Premium
A novel measure characterized by a polar energy surface approximation for recognition and classification of transmembrane protein structures
Author(s) -
Suwa Makiko,
Yudate Henrik T.,
Masuho Yasuhiko,
Mitaku Sigeki
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20001201)41:4<504::aid-prot80>3.0.co;2-k
Subject(s) - bacteriorhodopsin , polar , transmembrane domain , transmembrane protein , rhodopsin , polar coordinate system , crystallography , similarity (geometry) , chemistry , helix (gastropod) , polarity (international relations) , physics , mathematics , artificial intelligence , biology , membrane , geometry , computer science , retinal , biochemistry , ecology , receptor , astronomy , snail , image (mathematics) , cell
A new theoretical method has been developed for recognition and classification of membrane proteins. The method is based on computation of a polar energy surface that can reveal characteristic interaction patterns for individual helices even if crystal or NMR structure coordinates are not available. A protein with N transmembrane helices is described as a set of N vectors that are derived from a Fourier analysis of this polar energy surface computed for each helix. We then derive a polarity difference score (PDS) for any two proteins computed as the root mean square deviation between the respective vector coordinate sets. The score was found to correlate with the degree of structural similarity between the following three protein families for which tertiary structures have been determined: bacteriorhodopsin, rhodopsin, and the cytochrome c oxidase III subunit. Proteins 2000;41:504–517. © 2000 Wiley‐Liss, Inc.