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This study introduces a new computational method to calculate particle transfer rates and kinetic isotope effects in enzymatic reactions like yeast alcohol dehydrogenase (YADH). The method accurately predicts experimental results by including quantum effects and simulating complex enzymatic systems.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Enzyme Kinetics

Background:

  • Enzymatic reactions involve complex particle transfer mechanisms.
  • Accurately determining kinetic isotope effects (KIEs) is crucial for understanding enzyme mechanisms.
  • Previous computational methods have limitations in simulating large enzyme systems and incorporating quantum effects.

Purpose of the Study:

  • To develop and validate a first-principles computational method for calculating particle transfer rates and KIEs in enzymatic reactions.
  • To apply this method to the yeast alcohol dehydrogenase (YADH) enzyme.
  • To assess the accuracy of the method by comparing calculated KIEs with experimental data.

Main Methods:

  • Utilizing transition path sampling (TPS) and normal mode centroid dynamics (CMD) for simulations.
  • Simulating enzymatic reactions without prior knowledge of reaction coordinates.
  • Incorporating quantum mechanical effects like zero-point energy and tunneling for the transferring particle.

Main Results:

  • Successfully applied TPS and CMD to the large YADH enzyme system.
  • Calculated primary H/D kinetic isotope effect for YADH.
  • Achieved agreement between calculated and experimental H/D KIEs within experimental error.

Conclusions:

  • The developed first-principles method accurately predicts experimental KIEs in enzymatic systems.
  • The method captures the kinetic isotope effect specifically for the particle transfer event.
  • This approach offers a powerful tool for studying enzyme mechanisms and reaction dynamics.