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

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 empiri...

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Bibliographic Details
Published in:Protein engineering, design and selection design and selection, 2006-09, Vol.19 (9), p.421-429
Main Authors: Tsuchiya, Yuko, Kinoshita, Kengo, Nakamura, Haruki
Format: Article
Language:English
Subjects:
complementary analysis
computational approach
Dimerization
homo-oligomer protein
Models, Molecular
Oligodeoxyribonucleotides - chemistry
Oligodeoxyribonucleotides - metabolism
Protein Binding
Protein Conformation
protein three-dimensional structure
Proteins - classification
Proteins - metabolism
protein–protein interactions
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Summary: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.
ISSN:1741-0126
1741-0134
DOI:10.1093/protein/gzl026