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J Chem Inf Model. 2016 Nov 28;56(11):2207-2215. Epub 2016 Oct 31.

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.

Author information

1
Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
2
Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland.

Abstract

The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.

PMID:
27775349
DOI:
10.1021/acs.jcim.6b00350
[Indexed for MEDLINE]

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