1
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Sahrmann P, Loose TD, Durumeric AEP, Voth GA. Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles. J Chem Theory Comput 2023; 19:4402-4413. [PMID: 36802592 PMCID: PMC10373655 DOI: 10.1021/acs.jctc.2c01183] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 02/22/2023]
Abstract
Coarse-grained (CG) models parametrized using atomistic reference data, i.e., "bottom up" CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG models of biomolecules remains challenging. We demonstrate in this work how virtual particles, CG sites with no atomistic correspondence, can be incorporated into CG models within the context of relative entropy minimization (REM) as latent variables. The methodology presented, variational derivative relative entropy minimization (VD-REM), enables optimization of virtual particle interactions through a gradient descent algorithm aided by machine learning. We apply this methodology to the challenging case of a solvent-free CG model of a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer and demonstrate that introduction of virtual particles captures solvent-mediated behavior and higher-order correlations which REM alone cannot capture in a more standard CG model based only on the mapping of collections of atoms to the CG sites.
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Affiliation(s)
- Patrick
G. Sahrmann
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United
States
| | - Timothy D. Loose
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United
States
| | - Aleksander E. P. Durumeric
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United
States
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center
for Theoretical Chemistry, James Franck Institute, and Institute for
Biophysical Dynamics, The University of
Chicago, Chicago, Illinois 60637, United
States
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2
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Ugarte La Torre D, Takada S. Coarse-grained implicit solvent lipid force field with a compatible resolution to the Cα protein representation. J Chem Phys 2020; 153:205101. [PMID: 33261497 DOI: 10.1063/5.0026342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biological membranes have been prominent targets for coarse-grained (CG) molecular dynamics simulations. While minimal CG lipid models with three beads per lipid and quantitative CG lipid models with >10 beads per lipid have been well studied, in between them, CG lipid models with a compatible resolution to residue-level CG protein models are much less developed. Here, we extended a previously developed three-bead lipid model into a five-bead model and parameterized it for two phospholipids, POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine). The developed model, iSoLF, reproduced the area per lipid, hydrophobic thickness, and phase behaviors of the target phospholipid bilayer membranes at the physiological temperature. The model POPC and DPPC membranes were in liquid and gel phases, respectively, in accordance with experiments. We further examined the spontaneous formation of a membrane bilayer, the temperature dependence of physical properties, the vesicle dynamics, and the POPC/DPPC two-component membrane dynamics of the CG lipid model, showing some promise. Once combined with standard Cα protein models, the iSoLF model will be a powerful tool to simulate large biological membrane systems made of lipids and proteins.
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Affiliation(s)
- Diego Ugarte La Torre
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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3
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Winkeljohn CM, Himberg B, Vanegas JM. Balance of Solvent and Chain Interactions Determines the Local Stress State of Simulated Membranes. J Phys Chem B 2020; 124:6963-6971. [DOI: 10.1021/acs.jpcb.0c03937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Conner M. Winkeljohn
- Department of Physics, University of Vermont, Burlington, Vermont 05405, United States
| | - Benjamin Himberg
- Materials Science Graduate Program, University of Vermont, Burlington, Vermont 05405, United States
| | - Juan M. Vanegas
- Department of Physics, University of Vermont, Burlington, Vermont 05405, United States
- Materials Science Graduate Program, University of Vermont, Burlington, Vermont 05405, United States
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4
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Dey S, Saha J. Minimal Coarse-Grained Modeling toward Implicit Solvent Simulation of Generic Bolaamphiphiles. J Phys Chem B 2020; 124:2938-2949. [DOI: 10.1021/acs.jpcb.0c00734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Somajit Dey
- Department of Physics, University of Calcutta, 92, A.P.C Road, Kolkata 700009, India
| | - Jayashree Saha
- Department of Physics, University of Calcutta, 92, A.P.C Road, Kolkata 700009, India
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5
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Miyazaki Y, Okazaki S, Shinoda W. pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. J Chem Theory Comput 2019; 16:782-793. [DOI: 10.1021/acs.jctc.9b00946] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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6
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F Brandner A, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Sci Rep 2019; 9:16450. [PMID: 31712588 PMCID: PMC6848203 DOI: 10.1038/s41598-019-52760-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/21/2019] [Indexed: 11/09/2022] Open
Abstract
In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.
