Literature DB >> 18512235

Modification of the CHARMM force field for DMPC lipid bilayer.

Carl-Johan Högberg1, Alexei M Nikitin, Alexander P Lyubartsev.   

Abstract

The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids. 2008 Wiley Periodicals, Inc.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 18512235     DOI: 10.1002/jcc.20974

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


  16 in total

1.  A new AMBER-compatible force field parameter set for alkanes.

Authors:  Alexei M Nikitin; Yury V Milchevskiy; Alexander P Lyubartsev
Journal:  J Mol Model       Date:  2014-02-19       Impact factor: 1.810

2.  Preferential binding of an odor within olfactory receptors: a precursor to receptor activation.

Authors:  Peter C Lai; Brandon Guida; Jing Shi; Chiquito J Crasto
Journal:  Chem Senses       Date:  2014-01-07       Impact factor: 3.160

3.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

4.  Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields.

Authors:  Brad A Bauer; Timothy R Lucas; David J Meninger; Sandeep Patel
Journal:  Chem Phys Lett       Date:  2011-05-27       Impact factor: 2.328

5.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Authors:  Jeffery B Klauda; Richard M Venable; J Alfredo Freites; Joseph W O'Connor; Douglas J Tobias; Carlos Mondragon-Ramirez; Igor Vorobyov; Alexander D MacKerell; Richard W Pastor
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

6.  LIPID11: a modular framework for lipid simulations using amber.

Authors:  Åge A Skjevik; Benjamin D Madej; Ross C Walker; Knut Teigen
Journal:  J Phys Chem B       Date:  2012-09-04       Impact factor: 2.991

7.  Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation.

Authors:  Jianjun Pan; Stephanie Tristram-Nagle; John F Nagle
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-08-25

8.  Statistical thermodynamics of biomembranes.

Authors:  Ram V Devireddy
Journal:  Cryobiology       Date:  2009-05-19       Impact factor: 2.487

9.  Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models.

Authors:  Joseph E Davis; Obaidur Rahaman; Sandeep Patel
Journal:  Biophys J       Date:  2009-01       Impact factor: 4.033

10.  Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads.

Authors:  Ilja V Khavrutskii; Alemayehu A Gorfe; Benzhuo Lu; J Andrew McCammon
Journal:  J Am Chem Soc       Date:  2009-02-11       Impact factor: 15.419

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.