title: Membrane protein native state discrimination by implicit membrane models.
abstract: Four implicit membrane models [IMM1, generalized Born (GB)-surface area-implicit membrane (GBSAIM), GB with a simple switching (GBSW), and heterogeneous dielectric GB (HDGB)] were tested for their ability to discriminate the native conformation of five membrane proteins from 450 decoys generated by the Rosetta-Membrane program. The energy ranking of the native state and Z-scores were used to assess the performance of the models. The effect of membrane thickness was examined and was found to be substantial. Quite satisfactory discrimination was achieved with the all-atom IMM1 and GBSW models at 25.4 Å thickness and with the HDGB model at 28.5 Å thickness. The energy components by themselves were not discriminative. Both van der Waals and electrostatic interactions contributed to native state discrimination, to a different extent in each model. Computational efficiency of the models decreased in the order: extended-atom IMM1 > all-atom IMM1 > GBSAIM > GBSW > HDGB. These results encourage the further development and use of implicit membrane models for membrane protein structure prediction.
authors.affiliation: Department of Chemistry, City College of the City University of New York, 160 Convent Avenue, New York, New York 10031, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Yuzlenko
authors.forename: Themis
authors.initials: T
authors.lastname: Lazaridis
mesh_terms: D000818:Animals; D001419:Bacteria; D001436:Bacteriorhodopsins / Q000737:chemistry*; D002462:Cell Membrane / Q000737:chemistry*; D003198:Computer Simulation; D006801:Humans; D026901:Membrane Transport Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012243:Rhodopsin / Q000737:chemistry*; D055672:Static Electricity; D013385:Succinate Dehydrogenase / Q000737:chemistry*; D013816:Thermodynamics; D025262:Vacuolar Proton-Translocating ATPases / Q000737:chemistry*
chemical_list: D026901:Membrane Transport Proteins; D001436:Bacteriorhodopsins; D012243:Rhodopsin; C021499:lactose permease; C033727:fumarate reductase complex; D013385:Succinate Dehydrogenase; D025262:Vacuolar Proton-Translocating ATPases