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 metho

SUBMITTER: Wang T 

PROVIDER: S-EPMC5522649 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature