BIOPHYSICAL THEORY AND MODELING |
ELECTROSTATIC PROPERTIES OF PROTEIN-PROTEIN COMPLEXES
Petras J Kundrotas 1 and Emil G Alexov 1*
1 Clemson University
* To whom correspondence should be addressed. E-mail: ealexov{at}clemson.edu.
Submitted on March 29, 2006
Revised on May 23, 2006
Accepted on 2 June 2006
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Abstract |
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Statistical electrostatic analysis of 37 protein-protein complexes extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom) is presented. It was shown that small interfaces have higher content of charged and polar groups compared to large interfaces. In a vast majority of the cases the average pKa shifts for acidic residues induced by the complex formation are negative indicating that complex formation stabilizes their ionizable states, while the histidines are predicted to destabilize the complex. The individual pKa shifts show the same tendency since 80% of the interfacial acidic groups were found to lower their pKa's while only 25% of histidines raise their pKa upon the complex formation. The interfacial groups have been divided into three sets according to the mechanism of their pKa shift and statistical analysis of each set was performed. It was shown that the optimum pH values (pH of maximal stability) of the complex tend to be the same as the optimum pH values of the complex components. This finding can be used in the homology-based prediction of the 3D structures of protein complexes, especially when one needs to evaluate and rank putative models. It is more likely for a model to be correct if both components of the model complex and the entire complex have the same or at least similar values of the optimum pH.
Key Words:
electrostatics, pH optimum, pKa calculations, protein complexes
