Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations

BMC Bioinformatics

Software

George Khelashvili¹  Daniel Harries²  Niklaus Johner³ 

[1] Department of Physiology and Biophysics, Weill Medical College of Cornell University, 10065, New York, NY, USA;Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, 91904, Jerusalem, Israel;Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, Basel, Switzerland;

关键词: Bending rigidity;    Lipid tilt and splay;    Helfrich theory of elasticity;    Tilt modulus;    Splay modulus;   

DOI  :  10.1186/s12859-016-1003-z

 received in 2015-11-27, accepted in 2016-03-27,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influence membrane reshaping and fusion processes as well as the organisation and function of membrane proteins. Determining these properties is therefore key for a mechanistic understanding of how the cell functions.ResultsWe have developed a method to determine the bending rigidity and tilt modulus, for lipidic assemblies of arbitrary lipid composition and shape, from molecular dynamics simulations. The method extracts the elastic moduli from the distributions of microscopic tilts and splays of the lipid components. We present here an open source implementation of the method as a set of Python modules using the computational framework OpenStructure. These modules offer diverse algorithms typically used in the calculatation the elastic moduli, including routines to align MD trajectories of complex lipidic systems, to determine the water/lipid interface, to calculate lipid tilts and splays, as well as to fit the corresponding distributions to extract the elastic properties. We detail the implementation of the method and give several examples of how to use the modules in specific cases.ConclusionsThe method presented here is, to our knowledge, the only available computational approach allowing to quantify the elastic properties of lipidic assemblies of arbitrary shape and composition (including lipid mixtures). The implementation as python modules offers flexibility, which has already allowed the method to be applied to diverse lipid assembly types, ranging from bilayers in the liquid ordered and disordered phases to a study of the inverted-hexagonal phase, and with different force-fields (both all-atom and coarse grained representations). The modules are freely available through GitHub at https://github.com/njohner/ost_pymodules/ while OpenStructure can be obtained at http://www.openstructure.org.

【 授权许可】

CC BY   
© Johner et al. 2016

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