Work

Membrane protein native state discrimination by implicit membrane models

Year: 2012

Type: article

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.

Source: Journal of Computational Chemistry

DOI: 10.1002/jcc.23189

Authors: Olga Yuzlenko, Themis Lazaridis

Institutions: City College of New York, City University of New York

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Center for Research Resources, National Institute on Minority Health and Health Disparities

Awards: G1193546451, Cellular/Molecular Basis of Development: Research Center, G3551758428, Cellular/Molecular Basis of Development: Research Center, Modeling Membrane Binding and Permeabilization by Antimicrobial Peptides