1
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Chachaj-Brekiesz A, Kobierski J, Wnętrzak A, Dynarowicz-Latka P, Pietruszewska P. Insight into the Molecular Mechanism of Surface Interactions of Phosphatidylcholines─Langmuir Monolayer Study Complemented with Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1473-1482. [PMID: 38320120 PMCID: PMC10875670 DOI: 10.1021/acs.jpcb.3c06810] [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: 10/13/2023] [Revised: 12/19/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Mutual interactions between components of biological membranes are pivotal for maintaining their proper biophysical properties, such as stability, fluidity, or permeability. The main building blocks of biomembranes are lipids, among which the most important are phospholipids (mainly phosphatidylcholines (PCs)) and sterols (mainly cholesterol). Although there is a plethora of reports on interactions between PCs, as well as between PCs and cholesterol, their molecular mechanism has not yet been fully explained. Therefore, to resolve this issue, we carried out systematic investigations based on the classical Langmuir monolayer technique complemented with molecular dynamics simulations. The studies involved systems containing 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) analogues possessing in the structure one or two polar functional groups similar to those of DPPC. The interactions and rheological properties of binary mixtures of DPPC analogues with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol were compared with reference systems (DPPC/POPC and DPPC/cholesterol). This pointed to the importance of the ternary amine group in PC/cholesterol interactions, while in PC mixtures, the phosphate group played a key role. In both cases, the esterified glycerol group had an effect on the magnitude of interactions. The obtained results are crucial for establishing structure-property relationships as well as for designing substitutes for natural lipids.
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Affiliation(s)
- Anna Chachaj-Brekiesz
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30–387 Kraków, Poland
| | - Jan Kobierski
- Department
of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30–688 Kraków, Poland
| | - Anita Wnętrzak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30–387 Kraków, Poland
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2
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Kumar J, Chng CP, Huang C. Hydrophobic Matching Dictates over the Linear Rule of Mixtures in Binary Lipid Membranes. J Phys Chem B 2023; 127:7946-7954. [PMID: 37674349 DOI: 10.1021/acs.jpcb.3c04502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Biological membranes feature heterogeneous mixtures of lipids with different head and tail characteristics. Their biophysical properties are dictated by the intimate interaction among different constituent lipids. Previous studies suggest that the membrane area-per-lipid (APL) deviates from the linear rule of mixtures (LRM) for binary lipid membranes, but the underlying mechanism remains elusive. Our molecular dynamics (MD) simulations of binary lipid membranes consisting of lipids with different tail characteristics reveal a competitive mechanism whereby lipids tend to deform each other to minimize the hydrophobic mismatch between their tails. Depending on the relative tail lengths and saturation levels, this may result in an either positive or negative deviation of APL from the LRM. As lipid packing plays an essential role in membrane fusion and peptide-membrane binding, our findings may help guide the selection of lipids for the effective rational design of nanoliposomes and membrane-targeting peptides.
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Affiliation(s)
- Jatin Kumar
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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3
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Close, but not too close: a mesoscopic description of (a)symmetry and membrane shaping mechanisms. Emerg Top Life Sci 2023; 7:81-93. [PMID: 36645200 DOI: 10.1042/etls20220078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/17/2023]
Abstract
Biomembranes are fundamental to our understanding of the cell, the basic building block of all life. An intriguing aspect of membranes is their ability to assume a variety of shapes, which is crucial for cell function. Here, we review various membrane shaping mechanisms with special focus on the current understanding of how local curvature and local rigidity induced by membrane proteins leads to emerging forces and consequently large-scale membrane deformations. We also argue that describing the interaction of rigid proteins with membranes purely in terms of local membrane curvature is incomplete and that changes in the membrane rigidity moduli must also be considered.
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4
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Kurki M, Poso A, Bartos P, Miettinen MS. Structure of POPC Lipid Bilayers in OPLS3e Force Field. J Chem Inf Model 2022; 62:6462-6474. [PMID: 36044537 PMCID: PMC9795559 DOI: 10.1021/acs.jcim.2c00395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters SCH of POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid bilayers at varying hydration conditions and ion concentrations. The results show that OPLS3e behaves similarly to the CHARMM36 force field and relatively accurately follows the experimentally measured SCH for the lipid headgroup, the glycerol backbone, and the acyl tails. Thus, OPLS3e is a good choice for POPC bilayer simulations under many biologically relevant conditions. The exception are systems with an abundancy of ions, as similarly to most other force fields OPLS3e strongly overestimates the membrane-binding of cations, especially Ca2+. This leads to undesirable positive charge of the membrane surface and drastically lowers the concentration of Ca2+ in the surrounding solvent, which might cause issues in systems sensitive to correct charge distribution profiles across the membrane.
