Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores

Proteins
Shide LiangHuarong Guo

Abstract

We show that residues at the interfaces of protein-protein complexes have higher side-chain energy than other surface residues. Eight different sets of protein complexes were analyzed. For each protein pair, the complex structure was used to identify the interface residues in the unbound monomer structures. Side-chain energy was calculated for each surface residue in the unbound monomer using our previously developed scoring function.1 The mean energy was calculated for the interface residues and the other surface residues. In 15 of the 16 monomers, the mean energy of the interface residues was higher than that of other surface residues. By decomposing the scoring function, we found that the energy term of the buried surface area of non-hydrogen-bonded hydrophilic atoms is the most important factor contributing to the high energy of the interface regions. In spite of lacking hydrophilic residues, the interface regions were found to be rich in buried non-hydrogen-bonded hydrophilic atoms. Although the calculation results could be affected by the inaccuracy of the scoring function, patch analysis of side-chain energy on the surface of an isolated protein may be helpful in identifying the possible protein-protein interface. A patc...Continue Reading

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Citations

Aug 9, 2006·Nucleic Acids Research·Shide LiangYaoqi Zhou
Nov 8, 2008·Nucleic Acids Research·Yao Chi Chen, Carmay Lim
Sep 24, 2009·BMC Bioinformatics·Shide LiangMartin Zacharias
Jan 12, 2012·BMC Bioinformatics·Bin Li, Daisuke Kihara
Oct 4, 2011·Archives of Physical Medicine and Rehabilitation·Glenn K KluteBrian Curless
Nov 17, 2009·Journal of Molecular Biology·Veena L ThomasBrian K Shoichet

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