The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Is allostery an intrinsic property of all dynamic proteins?
Abstract
Allostery involves coupling of conformational changes between two widely separated binding sites. The common view holds that allosteric proteins are symmetric oligomers, with each subunit existing in “at least” two conformational states with a different affinity for ligands. Recent observations such as the allosteric behavior of myoglobin, a classical example of a nonallosteric protein, call into question the existing allosteric dogma. Here we argue that all (nonfibrous) proteins are potentially allosteric. Allostery is a consequence of re‐distributions of protein conformational ensembles. In a nonallosteric protein, the binding site shape may not show a concerted second‐site change and enzyme kinetics may not reflect an allosteric transition. Nevertheless, appropriate ligands, point mutations, or external conditions may facilitate a population shift, leading a presumably nonallosteric protein to behave allosterically. In principle, practically any potential drug binding to the protein surface can alter the conformational redistribution. The question is its effectiveness in the redistribution of the ensemble, affecting the protein binding sites and its function. Here, we review experimental observations validating this view of protein allostery. Proteins 2004. © 2004 Wiley‐Liss, Inc.
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Citations
Cites
Implications of protein flexibility for drug discovery
Teague, S. J. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1129 · Cited by 755
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Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594
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MA, B., KUMAR, S., TSAI, C.-J., HU, Z., & NUSSINOV, R. (2000) · Journal of Theoretical Biology · doi:10.1006/jtbi.2000.1097 · Cited by 86
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Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008
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Motlagh, H. N., Wrabl, J. O., Li, J., & Hilser, V. J. (2014) · Nature · doi:10.1038/nature13001 · Cited by 1,247
Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?
Keskin, O., Gursoy, A., Ma, B., & Nussinov, R. (2008) · Chemical Reviews · doi:10.1021/cr040409x · Cited by 697
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Goodey, N. M., & Benkovic, S. J. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.98 · Cited by 667
An introduction to NMR-based approaches for measuring protein dynamics
Kleckner, I. R., & Foster, M. P. (2011) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2010.10.012 · Cited by 561
Protein Allostery and Conformational Dynamics
Guo, J., & Zhou, H.-X. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00590 · Cited by 484
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436
Self-citationAn NMR Perspective on Enzyme Dynamics
Boehr, D. D., Dyson, H. J., & Wright, P. E. (2006) · Chemical Reviews · doi:10.1021/cr050312q · Cited by 458
Allostery: Absence of a change in shape does not imply that allostery is not at play
Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.02.034 · Cited by 453
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Page, M. J., & Di Cera, E. (2008) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-008-7565-9 · Cited by 438
A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
Olson, C. A., Wu, N. C., & Sun, R. (2014) · Current Biology · doi:10.1016/j.cub.2014.09.072 · Cited by 408
Allostery 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
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Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003394 · Cited by 401
Self-citationHidden dynamic allostery in a PDZ domain
Petit, C. M., Zhang, J., Sapienza, P. J., Fuentes, E. J., & Lee, A. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904492106 · Cited by 344
Tsai, C.-J., del Sol, A., & Nussinov, R. (2009) · Molecular BioSystems · doi:10.1039/b819720b · Cited by 324
Self-citationIntrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
Bahar, I., Chennubhotla, C., & Tobi, D. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.09.011 · Cited by 306
Allostery: An Overview of Its History, Concepts, Methods, and Applications
Liu, J., & Nussinov, R. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004966 · Cited by 281
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Dokholyan, N. V. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00544 · Cited by 260
(2024) · doi:10.1038/s41467-024-45461-2 · Cited by 243
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Ma, B., Tsai, C.-J., Haliloğlu, T., & Nussinov, R. (2011) · Structure · doi:10.1016/j.str.2011.06.002 · Cited by 222
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Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612139114 · Cited by 204
“This finding can be viewed as a first step towards understanding why allosteric behavior is so common in biopolymers [5].”
BackgroundAllostery without a conformational change? Revisiting the paradigm
Nussinov, R., & Tsai, C.-J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.11.005 · Cited by 202
Self-citationPrinciples of Allosteric Interactions in Cell Signaling
Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154
Self-citationASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks
Shen, Q., Wang, G., Li, S., Liu, X., Lu, S., Chen, Z., Song, K., Yan, J., Geng, L., Huang, Z., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv902 · Cited by 122
Catalytic Contributions from Remote Regions of Enzyme Structure
Lee, J., & Goodey, N. M. (2011) · Chemical Reviews · doi:10.1021/cr100042n · Cited by 116
An update on the physiological and therapeutic relevance of GPCR oligomers
Farran, B. (2017) · Pharmacological Research · doi:10.1016/j.phrs.2017.01.008 · Cited by 115
The Design of Covalent Allosteric Drugs
Nussinov, R., & Tsai, C.-J. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124401 · Cited by 112
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Di Cera, E. (2020) · Biophysics Reviews · doi:10.1063/5.0020997 · Cited by 73
A Computational Investigation of Allostery in the Catabolite Activator Protein
Li, L., Uversky, V. N., Dunker, A. K., & Meroueh, S. O. (2007) · Journal of the American Chemical Society · doi:10.1021/ja076046a · Cited by 71
Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs
Nussinov, R., Zhang, M., Maloney, R., Liu, Y., Tsai, C.-J., & Jang, H. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167569 · Cited by 66
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Palazzesi, F., Barducci, A., Tollinger, M., & Parrinello, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313548110 · Cited by 62
Proctor, E. A., Kota, P., Aleksandrov, A. A., He, L., Riordan, J. R., & Dokholyan, N. V. (2015) · Chemical Science · doi:10.1039/c4sc01320d · Cited by 61
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Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure · doi:10.1016/j.str.2013.06.002 · Cited by 55
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Self-citationAmplification of signaling via cellular allosteric relay and protein disorder
Ma, B., & Nussinov, R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903024106 · Cited by 36
Self-citationDynamic Protein Allosteric Regulation and Disease
Nussinov, R., Tsai, C.-J., & Jang, H. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-981-13-8719-7_2 · Cited by 18
Self-citationTherapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families
Li, L., Meyer, C., Zhou, Z.-W., Elmezayen, A., & Westover, K. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167626 · Cited by 14
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Metadata
- Authors
- Gunasekaran, K., Ma, B., & Nussinov, R.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2004-07-22
- Volume
- 57
- Issue
- 3
- Pages
- 433-443
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2049682677
- Cited by
- 879
- References
- 3
- FWCI
- 7.22
- Type
- journal article
- Language
- en
- Open access
- closed
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