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Related Experiment Video

Updated: Mar 16, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

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Published on: July 19, 2019

Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions.

M W Dzierlenga¹, M J Varga¹, S D Schwartz¹

¹University of Arizona, Tucson, AZ, United States.

Methods in Enzymology

|August 7, 2016

Summary

This summary is machine-generated.

Computational methods now incorporate enzyme dynamics and quantum effects for studying particle transfer reactions. New techniques reveal tunneling

Keywords:

Centroid molecular dynamics Enzymatic reactions Free energy Hydride transfer Kinetic isotope effects Molecular dynamics Nuclear quantum effects Transition path sampling

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Quantitative FRET Förster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination

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Area of Science:

Biochemistry
Computational Chemistry
Enzyme Kinetics

Background:

Enzymatic reaction mechanisms are typically studied using computational techniques.
Existing methods often neglect enzyme dynamics, potentially leading to inaccurate results, especially for particle transfer reactions involving nuclear tunneling.

Purpose of the Study:

To outline previous computational methods for studying enzymatic reactions.
To discuss newly developed dynamical methods for investigating enzymatic particle transfer reactions.
To incorporate quantum effects and full enzyme dynamics into mechanism studies.

Main Methods:

Centroid Molecular Dynamics (CMD) for incorporating quantum effects.
Transition Path Sampling (TPS) for capturing enzyme dynamics.
Application of CMD and TPS to calculate free energy barriers and kinetic isotope effects (KIEs).

Main Results:

Tunneling was found to be insignificant in yeast alcohol dehydrogenase (YADH) but significant, though not dominant, in lactate dehydrogenase (LDH).
Calculated primary H/D KIE for YADH using TPS and CMD aligned with experimental values.
The developed methods accurately reflect particle transfer kinetics within enzymes.

Conclusions:

Newly developed dynamical methods, incorporating protein and quantum dynamics, offer advanced tools for studying enzyme mechanisms.
These methods provide accurate calculations of free energy barriers and KIEs, improving our understanding of enzymatic particle transfer.