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J Chem Theory Comput. 2016 Mar 8;12(3):1019-28. doi: 10.1021/acs.jctc.5b01106. Epub 2016 Feb 4.

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

Author information

1
Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.
2
Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS , F-38000 Grenoble, France.
3
Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich , 52425 Jülich, Germany.
4
Université Grenoble Alpes, LJK, F-38000 Grenoble, France.
5
CNRS, LJK, F-38000 Grenoble, France.
6
Inria, F-38000 Grenoble, France.

Abstract

Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

PMID:
26765212
DOI:
10.1021/acs.jctc.5b01106
[Indexed for MEDLINE]

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