Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
Interactive Molecular Dynamics (IMD) is a real-time simulation technique that allows scientists to interact with virtual molecular systems. Users can observe a simulation in progress in real time and manipulate the motion of individual atoms and molecules by applying forces, and receive feedback on the dynamic response of these systems in interactive time. The development of IMD has been influenced by technological and algorithmic advances in simulation tools as well as advances in human-computer interaction, including haptic devices or augmented and virtual reality approaches, and increasingly affordable devices. Scientific and practical applications include mechanobiology research, determination of experimental structures, and nanoscale property visualization for dissemination. IMD has made significant advances in performance, visualization, and data analysis.
Outer mitochondrial membrane (OMM) fusion is an important process for the cell and organism survival, as its dysfunction is linked to neurodegenerative diseases and cancer. The OMM fusion is mediated by members of the dynamin-related protein (DRP) family, named mitofusins. The exact mechanism by which the mitofusins contribute to these diseases, as well as the exact molecular fusion mechanism mediated by mitofusin, remains elusive. We have performed extensive multiscale molecular dynamics simulations using both coarse-grained and all-atom approaches to predict the dimerization of two transmembrane domain (TM) helices of the yeast mitofusin Fzo1. We identify specific residues, such as Lys716, that can modulate dimer stability. Comparison with a previous computational model reveals remarkable differences in helix crossing angles and interfacial contacts. Overall, however, the TM1-TM2 interface appears to be stable in the Martini and CHARMM force fields. Replica-exchange simulations further tune a detailed atomistic model, as confirmed by a remarkable agreement with an independent prediction of the Fzo1-Ugo1 complex by AlphaFold2. Functional implications, including a possible role of Lys716 that could affect membrane interactions during fusion, are suggested and consistent with experiments monitoring mitochondrial respiration of selected Fzo1 mutants.
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation, such as temperature and simulation length, and identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore collected MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and increase populating and standardizing metadata to reuse this valuable matter.
Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head-mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Further, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field (1), which requires us to understand this process at the atomic level. Using a multi-scale approach combining all-atom molecular dynamics and coarse- grain Brownian dynamics simulations, we investigated the adsorption behavior of ÎČ-glucosidase A (ÎČGA) on bare and SAM-functionalized gold surfaces (2). We monitored the enzyme position and orientation during the MD trajectories, and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity (3). Our results show that compared to the SAM-functionalized surface, the adsorption of ÎČGA on bare gold is more stable, but also less specific, and more likely to disrupt the enzymeâs function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a keypoint when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off (4). References 1Â Hitaishi, V.; Clement, R.; Bourassin, N.; Baaden, M.; de Poulpiquet, A.; Sacquin-Mora, S.; Ciaccafava, A.; Lojou, E., Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts 2018, 8 (5), 192. 2 Bourassin, N.; Barbault, F.; Baaden, M.; Sacquin-Mora, S., Between two walls : Modeling the adsorption behavior of ÎČ-glucosidase on bare and SAM-functionalised gold surfaces, Langmuir 2022, 38, 1313â1323 3Â Bourassin, N.; Baaden, M.; Lojou, E.; Sacquin-Mora, S., Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation. J Phys Chem B 2020, 124 (39), 8516-8523. 4 Weltz, J. S.; Kienle, D. F.; Schwartz, D. K.; Kaar, J. L., Reduced Enzyme Dynamics upon Multipoint Covalent Immobilization Leads to Stability-Activity Trade-off. J. Am. Chem. Soc. 2020, 142 (7), 3463-3471.
The insertion of proteins into membranes is crucial for understanding their function in many biological processes. In this work, we present UNILIPID, a universal implicit lipid-protein description as a methodology for dealing with implicit membranes. UNILIPID is independent of the scale of representation and can be applied at the level of all atoms, coarse-grained particles down to the level of a single bead per amino acid. We provide example implementations for these scales and demonstrate the versatility of our approach by accurately reflecting the free energy of transfer for each amino acid. In addition to single membranes, we describe the analytical implementation of double membranes and show that UNILIPID is well suited for modeling at multiple scales. We generalize to membranes of arbitrary shape. With UNILIPID, we provide a methodological framework for a simple and general parameterization tuned to reproduce a selected reference hydrophobicity scale. The software we provide along with the methodological description is optimized for specific user features such as real-time response, live visual analysis, and virtual reality experiences.
The enzyme OmpT of the outer membrane of Escherichia coli shows proteolytic activity and cleaves peptides and proteins. Using molecular dynamics simulations in a fully hydrated lipid bilayer on a time scale of hundreds of nanoseconds, we draw a detailed atomic picture of substrate recognition in the OmpT-holo enzyme complex. Hydrogen bonds and salt bridges are essential for maintaining the integrity of the active site and play a central role for OmpT in recognizing its substrate. Electrostatic interactions are critical at all stages from approaching the substrate to docking at the active site. Computational alanine scanning based on the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) approach confirms the importance of multiple residues in the active site that form salt bridges. The substrate fluctuates along the axis of the ÎČ-barrel, which is associated with oscillations of the binding cleft formed by the residue pairs D210-H212 and D83-D85. Principal component analysis suggests that substrate and protein movements are correlated. We observe the transient presence of putative catalytic water molecules near the active site, which may be involved in the nucleophilic attack on the cleavable peptide bond of the substrate.
AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable and effective methods for predicting protein structures. This article explores their impact and limitations, focusing on their integration into experimental pipelines and their application in diverse protein classes, including membrane proteins, intrinsically disordered proteins (IDPs), and oligomers.In experimental pipelines, AF2 models aid X-ray crystallography in resolving the phase problem, while complementarity with Mass Spectrometry and NMR data enhances structure determination and protein flexibility prediction. Predicting the structure of membrane proteins remains challenging for both AF2 and RF due to difficulties in capturing conformational ensembles and interactions with the membrane. Improvements in incorporating membrane-specific features and predicting the structural effect of mutations are crucial. For Intrinsically Disordered Proteins, AF2's confidence score (pLDDT) serves as a competitive disorder predictor, but integrative approaches with molecular dynamics simulations or hydrophobic cluster analyses are advocated for accurate dynamics representation. AF2 and RF show promising results for oligomeric models, outperforming traditional docking methods, with AlphaFold-Multimer showing improved performance, however, somes caveats remain in particular for membrane proteins. Real-life examples demonstrate AF2's predictive capabilities in unknown protein structures, but models should be evaluated for their agreement with experimental data. Furthermore, combining AF2 models with molecular dynamics simulations can be used complementarily. In this perspective we propose a "wish list" for improving deep learning-based protein folding prediction models, including using experimental data as constraints and modifying models with binding partners or post-translational modifications. Additionally, a meta-tool for ranking and suggesting composite models is suggested, driving future advancements in this rapidly evolving field.
Artificial water channels (AWCs) that selectively transport water and reject ions through bilayer membranes have potential to act as synthetic Aquaporins (AQPs). AWCs can have a similar osmotic permeability, better stability, with simpler manufacture on a largerâscale and have higher functional density and surface permeability when inserted into the membrane. Here, we report the screening of combinatorial libraries of symmetrical and unsymmetrical rimâfunctionalized PAs A â D that are able to transport ca. 10 7 â10 8 water molecules/s/channel, which is within 1 order of magnitude of AQPsâ and show total ion and proton rejection. Among the four channels, C and D are 3â4â times more water permeable than A and B when inserted in bilayer membranes. The binary combinations of A â D with different molar ratios could be expressed as an independent (linear ABA ), a recessive (inhibition AB , AC , DB , ACA ), or a dominant (amplification, DBD ) behavior of the water net permeation events.
Transport of water across cell membranes is a fundamental process for important biological functions. Herein, we focused our research on a new type of symmetrical saccharide rim-functionalized pillar[5]arene PA-S artificial water channels with variable pore structures. To point out the versatility of PA-S channels, we systematically varied the nature of anchoring/gate keepers D-Mannoside, D-Mannuronic acid or Sialic acid H-bonding groups on lateral PA arms, known as good membrane adhesives, to best describe the influence of the chemical structure on their transport activity. The control of hydrophobic membrane bindinghydrophilic water binding balance is an important feature influencing the channels' structuration and efficiency for a proper insertion into bilayer membranes. The glycosylated-PA channels transport performances were assessed in lipid bilayer membranes, and they were able to transport water at high rates (~10 6-10 7 waters/s/channel within one order of magnitude as for aquaporins.) serving as selective proton railways with total Na + and K + rejection. Molecular simulation substantiates the idea that the PAs can generate supramolecular pores, featuring hydrophilic carbohydrate gate-keepers that serve as water-sponge relays at the channel entrance, effectively absorbing and redirecting water within the channel. The present channels may be regarded as a rare biomimetic example of artificial channels presenting proton vs. cations transport selectivity performances.
(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an advanced molecular visualization software; MDDriver, a socket for data communication; and BioSpring, a Spring network simulation engine, were extended to perform IMS. These components are designed to easily communicate with each other, adapt to other molecular simulation software, and provide a development framework for adding new interaction models to simulate biological phenomena such as protein alignment in the membrane at a fast enough rate for real-time experiments. (3) Results: We describe in detail the integration of an implicit membrane model for Integral Membrane Protein And Lipid Association (IMPALA) into our IMS framework. Our implementation can cover multiple levels of representation, and the degrees of freedom can be tuned to optimize the experience. We explain the validation of this model in an interactive and exhaustive search mode. (4) Conclusions: Protein positioning in model membranes can now be performed interactively in real time.
Self-assembled Artificial Water Channels (AWCs) are reshaping current water desalination technologies. Recently, the improvements achieved by incorporating hydrophilic compounds into polyamide membranes (PA) at the interface have been experimentally confirmed. However, the determination of the nanoscale structure of AWCs remains unclear. An important step in the preparation of PA membranes is solubilization by colloidal suspension of the solid phase in a water-ethanol mixture. We perform molecular dynamics simulations to study the nanoscale structure of AWC aggregates. We characterize the size and shape of the aggregates at several key locations in the ternary phase diagram. The role of ethanol in forming the interface between the solvent and the solute phase is highlighted. We found that the structure of the aggregates formed in the ternary solution resembles the disordered sponge-like structures observed when AWCs were inserted into lipid membranes. Such permeable sponge architectures allow the passage of water despite their non-crystalline organization and have been previously shown to be consistent with AWC permeation measurements in membrane environments.
Background Digital twins offer rich potential for exploration in virtual reality (VR). Using interactive molecular simulation approaches, they enable a human operator to access the physical properties of molecular objects and to build, manipulate, and study their assemblies. Integrative modeling and drug design are important applications of this technology. Methods In this study, head-mounted virtual reality displays connected to molecular simulation engines were used to create interactive and immersive digital twins. They were used to perform tasks relevant to specific use cases. Results Three areas were investigated, including model building, rational design, and tangible models. Here, we report several membrane-embedded systems of ion channels, viral components, and artificial water channels. We were able to improve and create molecular designs based on digital twins. Conclusions The molecular application domain offers great opportunities, and most of the technical and technological aspects have been solved. Wider adoption is expected once the onboarding of VR is simplified and the technology gains wider acceptance.
Bioinformatics applies computer science approaches to the analysis of biological data. It is widely known for its genomics-based analysis approaches that have supported, for example, the 1000 Genomes Project. In addition, bioinformatics relates to many other areas, such as analysis of microscopic images (e.g., organelle localization), molecular modelling (e.g., proteins, biological membranes), and visualization of biological networks (e.g., protein-protein interaction networks, metabolism). Design is a highly interdisciplinary field that incorporates aspects such as aesthetic, economic, functional, philosophical, and/or socio-political considerations into the creative process and is usually determined by context. While visualization plays a critical role in bioinformatics, as reflected in a number of conferences and workshops in the field, design in bioinformatics-related research contexts in particular is not as well studied. With this special issue in conjunction with an international workshop, we aim to bring together bioinformaticians from different fields with designers, design researchers, and medical and scientific illustrators to discuss future challenges in the context of bioinformatics and design.
The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multi-scale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of ÎČ-glucosidase A (ÎČGA) on bare and SAM-functionalized gold surfaces. We monitored the enzyme position and orientation during the MD trajectories, and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of ÎČGA on bare gold is more stable, but also less specific, and more likely to disrupt the enzymeâs function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a keypoint when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.
Hedgehog (Hh) pathway inhibition by the conserved protein Suppressor of Fused (SuFu) is crucial to vertebrate development. By constrast, SuFu removal has little effect in drosophila. Previous publications showed that the crystal structures of human and drosophila SuFu consist of two ordered domains that are capable of breathing motions upon ligand binding. However, the crystal structure of human SuFu does not give information about 20 N-terminal residues (IDR1) and an eighty-residue-long disordered region (IDR2) in the C-terminus, whose function is important for the pathway repression. These two IDRs are species-dependent. We studied SuFuâs structure in solution, both with circular dichroism and small angle X-ray scattering, comparing drosophila, zebrafish and human species, to better understand this considerable difference. Our studies show that, in spite of similar crystal structures restricted to ordered domains, drosophila and vertebrate SuFu have very different structures in solution. The IDR2 of vertebrates spans a large area, thus enabling it to reach for partners and be accessible for post-translational modifications. Furthermore, we show that the IDR2 region is highly conserved within phyla but varies in length and sequence, with insects having a shorter disordered region while that of vertebrates is broad and mobile. This major variation may explain the different phenotypes observed upon SuFu removal.
Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.
We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.
PRACE (Partnership for Advanced Computing in Europe), an international not-for-profit association that brings together the five largest European supercomputing centers and involves 26 European countries, has allocated more than half a billion core hours to computer simulations to fight the COVID-19 pandemic. Alongside experiments, these simulations are a pillar of research to assess the risks of different scenarios and investigate mitigation strategies. While the world deals with the subsequent waves of the pandemic, we present a reflection on the use of urgent supercomputing for global societal challenges and crisis management.
Why is it so important to know the shape of molecules? How can virtual reality and advances in scientific visualization help? These are recurrent questions about the importance of understanding molecular shapes and molecular motions. In this brief feature article some background is provided to better understand the central role played by visual and computational analysis of molecular structures. The role of hardware devices and software tools to assist scientists in this quest is pointed out, along with challenges to share visual experiences more broadly. These topics touch upon many current questions in research. Examples related to biological membranes, molecular medicine, -omics data and SARS-Cov-2 structural data are provided to illustrate convincing use cases.
Synopsis Visualization renders structural molecular data accessible to a broad audience. We describe an approach to share molecular visualization experiences based on FAIR principles. Our workflow is exemplified with recent Covid-19 related data. Abstract Motivated by the current Covid-19 pandemic that has spurred a substantial flow of structural data we describe how molecular visualization experiences can be used to make these datasets accessible to a broad audience. Using a variety of technology vectors related to the cloud, 3D-and virtual reality gear, we examine how to share curated visualizations of structural biology, modeling and/or bioinformatics datasets for interactive and collaborative exploration. We discuss F.A.I.R. as overarching principle for sharing such visualizations. We provide four initial example scenes related to recent Covid-19 structural data together with a ready-to-use (and share) implementation in the UnityMol software.
Nanopores that efficiently and selectively transport water have been intensively studied at the nanoscale level. A key challenge relates to linking the nanoscale to the compound's macroscopic properties, which are hardly accessible at the smaller scale. Here we numerically investigate the influence of varying the dimensions of a self-assembled Imidazole I-quartet (I4) aggregate in lipid bilayers on the water permeation properties of these highly packed water channels. Quantitative transport studies reveal that water pathways in I4 crystal-like packing are not affected by small scaling factors, despite non-uniform contributions between central channels shielded from the bilayer and lateral, exposed channels. The permeation rate computed in simulations overestimates the experimental value by an order of magnitude, yet these in silico properties are very dependent on the force field parameters. The diversity of observed water pathways in such a small-scale in silico experiment yields some insights into modifying the current molecular designs in order to considerably improve water transport in scalable membranes.
Understanding water transport mechanisms at the nanoscale level remains a challenge for theoretical chemical physics. Major advances in chemical synthesis have allowed us to discover new artificial water channels, rivaling with or even surpassing water conductance and selectivity of natural protein channels. In order to interpret experimental features and understand microscopic determinants for performance improvements, numerical approaches based on all-atom molecular dynamics simulations and enhanced sampling methods have been proposed. In this study, we quantify the influence of microscopic observables such as channel radius and hydrogen bond connectivity, and of meso-scale features such as the size of self-assembly blocks, on the permeation rate of a self-assembled nanocrystal-like artificial water channel. Although the absolute permeation rate extrapolated from these simulations is overestimated by one order of magnitude compared to the experimental measurement, the detailed analysis of several observed conductive patterns in large assemblies opens new pathways to scalable membranes with enhanced water conductance for future design. Artificial Water Channels, nanopores, water dynamics, hydrogen bonds, pore radius.
NOX5 is a member of the NADPH oxidase family which is dedicated to the production of reactive oxygen species. The molecular mechanisms governing transmembrane electron transfer (ET) that permits to shuttle electrons over the biological membrane have remained elusive for a long time. Using computer simulations, we report conformational dynamics of NOX5 embedded within a realistic membrane environment. We assess the stability of the protein within the membrane and monitor the existence of cavities that could accommodate dioxygen molecules. We investigate the heme-to-heme electron transfer. We find a reaction free energy of a few tenths of eV (ca. â0.3 eV) and a reorganization free energy of around 1.1 eV (0.8 eV after including electrostatic induction corrections). The former indicates thermodynamically favorable ET, while the latter falls in the expected values for transmembrane inter-heme ET. We estimate the electronic coupling to fall in the range of the ÎŒeV. We identify electron tunneling pathways showing that not only the W378 residue is playing a central role, but also F348. Finally, we reveal the existence of two connected O 2â binding pockets near the outer heme with fast exchange between the two sites on the nanosecond timescale. We show that when the terminal heme is reduced, O 2 binds closer to it, affording a more efficient tunneling pathway than when the terminal heme is oxidized, thereby providing an efficient mechanism to catalyze superoxide production in the final step. Overall, our study reveals some key molecular mechanisms permitting reactive oxygen species production by NOX5 and paves the road for further investigation of ET processes in the wide family of NADPH oxidases by computer simulations.
Since the dawn of the computer age, scientists have designed devices to represent molecular structures and developed tools to simulate their dynamic behavior in silico. To this day, these tools remain central to our understanding of biomolecular phenomena. In contrast to other fields such as fluid mechanics or meteorology, the observation of molecular motions at the atomic level remains a major experimental challenge. Continuous advances in computer graphics and numerical computation, combined with the emergence of human-computer interaction approaches, led to the methodology of so-called "interactive molecular simulations", characterized by two main features. First, the possibility to visualize a running simulation in interactive time, i.e. compatible with human perception. Second, the possibility to manipulate the simulation interactively by imposing a force, changing a biophysical property, or editing runtime parameters on the fly. Such simulations are still little used in computational biology, where it is more common to run a series of offline simulations and then visualize and analyze the results. However, interactive molecular simulation tools promise to handle time-consuming tasks such as the modeling of particularly complex biomolecular structures more efficiently or to support approaches such as Rational Drug Design with regard to pharmaceutical applications.
Artificial water channels (AWCs) are known to selectively transport water, with ion exclusion. Similarly to natural porins, AWCs encapsulate water wires or clusters, offering continuous and iterative H-bonding that plays a vital role in their stabilization. Herein, we report octyl-ureido-polyol AWCs capable of self-assembly into hydrophilic hydroxy channels. Variants of ethanol, propanediol, and trimethanol are used as head groups to modulate the water transport permeabilities, with rejection of ions. The hydroxy channels achieve a single-channel permeability of 2.33 Ă 108 water molecules per second, which is within the same order of magnitude as the transport rates for aquaporins. Depending on their concentration in the membrane, adaptive channels are observed in the membrane. Over increased concentrations, a significant shift occurs, initiating unexpected higher water permeation. Molecular simulations probe that spongelike or cylindrical aggregates can form to generate transient cluster water pathways through the bilayer. Altogether, the adaptive self-assembly is a key feature influencing channel efficiency. The adaptive channels described here may be considered an important milestone contributing to the systematic discovery of artificial water channels for water desalination.
Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells, or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics, and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating local protein flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian dynamics simulations. The impact of protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e., residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.
Computer simulations provide crucial insights and rationales for the design of molecular approaches in medicine. Several case studies illustrate how molecular model building and molecular dynamics simulations of complex molecular assemblies such as membrane proteins help in that process. Important aspects relate to build relevant molecular models with and without a crystal structure, to model membrane aggregates, then to link (dynamic) models to function, and finally to understand key disease-triggering phenomena such as aggregation. Through selected examples-including key signaling pathways in neurotransmission-the links between a molecular-level understanding of biological mechanisms and original approaches to treat disease conditions will be illuminated. Such treatments may be symptomatic, e.g. by better understanding the function and pharmacology of macromolecular key players, or curative, e.g. through molecular inhibition of disease-inducing molecular processes.
In biology, metabolite transport across cell membranes occurs through natural channels and pores. Artificial ion-channel architectures represent potential mimics of natural ionic conduction. Many such systems were produced leading to a remarkable set of alternative artificial ion-channels. Far less advances were achieved in the area of synthetic biomimetic water channels, even though they could improve our understanding of the natural function of protein channels and may provide new strategies to generate highly selective, advanced water purification systems. Most realizations have used the selectivity components of natural protein channels embedded in artificial systems. Such biomolecules provide building blocks to constitute highly selective membrane-spanning water transport architec-tures. The simplification of such compounds, while preserving the high conduction activity of natural macromolecules, lead to fully synthetic artificial biomimet-ic channels. These simplified systems offer a particular chance to understand mechanistic and structural behaviors, providing rationales to engineer better artificial water-channels. Here we focus on computer simulations as a tool to complement experiment in understanding the properties of such systems with the aim to rationalize important concepts, design and optimize better compounds. Molecular dynamics simulations combined with advanced visual scrutiny thereof are central to such an approach. Novel technologies such as virtual reality headsets and stere-oscopic large-scale display walls offer immersive collaborative insight into the complex mechanisms underlying artificial water channel function.
Molecular visualisation is fundamental in the current scientific literature, textbooks and dissemination materials, forming an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Visual exploration has become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. Here we first describe a few Swiss Army knives geared towards protein visualisation for everyday use with an existing large user base, then focus on more specialised tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the APBS software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple \ac{GUI} for either a standard desktop or immersive virtual reality experience.
Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, ÎČ-sheet and random coil secondary structures, previous studies showed important discrepancies for ÎČ-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized ÎČ-turns in peptides, namely types I, II, IâČ and IIâČ. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of ÎČ-turn types (namely, type I/type IIâČ and type II/type IâČ), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of ÎČ-turns based on circular dichroism spectroscopy.
Artificial water channels mimicking natural aquaporins (AQPs) can be used for selective and fast transport of water. Here, we quantify the transport performances of peralkyl-carboxylate-pillar[5]arenes dimers in bilayer membranes. They can transport % 10 7 water molecules/channel/ second, within one order of magnitude of the transport rates of AQPs, rejecting Na + and K + cations. The dimers have a tubular structure, superposing pillar[5]arene pores of 5 diameter with twisted carboxy-phenyl pores of 2.8 diameter. This biomimetic platform, with variable pore dimensions within the same structure, offers size restriction reminiscent of natural proteins. It allows water molecules to selectively transit and prevents bigger hydrated cations from passing through the 2.8 pore. Molecular simulations prove that dimeric or multimeric honeycomb aggregates are stable in the membrane and form water pathways through the bilayer. Over time, a significant shift of the upper vs. lower layer occurs initiating new unexpected water permeation events through toroidal pores. &&Abstract was shortened to fit within allotted space. Please check.&&
In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.
Tethering and homotypic fusion of mitochondrial outer membranes is mediated by large GTPases of the dynamin-related proteins family called the mitofusins. The yeast mitofusin Fzo1 forms high molecular weight complexes and its assembly during membrane fusion likely involves the formation of high order complexes. Consistent with this possibility, mitofusins form oligomers in both cis (on the same lipid bilayer) and trans to mediate membrane attachment and fusion. Here, we utilize our recent Fzo1 model to investigate and discuss the formation of cis and trans mitofusin oligomers. We have built three distinct cis-assembly Fzo1 models that gave rise to three distinct trans-oligomeric models of mitofusin constructs. Each model involves two main components of mitofusin oligomerization: the GTPase and the trunk domains. The oligomeric models proposed in this study were further assessed for stability and dynamics in a membrane environment using a coarse-grained molecular dynamics (MD) simulation approach. A narrow opening âhead-to-headâ cis-oligomerization (via the GTPase domain) followed by the antiparallel âback-to-backâ trans-associations (via the trunk domain) appears to be in agreement with all of the available experimental data. More broadly, this study opens new possibilities to start exploring cis and trans conformations for Fzo1 and mitofusins in general.
Visualization of molecular structures is one of the most common tasks carried out by structural biologists, yet the technical details and advances required to e ciently display molecular structures are often hidden from the end user. During decades molecular viewer software such as Chimera, COOT, PyMOL, or VMD provided the most common solutions to quickly visualize structures. Nowadays, new and e cient ways to depict molecular objects are changing how structural biologists interact with their data. Such novelties are often driven by advances made by computer scientists, but an important gap remains between this community and the final users such as structural and computational biologists. In this perspective article, we clarify how developments from computer graphics and data visualization have led to novel ways of understanding protein structure. We present future developments from computer science that will be beneficial for structural biology. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we hope to promote communication between the diâ”erent communities to shape future developments in molecular graphics.
We present here an interdisciplinary workshop on the subject of biomolecules offered to undergraduate and high school students with the aim of boosting their interest toward all areas of science contributing to the study of life. The workshop involves mathematics, physics, chemistry, computer science and biology. Based on our own areas of research, molecular modelling is chosen as the central axis as it involves all disciplines. To provide a strong biological motivation for the study of the dynamics of biomolecules, the theme of the workshop is the origin of life. All sessions are built around active pedagogy, including games, and a final poster presentation.
