How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Lactate Dehydrogenase (LDH) is crucial for cellular metabolism, catalyzing the interconversion of pyruvate and lactate.
• The precise catalytic mechanism of LDH, specifically the transfer of hydride and protons, has been debated, with conflicting reports of concerted versus stepwise pathways.

Purpose of the Study:

• To apply the Transition Path Sampling (TPS) algorithm to investigate the reaction mechanism of Lactate Dehydrogenase.
• To demonstrate the scalability of TPS for complex, high-dimensional systems.
• To resolve the existing paradox regarding concerted versus stepwise catalytic mechanisms in LDH.

Main Methods:

• Utilized the Transition Path Sampling (TPS) algorithm, a Monte Carlo importance sampling technique.
• Applied TPS to simulate the enzyme-catalyzed reaction of Lactate Dehydrogenase.
• Analyzed time series data of donor-acceptor and residue distances to identify a reduced reaction coordinate.

Main Results:

• TPS successfully generated a transition path ensemble, confirming both concerted and stepwise mechanisms as viable pathways for LDH catalysis.
• The study demonstrated the efficiency of TPS in handling systems with many degrees of freedom and complex energy landscapes.
• Identified a collective compression/relaxation motion of active site residues during hydride transfer, crucial for reaction completion.

Conclusions:

• Transition Path Sampling provides a robust method for elucidating complex enzyme mechanisms.
• Both concerted and stepwise pathways are biologically relevant for Lactate Dehydrogenase.
• The identified residue compression/relaxation dynamics are critical for efficient enzymatic catalysis.