Literature DB >> 26610004

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

Jakob P Ulmschneider1, Martin B Ulmschneider1.   

Abstract

We have developed a new united-atom set of lipid force field parameters for dipalmitoylphosphatidylcholine (DPPC) lipid bilayers that can be combined with the all-atom optimized potentials for liquid simulations (OPLS-AA) protein force field. For this, all torsions have been refitted for a nonbonded 1-4 scale factor of 0.5, which is the standard in OPLS-AA. Improved van der Waals parameters have been obtained for the acyl lipid tails by matching simulation results of bulk pentadecane against recently improved experimental measurements. The charge set has been adjusted from previous lipid force fields to allow for an identical treatment of the alkoxy ester groups. This reduces the amount of parameters required for the model. Simulation of DPPC bilayers in the tension-free NPT ensemble at 50 °C gives the correct area per lipid of 62.9 ± 0.1 Å(2), which compares well with the recently refined experimental value of 63.0 Å(2). Electron density profiles and deuterium order parameters are similarly well reproduced. The new parameters will allow for improved simulation results in microsecond scale peptide partitioning simulations, which have proved problematic with prior parametrizations.

Entities:  

Year:  2009        PMID: 26610004     DOI: 10.1021/ct900086b

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  37 in total

1.  Peptide partitioning properties from direct insertion studies.

Authors:  Martin B Ulmschneider; Jeremy C Smith; Jakob P Ulmschneider
Journal:  Biophys J       Date:  2010-06-16       Impact factor: 4.033

2.  Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide.

Authors:  William G Glass; Jonathan W Essex; Franca Fraternali; James Gebbie-Rayet; Irene Marzuoli; Marley L Samways; Philip C Biggin; Syma Khalid
Journal:  Methods Mol Biol       Date:  2021

3.  Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations.

Authors:  Jakob P Ulmschneider; Jeremy C Smith; Martin B Ulmschneider; Anne S Ulrich; Erik Strandberg
Journal:  Biophys J       Date:  2012-08-08       Impact factor: 4.033

4.  N-Ras forms dimers at POPC membranes.

Authors:  Jörn Güldenhaupt; Till Rudack; Peter Bachler; Daniel Mann; Gemma Triola; Herbert Waldmann; Carsten Kötting; Klaus Gerwert
Journal:  Biophys J       Date:  2012-10-02       Impact factor: 4.033

5.  Conformational states of melittin at a bilayer interface.

Authors:  Magnus Andersson; Jakob P Ulmschneider; Martin B Ulmschneider; Stephen H White
Journal:  Biophys J       Date:  2013-03-19       Impact factor: 4.033

6.  Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.

Authors:  Martin B Ulmschneider; Claire Bagnéris; Emily C McCusker; Paul G Decaen; Markus Delling; David E Clapham; Jakob P Ulmschneider; B A Wallace
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-29       Impact factor: 11.205

7.  Local partition coefficients govern solute permeability of cholesterol-containing membranes.

Authors:  Florian Zocher; David van der Spoel; Peter Pohl; Jochen S Hub
Journal:  Biophys J       Date:  2013-12-17       Impact factor: 4.033

8.  The Photosystem II Subunit S under Stress.

Authors:  Vangelis Daskalakis; Sotiris Papadatos
Journal:  Biophys J       Date:  2017-12-05       Impact factor: 4.033

9.  Role of the Native Outer-Membrane Environment on the Transporter BtuB.

Authors:  Curtis Balusek; James C Gumbart
Journal:  Biophys J       Date:  2016-10-04       Impact factor: 4.033

10.  In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions.

Authors:  Jakob P Ulmschneider; Jeremy C Smith; Stephen H White; Martin B Ulmschneider
Journal:  J Am Chem Soc       Date:  2011-09-14       Impact factor: 15.419

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