The Cluster of Hydrophobic Residues Controls the Entrance to the Active Site of Choline Oxidase
Abstract
The active site of many enzymes is well-protected from solution by a gate. The opening and closing of these gates provide controlled access and could be the rate-limiting steps in catalytic processes. The gating mechanism of an enzyme is therefore very important in gaining broader insight into the entire catalytic process. However, the entrance to active sites and let alone the gating mechanisms are not always obvious from X-ray crystal structures of proteins. Here, we have proposed and quantitatively characterized an alternative gating mechanism controlled by a cluster of hydrophobic residues located on the solvent accessible surface of choline oxidase. We show that the opening and closing of the gate are very fast, and diffusion of choline to the active site is also fast and is partly controlled by the electrostatic potential of the enzyme. Using all-atom molecular dynamics and Brownian dynamics simulations, complete analyses of the mechanism of opening and closing of the gate, the rate of collision of the substrate with the enzyme, and the rate of formation of the complex have been conducted.
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For bacterial phosphotriesterase, maltose binding protein, choline oxidase, cytochrome bc1 complex, and many lid-gated enzymes, closed and open conformations are in equilibrium prior to ligand binding, permitting conformational selection at different catalytic steps.
“Conformational sampling for bacterial phosphotriesterase,443 maltose binding protein,444 and choline oxidase,445 cytochrome bc1 complex,446 and many other lid-gated enzymes indicated that the closed and open conformations are in equilibrium prior to ligand binding, permitting a conformational selection pathway at different catalytic steps.447”
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 [445]
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- Authors
- Xin, Y., Gadda, G., & Hamelberg, D.
- Affiliations
- Department of Chemistry
- Corresponding author
- Hamelberg, Donald
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-09-16
- Volume
- 48
- Issue
- 40
- Pages
- 9599-9605
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2010353539
- Cited by
- 33
- References
- 53
- Citations by year
- 2025: 2 · 2024: 2 · 2023: 1 · 2022: 3 · 2021: 1 · 2020: 2 · 2018: 2 · 2017: 4 · 2016: 6 · 2014: 2 · 2013: 2 · 2012: 2
- FWCI
- 0.80
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
- Keywords
- choline oxidase, substrate diffusion, electrostatic potential, enzyme-substrate complex formation, solvent accessibility
- MeSH terms
- Alcohol Oxidoreductases, Amino Acids, Catalysis, Ion Channel Gating, Crystallography, X-Ray, Catalytic Domain, Static Electricity, Hydrophobic and Hydrophilic Interactions
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