101
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Klug J, Masone D, Del Pópolo MG. Molecular-level insight into the binding of arginine to a zwitterionic Langmuir monolayer. RSC Adv 2017. [DOI: 10.1039/c7ra05359b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arginine molecules bind to a DPPC monolayer, altering the interfacial electrostatic potential and the lateral mobility of the lipids, while having little effect on the compression isotherm of the monolayer.
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Affiliation(s)
- Joaquín Klug
- CONICET & Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
- Atomistic Simulation Centre
| | - Diego Masone
- CONICET & Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
| | - Mario G. Del Pópolo
- CONICET & Facultad de Ciencias Exactas y Naturales
- Universidad Nacional de Cuyo
- Mendoza
- Argentina
- Atomistic Simulation Centre
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102
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Carvalho TC, McCook JP, Narain NR, McConville JT. Development of aqueous dispersions of Coenzyme Q 10 for pulmonary delivery and the dynamics of active vibrating-mesh aerosolization. Int J Pharm 2016; 514:407-419. [DOI: 10.1016/j.ijpharm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 11/16/2022]
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103
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McKiernan KA, Wang LP, Pande VS. Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field. J Chem Theory Comput 2016; 12:5960-5967. [DOI: 10.1021/acs.jctc.6b00801] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Lee-Ping Wang
- Department
of Chemistry, University of California—Davis, Davis, California 95618, United States
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104
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Drenscko M, Loverde SM. Characterisation of the hydrophobic collapse of polystyrene in water using free energy techniques. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1253840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mihaela Drenscko
- Department of Chemistry, College of Staten Island, City University of New York, USA
- Program in Physics, The Graduate Center of the City University of New York, USA
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, City University of New York, USA
- Program in Physics, The Graduate Center of the City University of New York, USA
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105
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Shi W. The structure and dynamics of Nano Particles encapsulated by the SDS monolayer collapse at the water/TCE interface. Sci Rep 2016; 6:37386. [PMID: 27853312 PMCID: PMC5112588 DOI: 10.1038/srep37386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/28/2016] [Indexed: 11/09/2022] Open
Abstract
The super-saturated surfactant monolayer collapses with the nanoparticles (NPs) at the water/trichloroethylene (TCE) interface are investigated using molecular dynamics (MD) simulations. The results show that sodium alkyl sulfate (SDS) monolayer collapse is initiated by buckling and followed primarily by budding and the bud encapsulating the NPs and oil molecules. The developed bud detaches from the monolayer into a water phase and forms the swollen micelle emulsion with NPs and oil molecules. We investigate the wavelength of the initial budding and the theoretical description of the budding process. The wavelength of the monolayer increases with bending modulus. The energy barrier of the budding can be easily overcome by thermal fluctuation energy, which indicates that budding process proceeds rapidly.
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Affiliation(s)
- Wenxiong Shi
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
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106
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Miguel V, Perillo MA, Villarreal MA. Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2903-2910. [DOI: 10.1016/j.bbamem.2016.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 02/04/2023]
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107
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Bunker A, Magarkar A, Viitala T. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2334-2352. [DOI: 10.1016/j.bbamem.2016.02.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/22/2023]
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108
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Mayne CG, Arcario MJ, Mahinthichaichan P, Baylon JL, Vermaas JV, Navidpour L, Wen PC, Thangapandian S, Tajkhorshid E. The cellular membrane as a mediator for small molecule interaction with membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:2290-2304. [PMID: 27163493 PMCID: PMC4983535 DOI: 10.1016/j.bbamem.2016.04.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 01/05/2023]
Abstract
The cellular membrane constitutes the first element that encounters a wide variety of molecular species to which a cell might be exposed. Hosting a large number of structurally and functionally diverse proteins associated with this key metabolic compartment, the membrane not only directly controls the traffic of various molecules in and out of the cell, it also participates in such diverse and important processes as signal transduction and chemical processing of incoming molecular species. In this article, we present a number of cases where details of interaction of small molecular species such as drugs with the membrane, which are often experimentally inaccessible, have been studied using advanced molecular simulation techniques. We have selected systems in which partitioning of the small molecule with the membrane constitutes a key step for its final biological function, often binding to and interacting with a protein associated with the membrane. These examples demonstrate that membrane partitioning is not only important for the overall distribution of drugs and other small molecules into different compartments of the body, it may also play a key role in determining the efficiency and the mode of interaction of the drug with its target protein. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Christopher G Mayne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Mark J Arcario
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
| | - Paween Mahinthichaichan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Javier L Baylon
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Josh V Vermaas
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States.
| | - Latifeh Navidpour
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Po-Chao Wen
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States.
| | - Sundarapandian Thangapandian
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States.