Recently, several fast methods to compute Solvent Excluded Surfaces (SES) on GPUs have been presented. While these published methods reportedly yield interesting and useful results, up to now no public, freely accessible implementation of a fast and open- source SES mesh computation method that runs on GPUs is available. Most molecular viewers, therefore, still use legacy CPU methods that run only on a single core, without GPU acceleration. In this paper, we present an in-depth explanation and a fully open-source CUDA implementation of the fast, grid-based computation method proposed by Hermosilla et al. [HKGâ17]. Our library called QuickSES runs on GPUs and is distributed with a permissive license. It comes with a standalone program that reads Protein Data Bank (PDB) files and outputs a complete SES mesh as a Wavefront OBJ file. Alternatively it can directly be integrated in classical molecular viewers as shared library. We demonstrate the low memory consumption to enable execution on lower-end GPUs, and compare the runtime speed-up to available state-of-the-art tools.
Biological membranes are fascinating. Santiago RamĂłn y Cajal, who received the Nobel prize in 1906 together with Camillo Golgi for their work on the nervous system, wrote â[âŠ]in the study of this membrane[âŠ] I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of lifeââ . The visualization and conceptualization of these biological objects have profoundly shaped many aspects of modern biology, drawing inspiration from experiments, computer simulations, and the imagination of scientists and artists. The aim of this review is to provide a fresh look on current ideas of biological membrane organization and dynamics by discussing selected examples across fields.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. The Faraday Discussion on Artificial Water Channels brought together experts from various fields related to water transport, including biological porins, artificial water channels, carbon nanotubes and graphene-based materials, and membranes for desalination and water treatment. During the discussion, the structure and function of natural proteins for water transport were discussed, as well as the formation of supramolecular tetrameric structures and structure-activity relationships in artificial water channels. The discussion also covered the modeling and enhancement of water hydrodynamics, and the application of artificial water channels to water transport systems, including reverse osmosis membranes integrated with aquaporins. The conference also featured poster presentations and social events for networking and discussion.
In this work we present a novel set of possible auto-oligomerisation states of yeast protein Fzo1 in the context of membrane docking. The dataset reports atomistic models and trajectories derived from a molecular dynamics study of the yeast mitofusin Fzo1, residues 101â855. The initial modelling was followed by coarse-grained molecular dynamics simulation to evaluate the stability and the dynamics of each structural model in a solvated membrane environment. Simulations were run for 1 ÎŒs and collected with GROMACS v5.0.4 using the martini v2.1 force field. For each structural model, the dataset comprises the production phase under semi-isotropic condition at 1 bar, 310 K and 150 mn NaCl. The integration step is 20 fs and coordinates have been saved every 1 ns. Each trajectory is associated with a ready-available visualization state for the VMD software. These structural detailed informations are a ready-available platform to plan integrative studies on the mitofusin Fzo1 and will aid the community to further elucidate the mitochondrial tethering process during membrane fusion. This dataset is based on the publication âPhysics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking.â (Brandner and De Vecchis et al., 2019)â.
Mitochondria are dynamic organelles characterized by an ultrastructural organization which is essential in maintaining their quality control and ensuring functional efficiency. The complex mitochondrial network is the result of the two ongoing forces of fusion and fission of inner and outer membranes. Understanding the functional details of mitochondrial dynamics is physiologically relevant as perturbations of this delicate equilibrium have critical consequences and involved in several neurological disorders. Molecular actors involved in this process are large GTPases from the dynamin-related protein family. They catalyze nucleotide-dependent membrane remodeling and are widely conserved from bacteria to higher eukaryotes. Although structural characterization of different family members has contributed in understanding molecular mechanisms of mitochondrial dynamics in more detail, the complete structure of some members as well as the precise assembly of functional oligomers remains largely unknown. As increasing structural data become available, the domain modularity across the dynamin superfamily emerged as a foundation for transfering the knowledge towards less characterized members. In this review, we will first provide an overview of the main actors involved in mitochondrial dynamics. We then discuss recent example of computational methodologies for the study of mitofusin oligomers, and present how the usage of integrative modeling in conjunction with biochemical data can be an asset in progressing the still challenging field of membrane dynamics.
Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an intramolecular disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Physiological reductases, thioredoxins and glutaredoxins, could not dissolve AtGAPC1 aggregates but could efficiently contrast their growth. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.
Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. The Laguerre partition specifies inter-atomic contacts, formalized in graphs. The deduced properties are the existence and count of water aggregates, possible passage ways and constrictions, the structure, connectivity, stability and depth of the water network. As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. Inside FepA, the solvent splits into isolated clusters and an intricate network connecting both sides of the lipid bilayer. The network is dynamic, connections set on and off, occasionally substantially relocating traversing paths. Subtle differences are detected between two forms of FepA, ligand-free and complexed with its natural iron carrier, the enterobactin. The complexed form has more constricted and more centered openings in the upper part whereas, in the lower part, constriction is released: two main channels between the plug and barrel lead directly to the periplasm. Reliability, precision and the variety of topological features are the main interest of the method.
In vivo, the primary molecular mechanotransductive events mechanically initiating cell differentiation remain unknown. Here we find the molecular stretching of the highly conserved Y654-ÎČ-catenin-D665-E-cadherin binding site as mechanically induced by tissue strain. It triggers the increase of accessibility of the Y654 site, target of the Src42A kinase phosphorylation leading to irreversible unbinding. Molecular dynamics simulations of the ÎČ-catenin/E-cadherin complex under a force mimicking a 6 pN physiological mechanical strain predict a local 45% stretching between the two α-helices linked by the site and a 15% increase in accessibility of the phosphorylation site. Both are quantitatively observed using FRET lifetime imaging and non-phospho Y654 specific antibody labelling, in response to the mechanical strains developed by endogenous and magnetically mimicked early mesoderm invagination of gastrulating Drosophila embryos. This is followed by the predicted release of 16% of ÎČ-catenin from junctions, observed in FRAP, which initiates the mechanical activation of the ÎČ-catenin pathway process.
Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural â usually molecular â data plays an important role in the aforementioned contexts. For decades, virtual reality (VR)-related technologies were developed and applied to Bioinformatics problems. Often, these approaches provide âjustâ visual support of the analysis, e.g. in the case of exploring and interacting with a protein on a 3D monitor and compatible interaction hardware. Moreover, in the past these approaches were limited to cost-intensive professional visualization facilities. The advent of new affordable, and often mobile technologies, provides high potential for using similar approaches on a regular basis for daily research. Visual Analytics is successfully being used for several years to analyze complex and heterogeneous datasets. Immersive Analytics combines these approaches now with new immersive and interactive technologies. This publication provides a short overview of related technologies, their history and Bioinformatics-related approaches. Six new applications on the path from VR to Immersive Analytics are being introduced and discussed.
Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins. We aim to understand underlying molecular mechanisms and structural determinants through integration of redox proteome data from gene- to structural level. Our interactive visual analytics approach on an 8.3 m2 display wall of 25 MPixel resolution features stereoscopic three dimensions (3D) representation performed by UnityMol WebGL. Virtual reality headsets complement the range of usage configurations for fully immersive tasks. Our experiments confirm that fast access to a rich cross-linked database is necessary for immersive analysis of structural data. We emphasize the possibility to display complex data structures and relationships in 3D, intrinsic to molecular structure visualization, but less common for omics-network analysis. Our setup is powered by MinOmics, an integrated analysis pipeline and visualization framework dedicated to multi-omics analysis. MinOmics integrates data from various sources into a materialized physical repository. We evaluate its performance, a design criterion for the framework.
The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.
Aquaporins (AQPs) feature highly selective water transport through cell membranes, where the dipolar orientation of structured water wires spanning the AQP pore is of considerable importance for the selective translocation of water over ions. We recently discovered that water permeability through artificial water channels formed by stacked imidazole I-quartet superstructures increases when the channel water molecules are highly organized. Correlating water structure with molecular transport is essential for understanding the underlying mechanisms of (fast) water translocation and channel selectivity. Chirality adds another factor enabling unique dipolar oriented water structures. We show that water molecules exhibit a dipolar oriented wire structure within chiral I-quartet water channels both in the solid state and embedded in supported lipid bilayer membranes (SLBs). X-ray single-crystal structures show that crystallographic water wires exhibit dipolar orientation, which is unique for chiral I-quartets. The integration of I-quartets into SLBs was monitored with a quartz crystal microbalance with dissipation, quantizing the amount of channel water molecules. Nonlinear sum-frequency generation vibrational spectroscopy demonstrates the first experimental observation of dipolar oriented water structures within artificial water channels inserted in bilayer membranes. Confirmation of the ordered confined water is obtained via molecular simulations, which provide quantitative measures of hydrogen bond strength, connectivity, and the stability of their dipolar alignment in a membrane environment. Together, uncovering the interplay between the dipolar aligned water structure and water transport through the self-assembled I-quartets is critical to understanding the behavior of natural membrane channels and will accelerate the systematic discovery for developing artificial water channels for water desalting.
Dystrophin, encoded by the gene, is critical for maintaining plasma membrane integrity during muscle contraction events. Mutations in the gene disrupting the reading frame prevent dystrophin production and result in severe Duchenne muscular dystrophy (DMD); in-frame internal deletions allow production of partly functional internally deleted dystrophin and result in less severe Becker muscular dystrophy (BMD). Many known BMD deletions occur in dystrophin's central domain, generally considered to be a monotonous rod-shaped domain based on the knowledge of spectrin family proteins. However, the effects caused by these deletions, ranging from asymptomatic to severe BMD, argue against the central domain serving only as a featureless scaffold. We undertook structural studies combining small-angle X-ray scattering and molecular modeling in an effort to uncover the structure of the central domain, as dystrophin has been refractory to characterization. We show that this domain appears to be a tortuous and complex filament that is profoundly disorganized by the most severe BMD deletion (loss of exons 45-47). Despite the preservation of large parts of the binding site for neuronal nitric oxide synthase (nNOS) in this deletion, computational approaches failed to recreate the association of dystrophin with nNOS. This observation is in agreement with a strong decrease of nNOS immunolocalization in muscle biopsies, a parameter related to the severity of BMD phenotypes. The structural description of the whole dystrophin central domain we present here is a first necessary step to improve the design of microdystrophin constructs toward the goal of a successful gene therapy for DMD.
Serious scientific games are games whose purpose is not just fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games (CSGs), games that allow people to produce and/or analyze scientific data. It is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience (Phylo, DocMolecules, the HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games.
Artificial water channels (AWCs) have been designed for water transport across membranes with the aim to mimic the high water permeability observed for biological systems such as aquaporins (similar to 10(8)-10(9) water molecules per s per channel), as well as their selectivity to reject ion permeation at the same time. Recent works on designed self-assembling alkylureido-ethylimidazole compounds forming imidazole-quartet channels (I-quartets), have shown both high water permeability and total ionic-rejection. I-quartets are thus promising candidates for further development of AWCs. However, the molecular mechanism of water permeation as well as I-quartet organization and stability in a membrane environment need to be fully understood to guide their optimal design. Here, we use a wide range of all-atom molecular dynamics (MD) simulations and their analysis to understand the structure/activity relationships of the I-quartet channels. Four different types with varying alkyl chain length or chirality have been studied in a complex fully hydrated lipid bilayer environment at both microsecond and nanosecond scale. Microsecond simulations show two distinct behaviors; (i) two out of four systems maintain chiral dipolar oriented water wires, but also undergo a strong reorganization of the crystal shape, (ii) the two other I-quartet channels completely lose the initial organization, nonetheless keeping a water transport activity. Short MD simulations with higher time resolution were conducted to characterize the dynamic properties of water molecules in these model channels and provided a detailed hypothesis on the molecular mechanism of water permeation. The ordered confined water was characterized with quantitative measures of hydrogen-bond life-time and single particle dynamics, showing variability among I-quartet channels. We will further discuss the underlying assumptions, currently based on self-aggregation simulations and crystal patches embedded in lipid bilayer simulations and attempt to describe possible alternative approaches to computationally capture the water permeation mechanism and the self-assembly process of these AWCs.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. Of the various topics discussed, a few are briefly mentioned below. A focus on biomimetic water channels concerned the formation of G4 quartet hydrogels. It was found that these hydrogels can form with several different monovalent cations (Li+, Na+, K+, Rb+, and NH4+), but not well with Cs+. The cations are separated from each other in the central channel by about 3.5 Angstroms. The location of anions in G4-potassium complexes or G4 complexes with any cations was also discussed, since the presence of anions affects column stack formation and ionic conductivity. The issue of selectivity for use in environmental remediation was briefly addressed. I4 quartet channels were also an important topic of discussion.
Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.
Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.
The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a superhelical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question of how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived nonelectrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in the superhelix possible by shielding the strong electrostatic repulsion of the charged phosphate groups. Overall, this study provides new insights on the nucleosome cohesion, explaining how DNA distortions can be maintained in a nucleoprotein complex.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. The discussion focused on the structure and function of natural proteins for water transport and examined, among other things, Finkelstein's model of the movement of water molecules. It was discussed that these water molecules move as a unit with a coefficient of friction proportional to the number of molecules, but do not allow electroosmotic transport in the opposite direction of water flow because of their narrow width. The entropy of water molecules entering the nanotubes has also been discussed. There is evidence that entropy increases for certain tube sizes and water distances. The group discussed that the activation barrier can only be determined by measuring the permeabilities at different temperatures, with the pores of carbon nanotubes having the highest water permeability and thus the lowest activation energy, which is even lower than the best of the aquaporins.
