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SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium
Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium
These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 22 March 2013; in revised form: 2 May 2013 / Accepted: 20 May 2013 / Published: 30 May 2013
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.
Keywords: molecular dynamics; elastic network; coarse-grained; MARTINI forcefield; membrane; lipids; protein structure; hydrogen bond; accessible surface
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Dony, N.; Crowet, J.M.; Joris, B.; Brasseur, R.; Lins, L. SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein. Int. J. Mol. Sci. 2013, 14, 11510-11526.
Dony N, Crowet JM, Joris B, Brasseur R, Lins L. SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein. International Journal of Molecular Sciences. 2013; 14(6):11510-11526.
Dony, Nicolas; Crowet, Jean M.; Joris, Bernard; Brasseur, Robert; Lins, Laurence. 2013. "SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein." Int. J. Mol. Sci. 14, no. 6: 11510-11526.