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; College of Medicine, University of Illinois at Urbana-Champaign, United States.
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109
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MacDermaid CM, Kashyap HK, DeVane RH, Shinoda W, Klauda JB, Klein ML, Fiorin G. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes. J Chem Phys 2016; 143:243144. [PMID: 26723629 DOI: 10.1063/1.4937153] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.
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Affiliation(s)
- Christopher M MacDermaid
- Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801, USA
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Russell H DeVane
- Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069, USA
| | - Wataru Shinoda
- Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801, USA
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801, USA
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110
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Kawamoto S, Klein ML, Shinoda W. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism. J Chem Phys 2016; 143:243112. [PMID: 26723597 DOI: 10.1063/1.4933087] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.
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Affiliation(s)
- Shuhei Kawamoto
- Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, SERC Building 1925 North 12th Street, Philadelphia, Pennsylvania 19122, USA
| | - Wataru Shinoda
- Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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111
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Li X, Murthy NS, Becker ML, Latour RA. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel. Biointerphases 2016; 11:021002. [PMID: 27013229 PMCID: PMC4808066 DOI: 10.1116/1.4944829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022] Open
Abstract
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
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Affiliation(s)
- Xianfeng Li
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
| | - N Sanjeeva Murthy
- New Jersey Center for Biomaterials, Rutgers University, Piscataway, New Jersey 08854
| | - Matthew L Becker
- Departments of Polymer Science and Biomedical Engineering, The University of Akron, Akron, Ohio 44325
| | - Robert A Latour
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634
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112
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Collapse of a lipid-coated nanobubble and subsequent liposome formation. Sci Rep 2016; 6:28164. [PMID: 27306704 PMCID: PMC4910104 DOI: 10.1038/srep28164] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/01/2016] [Indexed: 11/16/2022] Open
Abstract
We investigate the collapse of a lipid-coated nanobubble and subsequent formation of a lipid vesicle by coarse grained molecular dynamics simulations. A spherical nanobubble coated with a phospholipid monolayer in water is a model of an aqueous dispersion of phospholipids under negative pressure during sonication. When subjected to a positive pressure, the bubble shape deforms into an irregular spherical shape and the monolayer starts to buckle and fold locally. The local folds grow rapidly in multiple directions and forming a discoidal membrane with folds of various amplitudes. Folds of small amplitude disappear in due course and the membrane develops into a unilamellar vesicle via a bowl shape. Folds with large amplitude develop into a bowl shape and a multivesicular shape forms. The membrane shape due to bubble collapse can be an important factor governing the vesicular shape during sonication.
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113
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Yoo B, Zhu Y, Maginn EJ. Molecular Mechanism of Ionic-Liquid-Induced Membrane Disruption: Morphological Changes to Bilayers, Multilayers, and Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5403-5411. [PMID: 27159842 DOI: 10.1021/acs.langmuir.6b00768] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The application of ionic liquids (ILs) in many industrially relevant processes provides an urgent need to better understand their molecular interactions with biological systems. A detailed understanding of the cytotoxicity mechanism of ILs can be helpful in facilitating the molecular design of nontoxic ILs. Using coarse-grained molecular dynamics (MD) simulations, we investigate the effects of imidazolium-based ILs on several lipid bilayer morphologies. Our results demonstrate that the asymmetric insertion of IL cations into one side of a lipid bilayer leaflet enhances the leaflet strain, which upon reaching a critical value triggers a morphological disruption in the bilayer. Consistently, the bending modulus of the bilayer is reduced by 1 to 2 orders of magnitude relative to that of an IL-free planar bilayer prior to the disruption event. Our results suggest that ILs that can easily insert into the lipid bilayer without diffusing across or inducing lipid flip-flop can be more disruptive to a lipid biomembrane.
