Title

Interaction modes at protein hetero-dimer interfaces

Authors

Ayyappan Vaishnavi^1,3, Gopichandran Sowmya^1,3, Jayaseelan Kalaivanii^1,3, Selvarajan Ilakya^1,3, Uma Kangueane¹, Pandjassarame Kangueane^1,2*

Affiliation

¹Biomedical Informatics, Pondicherry 607 402, India; ²AIMST, Kedah 08100, Malaysia; ³Equal contributions

Email

kangueane@bioinformation.net

Article Type

Hypothesis

Date

Received November 15, 2009; Revised December 07, 2009; Accepted December 16, 2009; Published January 20, 2010

Abstract

Hetero dimer (different monomers) interfaces are involved in catalysis and regulation through the formation of interface active sites. This is critical in cell and molecular biology events. The physical and chemical factors determining the formation of the interface active sites is often large in numbers. The combined role of interacting features is frequently combinatorial and additive in nature. Therefore, it is important to determine the physical and chemical features of such interactions. A number of such features have been documented in literature since 1975. However, the use of such interaction features in the prediction of interaction partners and sites given their sequences is still a challenge. In a non-redundant dataset of 156 hetero-dimer structures determined by X-ray crystallography, the interacting partners are often varying in size and thus, size variation between subunits is an important factor in determining the mode of interface formation. The size of protein subunits interacting are either small-small, largelarge, medium-medium, large-small, large-medium and small-medium. It should also be noted that the interface formed between subunits have physical interactions at N terminal (N), C terminal (C) and middle (M) region of the protein with reference to their sequences in one dimension. These features are believed to have application in the prediction of interaction partners and sites from sequences. However, the use of such features for interaction prediction from sequence is not currently clear.

Keywords

protein-protein interaction, mode of interaction, protein size, interface

Citation

Vaishnavi et al., Bioinformation, 4 (7) 310-319, (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.