In silico modeling of pH‐optimum of protein–protein binding

Protein–protein association is a pH‐dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH‐optimum) or the pH at which stability is almost pH‐independent (pH‐flat) of monomers are correlated with the pH‐optimum of maximal affinity (pH‐optimum of binding) or pH interval at which affinity is almost pH‐independent (pH‐flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH‐dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH‐optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH‐optimum of binding. These findings are used to propose empirical rule for predicting pH‐optimum of binding provided that the amino acid compositions of the corresponding monomers are available. Proteins 2011. © 2010 Wiley‐Liss, Inc.