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Affiliation(s)
- Brian Yoo
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556-5637, United States
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University , 5050 Anthony Wayne Drive, Detroit, Michigan 48202, United States
| | - Edward J Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , 182 Fitzpatrick Hall, Notre Dame, Indiana 46556-5637, United States
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114
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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: 188] [Impact Index Per Article: 23.5] [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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115
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Skjevik ÅA, Madej BD, Dickson CJ, Lin C, Teigen K, Walker RC, Gould IR. Simulation of lipid bilayer self-assembly using all-atom lipid force fields. Phys Chem Chem Phys 2016; 18:10573-84. [PMID: 27034995 DOI: 10.1039/c5cp07379k] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.
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Affiliation(s)
- Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, USA.
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116
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Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083001. [PMID: 26828575 DOI: 10.1088/0953-8984/28/8/083001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.
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Affiliation(s)
- Zhen-lu Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
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117
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Baoukina S, Tieleman DP. Computer simulations of lung surfactant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2431-2440. [PMID: 26922885 DOI: 10.1016/j.bbamem.2016.02.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 01/26/2023]
Abstract
Lung surfactant lines the gas-exchange interface in the lungs and reduces the surface tension, which is necessary for breathing. Lung surfactant consists mainly of lipids with a small amount of proteins and forms a monolayer at the air-water interface connected to bilayer reservoirs. Lung surfactant function involves transfer of material between the monolayer and bilayers during the breathing cycle. Lipids and proteins are organized laterally in the monolayer; selected species are possibly preferentially transferred to bilayers. The complex 3D structure of lung surfactant and the exact roles of lipid organization and proteins remain important goals for research. We review recent simulation studies on the properties of lipid monolayers, monolayers with phase coexistence, monolayer-bilayer transformations, lipid-protein interactions, and effects of nanoparticles on lung surfactant. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Svetlana Baoukina
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
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118
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Yoo B, Jing B, Jones SE, Lamberti GA, Zhu Y, Shah JK, Maginn EJ. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach. Sci Rep 2016; 6:19889. [PMID: 26831599 PMCID: PMC4735680 DOI: 10.1038/srep19889] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/21/2015] [Indexed: 01/28/2023] Open
Abstract
Ionic liquids (ILs) are salts that remain liquid down to low temperatures, and sometimes well below room temperature. ILs have been called "green solvents" because of their extraordinarily low vapor pressure and excellent solvation power, but ecotoxicology studies have shown that some ILs exhibit greater toxicity than traditional solvents. A fundamental understanding of the molecular mechanisms responsible for IL toxicity remains elusive. Here we show that one mode of IL toxicity on unicellular organisms is driven by swelling of the cell membrane. Cytotoxicity assays, confocal laser scanning microscopy, and molecular simulations reveal that IL cations nucleate morphological defects in the microbial cell membrane at concentrations near the half maximal effective concentration (EC50) of several microorganisms. Cytotoxicity increases with increasing alkyl chain length of the cation due to the ability of the longer alkyl chain to more easily embed in, and ultimately disrupt, the cell membrane.
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Affiliation(s)
- Brian Yoo
- University of Notre Dame, Department of Chemical and Biomolecular Engineering, Notre Dame, IN 46556-5637, USA
| | - Benxin Jing
- University of Notre Dame, Department of Chemical and Biomolecular Engineering, Notre Dame, IN 46556-5637, USA
| | - Stuart E. Jones
- University of Notre Dame, Department of Biological Sciences, Notre Dame, IN 46556-0369, USA
| | - Gary A. Lamberti
- University of Notre Dame, Department of Biological Sciences, Notre Dame, IN 46556-0369, USA
| | - Yingxi Zhu
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI 46202 USA
| | - Jindal K. Shah
- Oklahoma State University, School of Chemical Engineering, Stillwater, OK 74078, USA
| | - Edward J. Maginn
- University of Notre Dame, Department of Chemical and Biomolecular Engineering, Notre Dame, IN 46556-5637, USA
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119
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Lyubartsev AP, Rabinovich AL. Force Field Development for Lipid Membrane Simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2483-2497. [PMID: 26766518 DOI: 10.1016/j.bbamem.2015.12.033] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Stockholm, Sweden.
| | - Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation.
