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Updated: May 27, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Wide transition-state ensemble as key component for enzyme catalysis.

Gabriel E Jara1, Francesco Pontiggia2, Renee Otten2

  • 1Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina.

Elife
|February 18, 2025
PubMed
Summary

Enzymes accelerate reactions using a broad transition-state ensemble (TSE) rather than a single structure. This conformational flexibility is key to overcoming entropic barriers in enzyme catalysis.

Keywords:
QM/MMadenylate kinasefree-energy calculationsmolecular biophysicsphosphoryl-transfer reactionssteered molecular dynamicsstructural biologytransition state

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Transition-state (TS) theory explains enzyme catalysis by accelerating reaction rates.
  • Proteins exist as conformational ensembles, posing challenges for unique TS identification.
  • Enzymatic phosphoryl-transfer reactions, like in adenylate kinase, are crucial biological processes.

Purpose of the Study:

  • To investigate the nature of the enzymatic transition-state ensemble (TSE) for phosphoryl-transfer in adenylate kinase.
  • To determine if enzymes utilize a broad TSE to overcome entropic bottlenecks.
  • To link computational findings with experimental enzyme kinetics data.

Main Methods:

  • Quantum-mechanics/molecular-mechanics (QM/MM) calculations were employed to model the enzymatic reaction.
  • Analysis of the reaction coordinate to identify the range of transition-state configurations.
  • Enzyme kinetics experiments were performed to measure the entropy of activation.

Main Results:

  • A structurally diverse and energetically equivalent set of configurations defines the TSE.
  • The enzyme's macroscopic nature leads to a conformationally delocalized and asymmetric TSE.
  • Experimental kinetics confirm a reduced entropy of activation consistent with a broad TSE.

Conclusions:

  • Enzymes employ broad transition-state ensembles, not unique structures, for efficient catalysis.
  • Conformational flexibility and delocalization are fundamental to enzymatic rate enhancement.
  • The concept of broad TSEs unifies understanding of protein folding, dynamics, and function.