The DOI matches its Crossref record; 99 of the 99 references it cites were found in a registry or an index.
Protein Allostery and Conformational Dynamics
Open accessAbstract
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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“AlphaFold, which predicts single ranked structures for a protein sequence, is unable to address directly allosteric mechanisms, which are based on the populations of conformational states in the ensembles.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [103]
In the citing paper
“A feature of this mechanism, first formalized by Cooper and Dryden (1984) and termed thermal fluctuations allostery by the author or “dynamic allostery” elsewhere (Guo and Zhou, 2016; Kern and Zuiderweg, 2003; Schueler-Furman and Wodak, 2016, is that soft global modes of motion rather than more local ones are recruited to enable allosteric cooperativity.”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Guo and Zhou, 2016
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Cites
Community structure in social and biological networks
Girvan, M., & Newman, M. E. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122653799 · Cited by 15,502
ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.
Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681
Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments
Carr, H. Y., & Purcell, E. M. (1954) · Physical Review · doi:10.1103/physrev.94.630 · Cited by 6,445
Modified Spin-Echo Method for Measuring Nuclear Relaxation Times
Meiboom, S., & Gill, D. (1958) · Review of Scientific Instruments · doi:10.1063/1.1716296 · Cited by 6,001
Chung, F. (1996) · Regional conference series in mathematics · doi:10.1090/cbms/092 · Cited by 5,918
Floyd, R. W. (1962) · Communications of the ACM · doi:10.1145/367766.368168 · Cited by 4,137
Lipari, G., & Szabo, A. (1982) · Journal of the American Chemical Society · doi:10.1021/ja00381a009 · Cited by 3,777
Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *
Koshland, D. E., Némethy, G., & Filmer, D. (1966) · Biochemistry · doi:10.1021/bi00865a047 · Cited by 3,019
Perutz, M. F. (1970) · Nature · doi:10.1038/228726a0 · Cited by 2,914
Pervushin, K. V., Riek, R., Wider, G., & Kurt Wüthrich, A. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.23.12366 · Cited by 2,450
Research works printed but not linked: 1
- Burgen A. S., 1981, Fed. Proc., 40, 2723
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Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation
Zhou, H., & Pang, X. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00305 · Cited by 1,214
Self-citationAllostery in Its Many Disguises: From Theory to Applications
Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404
“As seen above, such soft modes may be readily described by coarsegrained models like those Bahar et al. (2010) and others (Hawkins and McLeish, 2004; Zhu et al., 2011).”
BackgroundInduced Fit of C 2 H 2 in a Flexible MOF Through Cooperative Action of Open Metal Sites
Zeng, H., Xie, M., Huang, Y., Zhao, Y., Xie, X., Bai, J., Wan, M., Krishna, R., Lu, W., & Li, D. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201904160 · Cited by 307
Eigenvector centrality for characterization of protein allosteric pathways
Negre, C. F. A., Morzan, U. N., Hendrickson, H. P., Pal, R., Lisi, G. P., Loria, J. P., Rivalta, I., Ho, J., & Batista, V. S. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810452115 · Cited by 246
The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution
Campitelli, P., Modi, T., Kumar, S., & Ozkan, S. B. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-052118-115517 · Cited by 190
“Rather than forming a new structure, a ligand binding to a remote site promotes a shift in the dynamics of all residues in the protein, changing the distribution of accessible conformational states in the ensemble and, thus, promoting easier access to certain conformers for allosteric regulations while restricting oth…”
Background
Metadata
- Authors
- Guo, J., & Zhou, H.-X.
- Affiliations
- Henan Normal University (CN)
- Florida State University (US)
- Corresponding author
- 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
- 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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