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120
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Abbott LJ, Stevens MJ. A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide). J Chem Phys 2015; 143:244901. [DOI: 10.1063/1.4938100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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121
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Shen Z, Sun H. Prediction of Surface and Bulk Partition of Nonionic Surfactants Using Free Energy Calculations. J Phys Chem B 2015; 119:15623-30. [PMID: 26618714 DOI: 10.1021/acs.jpcb.5b10239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The surface-bulk partition of nonionic surfactants was predicted by calculating chemical potential differences using two simulation boxes representing the surface and the bulk phases separately. A published coarse grained force field was modified and validated for this application. Thermodynamic integration (TI) was applied to compute excess chemical potentials. The high concentration surface was stabilized by applying an external harmonic potential, and the bulk was treated as ideal solution, which was confirmed by simulation using a lattice model at conditions near the critical micelle concentration (∼10(-5) mol/L). Based on the calculated chemical potential differences with precision of ca. 1 kJ/mol, the equilibria of surface-bulk concentration was predicted well in comparison with the experimental data.
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Affiliation(s)
| | - Huai Sun
- State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, College of Chemistry, Jilin University , Changchun 130012, China
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122
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Skjevik ÅA, Madej BD, Dickson CJ, Teigen K, Walker RC, Gould IR. All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields. Chem Commun (Camb) 2015; 51:4402-5. [PMID: 25679020 DOI: 10.1039/c4cc09584g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication reports the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations. Using two different lipid force fields we show simulations started from random mixtures of lipids and water in which four different types of phospholipids self-assemble into organized bilayers in under 1 microsecond.
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Affiliation(s)
- Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, USA.
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123
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Darré L, Iglesias-Fernandez J, Kohlmeyer A, Wacklin H, Domene C. Molecular dynamics simulations and neutron reflectivity as an effective approach to characterize biological membranes and related macromolecular assemblies. J Chem Theory Comput 2015; 11:4875-84. [PMID: 26574275 DOI: 10.1021/acs.jctc.5b00635] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In combination with other spectroscopy, microscopy, and scattering techniques, neutron reflectivity is a powerful tool to characterize biological systems. Specular reflection of neutrons provides structural information at the nanometer and subnanometer length scales, probing the composition and organization of layered materials. Currently, analysis of neutron reflectivity data involves several simplifying assumptions about the structure of the sample under study, affecting the extraction and interpretation of information from the experimental data. Computer simulations can be used as a source of structural and dynamic data with atomic resolution. We present a novel tool to compare the structural properties determined by neutron reflectivity experiments with those obtained from molecular simulations. This tool allows benchmarking the ability of molecular dynamics simulations to reproduce experimental data, but it also promotes unbiased interpretation of experimentally determined quantities. Two application examples are presented to illustrate the capabilities of the new tool. The first example is the generation of reflectivity profiles for a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer from molecular dynamics simulations using data from both atomistic and coarse-grained models, and comparison with experimentally measured data. The second example is the calculation of lipid volume changes with temperature and composition from all atoms simulations of single and mixed 1,2-di-palmitoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC) bilayers.
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Affiliation(s)
- L Darré
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - J Iglesias-Fernandez
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - A Kohlmeyer
- Institute for Computational Molecular Science (035-07), College of Science and Technology, Temple University , 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - H Wacklin
- European Spallation Source ESS AB, P.O. Box. 176, 22100 Lund, Sweden.,Physical Chemistry, Department of Chemistry, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - C Domene
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom.,Chemistry Research Laboratory, Mansfield Road, University of Oxford , Oxford OX1 3TA, United Kingdom
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124
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Cao F, Sun H. Transferability and Nonbond Functional Form of Coarse Grained Force Field – Tested on Linear Alkanes. J Chem Theory Comput 2015; 11:4760-9. [DOI: 10.1021/acs.jctc.5b00573] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fenglei Cao
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School
of Chemistry and Chemical Engineering and Key Laboratory of Scientific
and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Inorganic Synthesis & Preparative Chemistry, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
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125
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Qi Y, Ingólfsson HI, Cheng X, Lee J, Marrink SJ, Im W. CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. J Chem Theory Comput 2015; 11:4486-94. [PMID: 26575938 DOI: 10.1021/acs.jctc.5b00513] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.
