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SAHBNET, an accessible surface-based elastic network: an application to membrane protein.

Abstract：

:Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins.

journal_name

Int J Mol Sci

journal_title

International journal of molecular sciences

authors

Dony N,Crowet JM,Joris B,Brasseur R,Lins L

doi

10.3390/ijms140611510

subject

Has Abstract

pub_date

2013-05-30 00:00:00

pages

11510-26

issue

6

issn

1422-0067

pii

ijms140611510

journal_volume

14

pub_type

杂志文章

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