Transition Path Sampling Study of Classical Rate-promoting Vibrations
Overview
Chemistry
Affiliations
It is now widely accepted that there is a class of enzymatic proton transfer reactions, which proceed through quantum tunneling. In a series of papers we have argued that some experimental features of these reactions can be explained by assuming the presence of a "rate-promoting" vibration which brings donor and acceptor closer together, thus leading to rate enhancement. There has never been a study of this effect for classical systems. We used transition path sampling to study the equivalent classical problem and found a complicated dynamical behavior that cannot be captured by transition state theory. Slow promoting vibrations lead to reactive trajectories that overshoot the saddle point, but on the other hand the short period of fast oscillations allows the reactants to stay only briefly in a low-barrier regime. There is a competition between these effects, which results to an intermediate value for the frequency of the rate-promoting vibration that is optimal for enhancing the rate.
The Evolution of the Acylation Mechanism in -Lactamase and Rapid Protein Dynamics.
Frost C, Antoniou D, Schwartz S ACS Catal. 2024; 14(18):13640-13651.
PMID: 39464311 PMC: 11507604. DOI: 10.1021/acscatal.4c03065.
Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters.
Chalopin Y, Cramer S, Arragain S Biophys J. 2023; 122(8):1557-1567.
PMID: 36960530 PMC: 10147833. DOI: 10.1016/j.bpj.2023.03.027.
Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase.
Frost C, Balasubramani S, Antoniou D, Schwartz S J Phys Chem B. 2022; 127(1):144-150.
PMID: 36538016 PMC: 9873402. DOI: 10.1021/acs.jpcb.2c07243.
Role of Protein Motions in Catalysis by Formate Dehydrogenase.
Antoniou D, Schwartz S J Phys Chem B. 2020; 124(43):9483-9489.
PMID: 33064490 PMC: 7697370. DOI: 10.1021/acs.jpcb.0c05725.
Heavy Enzymes and the Rational Redesign of Protein Catalysts.
Scott A, Luk L, Tunon I, Moliner V, Allemann R Chembiochem. 2019; 20(22):2807-2812.
PMID: 31016852 PMC: 6900096. DOI: 10.1002/cbic.201900134.