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Affiliation(s)
- Astrid F Brandner
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Simone Melchionna
- ISC-CNR, Dipartimento di Fisica, Università Sapienza, P.le A. Moro 5, 00185, Rome, Italy.,Lexma Technology 1337 Massachusetts Avenue, Arlington, MA, 02476, USA
| | - Philippe Derreumaux
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France. .,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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7
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 419] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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8
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Mortezazadeh S, Jamali Y, Naderi-Manesh H, Lyubartsev AP. Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure. PLoS One 2019; 14:e0214673. [PMID: 30951539 PMCID: PMC6450619 DOI: 10.1371/journal.pone.0214673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of formation of these phases and transitions between them are computationally prohibitive, hence development of coarse-grained models is an important part of the methodological development in this area. Here we apply systematic bottom-up coarse-graining to model different phase structures formed by 1,2-dioleoylphosphatidylethanolamine (DOPE) lipid molecules. We started from atomistic simulations of DOPE lipids in water carried out at two different water/lipid molar ratio corresponding to the lamellar Lα and inverted hexagonal HII structures at low and high lipid concentrations respectively. The atomistic trajectories were mapped to coarse-grained trajectories, in which each lipid was represented by 14 coarse-grained sites. Then the inverse Monte Carlo method was used to compute the effective coarse-grained potentials which for the coarse-grain model reproduce the same structural properties as the atomistic simulations. The potentials derived from the low concentration atomistic simulation were only able to form a bilayer structure, while both Lα and HII lipid phases were formed in simulations with potentials obtained at high concentration. The typical atomistic configurations of lipids at high concentration combine fragments of both lamellar and non-lamellar structures, that is reflected in the extracted coarse-grained potentials which become transferable and can form a wide range of structures including the inverted hexagonal, bilayer, tubule, vesicle and micellar structures.
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Affiliation(s)
- Saeed Mortezazadeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Yousef Jamali
- Department of Mathematics, Tarbiat Modares University, Tehran, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- * E-mail: (HN); (APL)
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- * E-mail: (HN); (APL)
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9
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Pak A, Dannenhoffer-Lafage T, Madsen JJ, Voth GA. Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. J Chem Theory Comput 2019; 15:2087-2100. [PMID: 30702887 PMCID: PMC6416712 DOI: 10.1021/acs.jctc.8b01033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Indexed: 12/15/2022]
Abstract
Despite the central role of lipids in many biophysical functions, the molecular mechanisms that dictate macroscopic lipid behavior remain elusive to both experimental and computational approaches. As such, there has been much interest in the development of low-resolution, implicit-solvent coarse-grained (CG) models to dynamically simulate biologically relevant spatiotemporal scales with molecular fidelity. However, in the absence of solvent, a key challenge for CG models is to faithfully emulate solvent-mediated forces, which include both hydrophilic and hydrophobic interactions that drive lipid aggregation and self-assembly. In this work, we provide a new methodological framework to incorporate semiexplicit solvent effects through the use of virtual CG particles, which represent structural features of the solvent-lipid interface. To do so, we leverage two systematic coarse-graining approaches, multiscale coarse-graining (MS-CG) and relative entropy minimization (REM), in a hybrid fashion to construct our virtual-site CG (VCG) models. As a proof-of-concept, we focus our efforts on two lipid species, 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC), which adopt a liquid-disordered and gel phase, respectively, at room temperature. Through our analysis, we also present, to our knowledge, the first direct comparison between the MS-CG and REM methods for a complex biomolecule and highlight each of their strengths and weaknesses. We further demonstrate that VCG models recapitulate the rich biophysics of lipids, which enable self-assembly, morphological diversity, and multiple phases. Our findings suggest that the VCG framework is a powerful approach for investigation into macromolecular biophysics.