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Affiliation(s)
- Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States
| | - Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States
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126
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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127
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Chen Y, Jena KC, Lütgebaucks C, Okur HI, Roke S. Three Dimensional Nano "Langmuir Trough" for Lipid Studies. NANO LETTERS 2015; 15:5558-5563. [PMID: 26151602 DOI: 10.1021/acs.nanolett.5b02143] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A three-dimensional-phospholipid monolayer with tunable molecular structure was created on the surface of oil nanodroplets from a mixture of phospholipids, oil, and water. This simple nanoemulsion preparation technique generates an in situ prepared membrane model system with controllable molecular surface properties that resembles a lipid droplet. The molecular interfacial structure of such a nanoscopic system composed of hexadecane, 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), and water was determined using vibrational sum frequency scattering and second harmonic scattering techniques. The droplet surface structure of DPPC can be tuned from a tightly packed liquid condensed phase like monolayer to a more dilute one that resembles the liquid condensed/liquid expanded coexistence phase by varying the DPPC/oil/water ratio. The tunability of the chemical structure, the high surface-to-volume ratio, and the small sample volume make this system an ideal model membrane for biochemical research.
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Affiliation(s)
- Yixing Chen
- †Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Kailash C Jena
- †Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- ‡Department of Physics, Indian Institute of Technology Ropar, Rupnagar, 140001, India
| | - Cornelis Lütgebaucks
- †Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Halil I Okur
- †Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sylvie Roke
- †Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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128
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Antonny B, Vanni S, Shindou H, Ferreira T. From zero to six double bonds: phospholipid unsaturation and organelle function. Trends Cell Biol 2015; 25:427-36. [DOI: 10.1016/j.tcb.2015.03.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 01/21/2023]
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129
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Skelton AA, Khedkar VM, Fried JR. All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion. J Biomol Struct Dyn 2015; 34:529-39. [PMID: 26046587 DOI: 10.1080/07391102.2015.1044473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
All-atom molecular dynamics is used to investigate the transport of Na(+) across a 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayer facilitated by a diazacrown hydraphile. Specifically, the free energy of Na(+) passing through the bilayer is calculated using the adaptive biasing force method to study the free energy associated with the increase in Na(+) transport in the presence of the hydraphile molecule. The results show that water interaction greatly influences Na(+) transport through the lipid bilayer as water is pulled through the bilayer with Na(+) forming a water channel. The hydraphile causes a reduction in the free energy barrier for the transport of Na(+) through the head group part of the lipid bilayer since it complexes the Na(+) reducing the necessity for water to be complexed and, therefore, dragged through with Na(+), an energetically unfavorable process. The free energy associated with Na(+) being desolvated within the bilayer is significantly decreased in the presence of the hydraphile molecule; the hydraphile increases the number of solvation states of Na(+) that can be adopted, and this increase in the number of available configurations provides an entropic explanation for the success of the hydraphile.