Visualizations for computational biology have been developing for over 50 years. With recent advances in both computational biology and computer graphics techniques, these fields have witnessed rapid technological advances in the last decade. Thus, coping with the large number of scientific articles from both fields is a challenging task. Furthermore, there remains a gap between the two communities of visualization and computational biology, resulting in additional challenges to bridge the divide. A team of computational biology and visualization scientists attempts to address these challenges by presenting unified state-of-the-art reviews from both communities. We apply a variety of data-driven analysis to highlight links or differences between studies from both communities. This approach facilitates the identification of present and future challenges in visualizing and analyzing computational biology data. It offers a distinctive step forward in managing the literature on visualization of molecular dynamics and related simulation approaches.
Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of ÎČ-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.
Mitofusins are large transmembrane GTPases of the dynamin-related protein family, and are required for the tethering and fusion of mitochondrial outer membranes. Their full-length structures remain unknown, which is a limiting factor in the study of outer membrane fusion. We investigated the structure and dynamics of the yeast mitofusin Fzo1 through a hybrid computational and experimental approach, combining molecular modelling and all-atom molecular dynamics simulations in a lipid bilayer with site-directed mutagenesis and in vivo functional assays. The predicted architecture of Fzo1 improves upon the current domain annotation, with a precise description of the helical spans linked by flexible hinges, which are likely of functional significance. In vivo site-directed mutagenesis validates salient aspects of this model, notably, the long-distance contacts and residues participating in hinges. GDP is predicted to interact with Fzo1 through the G1 and G4 motifs of the GTPase domain. The model reveals structural determinants critical for protein function, including regions that may be involved in GTPase domain-dependent rearrangements.
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures. Their structures and full trajectories have been analyzed statistically and compared to standard replica exchange molecular dynamics simulations. Our analyses show that participants gain easily chemical intelligence to fold simple and nontrivial topologies, with little computer time, and this result opens the door for the use of human-guided simulations to RNA folding. Our experiment shows that interactive simulations have better chances of success when the user widely explores the conformational space. Interestingly, providing on-the-fly feedback of the root mean square deviation with respect to the experimental structure did not improve the quality of the proposed models.
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.
In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.
Aquaporins (AQPs) are biological water channels known for fast water transport (similar to 10(8)-10(9) molecules/s/channel) with ion exclusion. Few synthetic channels have been designed to mimic this high water permeability, and none reject ions at a significant level. Selective water translocation has previously been shown to depend on water-wires spanning the AQP pore that reverse their orientation, combined with correlated channel motions. No quantitative correlation between the dipolar orientation of the water-wires and their effects on water and proton translocation has been reported. Here, we use complementary X-ray structural data, bilayer transport experiments, and molecular dynamics (MD) simulations to gain key insights and quantify transport. We report artificial imidazole-quartet water channels with 2.6 angstrom pores, similar to AQP channels, that encapsulate oriented dipolar water-wires in a confined chiral conduit. These channels are able to transport 106 water molecules/s, which is within 2 orders of magnitude of AQPs' rates, and reject all ions except protons. The proton conductance is high (similar to 5 H+/s/channel) and approximately half that of the M2 proton channel at neutral pH. Chirality is a key feature influencing channel efficiency.
Pentameric ligand-gated ion channels have been identified as the principal target of general anesthetics (GA), whose molecular mechanism of action remains poorly understood. Bacterial homologs, such as the Gloeobacter violaceus receptor (GLIC), have been shown to be valid functional models of GA action. The GA bromoform inhibits GLIC at submillimolar concentration. We characterize bromoform binding by crystallography and molecular dynamics (MD) simulations. GLIC's open form structure identified three intra-subunit binding sites. We crystallized the locally closed form with an additional bromoform molecule in the channel pore. We systematically compare binding with the multiple potential sites of allosteric channel regulation in the open, locally closed, and resting forms. MD simulations reveal differential exchange pathways between sites from one form to the other. GAs predominantly access the receptor from the lipid bilayer in all cases. Differential binding affinity among the channel forms is observed; the pore site markedly stabilizes the inactive versus active state.
Bringing together, in a unique immersive environment, visualization and analysis of scientific and complex data requires a thorough approach in order to fulfill scientists' specific expectations. Such an approach needs to consider the highly heterogeneous nature of data, the dynamic interactions between experts and data, and the large amount of data involved in scientific studies. Whereas small and static scientific datasets can quickly be deciphered thanks to standard immersive tools such as 3D visualization software packages, bigger and dynamic datasets exceed the analytical capacity of these tools, requiring an efficient platform for their manipulation. Through the example of the structural biology field we discuss the need for an approach based on a high-level definition of the content (scientific data) and the context (immersive environments and interfaces). Our design is illustrated by a platform for dynamic and intelligent representation of data to the user. The data hierarchical classification will provide new ways to interact with the data via intelligent and direct relationships between them. This approach is based on the semantic definition of all the concepts manipulated in the virtual environment, either abstract or concrete, which allows for an adaptive and interactive experience of both visualization and analysis.
Many mutations responsible of Fabry disease destabilize lysosomal alpha-galactosidase, but retain the enzymatic activity. These mutations are associated to a milder phenotype and are potentially curable with a pharmacological therapy either with chaperones or with drugs that modulate proteostasis. We demonstrate the effectiveness of molecular dynamics simulations to correlate the genotype to the severity of the disease. We studied the relation between protein flexibility and residual enzymatic activity of pathological missense mutants in the cell. We found that mutations occurring at flexible sites are likely to retain activity in vivo. The usefulness of molecular dynamics for diagnostic purposes is not limited to lysosomal galactosidase because destabilizing mutations are widely encountered in other proteins, too, and represent a large share of all the ones associated to human diseases.
The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results. Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org. benoist.laurent@gmail.com or baaden@smplinux.de Supplementary data are available at Bioinformatics online.
A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures.
Visualisation and exploration of molecular experimental results play a crucial role in structural biology. By visualizing and analysing the 3 dimensional structure of a molecule - possibly over time thanks to simulation tools - scientists try to understand its functional role in the cell. Stereoscopic rendering features are historically used in structural biology and experts are thus quite familiar with virtual environment and 3D interaction. Since the dawn of virtual reality, immersive environments have been used to bring scientists into the heart of complex molecular scenes while adding an interactive dimension. However, in immersive environments as well as in desktop contexts, many issues concerning navigation need to be addressed when exploring molecular content. Among these issues, lack of spatial awareness and the cybersickness phenomenom encountered in navigation tasks are major obstacles to overcome to avoid any degradation of the experience and efficiency. It is interesting to highlight the fact that even if navigation is very frequently studied in virtual environments, most of the studies produce generic paradigms that are only applicable to realistic virtual scenes. These approaches do not explicitly take into account the content of the 3D scene and the task of the end user. In this study, we present some new implementation of navigation paradigms based on tasks and contents, dedicated to molecular biology and designed with the involvement of experts in structural biology. These paradigms are independent of the interaction context and can be indifferently used in a daily desktop context or in immersive environments ranging from CAVEs to HMDs.
We present a general software architecture to carry out interactive molecular simulations in a game engine environment. Our implementation is based on the UnityMol framework and the HireRNA physics engine. With UnityMol, we pursue the goal to create an interactive virtual laboratory enabling researchers in biology to visualize biomolecular systems, run simulations and interact with physical models and data. Similarly, UnityMol enables game designers to build scientifically accurate molecular scenarios. We discuss four case studies, from simulation setup via immersive experiments, force-induced unfolding of RNA to teaching and collaborative research applications. Visual effects enrich the dynamic and immersive aspects. We combine an appealing visual feedback with a set of analysis features to extract information about properties of the fascinating biomolecular systems under study. Access to various input devices enables a natural interaction with the simulation.
The glycine receptor (GlyR) is a pentameric ligand-gated ion channel (pLGIC) mediating inhibitory transmission in the nervous system. Its transmembrane domain (TMD) is the target of allosteric modulators such as general anesthetics and ethanol and is a major locus for hyperekplexic congenital mutations altering the allosteric transitions of activation or desensitization. We previously showed that the TMD of the human α1GlyR could be fused to the extracellular domain of GLIC, a bacterial pLGIC, to form a functional chimera called Lily. Here, we overexpress Lily in Schneider 2 insect cells and solve its structure by X-ray crystallography at 3.5 à resolution. The TMD of the α1GlyR adopts a closed-channel conformation involving a single ring of hydrophobic residues at the center of the pore. Electrophysiological recordings show that the phenotypes of key allosteric mutations of the α1GlyR, scattered all along the pore, are qualitatively preserved in this chimera, including those that confer decreased sensitivity to agonists, constitutive activity, decreased activation kinetics, or increased desensitization kinetics. Combined structural and functional data indicate a pore-opening mechanism for the α1GlyR, suggesting a structural explanation for the effect of some key hyperekplexic allosteric mutations. The first X-ray structure of the TMD of the α1GlyR solved here using GLIC as a scaffold paves the way for mechanistic investigation and design of allosteric modulators of a human receptor.
The influenza virus is surrounded by an envelope composed of a lipid bilayer and integral membrane proteins. Understanding the structural dynamics of the membrane envelope provides biophysical insights into aspects of viral function, such as the wide-ranging survival times of the virion in different environments. We have combined experimental data from X-ray crystallography, nuclear magnetic resonance spectroscopy, cryo-electron microscopy, and lipidomics to build a model of the intact influenza A virion. This is the basis of microsecond-scale coarse-grained molecular dynamics simulations of the virion, providing simulations at different temperatures and with varying lipid compositions. The presence of the Forssman glycolipid alters a number of biophysical properties of the virion, resulting in reduced mobility of bilayer lipid and protein species. Reduced mobility in the virion membrane may confer physical robustness to changes in environmental conditions. Our simulations indicate that viral spike proteins do not aggregate and thus are competent for multivalent immunoglobulin G interactions.
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. HiRE-RNA is a coarse-grained phenomenological model for folding and assembly of RNA which fully accounts for non-canonical interactions including the possibility of simultaneous multiple base pairs to give rise to triple and quadruple helices. The model correctly predicts the structure of a triple helix pseudoknot of 49 nucleotides from the knowledge of the sequence only.
[NiFe]-hydrogenases catalyse the cleavage of molecular hydrogen into protons and electrons and represent promising tools for H2-based technologies such as biofuel cells. However, many aspects of these enzymes remain to be understood, in particular how the catalytic center can be protected from irreversible inactivation by O2. In this work, we combined homology modelling, all-atom Molecular Dynamics, and coarse-grain Brownian Dynamics simulations to investigate and compare the dynamic and mechanical properties of two [NiFe]-hydrogenases: the soluble O2-sensitive enzyme from Desulfovibrio fructosovorans, and the O2-tolerant membrane-bound hydrogenase from Aquifex aeolicus. We investigated the diffusion pathways of H2 from the enzyme surface to the central [NiFe] active site, and the possible proton pathways that are used to evacuate hydrogen after the oxidation reaction. Our results highlight common features of the two enzymes, such as a Val/Leu/Arg triad of key residues that controls ligand migration and substrate access in the vicinity of the active site, or the key role played by a Glu residue for proton transfer after hydrogen oxidation. We show specificities of each hydrogenase regarding the enzymes internal tunnel network or the proton transport pathways.
Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
Many techniques may be applied to overcome the physical limitations induced by the small workspace of most haptic devices in a navigational context, such as the Bubble technique , or to manipulate virtual objects, such as clutching techniques. Several assem bly tasks require high precision, and haptic - guide based approaches are often used in order to help the user to reach a precise and predefined assembly goal. However, the re are a few haptic interaction techniques designed to facilitate micro - assembly tasks for which haptic guidance is unsuitable, such as protein docking. The objective is to find an optimal but precise 3D configuration by interactive exploration. In this paper, we propose an innovat ive technique to both overcome the physical limitations of t he device and to reach the high accuracy required by micromanipulation tasks without a predefined goal. This approach is based on a non - isomorphic mapping around a neutral referential retrieved by an elastic haptic feedback, in addition to external haptic feedback. We present at the end of this paper an application and a preliminary ergonomic study of this approach in a molecula r docking application framework.
[NiFe] hydrogenases from Aquifex aeolicus (AaHase) and Desulfovibrio fructosovorans (DfHase) have been mainly studied to characterize physiological electron transfer processes, or to develop biotechnological devices such as biofuel cells. In this context, it remains difficult to control the orientation of AaHases on electrodes to achieve a fast interfacial electron transfer. Here, we study the electrostatic properties of these two proteins based on microsecond-long molecular dynamics simulations that we compare to voltammetry experiments. Our calculations show weak values and large fluctuations of the dipole direction in AaHase compared to DfHase, enabling the AaHase to absorb on both negatively and positively charged electrodes, with an orientation distribution that induces a spread in electron transfer rates. Moreover, we discuss the role of the transmembrane helix of AaHase and show that it does not substantially impact the general features of the dipole moment.
The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system.