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Affiliation(s)
- Milla Kurki
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland
| | - Antti Poso
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland
| | - Piia Bartos
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland,
| | - Markus S. Miettinen
- Department
of Chemistry, University of Bergen, 5007 Bergen, Norway,Computational
Biology Unit, Department of Informatics, University of Bergen, 5007 Bergen, Norway
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5
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Domínguez-Arca V, Sabín J, García-Río L, Bastos M, Taboada P, Barbosa S, Prieto G. On the structure and stability of novel cationic DPPC liposomes doped with gemini surfactants. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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6
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Bacle A, Buslaev P, Garcia-Fandino R, Favela-Rosales F, Mendes Ferreira T, Fuchs PFJ, Gushchin I, Javanainen M, Kiirikki AM, Madsen JJ, Melcr J, Milán Rodríguez P, Miettinen MS, Ollila OHS, Papadopoulos CG, Peón A, Piggot TJ, Piñeiro Á, Virtanen SI. Inverse Conformational Selection in Lipid-Protein Binding. J Am Chem Soc 2021; 143:13701-13709. [PMID: 34465095 DOI: 10.1021/jacs.1c05549] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
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Affiliation(s)
- Amélie Bacle
- Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, 1 rue Georges Bonnet, Poitiers 86000, France
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain.,CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, Zacatecas 99102, México
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Patrick F J Fuchs
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France.,UFR Sciences du Vivant, Université de Paris, Paris 75013, France
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, Prague CZ-16610, Czech Republic
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, Groningen9747 AG, The Netherlands
| | - Paula Milán Rodríguez
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Chris G Papadopoulos
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Antonio Peón
- CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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7
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Akutsu H. Structure and dynamics of phospholipids in membranes elucidated by combined use of NMR and vibrational spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183352. [DOI: 10.1016/j.bbamem.2020.183352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022]
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8
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Buslaev P, Mustafin K, Gushchin I. Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183253. [PMID: 32142820 DOI: 10.1016/j.bbamem.2020.183253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/06/2023]
Abstract
Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.
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Affiliation(s)
- P Buslaev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - K Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - I Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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9
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Hanashima S, Yano Y, Murata M. Enantiomers of phospholipids and cholesterol: A key to decipher lipid‐lipid interplay in membrane. Chirality 2020; 32:282-298. [DOI: 10.1002/chir.23171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of ScienceOsaka University Toyonaka Japan
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10
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Hanashima S, Murakami K, Yura M, Yano Y, Umegawa Y, Tsuchikawa H, Matsumori N, Seo S, Shinoda W, Murata M. Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup. Biophys J 2019; 117:307-318. [PMID: 31303249 DOI: 10.1016/j.bpj.2019.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 12/19/2022] Open
Abstract
Sphingomyelin (SM) and cholesterol (Cho) are the important lipids for the formation of biologically functional membrane domains, lipid rafts. However, the interaction between Cho and the headgroup of SM remains unclear. In this study, we performed solid-state NMR experiments to reveal the Cho effects on the headgroup conformation using 2H-labeled stearoyl-SM (SSM). Deuterated SSMs at the Cα, Cβ, and Cγ positions of a choline moiety were separately prepared and subjected to NMR measurements to determine the quadrupolar splitting of 2H signals in hydrated SSM unitary and SSM/Cho (1:1) bilayers. Using 2H NMR and 13C-31P REDOR data, the conformation and orientation of the choline moiety were deduced and compared with those derived from molecular dynamics simulations. In SSM unitary bilayers, three torsional angles in the phosphocholine moiety, P-O-Cα-Cβ, were found to be consecutive +gauche(g)/+g/+g or -g/-g/-g. The orientation and conformation of the SSM headgroup were consistent with the results of our molecular dynamics simulations and the previous results on phosphatidylcholines. The quadrupolar coupling at the α methylene group slightly increased in the presence of Cho, and those at the Cβ and Cγ decreased more significantly, thus suggesting that Cho reduced the gauche conformation at the Cα-Cβ torsion. The conformational ensemble in the presence of Cho may enhance the so-called umbrella effect of the SSM headgroup, resulting in the stabilization of Cho near the SM molecules by concealing the hydrophobic Cho core from interfacial water. We also examined the effect of the chiral centers at the sphingosine chain to the headgroup conformation by determining the enantiomeric excess between the diastereomeric +g/+g/+g and -g/-g/-g conformers using (S)-Cα-deuterated and (R)-Cα-deuterated SSMs. Their 2H NMR measurements showed that the chiral centers induced the slight diastereomeric excess in the SM headgroup conformation.
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Affiliation(s)
- Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Kazuhiro Murakami
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Michihiro Yura
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yo Yano
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan; ERATO Lipid Active Structure Project, Japan Science and Technology Agency, Graduate School of Science, Osaka University, Osaka, Japan.
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11
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An Y, Singh S, Bejagam KK, Deshmukh SA. Development of an Accurate Coarse-Grained Model of Poly(acrylic acid) in Explicit Solvents. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yaxin An
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Karteek K. Bejagam
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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12
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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: 399] [Impact Index Per Article: 79.8] [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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13
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Goossens K, De Winter H. Molecular Dynamics Simulations of Membrane Proteins: An Overview. J Chem Inf Model 2018; 58:2193-2202. [PMID: 30336018 DOI: 10.1021/acs.jcim.8b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of membrane proteins have been rising in popularity in the past decade. Advancements in technology and force fields made it possible to simulate behavior of membrane proteins. Membrane protein simulations can now be used as supporting evidence for experimental findings, for elucidating protein mechanisms, and validating protein crystal structures. Unrelated to experimental data, these simulations can also serve to investigate larger scale processes like protein sorting, protein-membrane interactions, and more. In this review, the history as well as the state-of-the-art methodologies in membrane protein simulations will be summarized. An emphasis will be put on how to set up the system and on the current models for the different components of the simulation system. An overview of the available tools for membrane protein simulation will be given, and current limitations and prospects will also be discussed.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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