Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems.

International Journal of Molecular Sciences
Peter SpijkerPeter A J Hilbers

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.

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Citations

Dec 4, 2012·International Journal of Molecular Sciences·Junfeng GuXicheng Wang
Oct 19, 2011·Future Medicinal Chemistry·Seetharama D Satyanarayanajois, Ronald A Hill
Jan 29, 2014·Journal of Bioinformatics and Computational Biology·Ismael Sanchez-OsorioEdgar Dantan
Jan 3, 2016·The Journal of Chemical Physics·Ghulam MustafaRebecca C Wade
Sep 7, 2019·International Journal of Molecular Sciences·Ghulam MustafaRebecca C Wade
Oct 3, 2012·The Journal of Physical Chemistry. B·Bram van HoofPeter A J Hilbers
Jul 12, 2011·The Journal of Physical Chemistry. B·Bram van HoofPeter A J Hilbers
Mar 7, 2014·The Journal of Physical Chemistry. B·Bram van HoofPeter A J Hilbers

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Methods Mentioned

BETA
protein folding

Software Mentioned

Marrink

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