1
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Kondrashov OV, Akimov SA. Gramicidin A as a mechanical sensor for mixed nonideal lipid membranes. Phys Rev E 2024; 109:064404. [PMID: 39020903 DOI: 10.1103/physreve.109.064404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/22/2024] [Indexed: 07/20/2024]
Abstract
Gramicidin A (gA) is a short hydrophobic β-helical peptide that forms cation-selective channels in lipid membranes in the course of transbilayer dimerization. The length of the gA helix is smaller than the thickness of a typical lipid monolayer. Consequently, elastic deformations of the membrane arise in the configurations of gA monomers, conducting dimer, and the intermediate state of coaxial pair, where gA monomers from opposing membrane monolayers are located one on top of the other. The gA channel is characterized by the average lifetime of the conducting state. The elastic properties of the membrane influence the average lifetime, thus making gA a convenient sensor of membrane elasticity. However, the utilization of gA to investigate the elastic properties of mixed membranes comprising two or more components frequently relies on the assumption of ideality, namely that the elastic parameters of mixed-lipid bilayers depend linearly on the concentrations of the components. Here, we developed a general approach that does not rely on the aforementioned assumption. Instead, we explicitly accounted for the possibility of inhomogeneous lateral distribution of all lipid components, as well as for membrane-mediated lateral interactions of gA monomers, dimer, coaxial pair, and minor lipid components. This approach enabled us to derive unknown elastic parameters of lipid monolayer from experimentally determined lifetimes of gA channel in mixed-lipid bilayers. A general algorithm was formulated that allows the unknown elastic parameters of a lipid monolayer to be obtained using gA as a mechanical sensor.
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2
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Park S, Pastor RW, Im W. Binary bilayer simulations for partitioning within membranes. Methods Enzymol 2024; 701:123-156. [PMID: 39025570 DOI: 10.1016/bs.mie.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Membrane proteins (MPs) often show preference for one phase over the other, which is characterized by the partition coefficient, Kp. The physical mechanisms underlying Kp have been only inferred indirectly from experiments due to the unavailability of detailed structures and compositions of ordered phases. Molecular dynamics (MD) simulations can complement these details and thus, in principle, provide further insights into the partitioning of MPs between two phases. However, the application of MD has remained difficult due to long time scales required for equilibration and large system size for the phase stability, which have not been fully resolved even in free energy simulations. This chapter describes the recently developed binary bilayer simulation method, where the membrane is composed of two laterally attached membrane patches. The binary bilayer system (BBS) is designed to preserve the lateral packing of both phases in a significantly smaller size compared to that required for macroscopic phase separation. These characteristics are advantageous in partitioning simulations, as the length scale for diffusion across the system can be significantly smaller. Hence the BBS can be efficiently employed in both conventional MD and free energy simulations, though sampling in ordered phases remains difficult due to slow diffusion. Development of efficient lipid swapping methods and its combination with the BBS would be a useful approach for partitioning in coexisting phases.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA, United States.
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3
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Chang L, Mondal A, Singh B, Martínez-Noa Y, Perez A. Revolutionizing Peptide-Based Drug Discovery: Advances in the Post-AlphaFold Era. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2024; 14:e1693. [PMID: 38680429 PMCID: PMC11052547 DOI: 10.1002/wcms.1693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/18/2023] [Indexed: 05/01/2024]
Abstract
Peptide-based drugs offer high specificity, potency, and selectivity. However, their inherent flexibility and differences in conformational preferences between their free and bound states create unique challenges that have hindered progress in effective drug discovery pipelines. The emergence of AlphaFold (AF) and Artificial Intelligence (AI) presents new opportunities for enhancing peptide-based drug discovery. We explore recent advancements that facilitate a successful peptide drug discovery pipeline, considering peptides' attractive therapeutic properties and strategies to enhance their stability and bioavailability. AF enables efficient and accurate prediction of peptide-protein structures, addressing a critical requirement in computational drug discovery pipelines. In the post-AF era, we are witnessing rapid progress with the potential to revolutionize peptide-based drug discovery such as the ability to rank peptide binders or classify them as binders/non-binders and the ability to design novel peptide sequences. However, AI-based methods are struggling due to the lack of well-curated datasets, for example to accommodate modified amino acids or unconventional cyclization. Thus, physics-based methods, such as docking or molecular dynamics simulations, continue to hold a complementary role in peptide drug discovery pipelines. Moreover, MD-based tools offer valuable insights into binding mechanisms, as well as the thermodynamic and kinetic properties of complexes. As we navigate this evolving landscape, a synergistic integration of AI and physics-based methods holds the promise of reshaping the landscape of peptide-based drug discovery.
