Protein-protein binding is often associated with changes in protonation state

pKa values of ionizable residues have been calculated using the PROPKA method and structures of 75 protein–protein complexes and their corresponding free forms. These pKa values were used to compute changes in protonation state of individual residues, net changes in protonation state of the complex relative to the uncomplexed proteins, and the correction to a binding energy calculated assuming standard protonation states at pH 7. For each complex, two different structures for the uncomplexed form of the proteins were used: the X‐ray structures determined for the proteins in the absence of the other protein and the individual protein structures taken from the structure of the complex (referred to as unbound and bound structures, respectively). In 28 and 77% of the cases considered here, protein–protein binding is accompanied by a complete (>95%) or significant (>50%) change in protonation state of at least one residue using unbound structures. Furthermore, in 36 and 61% of the cases, protein–protein binding is accompanied by a complete or significant net change in protonation state of the complex relative to the separated monomers. Using bound structures, the corresponding values are 12, 51, 20, and 48%. Comparison to experimental data suggest that using unbound and bound structures lead to over‐ and underestimation of binding‐induced protonation state changes, respectively. Thus, we conclude that protein–protein binding is often associated with changes in protonation state of amino acid residues and with changes in the net protonation state of the proteins. The pH‐dependent correction to the binding energy contributes at least one order of magnitude to the binding constant in 45 and 23%, using unbound and bound structures, respectively. Proteins 2008. © 2007 Wiley‐Liss, Inc.