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

Journal of Chemical Theory and Computation
Pavel BuslaevIvan Gushchin

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...Continue Reading

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Citations

Aug 17, 2016·Biochimica Et Biophysica Acta·Yin WangZoe Cournia
Dec 19, 2019·Frontiers in Molecular Biosciences·Olga NovitskaiaIvan Gushchin
Jul 24, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Paul SmithChristian D Lorenz
Sep 2, 2021·Journal of the American Chemical Society·Amélie BacleSalla I Virtanen

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