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Affiliation(s)
- Liwei Chang
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Arup Mondal
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Bhumika Singh
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | | | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL 32611
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4
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Kondrashov OV, Akimov SA. Alteration of Average Thickness of Lipid Bilayer by Membrane-Deforming Inclusions. Biomolecules 2023; 13:1731. [PMID: 38136602 PMCID: PMC10741968 DOI: 10.3390/biom13121731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Thickness of lipid bilayer membranes is a key physical parameter determining membrane permeability and stability with respect to formation of through pores. Most membrane inclusions or impurities like amphipathic peptides, transmembrane peptides, lipid inclusions of a different molecular shape, lipid domains, and protein-lipid domains, locally deform the membrane. The detailed structure of the locally deformed region of the membrane is a kind of "fingerprint" for the inclusion type. However, most experimental methods allow determining only averaged parameters of membranes with incorporated inclusions, thus preventing the direct obtaining of the characteristics of the inclusion. Here we developed a model that allows the obtaining of characteristic parameters of three types of membrane inclusions (amphipathic peptides, transmembrane peptides, monolayer lipid patches) from experimentally observable dependencies of the average thickness of lipid bilayer on the surface concentration of the inclusions. In the case of amphipathic peptides, the model provided the peptide parameters that were in qualitative agreement with the available experimental data.
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Affiliation(s)
- Oleg V. Kondrashov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Sergey A. Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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5
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Müller W, Beales PA, Muniz AR, Jeuken LJC. Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer-Lipid Hybrid Vesicles. Biomacromolecules 2023; 24:4156-4169. [PMID: 37539954 PMCID: PMC10498451 DOI: 10.1021/acs.biomac.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/20/2023] [Indexed: 08/05/2023]
Abstract
Hybrid vesicles consisting of natural phospholipids and synthetic amphiphilic copolymers have shown remarkable material properties and potential for biotechnology, combining the robustness of polymers with the biocompatibility of phospholipid membranes. To predict and optimize the mixing behavior of lipids and copolymers, as well as understand the interaction between the hybrid membrane and macromolecules like membrane proteins, a comprehensive understanding at the molecular level is essential. This can be achieved by a combination of molecular dynamics simulations and experiments. Here, simulations of POPC and PBD22-b-PEO14 hybrid membranes are shown, uncovering different copolymer configurations depending on the polymer-to-lipid ratio. High polymer concentrations created thicker membranes with an extended polymer conformation, while high lipid content led to the collapse of the polymer chain. High concentrations of polymer were further correlated with a decreased area compression modulus and altered lateral pressure profiles, hypothesized to result in the experimentally observed improvement in membrane protein reconstitution and resistance toward destabilization by detergents. Finally, simulations of a WALP peptide embedded in the bilayer showed that only membranes with up to 50% polymer content favored a transmembrane configuration. These simulations correlate with previous and new experimental results and provide a deeper understanding of the properties of lipid-copolymer hybrid membranes.
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Affiliation(s)
- Wagner
A. Müller
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - André R. Muniz
- Department
of Chemical Engineering, Universidade Federal
do Rio Grande do Sul, Porto
Alegre 90035-003, Brazil
| | - Lars J. C. Jeuken
- Leiden
Institute of Chemistry, University Leiden, PO Box 9502, 2300RA Leiden, The
Netherlands
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6
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Chávez-García C, Hénin J, Karttunen M. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. J Chem Inf Model 2022; 62:958-970. [PMID: 35130441 DOI: 10.1021/acs.jcim.1c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The malfunction of the methyl-CpG binding protein 2 (MeCP2) is associated with the Rett syndrome, one of the most common causes of cognitive impairment in females. MeCP2 is an intrinsically disordered protein (IDP), making its experimental characterization a challenge. There is currently no structure available for the full-length MeCP2 in any of the databases, and only the structure of its MBD domain has been solved. We used this structure to build a full-length model of MeCP2 by completing the rest of the protein via ab initio modeling. Using a combination of all-atom and coarse-grained simulations, we characterized its structure and dynamics as well as the conformational space sampled by the ID and transcriptional repression domain (TRD) domains in the absence of the rest of the protein. The present work is the first computational study of the full-length protein. Two main conformations were sampled in the coarse-grained simulations: a globular structure similar to the one observed in the all-atom force field and a two-globule conformation. Our all-atom model is in good agreement with the available experimental data, predicting amino acid W104 to be buried, amino acids R111 and R133 to be solvent-accessible, and having a 4.1% α-helix content, compared to the 4% found experimentally. Finally, we compared the model predicted by AlphaFold to our Modeller model. The model was not stable in water and underwent further folding. Together, these simulations provide a detailed (if perhaps incomplete) conformational ensemble of the full-length MeCP2, which is compatible with experimental data and can be the basis of further studies, e.g., on mutants of the protein or its interactions with its biological partners.
