Exploring transmembrane diffusion pathways with molecular dynamics

Molecular dynamics simulation for membrane separation and porous materials: A current state of art review

Computational frameworks have been under specific attention within the last two decades. Molecular Dynamics (MD) simulations, identical to the other computational approaches, try to address the unknown question, lighten the dark areas of unanswered questions, to achieve probable explanations and solutions. Owing to their complex microporous structure on one side and the intricate biochemical nature of various materials used in the structure, separative membrane materials possess peculiar degrees of complications. More notably, as nanocomposite materials are often integrated into separative membranes, thin-film nanocomposites and porous separative nanocomposite materials could possess an additional level of complexity with regard to the nanoscale interactions brought to the structure. This critical review intends to cover the recent methods used to assess membranes and membrane materials. Incorporation of MD in membrane technology-related fields such as desalination, fuel cell-based energy production, blood purification through hemodialysis, etc., were briefly covered. Accordingly, this review could be used to understand the current extent of MD applications for separative membranes. The review could also be used as a guideline to use the proper MD implementation within the related fields.

The Evolution of Cholesterol-Rich Membrane in Oxygen Adaption: The Respiratory System as a Model

The increase in atmospheric oxygen levels imposed significant environmental pressure on primitive organisms concerning intracellular oxygen concentration management. Evidence suggests the rise of cholesterol, a key molecule for cellular membrane organization, as a cellular strategy to restrain free oxygen diffusion under the new environmental conditions. During evolution and the increase in organismal complexity, cholesterol played a pivotal role in the establishment of novel and more complex functions associated with lipid membranes. Of these, caveolae, cholesterol-rich membrane domains, are signaling hubs that regulate important in situ functions. Evolution resulted in complex respiratory systems and molecular response mechanisms that ensure responses to critical events such as hypoxia facilitated oxygen diffusion and transport in complex organisms. Caveolae have been structurally and functionally associated with respiratory systems and oxygen diffusion control through their relationship with molecular response systems like hypoxia-inducible factors (HIF), and particularly as a membrane-localized oxygen sensor, controlling oxygen diffusion balanced with cellular physiological requirements. This review will focus on membrane adaptations that contribute to regulating oxygen in living systems.

Emerging Diversity in Lipid-Protein Interactions

Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Computational methods in drug discovery

The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.

The cellular membrane as a mediator for small molecule interaction with membrane proteins

The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Improving Luminol Blood Detection in Forensics

The aim of this study was to develop chemical improvements to the original Weber protocol, in order to increase the intensity and time length of light emission and to eliminate false-positive reactions. The intensity and duration of light were measured on serial blood dilutions using a plate reader chemiluminometer. Blood stains of various concentrations were impregnated in pure cellulose, dried, and luminol solution was added with/without the potential enhancers. An in silico study was also conducted, aiming to demonstrate the enhancing mechanism of hemoglobin denaturation using 8 M urea. The luminol blood detection test revealed important improvements after urea pretreatment or in the presence of monochloro-triazinyl-β-cyclodextrin. This approach also eliminated the false-positive reaction from sodium hypochlorite. These improvements could provide a higher sensitivity under particular circumstances such as old or washed blood stains, leading to a better localization for further DNA typing and higher quality photographic analysis.

Effect of colostrum and milk on small intestine expression of AQP4 and AQP5 in newborn buffalo calves

Functional studies indicate differences in newborn gastrointestinal morphology and physiology after a meal. Both water and solutes transfer across the intestinal epithelial membrane appear to occur via aquaporins (AQPs). Given that the physiological roles of AQP4 and AQP5 in the developing intestine have not been fully established, the objective of this investigation was to determine their distribution, expression and respective mRNA in the small intestine of colostrums-suckling buffalo calves by using immunohistochemistry, Western blot, and reverse transcriptase-PCR analysis. Results showed different tissue distribution between AQP4 and AQP5 with the presence of the former along the enteric neurons and the latter in the endocrine cells. Moreover, their expression levels were high in the ileum of colostrum-suckling buffalo calves. The data present a link between feeding, intestinal development and water homeostasis, suggesting the involvement of these channel proteins in intestinal permeability and fluid secretion/absorption during this stage of development after birth.

