Crucial Role of Protein Flexibility in Formation of a Stable Reaction Transition State in an α-Amylase Catalysis
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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MD simulations and free energy calculations revealed a crucial role of protein flexibility in forming a stable reaction transition state in α-amylase catalysis.
“MD simulations and free energy calculations revealed the crucial role of protein flexibility in formation of a stable reaction transition state in α-amylase catalysis.451”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [451]
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Self-citation
- Authors
- Kosugi, T., & Hayashi, S.
- Affiliations
- Kyoto University (JP)
- Corresponding author
- Hayashi, Shigehiko
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- 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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