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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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Mavioso ICVC, de Andrade VCR, Palace Carvalho AJ, Martins do Canto AMT. Molecular dynamics simulations of T-2410 and T-2429 HIV fusion inhibitors interacting with model membranes: Insight into peptide behavior, structure and dynamics. Biophys Chem 2017; 228:69-80. [PMID: 28711675 DOI: 10.1016/j.bpc.2017.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
Abstract
T-2410 and T-2429 are HIV fusion inhibitor peptides (FI) designed to present a higher efficiency even against HIV strains that developed resistance against other FIs. Similar peptides were shown to interact with model membranes both in the liquid disordered phase and in the liquid ordered state. Those results indicated that such interaction is important to function and could be correlated with their effectiveness. Extensive molecular dynamics simulations were carried out to investigate the interactions between both T-2410 and T-2429 with bilayers of pure 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and a mixture of POPC/cholesterol (Chol) (1:1). It was observed that both peptides interact strongly with both membrane systems, especially with the POPC/Chol systems, where these peptides show the highest number of H-bonds observed so far. T-2410 and T-2429 showed higher extent of interaction with bilayers when compared to T-20 or T-1249 in previous studies. This is most notable in POPC/Chol membranes where, although able to form H-bonds with Chol, they do so to a lesser extent than T-1249 does, the latter being the only FI peptide so far that was observed to form H-bonds with Chol. This behavior suggests that interaction of FI peptides with rigid Chol rich membranes may not be as dependent from peptide/Chol H-bond formation as previous results of T-1249 behavior led to believe. As in other similar peptides, the higher ability to interact with membranes shown by T-2410 and T2429 is probably correlated with its higher inhibitory efficiency.
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Affiliation(s)
- I C V C Mavioso
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - V C R de Andrade
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A J Palace Carvalho
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - A M T Martins do Canto
- Departamento de Química, Escola de Ciências e Tecnologia, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal; Centro de Química de Évora, IIFA, Universidade de Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal.
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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Abstract
Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA-approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs.
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Gapsys V, de Groot BL, Briones R. Computational analysis of local membrane properties. J Comput Aided Mol Des 2013; 27:845-58. [PMID: 24150904 PMCID: PMC3882000 DOI: 10.1007/s10822-013-9684-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
In the field of biomolecular simulations, dynamics of phospholipid membranes is of special interest. A number of proteins, including channels, transporters, receptors and short peptides are embedded in lipid bilayers and tightly interact with phospholipids. While the experimental measurements report on the spatial and/or temporal average membrane properties, simulation results are not restricted to the average properties. In the current study, we present a collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature. The local membrane property calculation allows for a direct mapping of the membrane features, which subsequently can be used for further analysis and visualization of the processes of interest. The main features of the described methods are highlighted in a number of membrane systems, namely: a pure dimyristoyl-phosphatidyl-choline (DMPC) bilayer, a fusion peptide interacting with a membrane, voltage-dependent anion channel protein embedded in a DMPC bilayer, cholesterol enriched bilayer and a coarse grained simulation of a curved palmitoyl-oleoyl-phosphatidyl-choline lipid membrane. The local membrane property analysis proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.
