SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein

[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 :

Issue :

Pages :

11510-26

Peer reviewed :

Peer Reviewed verified by ORBi

Tags :

CÉCI : Consortium des Équipements de Calcul Intensif

Available on ORBi :

since 03 June 2013

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