Identification of protons position in acid–base enzyme catalyzed reactions: The hepatitis C viral NS3 protease

General acid–base catalysis is a key element of the catalytic activity of most enzymes. Therefore, any explicit molecular modeling of enzyme‐catalyzed chemical reactions requires correct identification of protons location on the catalytic groups. In this work, we apply our quantum mechanical/self‐consistent reaction field in virtual solvent [QM/SCRF(VS)] method for identification of the position of protons shared by the enzyme catalytic groups and the polar groups of the inhibitor in a covalent tetrahedral complex (TC) of the hepatitis C virus NS3 protease with a peptidyl α‐ketoacid inhibitor. To identify the relevant protonation states, we have analyzed relative stabilities of R and S configurations of the TC that depend on the specific proton distribution over the polar groups and correlated it with experimental NMR and X‐ray crystallography data, both at low and neutral pH ranges. The tentative assignment of the single resonance in the 13 C NMR spectrum of the hemiketal carbon at physiological pH to the S configuration of TC is confirmed. Both R and S configurations are equally stable at acidic pH in our modeling, in good agreement with the 13 C NMR observation. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.