(117i) Rapid Calculation of Protein Pka Values Using Rosetta

We developed a Rosetta-based Monte Carlo method to calculate pK_a values of protein residues that commonly exhibit variable protonation states (Asp, Glu, Lys, His and Tyr). We tested the technique by calculating pK_a values for 270 residues from 34 proteins.  The standard Rosetta score function, which is independent of any environmental conditions, failed to capture pK_a shifts. After incorporating a Coulomb electrostatic potential and optimizing the solvation reference energies for pK_a calculations, a method allowing side-chain flexibility achieved a root-mean-square deviation (RMSD) of 0.83 from experimental values (0.68 after discounting 11 predictions with an error over 2 pH units). Additional degrees of side-chain conformational freedom for the proximal residues facilitated capture of charge-charge interactions in a few cases and achieved an overall RMSD of 0.85 pH units. Adding backbone flexibility increased overall RMSD to 0.94 pH units but improved relative pK_a predictions for proximal catalytic residues. The method also captures large pK_a shifts of lysine and some glutamate point mutations in staphylococcal nuclease. Thus, a simple and fast method based on the Rosetta score function and limited conformational sampling produces pK_a values that will be useful when rapid estimation is essential, as in docking, design and folding.