Conformational ensembles reveal the origins of serine protease catalysis
Siyuan Du, Rachael C. Kretsch, Jacob Parres-Gold, Elisa Pieri, Vinícius Wilian D. Cruzeiro, M.C. Zhu, Margaux M. Pinney, Filip Yabukarski, Jason P. Schwans, Todd J. Martı́nez, Daniel Herschlag
Abstract
Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. Our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.