Cited by 484Protein Structure and DynamicsAdvanced NMR Techniques and ApplicationsReceptor Mechanisms and Signaling

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Protein Allostery and Conformational Dynamics

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Guo, Jingjing, Zhou, Huan-Xiang·2016·Chemical Reviews

DOI 10.1021/acs.chemrev.5b00590PMC PMC5011433

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Abstract

The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond-nanosecond local and microsecond-millisecond conformational exchange dynamics, are presented.

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Site-selective dynamics of azidolysozyme
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“The actual mechanisms of allosteric signal transduction can be diverse, but in most proteins it can be explained by shifts between populations of different conformations, that are modified or induced by ligands binding at critical sites of the protein [5,9,10].”
Background
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“(9), it is assumed that all the φk = 0, then the initial fluctuation vector can be projected onto all the normal modes as”
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“…Gibbs energy basin locations in the conformational landscape and resulting in conformational transitions, but it also modulates the width of those Gibbs energy basins which dictates the dynamic properties of the conformational states and the rates of the conformational transitions [47, 48].”
Background
Programmable Allosteric Regulation of Three-Dimensional DNA Nanostructures for Targeted Membrane Protein Degradation
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Self-citation

Authors: Guo, J., & Zhou, H.-X.
Affiliations: Henan Normal University (CN)
Florida State University (US)
Corresponding author: Zhou, Huan-Xiang
ORCID: Guo, Jingjing
Zhou, Huan-Xiang
Venue: Chemical Reviews
Publisher: American Chemical Society (ACS)
Published: 2016-02-15
Volume: 116
Issue: 11
Pages: 6503-6515
ISSN: 0009-2665 (ISSN-L)
1520-6890
DOI: 10.1021/acs.chemrev.5b00590
PMC: PMC5011433
OpenAlex: W2283818235
Cited by: 484
References: 99
Citations by year: 2026: 66 · 2025: 59 · 2024: 54 · 2023: 58 · 2022: 41 · 2021: 37 · 2020: 43 · 2019: 48 · 2018: 35 · 2017: 26 · 2016: 17
FWCI: 3.80
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Chemical Reviews (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Department of Health and Human Services (GM058187)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
Keywords: protein allostery, conformational dynamics, allosteric regulation, free energy landscape, conformational change, substrate affinity, allosteric effectors, NMR spectroscopy, molecular dynamics simulation
MeSH terms: NIMA-Interacting Peptidylprolyl Isomerase, Allosteric Regulation, Protein Binding, Protein Conformation, Proteins, Thermodynamics, Nuclear Magnetic Resonance, Biomolecular, Catalytic Domain, Molecular Dynamics Simulation

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Protein Allostery and Conformational Dynamics

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