Issue 8, 2019

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

Abstract

In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.

Graphical abstract: Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

Associated articles

Article information

Article type
Review Article
Submitted
11 10 2018
Accepted
16 1 2019
First published
06 2 2019
This article is Open Access
Creative Commons BY license

RSC Adv., 2019,9, 4644-4658

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

S. Moradi, A. Nowroozi and M. Shahlaei, RSC Adv., 2019, 9, 4644 DOI: 10.1039/C8RA08441F

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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