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Affiliation(s)
- Alexander
J. Pak
- Department of Chemistry, The
University of Chicago, Chicago, Illinois 60637, United States
| | | | - Jesper J. Madsen
- Department of Chemistry, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department of Chemistry, The
University of Chicago, Chicago, Illinois 60637, United States
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10
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Leonov DV, Dzuba SA, Surovtsev NV. Normal vibrations of ternary DOPC/DPPC/cholesterol lipid bilayers by low-frequency Raman spectroscopy. RSC Adv 2019; 9:34451-34456. [PMID: 35530012 PMCID: PMC9073921 DOI: 10.1039/c9ra06114b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/20/2019] [Indexed: 11/23/2022] Open
Abstract
A lipid bilayer containing a ternary mixture of low- and high-melting lipids and cholesterol (Chol) can give rise to domain formation, referred to as lipid rafts. Low-frequency Raman spectroscopy at reduced temperatures allows detection of normal membrane mechanical vibrations. In this work, Raman spectra were obtained in the spectral range between 5 and 90 cm−1 for bilayers prepared from dioleoyl-glycero-phosphocholine (DOPC), dipalmitoyl-glycero-phosphocholine (DPPC) and Chol. A narrow peak detected between 13 and 16 cm−1 was attributed to the vibrational eigenmode of a lipid monolayer (a leaflet). For the equimolar DOPC/DPPC ratio, the Chol concentration dependence for the peak position, width and amplitude may be divided into three distinct ranges: below 9 mol%, the intermediate range between 9 mol% and 38 mol%, and above 38 mol%. In the intermediate range the peak position attains its minimum, and the peak width drops approximately by a factor of two as compared with the Chol-free bilayers. Meanwhile, this range is known for raft formation in a fluid state. The obtained results may be interpreted as evidence that bilayer structures in the raft-containing fluid state may be frozen at low temperatures. The drop of peak width indicates that at the spatial scale of the experiment (∼2.5 nm) the intermolecular bilayer structure with raft formation becomes more homogeneous and more cohesive. Upon lipid raft formation, the Raman peak corresponding to monolayer normal mechanical vibrations drops remarkably in position and width.![]()
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Affiliation(s)
- Dmitry V. Leonov
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
| | - Sergei A. Dzuba
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
- Voevodsky Institute of Chemical Kinetics and Combustion
| | - Nikolay V. Surovtsev
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
- Institute of Automation and Electrometry
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11
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Abstract
The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.
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Affiliation(s)
- Tanay Paul
- Department of Physics, University of Calcutta,92, A. P. C. Road, Kolkata 700009, India
| | - Jayashree Saha
- Department of Physics, University of Calcutta,92, A. P. C. Road, Kolkata 700009, India
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12
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Dey S, Saha J. Solvent-free, molecular-level modeling of self-assembling amphiphiles in water. Phys Rev E 2017; 95:023315. [PMID: 28297991 DOI: 10.1103/physreve.95.023315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 11/07/2022]
Abstract
Aggregation mesophases of self-assembling amphiphiles in water are highly important in the context of biology (biomembranes), therapy (liposomes), industry (polymer surfactants), and condensed-matter physics (lyotropic liquid crystals). Besides helping to increase fundamental understanding of collective molecular behavior, simulations of these lyotropic phases are pivotal to technological and medical developments such as smart drug carriers for gene therapy. Implicit-solvent, coarse-grained, low resolution modeling with a simple pair potential is the key to realizing the larger length and time scales associated with such mesoscopic phenomena during a computer simulation. Modeling amphiphiles by directed, soft, ellipsoidal cores interacting via a computationally simple yet tunable anisotropic pair potential, we have come to such a single-site model amphiphile that can rapidly self-assemble to give diverse lyotropic phases (such as fluid bilayers, micelles, etc.) without requiring the explicit incorporation of solvent particles. The model directly represents a tunable packing parameter that manifests in the spontaneous curvature of the amphiphile aggregates. Besides the all-important hydrophobic interaction, the hydration force is also treated implicitly. Thanks to the efficient solvent-free molecular-level coarse graining, this model is suitable for generic mesoscale studies of phenomena such as self-assembly, amphiphile mixing, domain formation, fusion, elasticity, etc., in amphiphile aggregates.
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Affiliation(s)
- Somajit Dey
- Department of Physics, University of Calcutta, 92, A.P.C. Road, Kolkata-700009, India
| | - Jayashree Saha
- Department of Physics, University of Calcutta, 92, A.P.C. Road, Kolkata-700009, India
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13
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Schindler T, Kröner D, Steinhauser MO. On the dynamics of molecular self-assembly and the structural analysis of bilayer membranes using coarse-grained molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1955-1963. [PMID: 27216316 DOI: 10.1016/j.bbamem.2016.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/27/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
We present a molecular dynamics simulation study of the self-assembly of coarse-grained lipid molecules from unbiased random initial configurations. Our lipid model is based on a well-tried CG polymer model with an additional potential that mimics the hydrophobic properties of lipid tails. We find that several stages of self-organization of lipid clusters are involved in the dynamics of bilayer formation and that the resulting equilibrium structures sensitively depend on the strength of hydrophobic interactions hc of the lipid tails and on temperature T. The obtained stable lipid membranes are quantitatively analyzed with respect to their local structure and their degree of order. At equilibrium, we obtain self-stabilizing bilayer membrane structures that exhibit a bending stiffness κB and compression modulus KC comparable to experimental measurements under physiological conditions. We present a phase diagram of our lipid model which covers a sol-gel transition, a liquid (or gel-like) phase including stable bilayer structures and vesicle formation, as well as a quasi-crystalline phase. We also determine the exact conditions for temperature T and degree of hydrophobicity hc for stable bilayer formation including closed vesicles.
