Conformational Ensembles Reveal the Origins of Serine Protease Catalysis

Despite a century of enzymology, we lack the ability to fully describe enzyme catalysis in molecular and energetic terms. Conformational ensembles built from 1231 structures of 17 serine proteases provide a comprehensive model that specifies the molecular features of their reaction path, reveals previously unknown catalytic features, and quantitates their catalytic contributions. The sum of these contributions fully accounts for the rate enhancement provided by serine proteases. These enzymes precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway motions. A local catalytic motif, the "nucleophilic elbow", generates ground state destabilization and has evolved in 50 proteases and 52 additional enzymes spanning 32 distinct structural folds. Ensemble-function analyses provide experimentally based, quantitative models for enzyme catalysis based on simple physical and chemical properties and identify molecular features that may be used as ingredients in enzyme design.