Optimizing pKA computation in proteins with pH adapted conformations

pKA in proteins are determined by electrostatic energy computations using a small number of optimized protein conformations derived from crystal structures. In these protein conformations hydrogen positions and geometries of salt bridges on the protein surface were determined self‐consistently with the protonation pattern at three pHs (low, ambient, and high). Considering salt bridges at protein surfaces is most relevant, since they open at low and high pH. In the absence of these conformational changes, computed pK  Acomp of acidic (basic) groups in salt bridges underestimate (overestimate) experimental pK  Aexp , dramatically. The pK  Acomp for 15 different proteins with 185 known pK  Aexp yield an RMSD of 1.12, comparable with two other methods. One of these methods is fully empirical with many adjustable parameters. The other is also based on electrostatic energy computations using many non‐optimized side chain conformers but employs larger dielectric constants at short distances of charge pairs that diminish their electrostatic interactions. These empirical corrections that account implicitly for additional conformational flexibility were needed to describe the energetics of salt bridges appropriately. This is not needed in the present approach. The RMSD of the present approach improves if one considers only strongly shifted pK  Aexp in contrast to the other methods under these conditions. Our method allows interpreting pK  Acomp in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. A web service is provided to perform pKA computations. Proteins 2008. © 2007 Wiley‐Liss, Inc.