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Affiliation(s)
- Tanja Schindler
- Fraunhofer-Institute for High-Speed Dynamics, Ernst-Mach-Institut, EMI, Eckerstrasse 4, 79104 Freiburg, Germany; Albert-Ludwigs University of Freiburg, Department of Applied Mathematics, Hermann-Herder-Strasse 10, 79104 Freiburg, Germany
| | - Dietmar Kröner
- Albert-Ludwigs University of Freiburg, Department of Applied Mathematics, Hermann-Herder-Strasse 10, 79104 Freiburg, Germany
| | - Martin O Steinhauser
- Fraunhofer-Institute for High-Speed Dynamics, Ernst-Mach-Institut, EMI, Eckerstrasse 4, 79104 Freiburg, Germany; Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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14
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15
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Arnarez C, Uusitalo JJ, Masman MF, Ingólfsson HI, de Jong DH, Melo MN, Periole X, de Vries AH, Marrink SJ. Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent. J Chem Theory Comput 2014; 11:260-75. [DOI: 10.1021/ct500477k] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Clément Arnarez
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Jaakko J. Uusitalo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Marcelo F. Masman
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - 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
| | - Djurre H. de Jong
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Manuel N. Melo
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - 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
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16
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Andrews CT, Elcock AH. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput 2014; 10:5178-5194. [PMID: 25400526 PMCID: PMC4230375 DOI: 10.1021/ct5006328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 02/06/2023]
Abstract
![]()
We describe the derivation of a set
of bonded and nonbonded coarse-grained
(CG) potential functions for use in implicit-solvent Brownian dynamics
(BD) simulations of proteins derived from all-atom explicit-solvent
molecular dynamics (MD) simulations of amino acids. Bonded potential
functions were derived from 1 μs MD simulations of each of the
20 canonical amino acids, with histidine modeled in both its protonated
and neutral forms; nonbonded potential functions were derived from
1 μs MD simulations of every possible pairing of the amino acids
(231 different systems). The angle and dihedral probability distributions
and radial distribution functions sampled during MD were used to optimize
a set of CG potential functions through use of the iterative Boltzmann
inversion (IBI) method. The optimized set of potential functions—which
we term COFFDROP (COarse-grained Force Field for Dynamic Representation
Of Proteins)—quantitatively reproduced all of the “target”
MD distributions. In a first test of the force field, it was used
to predict the clustering behavior of concentrated amino acid solutions;
the predictions were directly compared with the results of corresponding
all-atom explicit-solvent MD simulations and found to be in excellent
agreement. In a second test, BD simulations of the small protein villin
headpiece were carried out at concentrations that have recently been
studied in all-atom explicit-solvent MD simulations by Petrov and
Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions
seen in the MD study were reproduced in the COFFDROP simulations;
a simple scaling of COFFDROP’s nonbonded parameters, however,
produced results in better accordance with experiment. Overall, our
results suggest that potential functions derived from simulations
of pairwise amino acid interactions might be of quite broad applicability,
with COFFDROP likely to be especially useful for modeling unfolded
or intrinsically disordered proteins.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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17
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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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18
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Mirzoev A, Lyubartsev AP. Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids. J Comput Chem 2014; 35:1208-18. [DOI: 10.1002/jcc.23610] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Alexander Mirzoev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-10691 Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-10691 Sweden
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19
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Wüstner D, Sklenar H. Atomistic Monte Carlo simulation of lipid membranes. Int J Mol Sci 2014; 15:1767-803. [PMID: 24469314 PMCID: PMC3958820 DOI: 10.3390/ijms15021767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/06/2013] [Accepted: 01/09/2014] [Indexed: 02/07/2023] Open
Abstract
Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M DK-5230, Denmark.
| | - Heinz Sklenar
- Theoretical Biophysics Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, Berlin D-13125, Germany.
