Literature DB >> 27035634

A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers.

Kristyna Pluhackova1, Sonja A Kirsch1, Jing Han1, Liping Sun1, Zhenyan Jiang1, Tobias Unruh2, Rainer A Böckmann1.   

Abstract

Atomistic molecular dynamics simulations have become an important source of information for the structure and dynamics of biomembranes at molecular detail difficult to access in experiments. A number of force fields for lipid membrane simulations have been derived in the past; the choice of the most suitable force field is, however, frequently hampered by the availability of parameters for specific lipids. Additionally, the comparison of different quantities among force fields is often aggravated by varying simulation parameters. Here, we compare four atomistic lipid force fields, namely, the united-atom GROMOS54a7 and the all-atom force fields CHARMM36, Slipids, and Lipid14, for a broad range of structural and dynamical properties of saturated and monounsaturated phosphatidylcholine bilayers (DMPC and POPC) as well as for monounsaturated phosphatidylethanolamine bilayers (POPE). Additionally, the ability of the different force fields to describe the gel-liquid crystalline phase transition is compared and their computational efficiency estimated. Moreover, membrane properties like the water flux across the lipid bilayer and lipid acyl chain protrusion probabilities are compared.

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Year:  2016        PMID: 27035634     DOI: 10.1021/acs.jpcb.6b01870

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  39 in total

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4.  Phosphatidylinositol-3,5-bisphosphate lipid-binding-induced activation of the human two-pore channel 2.

Authors:  Sonja A Kirsch; Andreas Kugemann; Armando Carpaneto; Rainer A Böckmann; Petra Dietrich
Journal:  Cell Mol Life Sci       Date:  2018-04-28       Impact factor: 9.261

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Journal:  Eur Biophys J       Date:  2017-07-19       Impact factor: 1.733

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9.  Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Authors:  Yalun Yu; Andreas Krämer; Richard M Venable; Andrew C Simmonett; Alexander D MacKerell; Jeffery B Klauda; Richard W Pastor; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

10.  Membrane hydrophobicity determines the activation free energy of passive lipid transport.

Authors:  Julia R Rogers; Gustavo Espinoza Garcia; Phillip L Geissler
Journal:  Biophys J       Date:  2021-07-22       Impact factor: 3.699

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