The dissociation processes of clotrimazole (CLT) in several models are comparatively investigated by molecular dynamics simulations to explore the cooperative mechanism of clotrimazoles in P450. Our results suggest that when P450 only accommodates the active CLT (CLT1), CLT1 continually diffuses away from heme, and the partial BC loop (residues 73-88) and the extended FG loop (residues 173-186) first close and then open. When the enzyme binds to two CLT molecules, CLT1 basically keeps close to heme, and the partial BC loop and the extended FG loop move close to each other. Clearly, the effector CLT (CLT2) plays a cooperative role in the inhibition of CLT1 on P450. CLT2 restrains the dissociation of CLT1 first through direct Ï-Ï stacking interactions and then through the rearranged binding site induced by CLT2. The presence of CLT1 can help to stabilize the protein structure around CLT2 by interacting with M86, Q173, and M174.
We review foundations of biomolecular simulations that enable the study of membrane protein models with a particular focus on structureâfunction relationships and opportunities for drug design. A range of broadly used methods is presented comprising homology modeling, normal mode analysis, molecular dynamics simulations, and free energy calculations. These methods are illustrated with examples on several membrane protein systems, in particular ligand-gated ion channels such as the P2X receptors, the N-methyl-D-aspartate (NMDA) receptors, and the Cys-loop family of pentameric ion channels.
A broad challenge facing scientists today is the availability of huge amounts of data from various sources. Computers are required to store, analyze, explore and represent these data in order to extract useful information. With UnityMol, we pursue the ambitious goal to create an interactive virtual laboratory enabling researchers in biology to visualize biomolecular systems, run simulations and in- teract with physical models and data. Visual effects can enrich the dynamic and immersive aspects. Ultimately, we want to combine an appealing visual feedback already in place with a set of analysis features to extract information about properties of the fascinating biomolecular systems under study.
At present, our molecular knowledge of dystrophin, the protein encoded by the DMD gene and mutated in myopathy patients, remains limited. To get around the absence of its atomic structure, we have developed an innovative interactive docking method based on the BioSpring software in combination with Small-angle X-ray Scattering (SAXS) data. BioSpring allows interactive handling of biological macromolecules thanks to an augmented Elastic Network Model (aENM) that combines the spring network with non-bonded terms between atoms or pseudo-atoms. This approach can be used for building molecular assemblies even on a desktop or a laptop computer thanks to code optimizations including parallel computing and GPU programming. By combining atomistic and coarse-grained models, the approach significantly simplifies the set-up of multi-scale scenarios. BioSpring is remarkably efficient for the preparation of numeric simulations or for the design of biomolecular models integrating qualitative experimental data restraints. The combination of this program and SAXS allowed us to propose the first high-resolution models of the filamentous central domain of dystrophin, covering repeats 11 to 17. Low-resolution interactive docking experiments driven by a potential grid enabled us to propose how dystrophin may associate with F-actin and nNOS. This information provides an insight into medically relevant discoveries to come.
In the field of structural biology, molecular visualization is a critical step to study and understand 3D structures generated by experimental and theoretical technics. Numerous programs are dedicated to the exploration and analysis of structures in 3 dimensions. However, very few of them offer navigation algorithms that deal in an intelligent way with the content they display and the task to perform. This observation is emphasized in the case of navigation in immersive environments where users are immersed in their molecular systems, without any spatial landmark to guide their exploration. Starting from this observation, we propose to take into account some geometrical features found in multimeric molecular complexes to provide navigation guides to the users during the exploration process. It is possible thanks to the common symmetrical layout molecular complexes present. Beyond the biological meaning and importance that symmetric layouts have in proteins, they allow us to orient an d guide the exploration of molecular complexes in an intelligent and meaningful manner. We present then a current work on the design of navigation paradigms based on the content and the task for the molecular visualization.
Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separately described, but we note the parallel development that is present in both research fields with three important themes: firstly, combining CG modelling with knowledge-based approaches to predict and refine protein-protein complexes; secondly, using physics-based CG models for de novo prediction of protein-protein complexes; and thirdly modelling of large scale protein aggregates.
Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.
The association of hemagglutinin (HA) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A. Lipid rafts are thought to be small, fluctuating patches of membrane enriched in saturated phospholipids, sphingolipids, cholesterol and certain types of protein. However, raft-associating transmembrane (TM) proteins generally partition into Ld domains in model membranes, which are enriched in unsaturated lipids and depleted in saturated lipids and cholesterol. The reason for this apparent disparity in behavior is unclear, but model membranes differ from the plasma membrane in a number of ways. In particular, the higher protein concentration in the plasma membrane may influence the partitioning of membrane proteins for rafts. To investigate the effect of high local protein concentration, we have conducted coarse-grained molecular dynamics (CG MD) simulations of HA clusters in domain-forming bilayers. During the simulations, we observed a continuous increase in the proportion of raft-type lipids (saturated phospholipids and cholesterol) within the area of membrane spanned by the protein cluster. Lateral diffusion of unsaturated lipids was significantly attenuated within the cluster, while saturated lipids were relatively unaffected. On this basis, we suggest a possible explanation for the change in lipid distribution, namely that steric crowding by the slow-diffusing proteins increases the chemical potential for unsaturated lipids within the cluster region. We therefore suggest that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids. This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes.
To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Ă . Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.
Within the BioPac project, we aim to understand the molecular details of hydrogenase function in order to design and improve next generation biofuel cells. Hydrogenases are key enzymes for the enzymatic conversion of molecular hydrogen into protons and electrons, representing a promising replacement of chemical catalysts in fuel cell devices. To obtain a working biofuel cell, we have been studying the Aquifex Aeolicus (Aa) hydrogenase enzyme because of its resistance to oxygen and carbon monoxyde. Moreover, the presence of a putative transmembrane helix and protein-DDM interaction represent two challenging features to efficiently immobilize the protein on the electrode surface. Using classical molecular dynamics simulations in explicit solvent, we compare the properties of the enzyme from Desulfovibrio fructosovorans, a much studied bacterium, with the one from Aa. We focus mainly on surface properties with the aim to optimize immobilisation on an electrode surface. We also analyze differences among both enzymes as they might provide insight into the origin of oxygen resistance. Moreover, REFT simulations have been used to address both the DDM-protein interaction and the transmembrane helix conformational landscape. In the experimental counterpart of the project, a first working fuel cell prototype was realized yielding 300 ÎŒW cmâ2 power. Insights on the interaction between hydrogenase model and electrode will drive the experimental design of an improved electrode increasing the efficiency of the association and hence of electron transfer.
Pentameric ligand-gated ion channels (pLGICs) are a major family of membrane receptors that mediate fast chemical transmission of nerve signals in the central and peripheral nervous system [1]. In vertebrates, the family encompasses the cationic selective acetylcholine and serotonine receptors, and the anionic selective glycine and γ-amino-butyric acid receptors. pLGICs are dynamic proteins that couple neurotransmitter binding in their extracellular-domain (ECD) to the opening of ion channels embedded in their transmembrane domain (TMD). The receptors share a common architecture with a large ECD and a TMD that is composed of four α-helices, named M1 to M4, that form a transmembrane pore bordered by the M2 helices (Figure 52a). The flow of ions across the membrane is inhibited by a structurally-diverse class of molecules including tricyclic antidepressants, local anaesthetics and certain transition metals that bind to the transmembrane pore. The molecular understanding of ion permeation is thus a central issue in the study of these ion channels.
Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.
Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7 M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. Recent advances in experimental techniques allow us to solve ever larger 3D biomolecular structures. However, static states often lack dynamic information that is crucial for understanding subtle mechanisms at the molecular level. New simulation approaches specifically designed to study the formation and stability of very large biological structures need to be developed. BioSpring is unconventional and innovative software designed for molecular sketching and modeling. The main goals of BioSpring are to provide a tool to interactively get a quick overview of biomechanical properties, to support the user in the complex task of modeling large biomolecular complexes, to perform interactive flexible docking, and to provide and explore new hypotheses for complex molecular assemblies.
Accurate simulation of biomolecular systems requires the consideration of solvation effects. The arrangement and dynamics of water close to a solute are strongly influenced by the solute itself. However, as the solute-solvent distance increases, the water properties tend to those of the bulk liquid. This suggests that bulk regions can be treated at a coarse grained (CG) level, while keeping the atomistic details around the solute. Since water represents about 80% of any biological system, this approach may offer a significant reduction in the computational cost of simulations without compromising atomistic details. We show here that mixing the popular SPC water model with a CG model for solvation (called WatFour) can effectively mimic the hydration, structure, and dynamics of molecular systems composed of pure water, simple electrolyte solutions, and solvated macromolecules. As a nontrivial example, we present simulations of the SNARE membrane fusion complex, a trimeric protein-protein complex embedded in a double phospholipid bilayer. Comparison with a fully atomistic reference simulation illustrates the equivalence between both approaches.
Pentameric ligand-gated ion channels mediate signal transduction through conformational transitions between closed-pore and open-pore states. To stabilize a closed conformation of GLIC, a bacterial proton-gated homolog from Gloeobacter violaceus whose open structure is known, we separately generated either four cross-links or two single mutations. We found all six mutants to be in the same 'locally closed' conformation using X-ray crystallography, sharing most of the features of the open form but showing a locally closed pore as a result of a concerted bending of all of its M2 helices. The mutants adopt several variant conformations of the M2-M3 loop, and in all cases an interacting lipid that is observed in the open form disappears. A single cross-linked mutant is functional, according to electrophysiology, and the locally closed structure of this mutant indicates that it has an increased flexibility. Further cross-linking, accessibility and molecular dynamics data suggest that the locally closed form is a functionally relevant conformation that occurs during allosteric gating transitions.
An abstract was not provided in the original work, so a preliminary abstract has been prepared as follows. Interactive Molecular Simulation (IMS) is a method to study protein folding and interactions in real time using interactive manipulation and haptic devices. We particularly focus on our own BioSpring software. The approach involves building a spring network model of the protein, which can be manipulated using a particle-based simulation that accounts for spring forces and unbound interactions. The model can also include an electrostatic field to study conformational changes caused by electrostatic constraints. IMS enables the visualization of large biomolecular structures at high frame rates and can be enhanced by graphics techniques such as GPU shaders and HyperBalls. Haptic rendering or the use of force feedback is also possible, but is often not implemented in IMS frameworks due to the challenges of computing steric and electrostatic interactions at high frame rates. However, haptic rendering has the potential to significantly improve the user's ability to understand and manipulate protein structures.
Since the works of Leonardo da Vinci, scientific illustration has made much progress: going from simple drawings towards more and more refined and complex representations as knowledge progressed. The transition from the macroscopic to the microscopic level is, in reality, a continuous one. In practice, disciplines such as medical and molecular illustration do still represent separate universes. This may be explained by the great diversity of the objects that are represented.
Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of these huge structures remains an important way of unravelling some of their secrets. However, such visualization cannot conveniently be carried out using conventional rendering approaches, either due to performance limitations or due to lack of realism. Recent developments, in particular drawing benefit from the capabilities of Graphics Processing Units (GPUs), herald the next generation of molecular visualization solutions addressing these issues. In this article, we present advances in computer science and visualization that help biologists visualize, understand and manipulate large and complex molecular systems, introducing concepts that remain little-known in the bioinformatics field. Furthermore, we compile currently available software and methods enhancing the shape perception of such macromolecular assemblies, for example based on surface simplification or lighting ameliorations.
Ray-casting on Graphics Processing Units (GPUs) opens new possibilities for molecular visualization. We used this technique to develop HyperBalls, an improved ball & stick representation replacing tubes linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena and can routinely, accurately and interactively render huge macromolecular assemblies with more than 500,000 particles. Combined with Molecular Dynamics (MD) software and haptic devices, it is possible to manipulate molecular objects to study their properties.
Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball-and-stick, space-filling van der Waals spheres, and approximated solvent-accessible surfaces using GPUs. We introduce HyperBalls, an improved ball-and-stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse-grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray-casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly.
We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of apo-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, apo-versus-holo, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.
The mechanism of signal transduction mediated by G protein-coupled receptors is a subject of intense research in pharmacological and structural biology. Ligand association to the receptor constitutes a critical event in the activation process. Solution-state NMR can be amenable to high-resolution structure determination of agonist molecules in their receptor-bound state by detecting dipolar interactions in a transferred mode, even with equilibrium dissociation constants below the micromolar range. This is possible in the case of an inherent ultra-fast diffusive association of charged ligands onto a highly charged extracellular surface, and by slowing down the (1)H-(1)H cross-relaxation by perdeuterating the receptor. Here, we demonstrate this for two fatty acid molecules in interaction with the leukotriene BLT2 receptor, for which both ligands display a submicromolar affinity.
General anaesthetics have enjoyed long and widespread use but their molecular mechanism of action remains poorly understood. There is good evidence that their principal targets are pentameric ligand-gated ion channels (pLGICs) such as inhibitory GABA(A) (Îł-aminobutyric acid) receptors and excitatory nicotinic acetylcholine receptors, which are respectively potentiated and inhibited by general anaesthetics. The bacterial homologue from Gloeobacter violaceus (GLIC), whose X-ray structure was recently solved, is also sensitive to clinical concentrations of general anaesthetics. Here we describe the crystal structures of the complexes propofol/GLIC and desflurane/GLIC. These reveal a common general-anaesthetic binding site, which pre-exists in the apo-structure in the upper part of the transmembrane domain of each protomer. Both molecules establish van der Waals interactions with the protein; propofol binds at the entrance of the cavity whereas the smaller, more flexible, desflurane binds deeper inside. Mutations of some amino acids lining the binding site profoundly alter the ionic response of GLIC to protons, and affect its general-anaesthetic pharmacology. Molecular dynamics simulations, performed on the wild type (WT) and two GLIC mutants, highlight differences in mobility of propofol in its binding site and help to explain these effects. These data provide a novel structural framework for the design of general anaesthetics and of allosteric modulators of brain pLGICs.
