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Cover and spacer insertions: Small nonhydrophobic accessories that assist protein oligomerization
Author(s) -
Nishi Hafumi,
Koike Ryotaro,
Ota Motonori
Publication year - 2011
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.23084
Subject(s) - interface (matter) , cover (algebra) , protein structure , association (psychology) , crystallography , biology , computational biology , chemistry , biochemistry , mechanical engineering , pulmonary surfactant , gibbs isotherm , philosophy , epistemology , engineering
We investigated fragmental sequences that were inserted into proteins during long molecular evolution and relevant to the association of homo‐oligomers. Seventeen insertions in 12 SCOP (structure classification of proteins) families were examined and were classified into large and small insertions. The large insertions are composed of interface‐like residues and effectively increase the interface area. In contrast, small insertions are composed of the residues that are not commonly found at the interfaces and have a small interface area: their roles in the oligomerization process are unclear. We found that the small insertions were located in the middle of protein sequences and therefore must involve residues with strong turn and less interface‐like propensities. From a structural viewpoint, small insertions were found to mask hydrophobic patches or act as spacers to fill cavities present at interfaces. The presence or absence of small insertions coincides with the annotated oligomeric states for homologs in the SwissProt database, and the calculation of the association scores predicts that small insertions contribute to the stability of oligomers. These results support the significant role of small, nonhydrophobic insertions in protein oligomerization. Proteins 2011; © 2011 Wiley‐Liss, Inc.