Literature DB >> 21660129

Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field.

Zun-Jing Wang1, Markus Deserno.   

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.

Entities:  

Year:  2010        PMID: 21660129      PMCID: PMC3110073          DOI: 10.1088/1367-2630/12/9/095004

Source DB:  PubMed          Journal:  New J Phys        ISSN: 1367-2630            Impact factor:   3.729


  56 in total

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Authors:  S L Veatch; I V Polozov; K Gawrisch; S L Keller
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

2.  Pore nucleation in mechanically stretched bilayer membranes.

Authors:  Zun-Jing Wang; Daan Frenkel
Journal:  J Chem Phys       Date:  2005-10-15       Impact factor: 3.488

3.  Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers.

Authors:  Sukit Leekumjorn; Amadeu K Sum
Journal:  J Phys Chem B       Date:  2007-05-09       Impact factor: 2.991

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Authors:  J M Drouffe; A C Maggs; S Leibler
Journal:  Science       Date:  1991-11-29       Impact factor: 47.728

5.  Tunable generic model for fluid bilayer membranes.

Authors:  Ira R Cooke; Kurt Kremer; Markus Deserno
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-07-26

6.  A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers.

Authors:  Vagelis A Harmandaris; Markus Deserno
Journal:  J Chem Phys       Date:  2006-11-28       Impact factor: 3.488

7.  Tension-stabilized pores in giant vesicles: determination of pore size and pore line tension.

Authors:  D V Zhelev; D Needham
Journal:  Biochim Biophys Acta       Date:  1993-04-08

8.  Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints.

Authors:  Teemu Murtola; Emma Falck; Mikko Karttunen; Ilpo Vattulainen
Journal:  J Chem Phys       Date:  2007-02-21       Impact factor: 3.488

9.  Effect of chain length and unsaturation on elasticity of lipid bilayers.

Authors:  W Rawicz; K C Olbrich; T McIntosh; D Needham; E Evans
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

10.  A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.

Authors:  Zun-Jing Wang; Markus Deserno
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

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  8 in total

1.  Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.

Authors:  Tristan Bereau; Markus Deserno
Journal:  J Membr Biol       Date:  2014-10-14       Impact factor: 1.843

2.  Determining the Gaussian curvature modulus of lipid membranes in simulations.

Authors:  Mingyang Hu; John J Briguglio; Markus Deserno
Journal:  Biophys J       Date:  2012-03-20       Impact factor: 4.033

3.  More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.

Authors:  Tristan Bereau; Zun-Jing Wang; Markus Deserno
Journal:  J Chem Phys       Date:  2014-03-21       Impact factor: 3.488

4.  Structural behavior of amphiphilic polyion complexes interacting with saturated lipid membranes investigated by coarse-grained molecular dynamic simulations.

Authors:  Daniel G Angelescu
Journal:  RSC Adv       Date:  2020-10-26       Impact factor: 4.036

5.  Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.

Authors:  Parimal Kar; Srinivasa Murthy Gopal; Yi-Ming Cheng; Afra Panahi; Michael Feig
Journal:  J Chem Theory Comput       Date:  2014-06-16       Impact factor: 6.006

6.  Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme.

Authors:  Mingwei Wan; Lianghui Gao; Weihai Fang
Journal:  PLoS One       Date:  2018-05-24       Impact factor: 3.240

7.  The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study.

Authors:  Ankush Singhal; G J Agur Sevink
Journal:  Nanoscale Adv       Date:  2021-09-22

8.  Effect of Cholesterol on the Structure of a Five-Component Mitochondria-Like Phospholipid Membrane.

Authors:  Kelly Cathcart; Amit Patel; Hannah Dies; Maikel C Rheinstädter; Cécile Fradin
Journal:  Membranes (Basel)       Date:  2015-10-30
  8 in total

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