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SAHBNET, An Accessible Surface-Based Elastic Network to Insert a Protein in a Complex Lipid Membrane
Dony, Nicolas; Crowet, Jean-Marc; Joris, Bernard et al.
201316th GEM – 10th GERLI lipidomics meeting “From Membranes to Pathologies”
 

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Keywords :
Molecular dynamics; Elastic network; Coarse-grained; Membrane; Protein Structure
Abstract :
[en] Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the recent advances in membrane protein crystallization, it represents less than 1 % of the entries in the Protein Data Bank. Therefore, calculation methods to study membrane proteins are helpful to complement experimental studies and fill the gap between the information obtained from the sequence and/or structure, the experimental results and the biological activity. 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. However, these approaches have two main drawbacks, the preparation of complex systems and the preservation of the 3D protein structure, which is not trivial in coarse grained approach. To circumvent these problems, we propose to use a modified version of the Gromacs tool genbox to easily insert lipids and a network based on hydrogen bonds and accessible surface to maintain the protein 3D structure. This protocol is available through a website (gcgs.gembloux.ulg.ac.be).
Research center :
Centre de Biophysique Moléculaire Numérique
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 to Insert a Protein in a Complex Lipid Membrane
Publication date :
11 November 2013
Event name :
16th GEM – 10th GERLI lipidomics meeting “From Membranes to Pathologies”
Event organizer :
Groupe d’Etude des Membranes (GEM) / Groupe d’Etude et de Recherche en Lipidomique (GERLI)
Event place :
Saint-Jean-Cap-Ferrat, France
Event date :
10th-14th November 2013
Audience :
International
Name of the research project :
IAP/Belspo P7/44 project : Integrative Protein Science (iPROS)
Funders :
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
Pôles d'Attraction Interuniversitaires
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since 09 December 2013

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