molecular dynamics; elastic network; coarse-grained; MARTINI forcefield; membrane; lipids; protein structure; hydrogen bond; accessible surface
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Dony, Nicolas ; Université de Liège - ULiège > Centre d'ingénierie des protéines
Crowet, Jean-Marc ; Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Joris, Bernard ; Université de Liège - ULiège > Département des sciences de la vie > Physiologie et génétique bactériennes
Brasseur, Robert ; Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Lins, Laurence ; Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Language :
English
Title :
SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Publication date :
May 2013
Journal title :
International Journal of Molecular Sciences
ISSN :
1661-6596
eISSN :
1422-0067
Publisher :
Molecular Diversity Preservation International (MDPI), Basel, Switzerland
Volume :
14
Issue :
6
Pages :
11510-26
Peer reviewed :
Peer Reviewed verified by ORBi
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
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