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Affiliation(s)
- Cecilia Chávez-García
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique UPR 9080, CNRS and Université de Paris, Paris 75005, France
| | - Mikko Karttunen
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Physics and Astronomy, the University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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7
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Kondrashov OV, Akimov SA. Regulation of Antimicrobial Peptide Activity via Tuning Deformation Fields by Membrane-Deforming Inclusions. Int J Mol Sci 2021; 23:ijms23010326. [PMID: 35008752 PMCID: PMC8745196 DOI: 10.3390/ijms23010326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are considered prospective antibiotics. Some AMPs fight bacteria via cooperative formation of pores in their plasma membranes. Most AMPs at their working concentrations can induce lysis of eukaryotic cells as well. Gramicidin A (gA) is a peptide, the transmembrane dimers of which form cation-selective channels in membranes. It is highly toxic for mammalians as being majorly hydrophobic gA incorporates and induces leakage of both bacterial and eukaryotic cell membranes. Both pore-forming AMPs and gA deform the membrane. Here we suggest a possible way to reduce the working concentrations of AMPs at the expense of application of highly-selective amplifiers of AMP activity in target membranes. The amplifiers should alter the deformation fields in the membrane in a way favoring the membrane-permeabilizing states. We developed the statistical model that allows describing the effect of membrane-deforming inclusions on the equilibrium between AMP monomers and cooperative membrane-permeabilizing structures. On the example of gA monomer-dimer equilibrium, the model predicts that amphipathic peptides and short transmembrane peptides playing the role of the membrane-deforming inclusions, even in low concentration can substantially increase the lifetime and average number of gA channels.
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8
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Patel SJ, Van Lehn RC. Analysis of Charged Peptide Loop-Flipping across a Lipid Bilayer Using the String Method with Swarms of Trajectories. J Phys Chem B 2021; 125:5862-5873. [PMID: 34033491 DOI: 10.1021/acs.jpcb.1c02810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The hydrophobic core of the lipid bilayer is conventionally considered a barrier to the translocation of charged species such that the translocation of even single ions occurs on long time scales. In contrast, experiments have revealed that some materials, including peptides, proteins, and nanoparticles, can translocate multiple charged moieties across the bilayer on experimentally relevant time scales. Understanding the molecular mechanisms underlying this behavior is challenging because resolving corresponding free-energy landscapes with molecular simulation techniques is computationally expensive. To address this challenge, we use atomistic molecular dynamics simulations with the swarms-of-trajectories (SOT) string method to analyze charge translocation pathways across single-component lipid bilayers as a function of multiple collective variables. We first demonstrate that the SOT string method can reproduce the free-energy barrier for the translocation of a charged lysine amino acid analogue in good agreement with the literature. We then obtain minimum free-energy pathways for the translocation, or flipping, of charged peptide loops across the lipid bilayer by utilizing trajectories from prior temperature-accelerated molecular dynamics (TAMD) simulations as initial configurations. The corresponding potential of mean force calculations reveal that the protonation of a central membrane-exposed aspartate residue substantially reduces the free-energy barrier for flipping charged loops by modulating the water content of the bilayer. These results provide new insight into the thermodynamics underlying loop-flipping processes and highlight how the combination of TAMD and the SOT string method can be used to understand complex charge translocation mechanisms.
