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Common occurrence of internal repeat symmetry in membrane proteins
Author(s) -
Choi Sungwon,
Jeon Jouhyun,
Yang JaeSeong,
Kim Sanguk
Publication year - 2008
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/prot.21656
Subject(s) - symmetry (geometry) , protein structure , biophysics , divergence (linguistics) , crystallography , physics , biology , chemistry , chemical physics , geometry , biochemistry , mathematics , linguistics , philosophy
Symmetry plays significant roles in protein structure and function. Particularly, symmetric interfaces are known to act as switches for two‐state conformational change. Membrane proteins often undergo two‐state conformational change during the transport process of ion channels or the active/inactive transitions in receptors. Here, we provide the first comprehensive analyses of internal repeat symmetry in membrane proteins. We examined the known membrane protein structures and found that, remarkably, nearly half of them have internal repeat symmetry. Moreover, we found that the conserved cores of these internal repeats are positioned at the interface of symmetric units when they are mapped on structures. Because of the large sequence divergence that occurs between internal repeats, the inherent symmetry present in protein sequences often has only been detected after structure determination. We therefore developed a sensitive procedure to predict the internal repeat symmetry from sequence information and identified 4653 proteins that are likely to have internal repeat symmetry. Proteins 2008. © 2007 Wiley‐Liss, Inc.