title: 7×7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors.
abstract: The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7×7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs. Compared to the commonly used overall TM bundle RMSD as a single parameter, a 7×7 RMSD matrix contains 49 parameters, which reveal changes of the relative orientations of the seven TMs. We demonstrate the novelty and advantages of this method by tackling two problems that are challenging for the existing methods. With this method, we are able to identify and quantify the helix movements in the activated receptor structures and reveal structural conservation and divergence as well as the structural relationships of different GPCRs in terms of the relative orientations of the seven TMs.
authors.affiliation: Complex Systems Division, Beijing Computational Science Research Center, 10 W. Dongbeiwang Rd, Haidian District, Beijing 100193, China; Genome Center, 451 East Health Science Drive, University of California, Davis, CA 95616, United States. Electronic address: twang@ucdavis.edu.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: Complex Systems Division, Beijing Computational Science Research Center, 10 W. Dongbeiwang Rd, Haidian District, Beijing 100193, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Complex Systems Division, Beijing Computational Science Research Center, 10 W. Dongbeiwang Rd, Haidian District, Beijing 100193, China.
authors.forename: Leihan
authors.initials: L
authors.lastname: Tang
authors.affiliation: Genome Center, 451 East Health Science Drive, University of California, Davis, CA 95616, United States. Electronic address: duan@ucdavis.edu.
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
authors.affiliation: Complex Systems Division, Beijing Computational Science Research Center, 10 W. Dongbeiwang Rd, Haidian District, Beijing 100193, China. Electronic address: hgliu@csrc.ac.cn.
authors.forename: Haiguang
authors.initials: H
authors.lastname: Liu
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry; D008722:Methods; D000072756:Protein Conformation, alpha-Helical; D000072417:Protein Domains; D017510:Protein Folding; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry*
chemical_list: D008565:Membrane Proteins; D043562:Receptors, G-Protein-Coupled
keywords: Classification; GPCR; Helix movement; Membrane proteins; RMSD; Transmembrane