Reactivity Tracking of an Enzyme Progress Coordinate

• Type of Material: Article
• Authors: Wei Li, Emory University; Meghan Kohne, Emory University; Kurt Warncke, Emory University
• Language: English
• Date: 2023-08-04
• Publisher: AMER CHEMICAL SOC
• Publication Version: Final Published Version
• Copyright Statement: © 2023 The Authors. Published by American Chemical Society
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1021/acs.jpclett.3c01464
• Title of Journal or Parent Work: JOURNAL OF PHYSICAL CHEMISTRY LETTERS
• Volume: 14
• Issue: 32
• Start Page: 7157
• End Page: 7164
• Grant/Funding Information: This work was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) of the National Institutes of Health (NIH) under Grant R01 DK054514 and the National Institute of General Medical Sciences (NIGMS) of the NIH under Grant R01 GM142113. The Bruker E500 EPR spectrometer was funded by the National Center for Research Resources of the NIH under Grant No. RR 17767 and by Emory University.
• Keywords: Technology; ETHANOLAMINE AMMONIA-LYASE; Science & Technology - Other Topics; BOND HOMOLYSIS; LOW-TEMPERATURES; LIGAND-BINDING; Physical Sciences; ETHYLENE-GLYCOL SOLUTIONS; ELECTRON-PARAMAGNETIC-RESONANCE; Chemistry, Physical; CONFORMATIONAL SELECTION; AQUEOUS-SOLUTION; Nanoscience & Nanotechnology; RADICAL CATALYSIS; Physics, Atomic, Molecular & Chemical; Science & Technology; Materials Science; SINGLE-MOLECULE; Chemistry; Physics; Materials Science, Multidisciplinary
• Research Categories: Chemistry, Physical

Abstract

The reactivity of individual solvent-coupled protein configurations is used to track and resolve the progress coordinate for the core reaction sequence of substrate radical rearrangement and hydrogen atom transfer in the ethanolamine ammonia-lyase (EAL) enzyme from Salmonella enterica. The first-order decay of the substrate radical intermediate is the monitored reaction. Heterogeneous confinement from sucrose hydrates in the mesophase solvent surrounding the cryotrapped protein introduces distributed kinetics in the non-native decay of the substrate radical pair capture substate, which arise from an ensemble of configurational microstates. Reaction rates increase by >103-fold across the distribution to approach that for the native enabled substate for radical rearrangement, which reacts with monotonic kinetics. The native progress coordinate thus involves a collapse of the configuration space to generate optimized reactivity. Reactivity tracking reveals fundamental features of solvent-protein-reaction configurational coupling and leads to a model that refines the ensemble paradigm of enzyme catalysis for strongly adiabatic chemical steps.