Molecular simulation is nowadays becoming a routine technique in structural biology. Recent progress along with increasingly widespread access to substantial computing power now enables the study of macromolecular systems in interactive time. Visual inspection of MD trajectories is a good way to quickly discover general trends and perform initial analysis. Interactive Molecular Simulation (IMS) provides visualisation of and interaction with a simulation in progress, as well as possible on-the-fly control over simulation settings. Yet, few simulation and visualisation programs implement these features or often lack functionalities such as dynamic âliveâ analysis tools or efficient rendering.
The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study such phenomena using a method for investigating local flexibility on the residue scale that combines a reduced protein representation with Brownian dynamics simulations. We performed calculations on the enzyme guanylate kinase to study its mechanical response when submitted to anisotropic deformations. The resulting modifications of the protein's rigidity profile can be related to the changes in substrate binding affinity observed experimentally. Further analysis of the principal components of motion of the trajectories shows how the application of a mechanical constraint on the protein can disrupt its dynamics, thus leading to a decrease of the enzyme's catalytic rate. Eventually, a systematic probe of the protein surface led to the prediction of potential hotspots where the application of an external constraint would produce a large functional response both from the mechanical and dynamical points of view. Such enzyme-engineering approaches open the possibility to tune catalytic function by varying selected external forces.
Most mitochondrial proteins are synthesized in the cytosol as precursor and imported into the mitochondria by Tom complexes (translocase of outer membrane complexes). Knowledge of the binding mechanism between precursor and Tom20 in plants is very limited. Here, computational methods are employed to improve our understanding of the interactions between both molecules. To this end, we model mitochondrial superoxide dismutase precursor (pSOD) in complex with Tom20 in Oryza sativa (OsTom20). In a first stage, five main binding modes were generated using clustering analysis, energy minimization, and expert knowledge. In a second stage, the quality and validity of the resulting complexes is assessed by molecular dynamics (MD) simulations with a generalized Born solvation model. The change in binding free energies is estimated using a computational alanine scanning technique. We identified a particularly favorable complex between pSOD and OsTom20, exhibiting the lowest binding free energy among all candidates and correlating well with experimental data. Furthermore, three independent explicit solvent MD simulations of this structure, each of 100 ns duration, reveal that hydrophobic interactions occur between pSOD and OsTom20, in particular between L158 of pSOD and W81 of OsTom20, as evidenced by analysis of intermolecular distances and corresponding relative free energy landscapes. L158 is part of an interacting LRTLA motif. These results provide new insight into the structural basis and dynamics of precursor recognition by Tom20 in plant, and their generality is supported by sequence alignments with seven other plants.
Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson-Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the Gloeobacter violaceus receptor (GLIC), are increasingly used as structural and functional models of signal transduction in the nervous system. Here we present a one-microsecond-long molecular dynamics simulation of the GLIC channel pH stimulated gating mechanism. The crystal structure of GLIC obtained at acidic pH in an open-channel form is equilibrated in a membrane environment and then instantly set to neutral pH. The simulation shows a channel closure that rapidly takes place at the level of the hydrophobic furrow and a progressively increasing quaternary twist. Two major events are captured during the simulation. They are initiated by local but large fluctuations in the pore, taking place at the top of the M2 helix, followed by a global tertiary relaxation. The two-step transition of the first subunit starts within the first 50 ns of the simulation and is followed at 450 ns by its immediate neighbor in the pentamer, which proceeds with a similar scenario. This observation suggests a possible two-step domino-like tertiary mechanism that takes place between adjacent subunits. In addition, the dynamical properties of GLIC described here offer an interpretation of the paradoxical properties of a permeable A13'F mutant whose crystal structure determined at 3.15 A shows a pore too narrow to conduct ions.
We have implemented a noninvasive optical method for the fast control of protein activity in a live zebrafish embryo. It relies on releasing a protein fused to a modified estrogen receptor ligand binding domain from its complex with cytoplasmic chaperones, upon the local photoactivation of a nonendogenous caged inducer. Molecular dynamics simulations were used to design cyclofen-OH, a photochemically stable inducer of the receptor specific for 4-hydroxy-tamoxifen (ERT2). Cyclofen-OH was easily synthesized in two steps with good yields. At submicromolar concentrations, it activates proteins fused to the ERT2 receptor. This was shown in cultured cells and in zebrafish embryos through emission properties and subcellular localization of properly engineered fluorescent proteins. Cyclofen-OH was successfully caged with various photolabile protecting groups. One particular caged compound was efficient in photoinducing the nuclear translocation of fluorescent proteins either globally (with 365 nm UV illumination) or locally (with a focused UV laser or with two-photon illumination at 750 nm). The present method for photocontrol of protein activity could be used more generally to investigate important physiological processes (e.g., in embryogenesis, organ regeneration and carcinogenesis) with high spatiotemporal resolution.
Pentameric ligand-gated ion channels (pLGICs) are widely expressed in the animal kingdom and are key players of neurotransmission by acetylcholine (ACh), gamma-amminobutyric acid (GABA), glycine and serotonin. It is now established that this family has a prokaryotic origin, since more than 20 homologues have been discovered in bacteria. In particular, the GLIC homologue displays a ligand-gated ion channel function and is activated by protons. The prokaryotic origin of these membrane proteins facilitated the X-ray structural resolution of the first members of this family. ELIC was solved at 3.3 A in a closed-pore conformation, and GLIC at up to 2.9 A in an apparently open-pore conformation. These data reveal many structural features, notably the architecture of the pore, including its gate and its selectivity filter, and the interactions between the protein and lipids. In addition, comparison of the structures of GLIC and ELIC hints at a mechanism of channel opening, which consists of both a quaternary twist and a tertiary deformation. This mechanism couples opening-closing motions of the channel with a global reorganization of the protein, including the subunit interface that holds the neurotransmitter binding sites in eukaryotic pLGICs.
DNase I requires CaÂČ+ and MgÂČ+ for hydrolyzing double-stranded DNA. However, the number and the location of DNase I ion-binding sites remain unclear, as well as the role of these counter-ions. Using molecular dynamics simulations, we show that bovine pancreatic (bp) DNase I contains four ion-binding pockets. Two of them strongly bind CaÂČ+ while the other two sites coordinate MgÂČ+. These theoretical results are strongly supported by revisiting crystallographic structures that contain bpDNase I. One CaÂČ+ stabilizes the functional DNase I structure. The presence of MgÂČ+ in close vicinity to the catalytic pocket of bpDNase I reinforces the idea of a cation-assisted hydrolytic mechanism. Importantly, Poisson-Boltzmann-type electrostatic potential calculations demonstrate that the divalent cations collectively control the electrostatic fit between bpDNase I and DNA. These results improve our understanding of the essential role of cations in the biological function of bpDNase I. The high degree of conservation of the amino acids involved in the identified cation-binding sites across DNase I and DNase I-like proteins from various species suggests that our findings generally apply to all DNase I-DNA interactions.
Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of ⌠25 OMPs are currently known, the relationship between structure, dynamics and function is often unclear. Furthermore, relatively little is known about the effect of the local environment on the protein dynamics. Over the past 10 years or so, molecular dynamics simulations have been successful in revealing insights into aspects of outer membrane proteins that are difficult to study with experimental methods alone. Indeed in some cases simulations have aided the interpretation of structural data e.g. the apparent discrepancy between the x-ray structure of OmpA from E. coli and the observed conductance data. Simulations have also been employed to design mutants of OMPs with desired properties, e.g mutants of OmpG that may serve as components of stochastic biosensors. In general, more OMPs have been studied via MD simulations than perhaps any other family of membrane protein, yielding a wealth of information that provides an ideal complement to experimental determined data.
Metal ions drive important parts of biology, yet it remains experimentally challenging to locate their binding sites. Here we present an innovative computational approach. We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites. The user interacts with a haptic device and experiences tactile feedback related to the strength of binding at a given site. The potential field is the first level of resolution used in this model. Any type of potential field can be used, implicitly taking into account various conditions such as ionic strength, dielectric constants or the presence of a membrane. At a second level, we represent the accessibility of all binding sites by modelling the shape of the target macromolecule via non-bonded van der Waals interactions between its static atomic or coarse-grained structure and the probe molecule(s). The third independent level concerns the representation of the molecular probe itself. Ion selectivity can be assessed by using multiple interacting ions as probes. This method was successfully applied to the DNase I enzyme, where we recently identified two new cation binding sites by computationally expensive extended molecular dynamics simulations.
Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example.
Coarse-grain molecular dynamics are used to look at conformational and dynamic aspects of an R-SNARE peptide inserted in a lipid bilayer. This approach allows carrying out microsecond-scale simulations which bring to light long-lived conformational sub-states potentially interesting in the context of the membrane fusion mechanism mediated by the SNARE proteins. We show that these coarse-grain models are in agreement with most experimental data on the SNARE system, but differ in some details that may have a functional interest, most notably in the orientation of the soluble part of R-SNARE that does not appear to be spontaneously accessible for SNARE complex formation. We also compare rat and yeast sequences of R-SNARE and find some minor differences in their behavior.
Pentameric ligand-gated ion channels from the Cys-loop family mediate fast chemo-electrical transduction, but the mechanisms of ion permeation and gating of these membrane proteins remain elusive. Here we present the X-ray structure at 2.9 A resolution of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel homologue (GLIC) at pH 4.6 in an apparently open conformation. This cationic channel is known to be permanently activated by protons. The structure is arranged as a funnel-shaped transmembrane pore widely open on the outer side and lined by hydrophobic residues. On the inner side, a 5 A constriction matches with rings of hydrophilic residues that are likely to contribute to the ionic selectivity. Structural comparison with ELIC, a bacterial homologue from Erwinia chrysanthemi solved in a presumed closed conformation, shows a wider pore where the narrow hydrophobic constriction found in ELIC is removed. Comparative analysis of GLIC and ELIC reveals, in concert, a rotation of each extracellular beta-sandwich domain as a rigid body, interface rearrangements, and a reorganization of the transmembrane domain, involving a tilt of the M2 and M3 alpha-helices away from the pore axis. These data are consistent with a model of pore opening based on both quaternary twist and tertiary deformation.
Molecular Dynamics is nowadays routinely used to complement experimental studies and overcome some of their limitations. In particular, current experimental techniques do not allow to directly observe the full dynamics of a macromolecule at atomic detail. Molecular simulation provides time-dependent atomic positions, velocities and system energies according to biophysical models. Many molecular simulation engines can now compute a molecular dynamics trajectory of interesting biological systems in interactive time. This progress has lead to a new approach called interactive molecular dynamics. It allows to control and visualise a molecular simulation in progress. We have developed a generic library, called MDDriver, to facilitate the implementation of such interactive simulations. It allows to easily create a network between a molecular user interface and a physically-based simulation. We use this library in order to study an interesting biomolecular system, simulated by various interaction-enabled molecular engines and models. We use a classical molecular visualisation tool and a haptic device to control the dynamic behavior of the molecule. This approach provides encouraging results for interacting with a biomolecule and understanding its dynamics. Starting from this initial success, we decided to use VR functionalities more intensively, by designing a VR framework dedicated to immersive and interactive molecular simulations. This framework is based on MDDriver, on the visualisation toolkit VTK, and on the vtkVRPN library, which encapsulates the VRPN library into VTK.
The structures of three bacterial outer membrane proteins (OmpA, OmpX and PagP) have been determined by both X-ray diffraction and NMR. We have used multiple (7 x 15 ns) MD simulations to compare the conformational dynamics resulting from the X-ray versus the NMR structures, each protein being simulated in a lipid (DMPC) bilayer. Conformational drift was assessed via calculation of the root mean square deviation as a function of time. On this basis the 'quality' of the starting structure seems mainly to influence the simulation stability of the transmembrane beta-barrel domain. Root mean square fluctuations were used to compare simulation mobility as a function of residue number. The resultant residue mobility profiles were qualitatively similar for the corresponding X-ray and NMR structure-based simulations. However, all three proteins were generally more mobile in the NMR-based than in the X-ray simulations. Principal components analysis was used to identify the dominant motions within each simulation. The first two eigenvectors (which account for >50% of the protein motion) reveal that such motions are concentrated in the extracellular loops and, in the case of PagP, in the N-terminal alpha-helix. Residue profiles of the magnitude of motions corresponding to the first two eigenvectors are similar for the corresponding X-ray and NMR simulations, but the directions of these motions correlate poorly reflecting incomplete sampling on a approximately 10 ns timescale.