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Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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9
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Berressem F, Scherer C, Andrienko D, Nikoubashman A. Ultra-coarse-graining of homopolymers in inhomogeneous systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:254002. [PMID: 33845463 DOI: 10.1088/1361-648x/abf6e2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
We develop coarse-grained (CG) models for simulating homopolymers in inhomogeneous systems, focusing on polymer films and droplets. If the CG polymers interact solely through two-body potentials, then the films and droplets either dissolve or collapse into small aggregates, depending on whether the effective polymer-polymer interactions have been determined from reference simulations in the bulk or at infinite dilution. To address this shortcoming, we include higher order interactions either through an additional three-body potential or a local density-dependent potential (LDP). We parameterize the two- and three-body potentials via force matching, and the LDP through relative entropy minimization. While the CG models with three-body interactions fail at reproducing stable polymer films and droplets, CG simulations with an LDP are able to do so. Minor quantitative differences between the reference and the CG simulations, namely a slight broadening of interfaces accompanied by a smaller surface tension in the CG simulations, can be attributed to the deformation of polymers near the interfaces, which cannot be resolved in the CG representation, where the polymers are mapped to spherical beads.
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Affiliation(s)
- Fabian Berressem
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Christoph Scherer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Denis Andrienko
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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10
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Ozgur B, Sayar M. Representation of the conformational ensemble of peptides in coarse grained simulations. J Chem Phys 2020; 153:054108. [DOI: 10.1063/5.0012391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Mehmet Sayar
- Chemical and Biological Engineering and Mechanical Engineering Departments, College of Engineering, Koç University, 34450 Istanbul, Turkey
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11
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Jefferies D, Khalid S. Atomistic and coarse-grained simulations of membrane proteins: A practical guide. Methods 2020; 185:15-27. [PMID: 32084518 DOI: 10.1016/j.ymeth.2020.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are amphipathic macromolecules whose exposed hydrophobic surfaces promote interactions with lipid membranes. Membrane proteins are remarkably diverse in terms of chemical composition and correspondingly, their biological functions and general biophysical behavior. Conventional experimental techniques provide an approach to study specific properties of membrane proteins e.g. their surface features, the nature and abundance of stabilizing intramolecular forces, preferred bilayer orientation, and the characteristics of their annular lipid shells. Molecular modeling software-and in particular, the suite of molecular dynamics algorithms-enables a more comprehensive exploration of dynamic membrane protein behavior. Molecular dynamics methods enable users to produce stepwise trajectories of proteins on arbitrary spatiotemporal scales that enable the easy identification of dynamic interactions that are beyond the scope of conventional analytical techniques. This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions.
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Affiliation(s)
- Damien Jefferies
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.
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12
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Matubayasi N. Energy-Representation Theory of Solutions: Its Formulation and Application to Soft, Molecular Aggregates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190246] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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13
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Park S, Yeom MS, Andersen OS, Pastor RW, Im W. Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers. J Chem Theory Comput 2019; 15:6491-6503. [PMID: 31560853 PMCID: PMC7076909 DOI: 10.1021/acs.jctc.9b00815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a recently developed binary bilayer system (BBS) consisting of two patches of laterally contacting bilayers, umbrella sampling molecular dynamics (MD) simulations were performed for quantitative characterization of protein-lipid interactions. The BBS is composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) with an embedded model membrane protein, a gramicidin A (gA) channel. The calculated free energy difference for the transfer of a gA channel from DLPC (hydrophobic thickness ≈ 21.5 Å) to DMPC (hydrophobic thickness ≈ 25.5 Å) bilayers, ΔG(DLPC → DMPC), is -2.2 ± 0.7 kcal/mol. This value appears at odds with the traditional view that the hydrophobic length of the gA channel is ∼22 Å. To understand this discrepancy, we first note that recent MD simulations by different groups have shown that lipid bilayer thickness profiles in the vicinity of a gA channel differ qualitatively from the deformation profile predicted from continuum elastic bilayer models. Our MD simulations at low and high gA:lipid molar ratios and different membrane compositions indicate that the gA channel's effective hydrophobic length is ∼26 Å. Using this effective hydrophobic length, ΔG(DLPC → DMPC) determined here is in excellent agreement with predictions based on continuum elastic models (-3.0 to -2.2 kcal/mol) where the bilayer deformation energy is approximated as a harmonic function of the mismatch between the channel's effective hydrophobic length and the hydrophobic thickness of the bilayer. The free energy profile for gA in the BBS includes a barrier at the interface between the two bilayers which can be attributed to the line tension at the interface between two bilayers with different hydrophobic thicknesses. This observation implies that translation of a peptide between two different regions of a cell membrane (such as between the liquid ordered and disordered phases) may include effects of a barrier at the interface in addition to the relative free energies of the species far from the interface. The BBS allows for direct transfer free energy calculations between bilayers without a need of a reference medium, such as bulk water, and thus provides an efficient simulation protocol for the quantitative characterization of protein-lipid interactions at all-atom resolution.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information , Daejeon , Korea