Beyond water homeostasis: Diverse functional roles of mammalian aquaporins

BACKGROUND

Aquaporin (AQP) water channels are best known as passive transporters of water that are vital for water homeostasis.

SCOPE OF REVIEW

AQP knockout studies in whole animals and cultured cells, along with naturally occurring human mutations suggest that the transport of neutral solutes through AQPs has important physiological roles. Emerging biophysical evidence suggests that AQPs may also facilitate gas (CO2) and cation transport. AQPs may be involved in cell signalling for volume regulation and controlling the subcellular localization of other proteins by forming macromolecular complexes. This review examines the evidence for these diverse functions of AQPs as well their physiological relevance.

MAJOR CONCLUSIONS

As well as being crucial for water homeostasis, AQPs are involved in physiologically important transport of molecules other than water, regulation of surface expression of other membrane proteins, cell adhesion, and signalling in cell volume regulation.

GENERAL SIGNIFICANCE

Elucidating the full range of functional roles of AQPs beyond the passive conduction of water will improve our understanding of mammalian physiology in health and disease. The functional variety of AQPs makes them an exciting drug target and could provide routes to a range of novel therapies.

Molecular dynamics simulations of the transport of reactive oxygen species by mammalian and plant aquaporins

BACKGROUND

Aquaporins are responsible for water transport across lipid membranes. They are also able to transport reactive oxygen species, playing an important role in redox signaling. Certain plant aquaporins have even the ability to be regulated by oxidative stress. However, the underlying mechanisms are still not fully understood.

METHODS

Here, molecular dynamics simulations were employed to determine the activation free energies related to the transport of reactive oxygen species through both mammalian and plant aquaporin models.

RESULTS AND CONCLUSIONS

Both aquaporins may transport hydrogen peroxide (H2O2) and the protonated form of superoxide radicals (HO2). The solution-to-pore transfer free energies were low for small oxy-radicals, suggesting that even highly reactive hydroxyl radicals (HO) might have access to the pore interior and oxidize amino acids responsible for channel selectivity. In the plant aquaporin, no significant change in water permeability was observed upon oxidation of the solvent-exposed disulfide bonds at the extracellular region. During the simulated time scale, the existence of a direct oxidative gating mechanism involving these disulfide bonds could not be demonstrated.

GENERAL SIGNIFICANCE

Simulation results may improve the understanding of redox signaling mechanisms and help in the interpretation of protein oxidative labeling experiments.

Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach

In order to elucidate how phosphatidylserine (PS6) interacts with AQP5 in a cell membrane, we developed a hybrid steered molecular dynamics (hSMD) method that involved: (1) Simultaneously steering two centers of mass of two selected segments of the ligand, and (2) equilibrating the ligand-protein complex with and without biasing the system. Validating hSMD, we first studied vascular endothelial growth factor receptor 1 (VEGFR1) in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide (8ST), for which the binding energy is known from in vitro experiments. In this study, our computed binding energy well agreed with the experimental value. Knowing the accuracy of this hSMD method, we applied it to the AQP5-lipid-bilayer system to answer an outstanding question relevant to AQP5's physiological function: Will the PS6, a lipid having a single long hydrocarbon tail that was found in the central pore of the AQP5 tetramer crystal, actually bind to and inhibit AQP5's central pore under near-physiological conditions, namely, when AQP5 tetramer is embedded in a lipid bilayer? We found, in silico, using the CHARMM 36 force field, that binding PS6 to AQP5 was a factor of 3 million weaker than "binding" it in the lipid bilayer. This suggests that AQP5's central pore will not be inhibited by PS6 or a similar lipid in a physiological environment.

Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway?