Conformational fluctuations of enzymes may play an important role for substrate recognition and/or catalysis, as it has been suggested in the case of the protease enzymatic superfamily. Unfortunately, theoretically addressing this issue is a problem of formidable complexity, as the number of the involved degrees of freedom is enormous: indeed, the biological function of a protein depends, in principle, on all its atoms and on the surrounding water molecules. Here we investigated a membrane protease enzyme, the OmpT from Escherichia coli, by a hybrid molecular mechanics/coarse-grained approach, in which the active site is treated with the GROMOS force field, whereas the protein scaffold is described with a Go-model. The method has been previously tested against results obtained with all-atom simulations. Our results show that the large-scale motions and fluctuations of the electric field in the microsecond timescale may impact on the biological function and suggest that OmpT employs the same catalytic strategy as aspartic proteases. Such a conclusion cannot be drawn within the 10- to 100-ns timescale typical of current molecular dynamics simulations. In addition, our studies provide a structural explanation for the drop in the catalytic activity of two known mutants (S99A and H212A), suggesting that the coarse-grained approach is a fast and reliable tool for providing structure/function relationships for both wild-type OmpT and mutants.
Molecular Dynamics simulations are nowadays routinely used to complement experimental studies and overcome some of their limitations. In particular, current experimental techniques do not allow to directly observe the full dynamics of a macromolecule at atomic detail. Molecular simulation engines provide time-dependent atomic positions, velocities and system energies according to biophysical models. Many molecular simulation engines can now compute a molecular dynamics trajectory of interesting biological systems in interactive time. This progress has lead to a new approach called Interactive Molecular Dynamics. It allows the user to control and visualise a molecular simulation in progress. We have developed a generic library, called MDDriver, in order to facilitate the implementation of such interactive simulations. It allows one to easily create a network connection between a molecular user interface and a physically-based simulation. We use this library in order to study a biomolecular system, simulated by various interaction-enabled molecular engines and models. We use a classical molecular visualisation tool and a haptic device to control the dynamic behavior of the molecule. This approach provides encouraging results for interacting with a biomolecule and understanding its dynamics. Starting from this initial success, we decided to use Virtual Reality (VR) functionalities more intensively, by designing a VR framework dedicated to immersive and interactive molecular simulations. This framework is based on MDDriver, on the visualisation toolkit VTK, and on the vtkVRPN library, which encapsulates the VRPN library into VTK.
In this report, we present features of the neuronal SNARE complex determined by atomistic molecular dynamics simulations. The results are robust for three models, varying force fields (AMBER and GROMOS) and solvent environment (explicit and implicit). An excellent agreement with experimental findings is observed. The SNARE core complex behaves like a stiff rod, with limited conformational dynamics. An accurate picture of the interactions within the complex emerges with a characteristic pattern of atomic contacts, hydrogen bonds, and salt bridges reinforcing the underlying layer structure. This supports the metaphor of a molecular Velcro strip that has been used by others to describe the neuronal fusion complex. No evidence for directionality in the formation of these interactions was found. Electrostatics largely dominates all interactions, with an acidic surface patch structuring the hydration layers surrounding the complex. The interactions within the four-helix bundle are asymmetric, with the synaptobrevin R-SNARE notably exhibiting an increased rigidity with respect to the three Q-SNARE helices. The interaction patterns we observe provide a new tool for interpreting the impact of mutations on the complex.In this report, we present features of the neuronal SNARE complex determined by atomistic molecular dynamics simulations. The results are robust for three models, varying force fields (AMBER and GROMOS) and solvent environment (explicit and implicit). An excellent agreement with experimental findings is observed. The SNARE core complex behaves like a stiff rod, with limited conformational dynamics. An accurate picture of the interactions within the complex emerges with a characteristic pattern of atomic contacts, hydrogen bonds, and salt bridges reinforcing the underlying layer structure. This supports the metaphor of a molecular Velcro strip that has been used by others to describe the neuronal fusion complex. No evidence for directionality in the formation of these interactions was found. Electrostatics largely dominates all interactions, with an acidic surface patch structuring the hydration layers surrounding the complex. The interactions within the four-helix bundle are asymmetric, with the synaptobrevin R-SNARE notably exhibiting an increased rigidity with respect to the three Q-SNARE helices. The interaction patterns we observe provide a new tool for interpreting the impact of mutations on the complex.
The SNARE protein complex is central to membrane fusion, a ubiquitous process in biology. Modelling this system in order to better understand its guiding principles is a challenging task. This is mainly due to the complexity of the environment: two adjacent membranes and a central bundle of four helices formed by vesicular and plasma membrane proteins. Not only the size of the actual system, but also the computing time required to equilibrate it render this a demanding task requiring exceptional computing resources. Within the DEISA Extreme Computing Initiative (DECI), we have performed 40 ns of atomistic molecular dynamics simulations with an average performance of 81.5 GFlops on 96 processors using 218 000 CPU hours. Here we describe the setup of the simulation system and the computational performance characteristics.
Comparative molecular dynamics (MD) simulations enable us to explore the conformational dynamics of the active sites of distantly related enzymes. We have used the BioSimGrid (http://www.biosimgrid.org) database to facilitate such a comparison. Simulations of four enzymes were analyzed. These included three hydrolases and a transferase, namely acetylcholinesterase, outer-membrane phospholipase A, outer-membrane protease T, and PagP (an outer-membrane enzyme which transfers a palmitate chain from a phospholipid to lipid A). A set of 17 simulations were analyzed corresponding to a total of approximately 0.1 micros simulation time. A simple metric for active-site integrity was used to demonstrate the existence of clusters of dynamic conformational behaviour of the active sites. Small (i.e. within a cluster) fluctuations appear to be related to the function of an enzymatically active site. Larger fluctuations (i.e. between clusters) correlate with transitions between catalytically active and inactive states. Overall, these results demonstrate the potential of a comparative MD approach to analysis of enzyme function. This approach could be extended to a wider range of enzymes using current high throughput MD simulation and database methods.
Understanding proteins well enough to rationally modify their biological function requires understanding how these biomolecules behave in their natural cellular, or extra-cellular, environments. This, in turn, implies understanding their interactions with a wide variety of other species within a dense and heterogeneous medium. Molecular modelling and simulation can certainly contribute to improving our understanding in this area, however the range of molecules and processes involved in the biological systems implies that a range of modelling techniques will have to be applied, balancing the requirements for accuracy and precision against the constraints imposed by the size, time and energy scales involved. This article attempts to summarize the various representations, methodologies and target functions presently available to molecular modellers, discusses how different combinations of these basic features can be combined to attack different problems and then considers the role of hybrid methods, an area where there is still much scope for development.
Our goal was to assess the relationship between membrane protein quality, output from protein quality checkers and output from molecular dynamics (MD) simulations. Membrane transport proteins are essential for a wide range of cellular processes. Structural features of integral membrane proteins are still under-explored due to experimental limitations in structure determination. Computational techniques can be used to exploit biochemical and medium resolution structural data, as well as sequence homology to known structures, and enable us to explore the structure-function relationships in several transmembrane proteins. The quality of the models produced is vitally important to obtain reliable predictions. An examination of the relationship between model stability in molecular dynamics (MD) simulations derived from RMSD (root mean squared deviation) and structure quality assessment from various protein quality checkers was undertaken. The results were compared to membrane protein structures, solved at various resolution, by either X-ray or electron diffraction techniques. The checking programs could predict the potential success of MD in making functional conclusions. MD stability was shown to be a good indicator for the quality of structures. The quality was also shown to be dependent on the resolution at which the structures were determined.
In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging from helical pores such as gramicidin and small beta-barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the C(alpha)-atom trajectories was employed to assess the convergence of the conformational sampling in both the transmembrane domains and the whole proteins, while the time-dependence of the average structure was analyzed to obtain single-domain information. The membrane-embedded regions, particularly those of small or structurally simple proteins, were found to achieve reasonable convergence. By contrast, extra-membranous domains lacking secondary structure are often markedly under-sampled, exhibiting a continuous structural drift. This drift results in a significant imprecision in the calculated B-factors, which detracts from any quantitative comparison to experimental data. In view of such limitations, we suggest that similar analyses may be valuable in simulation studies of membrane protein dynamics, in order to attach a level of confidence to any biologically relevant observations.
Five molecular dynamics simulations (total duration >25 ns) have been performed on the Escherichia coli outer membrane protease OmpT embedded in a dimyristoylphosphatidylcholine lipid bilayer. Globally the protein is conformationally stable. Some degree of tilt of the beta-barrel is observed relative to the bilayer plane. The greatest degree of conformational flexibility is seen in the extracellular loops. A complex network of fluctuating H-bonds is formed between the active site residues, such that the Asp210-His212 interaction is maintained throughout, whereas His212 and Asp83 are often bridged by a water molecule. This supports a catalytic mechanism whereby Asp83 and His212 bind a water molecule that attacks the peptide carbonyl. A configuration yielded by docking calculations of OmpT simulation snapshots and a model substrate peptide Ala-Arg-Arg-Ala was used as the starting point for an extended Huckel calculation on the docked peptide. These placed the lowest unoccupied molecular orbital mainly on the carbon atom of the central C=O in the scissile peptide bond, thus favoring attack on the central peptide by the water held by residues Asp83 and His212. The trajectories of water molecules reveal exchange of waters between the intracellular face of the membrane and the interior of the barrel but no exchange at the extracellular mouth. This suggests that the pore-like region in the center of OmpT may enable access of water to the active site from below. The simulations appear to reveal the presence of specific lipid interaction sites on the surface of the OmpT barrel. This reveals the ability of extended MD simulations to provide meaningful information on protein-lipid interactions.
OMPLA is a phospholipase found in the outer membranes of many Gram-negative bacteria. Enzyme activation requires calcium-induced dimerisation plus bilayer perturbation. As the conformation of OMPLA in the different crystal forms (monomer versus dimer; with/without bound Ca(2+)) is remarkably similar we have used multi-nanosecond molecular dynamics (MD) simulations to probe possible differences in conformational dynamics that may be related to enzyme activation. Simulations of calcium-free monomeric OMPLA, of the Ca(2+)-bound dimer, and of the Ca(2+)-bound dimer with a substrate analogue covalently linked to the active site serine have been performed, all with the protein embedded in a phospholipid (POPC) bilayer. All simulations were stable, but differences in the dynamic behaviour of the protein between the various states were observed. In particular, the stability of the active site and the hydrophobic substrate-binding cleft varied. Dimeric OMPLA is less flexible than monomeric OMPLA, especially around the active site. In the absence of bound substrate analogue, the hydrophobic substrate-binding cleft of dimeric OMPLA collapses. A model is proposed whereby the increased stability of the active site in dimeric OMPLA is a consequence of the local ordering of water around the nearby calcium ion. The observed collapse of the substrate-binding cleft may explain the experimentally observed occurrence of multiple dimer conformations of OMPLA, one of which is fully active while the other shows significantly reduced activity.
Molecular modeling and simulation approaches have been use to generate a complete model of the prokaryotic ABC transporter MsbA from Escherichia coli, starting from the low-resolution structure-based Calpha trace (PDB code 1JSQ). MsbA is of some biomedical interest as it is homologous to mammalian transporters such as P-glycoprotein and TAP. The quality of the MsbA model is assessed using a combination of molecular dynamics simulations and static structural analysis. These results suggest that the approach adopted for MsbA may be of general utility for generating all atom models from low-resolution crystal structures of membrane proteins. Molecular dynamics simulations of the MsbA model inserted in a fully solvated octane slab (a membrane mimetic environment) reveal that while the monomer is relatively stable, the dimer is unstable and undergoes significant conformational drift on a nanosecond time scale. This suggests that the MsbA crystal dimer may not correspond to the MsbA dimer in vivo. An alternative model of the dimer is discussed in the context of available experimental data.
We report theoretical investigations on the complexation and liquid-liquid extraction of trivalent lanthanide cations by picolinamide ligands L. The relative contributions of pyridine vs. amide moieties of L and the effect of alkyl substituents are investigated in the gas phase by quantum mechanical calculations. The uncomplexed ligands L with different lipophilic substituents and Eu(NO(3))(3)L(3) complexes are simulated at a water-"oil" interface, where "oil" is modeled by chloroform. The simulations point to the importance of interfacial phenomena in the liquid-liquid extraction of cations by picolinamide ligands and the difference between pyridine vs. amide substituted ligands.
We report molecular dynamics simulations on the phase separation of "perfectly mixed" water/oil/tri-n-butylphosphate (TBP) solutions containing 30 or 60 TBP molecules and 5 UO(2)(NO(3))(2) complexes. The oil phase is mimicked by one of two liquids, either chloroform or supercritical CO(2) (SC-CO(2)). The simulations demonstrate the importance of TBP concentration. In the TBP(30) systems, the water and oil phases separate on the nanosecond time scale, leading to two interfaces onto which all TBPs adsord. Some of them spontaneously form 1:1 and 1:2 complexes with UO(2)(NO(3))(2) at the interface. With the more concentrated TBP(60) systems, water and oil do not separate but form microemulsions containing neat water "droplets" surrounded by oil in which TBP is solubilized, sitting at the oil-water boundaries delimiting the droplets. All UO(2)(NO(3))(2) salts are complexed by TBP at the liquid boundaries, sitting somewhat more in oil than in water. Following the Le Chatelier rule, the proportion of 1:2 complexes is larger in the TBP60 system than in the TBP(30) system. Thus, TBP acts not only as a complexant but also as an "interface modifier". The simulations reveal strong analogies between chloroform and SC-CO(2) as organic phases. These novel results are crucial for our understanding of the state of heterogeneous solutions involved in uranyl extraction by TBP as well as assisted cation extraction by other extractants.
