Literature DB >> 19827145

A new force field for simulating phosphatidylcholine bilayers.

David Poger1, Wilfred F Van Gunsteren, Alan E Mark.   

Abstract

A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid-crystalline, fluid phase at zero surface tension is presented. The structure of the bilayer with the area per lipid (0.629 nm(2); experiment 0.629-0.64 nm(2)), the volume per lipid (1.226 nm(3); experiment 1.229-1.232 nm(3)), and the ordering of the palmitoyl chains (order parameters) are all in very good agreement with experiment. Experimental electron density profiles are well reproduced in particular with regard to the penetration of water into the bilayer. The force field was further validated by simulating the spontaneous assembly of DPPC into a bilayer in water. Notably, the timescale on which membrane sealing was observed using this model appears closer to the timescales for membrane resealing suggested by electroporation experiments than previous simulations using existing models. 2009 Wiley Periodicals, Inc.

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Year:  2010        PMID: 19827145     DOI: 10.1002/jcc.21396

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  72 in total

1.  Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations.

Authors:  Kevin C Song; Philip W Livanec; Jeffery B Klauda; Krzysztof Kuczera; Robert C Dunn; Wonpil Im
Journal:  J Phys Chem B       Date:  2011-04-22       Impact factor: 2.991

Review 2.  The effect of H3O+ on the membrane morphology and hydrogen bonding of a phospholipid bilayer.

Authors:  Evelyne Deplazes; David Poger; Bruce Cornell; Charles G Cranfield
Journal:  Biophys Rev       Date:  2018-09-15

3.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

Authors:  Nathan Schmid; Andreas P Eichenberger; Alexandra Choutko; Sereina Riniker; Moritz Winger; Alan E Mark; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2011-04-30       Impact factor: 1.733

4.  Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables.

Authors:  S M Gruenbaum; J L Skinner
Journal:  J Chem Phys       Date:  2011-08-21       Impact factor: 3.488

5.  Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer.

Authors:  Pedro R Magalhães; Miguel Machuqueiro; António M Baptista
Journal:  Biophys J       Date:  2015-05-05       Impact factor: 4.033

6.  The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II.

Authors:  ZhiGuang Jia; Megan L O'Mara; Johannes Zuegg; Matthew A Cooper; Alan E Mark
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

7.  Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry.

Authors:  Shan Guo; Timothy C Moore; Christopher R Iacovella; L Anderson Strickland; Clare McCabe
Journal:  J Chem Theory Comput       Date:  2013-11-12       Impact factor: 6.006

8.  Oligomerization of the Tetraspanin CD81 via the Flexibility of Its δ-Loop.

Authors:  Thomas H Schmidt; Yahya Homsi; Thorsten Lang
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

9.  Organization and Structure of Branched Amphipathic Oligopeptide Bilayers.

Authors:  Zhiguang Jia; Susan K Whitaker; John M Tomich; Jianhan Chen
Journal:  Langmuir       Date:  2016-09-13       Impact factor: 3.882

10.  Scaling and alpha-helix regulation of protein relaxation in a lipid bilayer.

Authors:  Liming Qiu; Creighton Buie; Kwan Hon Cheng; Mark W Vaughn
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

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