title: Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases.
abstract: General-base catalysis in serine proteases still poses mechanistic challenges despite decades of research. Whether proton transfer from the catalytic Ser to His and nucleophilic attack on the substrate are concerted or stepwise is still under debate, even for the classical Asp-His-Ser catalytic triad. To address these key catalytic steps, the transformation of the Michaelis complex to tetrahedral complex in the covalent inhibition of two prototype serine proteases was studied: chymotrypsin (with the catalytic triad) inhibition by a peptidyl trifluoromethane and GlpG rhomboid (with Ser-His dyad) inhibition by an isocoumarin derivative. The sampled MD trajectories of averaged pKa  values of catalytic residues were QM calculated by the MD-QM/SCRF(VS) method on molecular clusters simulating the active site. Differences between concerted and stepwise mechanisms are controlled by the dynamically changing pKa  values of the catalytic residues as a function of their progressively reduced water exposure, caused by the incoming ligand.
authors.affiliation: The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel.
authors.forename: Neta
authors.initials: N
authors.lastname: Uritsky
authors.affiliation: The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel. michael.shokhen@biu.ac.il.
authors.forename: Michael
authors.initials: M
authors.lastname: Shokhen
authors.affiliation: The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel. amnon.albeck@biu.ac.il.
authors.forename: Amnon
authors.initials: A
authors.lastname: Albeck
mesh_terms: D002384:Catalysis; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D057057:Serine Proteases / Q000378:metabolism*
chemical_list: D057057:Serine Proteases
keywords: acidity; enzyme catalysis; molecular modeling; proteases; reaction mechanisms