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Affiliation(s)
- A A Skelton
- a School of Health Sciences , University of KwaZulu Natal , Westville Campus, Durban , South Africa
| | - V M Khedkar
- a School of Health Sciences , University of KwaZulu Natal , Westville Campus, Durban , South Africa
| | - J R Fried
- b Chemical Engineering , University of Louisville , Louisville , KY , USA
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130
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Lobanova O, Avendaño C, Lafitte T, Müller EA, Jackson G. SAFT-γ force field for the simulation of molecular fluids: 4. A single-site coarse-grained model of water applicable over a wide temperature range. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1004804] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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131
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Tamai H, Okutsu N, Tokuyama Y, Shimizu E, Miyagi S, Shulga S, Danilov VI, Kurita N. A coarse grained molecular dynamics study on the structure and stability of small-sized liposomes. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1020487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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132
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Sovová Ž, Berka K, Otyepka M, Jurečka P. Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase. J Phys Chem B 2015; 119:3988-98. [PMID: 25679231 DOI: 10.1021/jp5092366] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ceramides are lipids that are involved in numerous biologically important structures (e.g., the stratum corneum and ceramide-rich platforms) and processes (e.g., signal transduction and membrane fusion), but their behavior is not fully understood. We report coarse-grain force field parameters for N-lignocerylsphingosine (ceramide NS, also known as ceramide 2) that are consistent with the Martini force field. These parameters were optimized for simulations in the gel phase and validated against atomistic simulations. Coarse-grained simulations with our parameters provide areas per lipid, membrane thicknesses, and electron density profiles that are in good agreement with atomistic simulations. Properties of the simulated membranes are compared with available experimental data. The obtained parameters were used to model the phase behavior of ceramide NS as a function of temperature and hydration. At low water content and above the main phase transition temperature, the bilayer melts into an irregular phase, which may correspond to the unstructured melted-chain phase observed in X-ray diffraction experiments. The developed parameters also reproduce the extended conformation of ceramide, which may occur in the stratum corneum. The parameters presented herein will facilitate studies on important complex functional structures such as the uppermost layer of the skin and ceramide-rich platforms in phospholipid membranes.
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Affiliation(s)
- Žofie Sovová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , 17 Listopadu 12, 77146 Olomouc, Czech Republic
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133
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Abstract
Molecular dynamics (MD) simulations at the atomic scale are a powerful tool to study the structure and dynamics of model biological systems. However, because of their high computational cost, the time and length scales of atomistic simulations are limited. Biologically important processes, such as protein folding, ion channel gating, signal transduction, and membrane remodeling, are difficult to investigate using atomistic simulations. Coarse-graining reduces the computational cost of calculations by reducing the number of degrees of freedom in the model, allowing simulations of larger systems for longer times. In the first part of this chapter we review briefly some of the coarse-grained models available for proteins, focusing on the specific scope of each model. Then we describe in more detail the MARTINI coarse-grained force field, and we illustrate how to set up and run a simulation of a membrane protein using the Gromacs software package. We explain step-by-step the preparation of the protein and the membrane, the insertion of the protein in the membrane, the equilibration of the system, the simulation itself, and the analysis of the trajectory.
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134
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Baoukina S, Tieleman DP. Computer simulations of phase separation in lipid bilayers and monolayers. Methods Mol Biol 2015; 1232:307-322. [PMID: 25331143 DOI: 10.1007/978-1-4939-1752-5_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Studying phase coexistence in lipid bilayers and monolayers is important for understanding lipid-lipid interactions underlying lateral organization in biological membranes. Computer simulations follow experimental approaches and use model lipid mixtures of simplified composition. Atomistic simulations give detailed information on the specificity of intermolecular interactions, while coarse-grained simulations achieve large time and length scales and provide a bridge towards state-of-the-art experimental techniques. Computer simulations allow characterizing the structure and composition of domains during phase transformations at Angstrom and picosecond resolution, and bring new insights into phase behavior of lipid membranes.
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Affiliation(s)
- Svetlana Baoukina
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, 2500 University Dr. NW, Calgary, AB, Canada, T2N 1N4,
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135
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Baowan D, Cox BJ, Hill JM. Instability of carbon nanoparticles interacting with lipid bilayers. RSC Adv 2015. [DOI: 10.1039/c4ra13496f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
For nanoparticles penetrating biological tissue, modelling indicates that without external forces, carbon nanoparticles will remain trapped in lipid bilayers.
