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Enzyme catalysis by entropy without Circe effect.

Masoud Kazemi1, Fahmi Himo2, Johan Åqvist3

  • 1Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden;

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Summary

Enzymes do not always use binding energy to reduce entropic penalties. Computer simulations reveal cytidine deaminase uses a different reaction mechanism, not binding energy, for its catalytic efficiency.

Keywords:
computational Arrhenius plotscytidine deaminasedensity functional theoryempirical valence bond method

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Enzymology

Background:

  • Enzymes are known for their catalytic power, often attributed to entropic effects.
  • A key hypothesis suggests enzymes utilize substrate-binding energy to offset entropic penalties in chemical transformations.
  • Cytidine deaminase's reaction has been considered a prime example supporting this hypothesis.

Purpose of the Study:

  • To investigate the entropic effects in the cytidine deaminase reaction using computer simulations.
  • To determine the origin of the near-zero activation entropy observed in the enzyme's rate-limiting step.
  • To test the hypothesis that enzymes use binding energy to reduce entropic penalties.

Main Methods:

  • Density functional theory (DFT) calculations to determine reaction energetics.
  • Empirical valence bond (EVB) modeling parameterized with DFT results.
  • Molecular dynamics (MD) simulations for efficient sampling and Arrhenius plot computation.
  • Analysis of thermodynamic activation parameters and comparison with experimental data.

Main Results:

  • Computer simulations accurately reproduced experimental thermodynamic activation parameters.
  • The rate-limiting step of the enzyme-catalyzed reaction exhibits an activation entropy close to zero.
  • The origin of the near-zero activation entropy is a shift to a hydroxide ion attack mechanism.
  • This mechanism is intrinsically associated with favorable activation entropy, unlike the uncatalyzed reaction.

Conclusions:

  • The catalytic efficiency of cytidine deaminase is not due to utilizing binding free energy to pay entropic penalties.
  • The enzyme stabilizes an alternative reaction pathway (hydroxide ion attack) not operational in solution.
  • The preorganized active site facilitates a mechanism with favorable entropic characteristics, explaining the observed activation entropy.