title: Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.
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.
authors: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors: Wojciech
authors: W
authors: Pulawski
authors: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors: Michal
authors: M
authors: Jamroz
authors: Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland.
authors: Michal
authors: M
authors: Kolinski
authors: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors: Andrzej
authors: A
authors: Kolinski
authors: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors: Sebastian
authors: S
authors: Kmiecik
mesh_terms: D002462:Cell Membrane / Q000378:metabolism*; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D000072756:Protein Conformation, alpha-Helical; D017510:Protein Folding
chemical_list: D008565:Membrane Proteins