| | - Olaf S Andersen
- Department of Physiology and Biophysics , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.,School of Computational Sciences , Korea Institute for Advanced Study , Seoul 02455 , Republic of Korea
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14
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Nangia S, Boyd KJ, May ER. Molecular dynamics study of membrane permeabilization by wild-type and mutant lytic peptides from the non-enveloped Flock House virus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183102. [PMID: 31678020 DOI: 10.1016/j.bbamem.2019.183102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022]
Abstract
Flock House virus (FHV) serves as a model system for understanding infection mechanisms utilized by non-enveloped viruses to transport across cellular membranes. During the infection cycle of FHV, a fundamental stage involves disruption of the endosomal membrane by membrane active peptides, following externalization of the peptides from the capsid interior. The FHV lytic agents are the 44 C-terminal amino acids residues of the capsid protein, which are auto-catalytically cleaved during the capsid maturation process. The cleaved peptides are termed γ peptides. In this study, we perform multi-scale molecular dynamics simulations including 40 μs all-atom molecular dynamics simulations to study the behavior of pre-inserted transmembrane lytic peptides at a high concentration in a neutral membrane. We study the dynamical organization among peptides to form oligomeric bundles in four systems including the wild-type γ peptide and three mutant forms; namely, a truncation mutant in which the 23 C-terminal residues are deleted (γ1), a construct where the 8 C-terminal residues of γ are fused to γ1 (Δ385-399 γ) and a single-point mutant (F402A γ), all of which have been experimentally shown to drastically affect infectivity and lytic activity compared to the wild-type γ. Our results shed light on the actions of varied forms of the FHV lytic peptide including membrane insertion, trans-membrane stability, peptide oligomerization, water permeation activity and dynamic pore formation. Findings from this study provide detailed structural information and rationale for the differences in lytic activity among variants of FHV γ.
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Affiliation(s)
- Shivangi Nangia
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America
| | - Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, United States of America.
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15
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 422] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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16
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Patel SJ, Van Lehn RC. Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer. J Phys Chem B 2018; 122:10337-10348. [PMID: 30376710 DOI: 10.1021/acs.jpcb.8b06613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell membrane largely prevents the passive diffusion of charged molecules due to the large free energy barrier associated with translocating charged groups across the hydrophobic lipid bilayer core. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. The transmembrane helices of some multispanning membrane proteins undergo similar reorientation processes, suggesting that loop-flipping may be a mechanism for regulating membrane protein topology; however, the molecular mechanisms underlying this behavior remain unknown. In this work, we study the loop-flipping behavior exhibited by a peptide with a hydrophobic transmembrane helix, charged flanking loops, and a central, membrane-exposed aspartate residue of varying protonation state. We utilize all-atom temperature accelerated molecular dynamics simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways. We demonstrate that this approach can identify multiple possible flipping pathways, with the prevalence of each pathway depending on the protonation state of the central residue. In particular, we find that a charged central residue facilitates loop-flipping by stabilizing membrane water defects, enabling the "self-catalysis" of charge translocation. These findings provide detailed molecular-level insights into charged loop-flipping pathways that may generalize to other charge translocation processes, such as lipid flip-flop or the large-scale conformational rearrangements of multispanning membrane proteins.
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Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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17
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Lipopeptide daptomycin: Interactions with bacterial and phospholipid membranes, stability of membrane aggregates and micellation in solution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1949-1954. [DOI: 10.1016/j.bbamem.2018.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/17/2022]
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18
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
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19
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
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Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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20
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Rudzinski JF, Bereau T. Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. J Chem Phys 2018; 148:204111. [PMID: 29865838 DOI: 10.1063/1.5025125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.