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Affiliation(s)
- Duangkamon Baowan
- Department of Mathematics
- Faculty of Science
- Mahidol University
- Bangkok 10400
- Thailand
| | - Barry J. Cox
- Nanomechanics Group
- School of Mathematical Sciences
- The University of Adelaide
- Australia
| | - James M. Hill
- Nanomechanics Group
- School of Mathematical Sciences
- The University of Adelaide
- Australia
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136
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137
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Ma Z, LeBard DN, Loverde SM, Sharp KA, Klein ML, Discher DE, Finkel TH. TCR triggering by pMHC ligands tethered on surfaces via poly(ethylene glycol) depends on polymer length. PLoS One 2014; 9:e112292. [PMID: 25383949 PMCID: PMC4226474 DOI: 10.1371/journal.pone.0112292] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 10/10/2014] [Indexed: 11/29/2022] Open
Abstract
Antigen recognition by T cells relies on the interaction between T cell receptor (TCR) and peptide-major histocompatibility complex (pMHC) at the interface between the T cell and the antigen presenting cell (APC). The pMHC-TCR interaction is two-dimensional (2D), in that both the ligand and receptor are membrane-anchored and their movement is limited to 2D diffusion. The 2D nature of the interaction is critical for the ability of pMHC ligands to trigger TCR. The exact properties of the 2D pMHC-TCR interaction that enable TCR triggering, however, are not fully understood. Here, we altered the 2D pMHC-TCR interaction by tethering pMHC ligands to a rigid plastic surface with flexible poly(ethylene glycol) (PEG) polymers of different lengths, thereby gradually increasing the ligands' range of motion in the third dimension. We found that pMHC ligands tethered by PEG linkers with long contour length were capable of activating T cells. Shorter PEG linkers, however, triggered TCR more efficiently. Molecular dynamics simulation suggested that shorter PEGs exhibit faster TCR binding on-rates and off-rates. Our findings indicate that TCR signaling can be triggered by surface-tethered pMHC ligands within a defined 3D range of motion, and that fast binding rates lead to higher TCR triggering efficiency. These observations are consistent with a model of TCR triggering that incorporates the dynamic interaction between T cell and antigen-presenting cell.
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Affiliation(s)
- Zhengyu Ma
- Department of Biomedical Research, Nemours/A.I. duPont Hospital for Children, Wilmington, Delaware, United States of America
| | - David N. LeBard
- Department of Chemistry, Yeshiva University, New York, New York, United States of America
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, City University of New York, Staten Island, New York, United States of America
| | - Kim A. Sharp
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael L. Klein
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Dennis E. Discher
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Terri H. Finkel
- Department of Pediatrics, Nemours Children’s Hospital, Orlando, Florida, United States of America
- Department of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
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138
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Ikeda A, Kiguchi K, Hida T, Yasuhara K, Nobusawa K, Akiyama M, Shinoda W. [70]Fullerenes assist the formation of phospholipid bicelles at low lipid concentrations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12315-12320. [PMID: 25275703 DOI: 10.1021/la503732q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The incorporation of neutral [70]fullerenes (C70) led to bicelle formation in a relatively low lipid concentration range from neutral lipid mixtures (DMPC/DHPC). Furthermore, C70 addition resulted in the formation of large bicelles with a radius of ca. 100 nm, in contrast to C70-free bicelles that were formed from anionic lipid mixtures (DMPC/DHPC/DMPG). The stabilization of these bicelles was attributed to C70 incorporation into the membranes.
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Affiliation(s)
- Atsushi Ikeda
- Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University , Higashi-Hiroshima 739-8527, Japan
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139
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Interactions of peripheral proteins with model membranes as viewed by molecular dynamics simulations. Biochem Soc Trans 2014; 42:1418-24. [DOI: 10.1042/bst20140144] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many cellular signalling and related events are triggered by the association of peripheral proteins with anionic lipids in the cell membrane (e.g. phosphatidylinositol phosphates or PIPs). This association frequently occurs via lipid-binding modules, e.g. pleckstrin homology (PH), C2 and four-point-one, ezrin, radixin, moesin (FERM) domains, present in peripheral and cytosolic proteins. Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. Comparisons with experimental data indicate that such simulations can predict specific peripheral protein–lipid interactions. We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules.
