The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulations.

Rhomboid proteases are a ubiquitous family of intramembrane serine proteases in prokaryotic and eukaryotic organisms that cleave membrane proteins in their transmembrane region. Their catalytic activity is centered at a His-Ser catalytic dyad. We applied molecular dynamics and quantum mechanics calculations in order to clarify the protonation state of the catalytic residues of E. coli GlpG rhomboid protease and how it is affected by the immersion of the enzyme in the membrane. We identified (Nε)H150(dpr)_H254(dpr)_S201(pr) as the protonation (and H150 tautomeric) state of free GlpG in both lipid-solubilized and membrane environments. We used our MD-QM/SCRF(VS) computational protocol to rationalize and predict the trend of pKa change caused by the decrease of water exposure of the active site of GlpG due to ligand binding. The catalytic diad of lipid-solubilized GlpG exists as an H254(+)_S201(-) ion pair at the Michaelis complex stage, with Ser201 ready for nucleophilic attack on the substrate. Therefore, deprotonation of S201 does not contribute to the activation barrier of covalent tetrahedral complex formation. In contrast, both catalytic residues, H254 and S201, are neutral in the Michaelis complex of GlpG in the membrane. Therefore, S201 deprotonation by H254 general base catalysis should contribute to the activation barrier of the covalent tetrahedral complex formation.