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20
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Vanegas JM, Torres-Sánchez A, Arroyo M. Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations. J Chem Theory Comput 2014; 10:691-702. [DOI: 10.1021/ct4008926] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Juan M. Vanegas
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
| | | | - Marino Arroyo
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, 08034 Barcelona, Spain
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21
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Abstract
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
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Affiliation(s)
- Ryan Bradley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-215-898-0487; Fax: +1-215-573-2071
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22
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Srivastava A, Voth GA. A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J Chem Theory Comput 2012; 9:750-765. [PMID: 25100925 DOI: 10.1021/ct300751h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a systematic methodology to develop highly coarse-grained (CG) lipid models for large scale bio-membrane simulations, in which we derive CG interactions using a powerful combination of the multiscale coarse-graining (MS-CG) method, and an analytical form of the CG potential to model interactions at short range. The resulting hybrid coarse-graining (HCG) methodology is used to develop a three-site solvent-free model for 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and a 1:1 mixture of 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and DOPC. In addition, we developed a four-site model of DOPC, demonstrating the capability of the HCG methodology in designing model lipid systems of a desired resolution. We carried out microsecond-scale molecular dynamics (MD) simulations of large vesicles, highlighting the ability of the model to study systems at mesoscopic length and time scales. The models of DLPC, DOPC and DOPC-DOPS have elastic properties consistent with experiment and structural properties such as the radial distribution functions (RDF), bond and angle distributions, and the z-density distributions that compare well with reference all-atom systems.
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Affiliation(s)
- Anand Srivastava
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and Computation Institute, University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and Computation Institute, University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
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23
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Huang MJ, Kapral R, Mikhailov AS, Chen HY. Coarse-grain model for lipid bilayer self-assembly and dynamics: Multiparticle collision description of the solvent. J Chem Phys 2012; 137:055101. [DOI: 10.1063/1.4736414] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mu-Jie Huang
- Department of Physics, National Central University, Jhongli 32001, Taiwan
| | - Raymond Kapral
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Alexander S. Mikhailov
- Abteilung Physikalische Chemie, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Hsuan-Yi Chen
- Department of Physics, National Central University, Jhongli 32001, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11520, Taiwan
- Physics Division, National Center for Theoretical Sciences, Hsinchu, 30013, Taiwan
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24
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Computer simulation studies of self-assembling macromolecules. Curr Opin Struct Biol 2012; 22:175-86. [DOI: 10.1016/j.sbi.2012.01.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 11/20/2022]
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25
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Determining the Gaussian curvature modulus of lipid membranes in simulations. Biophys J 2012; 102:1403-10. [PMID: 22455923 DOI: 10.1016/j.bpj.2012.02.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/25/2012] [Accepted: 02/08/2012] [Indexed: 11/20/2022] Open
Abstract
The Gaussian curvature modulus κ¯ of lipid bilayers likely contributes more than 100 kcal/mol to every cellular fission or fusion event. This huge impact on membrane remodeling energetics might be a factor that codetermines the complex lipid composition of biomembranes through tuning of κ¯. Yet, its value has been measured only for a handful of simple lipids, and no simulation has so far determined it better than a factor of two, rendering a systematic investigation of such enticing speculations impossible. Here we propose a highly accurate method to determine κ¯ in computer simulations. It relies on the interplay between curvature stress and edge tension of partially curved axisymmetric membrane disks and requires determining their closing probability. For a simplified lipid model we obtain κ¯ and its relation to the normal bending modulus κ for membranes differing both in stiffness and spontaneous lipid curvature. The elastic ratio κ¯/κ can be determined with a few percent statistical accuracy. Its value agrees with the scarce experimental data, and its change with spontaneous lipid curvature is compatible with theoretical expectations, thereby granting additional information on monolayer properties. We also show that an alternative determination of these elastic parameters based on moments of the lateral stress profile gives markedly different and unphysical values.
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26
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Patti A, Ramsch R, Marsà CS. Solvent-Free Model for Self-Assembling Amphiphilic Cyclodextrins. An Off-Lattice Monte Carlo Approach in Two Dimensions. J Phys Chem B 2012; 116:2687-95. [DOI: 10.1021/jp212448q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandro Patti
- Institute of Advanced Chemistry of Catalonia
(IQAC−CSIC) and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Jordi Girona,
18-26−08034 Barcelona, Spain
| | - Roland Ramsch
- Institute of Advanced Chemistry of Catalonia
(IQAC−CSIC) and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Jordi Girona,
18-26−08034 Barcelona, Spain
| | - Conxita Solans Marsà
- Institute of Advanced Chemistry of Catalonia
(IQAC−CSIC) and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Jordi Girona,
18-26−08034 Barcelona, Spain
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27
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Wang ZJ, Deserno M. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field. NEW JOURNAL OF PHYSICS 2010; 12:095004. [PMID: 21660129 PMCID: PMC3110073 DOI: 10.1088/1367-2630/12/9/095004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
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Affiliation(s)
- Zun-Jing Wang
- Authors to whom any correspondence should be addressed. and
| | - Markus Deserno
- Authors to whom any correspondence should be addressed. and
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