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140
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Lamberg A, Taniguchi T. Coarse-Grained Computational Studies of Supported Bilayers: Current Problems and Their Root Causes. J Phys Chem B 2014; 118:10643-52. [DOI: 10.1021/jp5053419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antti Lamberg
- Department of Chemical Engineering, Kyoto University, Kyoto 615−8510, Japan
| | - Takashi Taniguchi
- Department of Chemical Engineering, Kyoto University, Kyoto 615−8510, Japan
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141
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Falk K, Fillot N, Sfarghiu AM, Berthier Y, Loison C. Interleaflet sliding in lipidic bilayers under shear flow: comparison of the gel and fluid phases using reversed non-equilibrium molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:2154-66. [PMID: 24346163 DOI: 10.1039/c3cp53238k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The friction between two rubbing surfaces lubricated by water can be diminished if they are coated with phospholipidic bilayers or brushes of polyelectrolytes. In the case of a coating by lipid membranes, the friction is lower when the lipids are in the gel phase rather than in the liquid phase. We investigated the response of fluid or gel bilayers to a mechanical load or under shear using non-equilibrium molecular dynamics simulations (NEMD) to understand whether this difference could come from intermonolayer sliding. The system is composed of a single fully hydrated bilayer of coarse grained phospholipids under a parallel shear with vorticity parallel to the bilayer. In both the liquid and the gel phases, an intermonolayer slip was measured in the velocity profile. In the liquid phase this slip is proportional to the shear stress. In the tilted gel phase of our model the stress is not systematically linear and relaxes differently when the shear is in the direction of the tilt or perpendicular to it. The impact of surface tension (or load) on the friction is different for the liquid and gel phases, but grossly the slip remains of the same order of magnitude.
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Affiliation(s)
- Kerstin Falk
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex, France
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142
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Yang C, Sun H. Surface–Bulk Partition of Surfactants Predicted by Molecular Dynamics Simulations. J Phys Chem B 2014; 118:10695-703. [DOI: 10.1021/jp506768b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chunwei Yang
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huai Sun
- School of Chemistry and Chemical
Engineering and Ministry of Education Key Laboratory of Scientific
and Engineering Computing, Shanghai Jiao Tong University, Shanghai, 200240, China
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143
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Liu Y, Li M, Yang Y, Xia Y, Nieh MP. The effects of temperature, salinity, concentration and PEGylated lipid on the spontaneous nanostructures of bicellar mixtures. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1871-80. [DOI: 10.1016/j.bbamem.2014.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/23/2013] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
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144
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Kawamoto S, Shinoda W. Free energy analysis along the stalk mechanism of membrane fusion. SOFT MATTER 2014; 10:3048-3054. [PMID: 24695575 DOI: 10.1039/c3sm52344f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The free energy profile of the stalk model of membrane fusion has been calculated using coarse-grained molecular dynamics simulations. The proposed method guides the lipid configuration using a guiding wall potential to make the transition from two apposed membranes to a stalk and a fusion pore. The free energy profile is obtained with a thermodynamic integration scheme using the mean force working on the guiding wall as a response of the system. We applied the method to two apposed flat bilayers composed of dioleoyl phosphatidylethanolamine/dioleoyl phosphatidylcholine expanding over the simulation box under the periodic boundary conditions. The two transition states are identified as pre-stalk and pre-pore states. The free energy barrier for the latter is confirmed to be in good agreement with that estimated by the pulling method. The present method provides a practical way to calculate the free energy profile along the stalk mechanism.
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Affiliation(s)
- Shuhei Kawamoto
- Health Research Institute, National Institute of Advanced Industrial Science & Technology (AIST), 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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145
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Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
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Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
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146
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LeBard DN. Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.899700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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147
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148
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Estimation of interfacial tension for immiscible and partially miscible liquid systems by Dissipative Particle Dynamics. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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149
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Loverde SM. Computer simulation of polymer and biopolymer self-assembly for drug delivery. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.898118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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150
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Kawamoto S, Nakamura T, Nielsen SO, Shinoda W. A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation. J Chem Phys 2014; 139:034108. [PMID: 23883011 DOI: 10.1063/1.4811677] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that accounts for thermal fluctuations of the membrane surface. The method has been successfully applied to a dimyristoyl phosphatidylcholine bilayer simulated with a coarse-grained model. A well-converged bending rigidity was obtained for the tension-free membrane and showed reasonable agreement with that obtained from the height fluctuation spectrum.
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Affiliation(s)
- Shuhei Kawamoto
- National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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