Molecular dynamics simulations provide microscopic pictures of the behavior of TBP (tri-n-butyl phosphate) at the waterââoilâ interface, and in waterââoilâ mixtures where âoilâ is modeled by chloroform. It is shown that, depending on the TBP concentration and water acidity, TBP behaves as a surfactant, an interface modifier, or a solute in oil. At low concentrations, TBP is surface active and forms an unsaturated monolayer at the âplanarâ interface between the pure water and oil phases, adopting an âamphiphilic orientationâ. Increasing the TBP concentration induces waterâoil mixing at the interface which becomes very rough while TBP orientations at the phase boundary are more random and TBP molecules solubilize in oil. The effect of water acidity is investigated with three nitric acid models: neutral NO3H, ionic NO3- H3O+ and TBPH+ NO3-. The role of these species on the properties of the waterâoil boundaries and on the outcome of waterâoil demixing experiments is presented. The neutral NO3H form is highly surface active. Hydrogen bonding between TBP and NO3H, TBPH+, or H3O+ disrupts the first TBP layer and leads, at high TBP concentrations, to a mixed third phase or to a microemulsion. These results are important for our understanding of the microscopic solution state of liquidâliquid extraction systems.
Molecular dynamics simulations on the 1:1 M3+ lanthanide (La3+, Eu3+ and Yb3+) âinclusionâ complex of a t-butyl-calix[4]arene L substituted at the narrow rim by four CH2âP(O)Ph2 arms demonstrate the role of hydration and counterions on the cation binding mode and shielding. In dry chloroform and in the absence of counterions, the cation is âendoâ, fully encapsulated within the pseudo-cavity delineated by the four phosphoryl arms and the four phenolic oxygens. This âendoâ bidentate binding mode is supported by full ab initio quantum mechanical optimization of the calixarene M3+ complexes. In biphasic solution, the complexes are shown to be surface active and to adsorb at an âoilâ/water interface with the cationic site pointing towards water and the hydrophobic t-butyl groups in âoilâ. The cation is not encapsulated, but adopts an âexo â position, coordinated to the four P[double bond, length half m-dash]O oxygens of L, to water molecules, and to counterions. This complex is too hydrophilic to be extracted from the interface to an organic phase. The unexpected binding mode has important implications concerning the mechanism of liquidâliquid ion extraction and the microscopic state of the extracted complex in the organic phase.
We report MD studies on a chloroform / nitric acid water interface, either neat, or saturated by TBP molecules. Two extreme models are compared, where the acid is either neutral HNO3 or dissociated to NO3â and H3O+. The latter species are found to be ârepelledâ by the neat interface, while the neutral HNO3 molecules are surface active. When the neat interface is saturated by TBP molecules, the latter form highly disordered arrangements instead of a regular monolayer, and water is dragged to the organic phase as 1:1, 1:2 and 2:2 hydrates of TBP. Simulations with the neutral HNO3 model lead to extraction of acid to the organic phase, hydrogen bonded to the phosphoryl oxygen of TBP, forming HNO3:TBP adducts of 1:1 and 2:1 types. Simulations with the ionic model lead to H3O+:TBP adducts of 1:1, 1:2 and 1:3 types in the organic phase and significant mixing of the chloroform, TBP and water liquids in the interfacial region.
This document provides user feedback by Marc Baaden on the ChemOffice Ultra 4.5 software experienced during his PhD. The software suite includes Chem3D, a program for visualizing and exploring 3D molecular models, and ChemDraw, which offers powerful options for modifying 2D structures and creating high-quality illustrations. The software can visualize optimized geometries and molecular surfaces obtained through first-principle calculations and is compatible with molecular dynamics calculations and ab initio studies. However, it has some flaws and shortcomings, such as B. the lack of an interface to deal with z-matrices and high CPU and memory requirements. The software has extensive documentation and is useful for a variety of tasks.
We report a molecular dynamics (MD) study on M3+ lanthanide (La3+, Eu3+, and Yb3+) cations in dry acetonitrile solution and in M(MeCN)n3+ clusters (n = 1â15) where two classical force-field representations of the cations are compared, in conjunction with the OPLS model of acetonitrile. It is shown that a set of van der Waals cation parameters (set2) fitted from free energies of hydration overestimates the cation coordination numbers (CNs). Another set of parameters (set1), where the size of cations is scaled down by 21/6 (using the Ï van der Waals value for R*) yields better results. Quantum mechanical calculations performed on M(MeCN)n3+ aggregates (n = 1â9) demonstrate the importance of charge-transfer and polarization effects. They confirm the preferred coordination number of eight for Yb3+, the Yb(MeCN)8+13+ species with one MeCN molecule in the outer coordination sphere being somewhat more stable than Yb(MeCN)93+D3h. Adding a polarization term for the 1â6â12 OPLS acetonitrile to the force field (set2+pol) indeed markedly improves the calculated CNs. In all MD simulations, a remarkable dynamic feature is observed in the first solvation shell where the lifetime of acetonitrile molecules increases from Yb3+ to La3+, that is, inversely to the cationâsolvent interaction energies and to the aqueous phase behavior. Rare-earth salts with ClO4- and F3CSO3- anions and the question of ion binding selectivity by L ligands (formation of ML33+ complexes, where L is a pyridineâdicarboxamide ligand) in acetonitrile solution are investigated by free-energy perturbation simulations, comparing the set1, set2, and set2+pol models. It is found that selectivities are markedly determined by the change in solvation-free energies of the uncomplexed cations, with pronounced counterion effects. The two simplest models (set1 or set2 without polarization) predict the correct order of complexation (Yb3+ > Eu3+ > La3+), whereas addition of polarization contribution leads to the inverse order, because of overestimation of the cationâanion interactions in the salt solutions.
We report molecular dynamics studies on the interfacial behavior of species involved in the assisted liquid-liquid extraction of cesium and uranyl cations. The distribution of uncomplexed Cs+Pic- and UO2(NO3)2 salts is first described at the water / chloroform interface. This is followed by simulations of monolayers of calix[4]arene-crown6 Cs+Pic- complexes at the interface, where they are found to remain adsorbed, contrary to expectations from extraction experiments. The question of synergistic effects is addressed by simulating these calixarenes at a TBP saturated interface (TBP = tributylphosphate). Finally, in relation with the extraction of uranyl by TBP, we report a computer demixing experiment of a "perfectly mixed" ternary water / chloroform / TBP mixture containing 5 UO2(NO3)2 molecules. The phase separation is found to be rapid, leading to the formation of a TBP layer between the aqueous and organic phases and to spontaneous complexation of the uranyl salts by TBP. The complexes formed are not extracted to chloroform, but remain close to the water / organic phase boundary. The simulations reveal the importance of interfacial phenomena in the ion extraction and recognition processes.
Combined spectroscopic and theoretical studies have been performed on two recently developed calix[4]arenes in the cone conformation, L1 (bearing two âCH2C(O)NEt2 and two âCH2P(O)Ph2 substituents occupying respectively distal phenolic positions) and L2 (with four âCH2P(O)Ph2 substituents), in order to compare the Li+vs. Na+ cation binding mode. Molecular dynamics simulations indicate that coordination of the Li+ cation involves three of the four substituents (the two phosphoryl groups and one of the two amide functions of L1; three phosphoryl arms of L2). A variable temperature NMR study carried out with L1·Li+ confirms this fourfold coordination and reveals that in solution the lithium cation moves between the two adjacent OPOPOamide units. The weaker binding of the Na+ cation results in a more symmetrical coordination of the four phenolic oxygen atoms and two carbonyls of L1 or four phosphoryls of L2.
The lanthanide and Th4+ complexes with calix[4]arene ligands substituted either on the narrow or at the wide rim by four coordinating groups behave totally differently as shown by an NMR investigation of the dia- and paramagnetic complexes. Solutions of complexes were prepared by reacting anhydrous metal perchlorate salts with the ligands in dry acetonitrile (CAUTION). Relaxation time T1 titrations of acetonitrile solutions of Gd3+ by calixarenes indicate that ligands substituted on the narrow rim form stable 1:1 complexes whether they feature four amide groups (1) or four phosphine oxide functions. In contrast, a ligand substituted by four (carbamoylmethyl)diphenylphosphine oxide moieties on the wide rim (3) and its derivatives form polymeric species even at a 1:1 ligand/metal concentration ratio. Nuclear magnetic relaxation dispersion (NMRD) curves (relaxation rates 1/T1 vs magnetic field strength) of Gd3+, Gd3+·1 and Gd3+·3 perchlorates in acetonitrile are analyzed by an extended version of the SolomonâBloembergenâMorgan equations. A comparison of the calculated rotational correlation times Ïr shows that ligand 3 forms oligomeric Gd3+ species. The chelates of ligand 1 are axially symmetric (C4 symmetry), and the paramagnetic shifts induced by the Yb3+ ion are accounted for quantitatively. The addition of water or of nitrate ions does not modify the geometry of the complex. The metal chelates of 3 and its derivatives adopt a C2 symmetry, and the paramagnetic shifts are interpreted on a semiquantitative basis only. Water and NO3- ions completely labilize the complexes of the heavy lanthanides. The very high selectivity of ligand 3 through the lanthanide series stems from a complex interplay of factors.
The âGauge Including Atomic Orbitalsâ (GIAO) approach is used to investigate the question of intramolecular rotation. Ab initio GIAO calculations of NMR chemical shielding tensors carried out with GAUSSIAN 94 within the SCF-Hartree-Fock approximation are described. In order to compare the calculated chemical shifts with experimental ones, it is important to use consistent nuclear shieldings for NMR reference compounds like TMS. The influence of rotating functional groups X=CH3, CHO, NO2, NH2, CONH2, COOH or C6H5 on the shielding tensors in seven vinylic derivatives H2C=CH-X is studied; the molecules are propene, acrolein, nitroethylene, ethyleneamine, acrylamide, acrylic acid and styrene. We observe a marked dependence of nuclear shielding and chemical shift on the torsional movement. Different Boltzmann averages over the conformational states are considered and compared for gas phase, liquid and solid state NMR. Their applicability to model cases for rigid or freely rotating molecules and for fixed molecules (e.g. polymers or proteins) with rapidly rotating groups is discussed and simple calculation models are presented. On the basis of this work it can be concluded that intramolecular rotation clearly affects the observed averages. Effects of up to 2 ppm have been observed for isotropic chemical shifts, and up to 17 ppm difference have been observed for individual tensor components, for example, of the carboxylic 13C atom in acrylic acid. The variation of the shielding tensor on a nucleus in a fixed molecular backbone resulting from an attached rotating group furthermore leads to a new relaxation mechanism by chemical shift anisotropy.
We report a molecular dynamics study on the 1:1 M3+ lanthanide (La3+, Eu3+ and Yb3+) inclusion complexes of an important extractant molecule L: a calix[4]arene-tetraalkyl ether substituted at the wide rim by four NH-C(O)-CH2-P(O)Ph2 arms. The M(NO3)3 and MCl3 complexes of L are compared in methanol solution and at a water / chloroform interface. In the different environments the coordination sphere of M3+ involves the four phosphoryl oxygens and three to four loosely bound carbonyl oxygens of the CMPO-like arms. Based on free energy simulations, we address the question of ion binding selectivity in pure liquid phases and at the liquid-liquid interface where L and the complexes are found to adsorb. According to the simulations, the enhancement of M3+ cation extraction in the presence of the calixarene platform, examined by comparing L to the (CMPO)4 âligandâ at the interface, is related to the fact that (i) the (CMPO)4Eu(NO3)3 complex is more hydrophilic than the LEu(NO3) one and (ii) the free CMPO ligands spread at the interface, and are therefore less organized for cation capture than L.
We report ab initio quantum mechanical calculations on charged LM3+ and neutral LMCl3 complexes formed by lanthanide M3+ cations (M = La, Eu, Yb) and model ligands L, where L are phosphorous derivatives R3PO (R = alkyl/O-alkyl/phenyl), R3PS and R2PS2- (R = alkyl/phenyl), and amide, pyridine, triazine and anisole ligands. Among all neutral ligands studied, Ph3PO is intrinsically clearly the best. However, the comparison of LM3+ to LMCl3 complexes demonstrates that the concept of 'ligand basicity' is not sufficient to compare the efficiency of cation coordination. Counterions play an important role in the structures of the complexes and for the consequences of substitution in the Ligand. For instance, in the absence of competing interactions, phenyl substituted R3PS or R2PS2- ligands interact better than alkyl substituted ones, but the order is reversed in the presence of counterions. Counterions also amplify the alkyl vs. O-alkyl substituent effect in R3PO complexes. Bidentate anions or more bulky anions are expected to amplify the effects observed with chloride anions. Thus, multiple interactions between counterions and the other species in the first coordination sphere markedly contribute to the 'effectiveness' and stereochemistry of ligand-cation interactions. (C) 2000 Elsevier Science S.A. All rights reserved.
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