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Affiliation(s)
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
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21
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Folding a viral peptide in different membrane environments: pathway and sampling analyses. J Biol Phys 2018; 44:195-209. [PMID: 29644513 DOI: 10.1007/s10867-018-9490-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/16/2018] [Indexed: 10/17/2022] Open
Abstract
Flock House virus (FHV) is a well-characterized model system to study infection mechanisms in non-enveloped viruses. A key stage of the infection cycle is the disruption of the endosomal membrane by a component of the FHV capsid, the membrane active γ peptide. In this study, we perform all-atom molecular dynamics simulations of the 21 N-terminal residues of the γ peptide interacting with membranes of differing compositions. We carry out umbrella sampling calculations to study the folding of the peptide to a helical state in homogenous and heterogeneous membranes consisting of neutral and anionic lipids. From the trajectory data, we evaluate folding energetics and dissect the mechanism of folding in the different membrane environments. We conclude the study by analyzing the extent of configurational sampling by performing time-lagged independent component analysis.
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22
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The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions. COMPUTATION 2018. [DOI: 10.3390/computation6010021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.
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23
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Naughton FB, Kalli AC, Sansom MS. Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition. J Mol Biol 2018; 430:372-388. [DOI: 10.1016/j.jmb.2017.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 11/30/2022]
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24
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Bagheri B, Baumeier B, Karttunen M. Getting excited: challenges in quantum-classical studies of excitons in polymeric systems. Phys Chem Chem Phys 2018; 18:30297-30304. [PMID: 27453482 DOI: 10.1039/c6cp02944b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe the conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM/MD simulations. Many-body Green's function theory within the GW approximation and the Bethe-Salpeter (GW-BSE) equation were utilized to describe the excited states of the systems. The reliability of the excitation energies based on the MM/MD conformations was examined and compared to the excitation energies from DFT conformations. The results show an overall agreement between the optical excitations based on MM/MD conformations and DFT conformations. This allows for the calculation of excitation energies based on MM/MD conformations.
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Affiliation(s)
- Behnaz Bagheri
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Björn Baumeier
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
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25
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Mizuguchi T, Matubayasi N. Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions. J Phys Chem B 2018; 122:3219-3229. [DOI: 10.1021/acs.jpcb.7b08241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomoko Mizuguchi
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Institute for the Promotion of University Strategy, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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26
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Hills RD. Refining amino acid hydrophobicity for dynamics simulation of membrane proteins. PeerJ 2018; 6:e4230. [PMID: 29340240 PMCID: PMC5767086 DOI: 10.7717/peerj.4230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, United States of America
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27
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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28
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Ward MD, Nangia S, May ER. Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. J Comput Chem 2017; 38:1462-1471. [PMID: 28102001 PMCID: PMC5407926 DOI: 10.1002/jcc.24694] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/20/2016] [Accepted: 11/17/2016] [Indexed: 12/29/2022]
Abstract
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael D. Ward
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Shivangi Nangia
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
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29
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Fosso-Tande J, Black C, G. Aller S, Lu L, D. Hills Jr R. Simulation of lipid-protein interactions with the CgProt force field. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Pulawski W, Jamroz M, Kolinski M, Kolinski A, Kmiecik S. Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model. J Chem Inf Model 2016; 56:2207-2215. [PMID: 27775349 DOI: 10.1021/acs.jcim.6b00350] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.
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Affiliation(s)
- Wojciech Pulawski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Jamroz
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland
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31
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Hung HM, Nguyen VP, Ngo ST, Nguyen MT. Theoretical study of the interactions between the first transmembrane segment of NS2 protein and a POPC lipid bilayer. Biophys Chem 2016; 217:1-7. [DOI: 10.1016/j.bpc.2016.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 07/16/2016] [Accepted: 07/16/2016] [Indexed: 01/22/2023]
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32
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Bereau T, Kremer K. Protein-Backbone Thermodynamics across the Membrane Interface. J Phys Chem B 2016; 120:6391-400. [DOI: 10.1021/acs.jpcb.6b03682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
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33
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Permeability across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2254-2265. [PMID: 27085977 DOI: 10.1016/j.bbamem.2016.03.032] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/22/2022]
Abstract
Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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34
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Yue T, Sun M, Zhang S, Ren H, Ge B, Huang F. How transmembrane peptides insert and orientate in biomembranes: a combined experimental and simulation study. Phys Chem Chem Phys 2016; 18:17483-94. [DOI: 10.1039/c6cp01133k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
After the synthesis of transmembrane peptides/proteins (TMPs), their insertion into a lipid bilayer is a fundamental biophysical process.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Mingbin Sun
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Shuai Zhang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
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