Coarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model.

TitleCoarse-grained simulations of membrane insertion and folding of small helical proteins using CABS model.
Publication TypeJournal Article
Year of Publication2016
AuthorsPulawski, Wojciech, Jamroz Michal, Koliński Michał, Koliński Andrzej, and Kmiecik Sebastian
JournalJ Chem Inf Model
Date Published2016 Oct 24
ISSN1549-960X
Abstract<p>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 CABS representation and force field (CABS-membrane) to the modeling of the effect of 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 all-atom representation and all-atom scoring. In conclusion, the CABS-membrane model is a promising approach for further development towards modeling of large protein-membrane systems.</p>
DOI10.1021/acs.jcim.6b00350
Alternate JournalJ Chem Inf Model
PubMed ID27775349