Cited by 58Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsChemical Reaction Mechanisms

Crucial Role of Protein Flexibility in Formation of a Stable Reaction Transition State in an α-Amylase Catalysis

Kosugi, Takahiro, Hayashi, Shigehiko·2012·Journal of the American Chemical Society

Abstract

Conformational flexibility of proteins provides enzymes with high catalytic activity. Although the conformational flexibility is known to be pivotal for the ligand binding and release, its role in the chemical reaction process of the reactive substrate remains unclear. We determined a transition state of an enzymatic reaction in a psychrophilic α-amylase by a hybrid molecular simulation that allows one to identify the optimal chemical state in an extensive conformational ensemble of protein. The molecular simulation uncovered that formation of the reaction transition state accompanies a large and slow movement of a loop adjacent to the catalytic site. Free energy calculations revealed that, although catalytic electrostatic potentials on the reactive moiety are formed by local and fast reorganization around the catalytic site, reorganization of the large and slow movement of the loop significantly contributes to reduction of the free energy barrier by stabilizing the local reorganization.

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Crossref · 10.1021/ja212117m

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Authors
Kosugi, T., & Hayashi, S.
Affiliations
Kyoto University (JP)
Corresponding author
Hayashi, Shigehiko
Venue
Journal of the American Chemical Society
Published
2012-04-11
Volume
134
Issue
16
Pages
7045-7055
ISSN
  • 0002-7863 (ISSN-L)
  • 1520-5126
OpenAlex
W2320834017
Cited by
58
References
40
Citations by year
2025: 6 · 2024: 2 · 2023: 3 · 2022: 5 · 2021: 4 · 2020: 2 · 2019: 5 · 2018: 1 · 2017: 3 · 2016: 5 · 2015: 5 · 2014: 6 · 2013: 7 · 2012: 4
FWCI
2.83
Type
journal article
Language
en
Open access
closed
Locations
  • Journal of the American Chemical Society (publishedVersion)
  • PubMed (publishedVersion)
Funders
Japan Society for the Promotion of Science (22370058)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
Keywords
protein flexibility, transition state, alpha-amylase, cold-adapted enzymes, enzyme catalysis, activation barrier, free energy calculation
MeSH terms
alpha-Amylases, Models, Molecular, Protein Conformation, Surface Properties, Biocatalysis, Molecular Dynamics Simulation

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