MAIN CONCLUSION

Enhancing the membrane content of PtdInsP 2 , the already-recognized protein-regulating lipid, increased the osmotic water permeability of tobacco protoplasts, apparently by increasing the abundance of active aquaporins in their membranes. While phosphoinositides are implicated in cell volume changes and are known to regulate some ion channels, their modulation of aquaporins activity has not yet been reported for any organism. To examine this, we compared the osmotic water permeability (P f) of protoplasts isolated from tobacco (Nicotiana tabacum) cultured cells (NT1) with different (genetically lowered or elevated relative to controls) levels of inositol trisphosphate (InsP3) and phosphatidyl inositol [4,5] bisphosphate (PtdInsP2). To achieve this, the cells were transformed with, respectively, the human InsP3 5-phosphatase ('Ptase cells') or human phosphatidylinositol (4) phosphate 5-kinase ('PIPK cells'). The mean P f of the PIPK cells was several-fold higher relative to that of controls and Ptase cells. Three results favor aquaporins over the membrane matrix as underlying this excessive P f: (1) transient expression of the maize aquaporin ZmPIP2;4 in the PIPK cells increased P f by 12-30 μm s(-1), while in the controls only by 3-4 μm s(-1). (2) Cytosol acidification-known to inhibit aquaporins-lowered the P f in the PIPK cells down to control levels. (3) The transcript of at least one aquaporin was elevated in the PIPK cells. Together, the three results demonstrate the differences between the PIPK cells and their controls, and suggest a hitherto unobserved regulation of aquaporins by phosphoinositides, which could occur through direct interaction or indirect phosphoinositides-dependent cellular effects.

Chemical reactivity drives spatiotemporal organisation of bacterial metabolism

In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.

How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion

One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.

Current state-of-the-art molecular dynamics methods and applications

Molecular dynamics simulations are used to describe the patterns, strength, and properties of protein behavior, drug-receptor interactions, the solvation of molecules, the conformational changes that a protein or molecule may undergo under various conditions, and other events that require the systematic evaluation of molecular properties in dynamic molecular systems. Only few years ago proteins were considered to be rigid body structures with very limited conformational flexibility. However, it is now clear that proteins are highly dynamic structures, the internal organization of which is the key to their 3D spatial arrangement and hence biological function. The study of protein dynamics in the lab is a very complicated, expensive, and time-consuming process. Therefore, a lot of effort and hope lies with the computers and the in silico study of protein structure and molecular dynamics. Herein, an effort has been made to describe the ever-evolving field of molecular dynamics, the different algorithms, and force fields that are being used as well as to provide some insight on what the near future holds for this auspicious field of computational structural biology.

Visualizing functional motions of membrane transporters with molecular dynamics simulations

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Permeation pathway of homomeric connexin 26 and connexin 30 channels investigated by molecular dynamics

Mutations in the genes GJB2 and GJB6 encoding human connnexin26 (hCx26) and connexin30 (hCx30), respectively, are the leading cause of non-syndromic prelingual deafness in several human populations. In this work, we exploited the high degree (77%) of sequence similarity shared by hCx26 and hCx30 to create atomistic models of homomeric hCx26 and hCx30 connexons starting from the X-ray crystallographic structure of an intercellular channel formed by hCx26 protomers at 3.5-å resolution. The equilibrium dynamics of the two protein complexes was followed for 40 ns each by Molecular Dynamics (MD) simulations. Our results indicate that, in hCx26, positively charged Lys41 residues establish a potential barrier within the fully open channel, hindering ion diffusion in the absence of an electrochemical gradient. A similar role is played, in hCx30, by negatively charged Glu49 residues. The different position and charge of these two ion sieves account for the differences in unitary conductance observed experimentally. Our results are discussed in terms of present models of voltage gating in connexin channels.

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins-ion channels and transporters-which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.

Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase

Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N₂O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb₃ oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed.

Denitrification is an anaerobic process performed by several bacteria as an alternative to aerobic respiration. A key intermediate step is catalyzed by the nitric oxide reductase (NOR) enzyme, which is situated in the cytoplasmic membrane. Proton delivery to the catalytic site inside NOR is an important part of its functioning. In this work we use molecular dynamics simulations to describe water distribution and to identify proton transfer pathways in cNOR. Our results reveal two channels from the periplasmic side of the membrane and none from the cytoplasmic side, indicating that cNOR is not a proton pump. It is our hope that these results will provide a basis for further experimental and computational studies aimed to understand details of the NOR mechanism. Furthermore, this work sheds light on the molecular evolution of respiratory enzymes.

Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z

Aquaporin Z (AQPZ) is a tetrameric protein that forms water channels in the cell membrane of Escherichia coli. The histidine residue (residue 174) in the selectivity filter (SF) region plays an important role in the transport of water across the membrane. In this work, we perform equilibrium molecular dynamics (MD) simulations to illustrate the gating mechanism of the SF and the influences of residue 174 in two different protonation states: Hsd174 with the proton at Nδ, and Hse174 with the proton at Nε. We calculate the pore radii in the SF region versus the simulation time. We perform steered MD to compute the free-energy profile, i.e., the potential of mean force (PMF) of a water molecule through the SF region. We conduct a quantum mechanics calculation of the binding energy of one water molecule with the residues in the SF region. The hydrogen bonds formed between the side chain of Hsd174 and the side chain of residue 189 (Arg189) play important roles in the selectivity mechanism of AQPZ. The radii of the pores, the hydrogen-bond analysis, and the free energies show that it is easier for water molecules to permeate through the SF region of AQPZ with residue 174 in the Hse state than in the Hsd state.

Water homeostasis: evolutionary medicine

As a major component of homeostasis, all organisms regulate the water composition of various compartments. Through the selective use of barrier membranes and surface glycoproteins, as well as aquaporin water channels, organisms ranging from Archaebacteria to humans can vary water permeabilities across their cell membranes by 4 to 5 orders of magnitude. In barrier epithelia the outer, or exofacial, leaflet acts as the main resistor to water flow; this leaflet restricts water flow by minimizing the surface area of lipid molecules which is not covered by phosphate headgroups and by packing hydrocarbon chains at maximal density. Cells may enhance the barrier by expressing glycoproteins that augment the "thickness" of unstirred layers at their surfaces, reducing osmotic gradients at the lipid bilayer surface. Aquaporins markedly and highly selectively accelerate water flux and are "switched on" either by deployment into membranes or gating. This review summarizes these mechanisms in many species, and indicates potential roles for manipulating water permeabilities in treating disease.

Reviewing ligand-based rational drug design: the search for an ATP synthase inhibitor

Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs.

Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors

Despite many years of dedicated efforts, high-resolution structural determination of membrane proteins lags far behind that of soluble proteins. Computational methods in general, and molecular dynamics (MD) simulations in particular, have represented important alternative resources over the years to advance understanding of membrane protein structure and function. However, it is only recently that much progress has been achieved owing to new high-resolution membrane protein structures, specialized parallel computer architectures, and efficient simulation algorithms. This has definitely been the case for G protein-coupled receptors (GPCRs), which have assumed a leading role in the area of structural biology with several new structures appearing in the literature during the past five years. We provide here a concise overview of recent developments in computational biophysics of membrane proteins, using GPCRs as an example to showcase important information that can be derived from modern MD simulations.

dxTuber: detecting protein cavities, tunnels and clefts based on protein and solvent dynamics

Empty space in a protein structure can provide valuable insight into protein properties such as internal hydration, structure stabilization, substrate translocation, storage compartments or binding sites. This information can be visualized by means of cavity analysis. Numerous tools are available depicting cavities directly or identifying lining residues. So far, all available techniques base on a single conformation neglecting any form of protein and cavity dynamics. Here we report a novel, grid-based cavity detection method that uses protein and solvent residence probabilities derived from molecular dynamics simulations to identify (I) internal cavities, (II) tunnels or (III) clefts on the protein surface. Driven by a graphical user interface, output can be exported in PDB format where cavities are described as individually selectable groups of adjacent voxels representing regions of high solvent residence probability. Cavities can be analyzed in terms of solvent density, cavity volume and cross-sectional area along a principal axis. To assess dxTuber performance we performed test runs on a set of six example proteins representing the three main classes of protein cavities and compared our findings to results obtained with SURFNET, CAVER and PyMol.