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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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BackgroundEmerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids
Arantes, P. R., Patel, A. C., & Palermo, G. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167518 · Cited by 40
Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to
Carofiglio, F., Trisciuzzi, D., Gambacorta, N., Leonetti, F., Stefanachi, A., & Nicolotti, O. (2020) · Molecules · doi:10.3390/molecules25184210 · Cited by 38
Role of Proteome Physical Chemistry in Cell Behavior
Ghosh, K., de Graff, A. M. R., Sawle, L., & Dill, K. A. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b04886 · Cited by 39
Applications of NMR and computational methodologies to study protein dynamics
Narayanan, C., Bafna, K., Roux, L. D., Agarwal, P. K., & Doucet, N. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.05.002 · Cited by 40
“MD simulations have been used in combination with NMR to identify allosteric networks of conformational motions that play an important role in enzyme function 10,56,57 .”
MethodEffect of ligand binding on a protein with a complex folding landscape
Mazal, H., Aviram, H. Y., Riven, I., & Haran, G. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp03327c · Cited by 37
Conformational control of mechanical networks
Kim, J. Z., Lu, Z., Strogatz, S. H., & Bassett, D. S. (2019) · Nature Physics · doi:10.1038/s41567-019-0475-y · Cited by 37
Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions
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Das, N., & Sen, P. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp04842b · Cited by 36
Probing allosteric communication with combined molecular dynamics simulations and network analysis
Bernetti, M., Bosio, S., Bresciani, V., Falchi, F., & Masetti, M. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102820 · Cited by 35
Macromolecular crowding effects on protein dynamics
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“1 to 1 s [74,75], so that sequential phosphorylations of several residues is on the timescale of seconds.”
BackgroundRecognition of protein allosteric states and residues: Machine learning approaches
Zhou, H.-Y., Dong, Z., & Tao, P. (2018) · Journal of Computational Chemistry · doi:10.1002/jcc.25218 · Cited by 36
Self-citationAbrusán, G., & Marsh, J. A. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz093 · Cited by 35
Autoinhibition can identify rare driver mutations and advise pharmacology
Nussinov, R., Tsai, C., & Jang, H. (2019) · The FASEB Journal · doi:10.1096/fj.201901341r · Cited by 35
Božović, O., Janković, B. G., & Hamm, P. M. (2020) · Nature Communications · doi:10.1038/s41467-020-19689-7 · Cited by 31
Son, A., Kim, W., Park, J., Lee, W., Lee, Y., Choi, S., & Kim, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25179725 · Cited by 39
“Advanced NMR techniques and MD simulations have revealed how allosteric signals propagate through protein structures, providing insights into the design of allosteric drugs and the evolution of protein function [23].”
BackgroundZhang, Y., Liu, Y., Li, W., & Han, W. (2024) · LWT · doi:10.1016/j.lwt.2024.117019 · Cited by 36
Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1
Campitelli, P., Guo, J., Zhou, H., & Ozkan, S. B. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b11971 · Cited by 35
Self-citation
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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