Sequence and structural features of binding site residues in protein-protein complexes

• Published in: 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) pp. 53 - 56
• Main Authors: Gromiha, M M, Saranya, N, Selvaraj, S, Jayaram, B, Fukui, K
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.12.2010
• Subjects: Amino acids; Bioinformatics; Coils; Electrostatics; Protein engineering; Proteins; Switches
• DOI: 10.1109/BIBM.2010.5706535
• ISBN: 1424483069; 9781424483068

We have developed an energy based approach for identifying the binding site residues in protein-protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as neighboring residues in the vicinity of binding sites and conformational switching. We observed specific preferences of dipeptides and tripeptides for binding, which is unique to protein-protein complexes. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.