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PEDS Advance Access published online on July 12, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzl026
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© 2006 The Author(s).
Received April 23, 2006
Accepted May 4, 2006

Article

Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity

Yuko Tsuchiya 1, Kengo Kinoshita 2 *, and Haruki Nakamura 1

1 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
2 Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan; Structure and Function of Biomolecules, SORST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

* To whom correspondence should be addressed.
Kengo Kinoshita, E-mail: kino{at}ims.u-tokyo.ac.jp


  Abstract

To extract the general structural features of interacting protein pairs, the non-redundant homo-oligomer interfaces (393 interfaces) in the PDB were analyzed using the fine-grained molecular surface, electrostatic potentials and the hydrophobicity calculated as the solvation free energy using empirical parameters. For each property, statistical analyses of the degree of complementarity were carried out, and we developed a method to judge whether interfaces were shape-complementary, electrostatic-complementary and/or hydrophobic-complementary or not. In order to search for the correlation between the property complementarity and structure of the interfaces, at first, we roughly classified all the interfaces into the following five groups according to the structure of the interface and surveyed the correlation between the shape classification and the complementary: cyclic-oligomer (69), twisted-dimer (27), dimer-parallel (14), dimer-perpendicular (109) and dimer-circular (174), where the number in the parenthesis is the number of interfaces in each group. As a result, we found the new characteristic trends as the possible necessary conditions in the formation of homo-oligomer interfaces, especially from the viewpoint of electrostatic complementarity. In addition, we also show that complementarity analyses can be used to discriminate the biological-interface from the crystallographic-interface in homo-oligomer proteins.

Keywords: complementary analysis; computational approach; homo-oligomer protein; protein three-dimensional structure; protein-protein interactions.
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