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Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany,
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Martins do Canto AMT, Palace Carvalho AJ, Prates Ramalho JP, Loura LMS. Effect of amphipathic HIV fusion inhibitor peptides on POPC and POPC/cholesterol membrane properties: a molecular simulation study. Int J Mol Sci 2013; 14:14724-43. [PMID: 23860208 PMCID: PMC3742270 DOI: 10.3390/ijms140714724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/16/2022] Open
Abstract
T-20 and T-1249 fusion inhibitor peptides were shown to interact with 1-palmitoyl-2-oleyl-phosphatidylcholine (POPC) (liquid disordered, ld) and POPC/cholesterol (1:1) (POPC/Chol) (liquid ordered, lo) bilayers, and they do so to different extents. Although they both possess a tryptophan-rich domain (TRD), T-20 lacks a pocket binding domain (PBD), which is present in T-1249. It has been postulated that the PBD domain enhances FI interaction with HIV gp41 protein and with model membranes. Interaction of these fusion inhibitor peptides with both the cell membrane and the viral envelope membrane is important for function, i.e., inhibition of the fusion process. We address this problem with a molecular dynamics approach focusing on lipid properties, trying to ascertain the consequences and the differences in the interaction of T-20 and T-1249 with ld and lo model membranes. T-20 and T-1249 interactions with model membranes are shown to have measurable and different effects on bilayer structural and dynamical parameters. T-1249’s adsorption to the membrane surface has generally a stronger influence in the measured parameters. The presence of both binding domains in T-1249 appears to be paramount to its stronger interaction, and is shown to have a definite importance in membrane properties upon peptide adsorption.
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Affiliation(s)
- António M. T. Martins do Canto
- Department of Chemistry, School of Science and Technology, University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal; E-Mails: (A.M.T.M.C.); (A.J.P.C.); (J.P.P.R.)
- Centre for Chemistry-Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Alfredo J. Palace Carvalho
- Department of Chemistry, School of Science and Technology, University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal; E-Mails: (A.M.T.M.C.); (A.J.P.C.); (J.P.P.R.)
- Centre for Chemistry-Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - João P. Prates Ramalho
- Department of Chemistry, School of Science and Technology, University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal; E-Mails: (A.M.T.M.C.); (A.J.P.C.); (J.P.P.R.)
- Centre for Chemistry-Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Luís M. S. Loura
- Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centre for Chemistry-Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +351-239-488-485; Fax: +351-239-827-126
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Sensing hydration and behavior of pyrene in POPC and POPC/cholesterol bilayers: A molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1094-101. [DOI: 10.1016/j.bbamem.2012.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 01/24/2023]
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Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012; 2012:151854. [PMID: 22675399 PMCID: PMC3364549 DOI: 10.1155/2012/151854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 03/08/2012] [Accepted: 03/20/2012] [Indexed: 12/19/2022]
Abstract
T-1249 is a peptide that inhibits the fusion of HIV envelope with the target cell membrane. Recent results indicate that T-1249, as in the case of related inhibitor peptide T-20 (enfuvirtide), interacts with membranes, more extensively in the bilayer liquid disordered phase than in the liquid ordered state, which could be linked to its effectiveness. Extensive molecular dynamics simulations (100 ns) were carried out to investigate the interaction between T-1249 and bilayers of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and POPC/cholesterol (1 : 1). It was observed that T-1249 interacts to different extents with both membrane systems and that peptide interaction with the bilayer surface has a local effect on membrane structure. Formation of hydrogen bonding between certain peptide residues and several acceptor and donor groups in the bilayer molecules was observed. T-1249 showed higher extent of interaction with bilayers when compared to T-20. This is most notable in POPC/Chol membranes, owing to more peptide residues acting as H bond donors and acceptors between the peptide and the bilayer lipids, including H-bonds formed with cholesterol. This behavior is at variance with that of T-20, which forms no H bonds with cholesterol. This higher ability to interact with membranes is probably correlated with its higher inhibitory efficiency.
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Martins PT, Velazquez-Campoy A, Vaz WLC, Cardoso RMS, Valério J, Moreno MJ. Kinetics and Thermodynamics of Chlorpromazine Interaction with Lipid Bilayers: Effect of Charge and Cholesterol. J Am Chem Soc 2012; 134:4184-95. [DOI: 10.1021/ja209917q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrícia T. Martins
- Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation
and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain, Unidad Asociada BIFI-IQFR,
CSIC, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Spain
| | - Winchil L. C. Vaz
- Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
| | - Renato M. S. Cardoso
- Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
| | - Joana Valério
- Instituto de Tecnologia Química e Biológica − UNL, Av.
da República-EAN, 2780-157 Oeiras, Portugal
| | - Maria João Moreno
- Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra,
Portugal
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