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Int. J. Mol. Sci. 2010, 11(6), 2393-2420; doi:10.3390/ijms11062393
Article

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

1,†, 1,2, 1,2, 1, 2 and 1,*
1 Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands 2 Division of Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA-91010, USA Present address: Ecole Polytechnique Fédérale de Lausanne, Switzerland.
* Author to whom correspondence should be addressed.
Received: 14 April 2010 / Revised: 16 May 2010 / Accepted: 30 May 2010 / Published: 9 June 2010
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Abstract

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
Keywords: molecular dynamics; coarse grained; transmembrane proteins; α-helices; WALP-peptides; hydrophobic mismatch molecular dynamics; coarse grained; transmembrane proteins; α-helices; WALP-peptides; hydrophobic mismatch
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Spijker, P.; Van Hoof, B.; Debertrand, M.; Markvoort, A.J.; Vaidehi, N.; Hilbers, P.A.J. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems. Int. J. Mol. Sci. 2010, 11, 2393-2420.

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