Allostery without a conformational change? Revisiting the paradigm

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 · see citing works

The Energy Landscapes and Motions of Proteins

Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250 · see citing works

Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery

Perutz, M. F. (1970) · Nature · doi:10.1038/228726a0 · Cited by 2,931 · see citing works

The role of dynamic conformational ensembles in biomolecular recognition

Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008 · see citing works

Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

Lockless, S. W., & Ranganathan, R. (1999) · Science · doi:10.1126/science.286.5438.295 · Cited by 1,288 · see citing works

Crystal Structure of a CAP-DNA Complex: the DNA Is Bent by 90°

Schultz, S. C., Shields, G. C., & Steitz, T. A. (1991) · Science · doi:10.1126/science.1653449 · Cited by 1,116 · see citing works

Is allostery an intrinsic property of all dynamic proteins?

Gunasekaran, K., Ma, B., & Nussinov, R. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20232 · Cited by 882 · see citing works

Haemoglobin: The structural changes related to ligand binding and its allosteric mechanism

Baldwin, J. M., & Chothia, C. (1979) · Journal of Molecular Biology · doi:10.1016/0022-2836(79)90277-8 · Cited by 872 · see citing works

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821 · see citing works

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 764 · see citing works

Allosteric Mechanisms of Signal Transduction

Changeux, J., & Edelstein, S. J. (2005) · Science · doi:10.1126/science.1108595 · Cited by 748 · see citing works

Allostery without conformational change

Cooper, A., & Dryden, D. T. F. (1984) · European Biophysics Journal · doi:10.1007/bf00276625 · Cited by 740 · see citing works

Dynamically driven protein allostery

Popovych, N., Sun, S., Ebright, R. H., & Kalodimos, C. G. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1132 · Cited by 637 · see citing works

Folding and binding cascades: Dynamic landscapes and population shifts

Kumar, S., Ma, B., Tsai, C., Sinha, N., & Nussinov, R. (2000) · Protein Science · doi:10.1110/ps.9.1.10 · Cited by 595 · see citing works

THE STEREOCHEMICAL MECHANISM OF THE COOPERATIVE EFFECTS IN HEMOGLOBIN REVISITED

Perutz, M. F., Wilkinson, A. J., Paoli, M., & Dodson, G. G. (1998) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.27.1.1 · Cited by 562 · see citing works

Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine

Dore, A. S., Robertson, N. J., Errey, J. C., Ng, I. W., Hollenstein, K., Tehan, B. G., Hurrell, E., Bennett, K. A., Congreve, M., Magnani, F., et al. (2011) · Structure · doi:10.1016/j.str.2011.06.014 · Cited by 557 · see citing works

Structure of the agonist-bound neurotensin receptor

White, J. F., Noinaj, N., Shibata, Y., Love, J. D., Kloss, B., Xu, F., Gvozdenovic‐Jeremic, J., Shah, P., Shiloach, J., Tate, C. G., et al. (2012) · Nature · doi:10.1038/nature11558 · Cited by 511 · see citing works

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Miao, Y., Sinko, W., Pierce, L., Bucher, D., Walker, R. C., & McCammon, J. A. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500090q · Cited by 460 · see citing works

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 · see citing works

A Unified View of “How Allostery Works”

Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003394 · Cited by 401 · see citing works

Folding and binding cascades: Shifts in energy landscapes

Tsai, C.-J., Ma, B., & Nussinov, R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.9970 · Cited by 365 · see citing works

Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

Parkinson, G. N., Wilson, C., Gunasekera, A. H., Ebright, R. H., Ebright, R. H., & Berman, H. M. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0409 · Cited by 273 · see citing works

Restructuring G-Protein- Coupled Receptor Activation

Audet, M., & Bouvier, M. (2012) · Cell · doi:10.1016/j.cell.2012.09.003 · Cited by 261 · see citing works

The Src, Syk, and Tec family kinases: Distinct types of molecular switches

Bradshaw, J. M. (2010) · Cellular Signalling · doi:10.1016/j.cellsig.2010.03.001 · Cited by 257 · see citing works

Mapping allostery through the covariance analysis of NMR chemical shifts

Selvaratnam, R., Chowdhury, S., VanSchouwen, B., & Melacini, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017311108 · Cited by 228 · see citing works

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

Popovych, N., Tzeng, S., Tonelli, M., Ebright, R. H., & Kalodimos, C. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900595106 · Cited by 218 · see citing works

The role of distant mutations and allosteric regulation on LovD active site dynamics

Jiménez‐Osés, G., Osuna, S., Gao, X., Sawaya, M. R., Gilson, L., Collier, S. J., Huisman, G. W., Yeates, T. O., Tang, Y., & Houk, K. N. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1503 · Cited by 211 · see citing works

Allosteric post-translational modification codes

Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.07.001 · Cited by 211 · see citing works

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis

Wart, A. T. V., Durrant, J. D., Votapka, L. W., & Amaro, R. E. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct4008603 · Cited by 183 · see citing works

Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition

Fenwick, R. B., Esteban-Martín, S., Richter, B., Lee, D., Walter, K. F. A., Milovanović, D., Becker, S., Lakomek, N., Griesinger, C., & Salvatella, X. (2011) · Journal of the American Chemical Society · doi:10.1021/ja200461n · Cited by 178 · see citing works

The Role of Ligands on the Equilibria Between Functional States of a G Protein-Coupled Receptor

Kim, T. H., Chung, K. Y., Manglik, A., Hansen, A. L., Dror, R. O., Mildorf, T. J., Shaw, D. E., Kobilka, B. K., & Prosser, R. S. (2013) · Journal of the American Chemical Society · doi:10.1021/ja404305k · Cited by 177 · see citing works

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 174 · see citing works

Structure-based model of allostery predicts coupling between distant sites

Weinkam, P., Pons, J., & Šali, A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116274109 · Cited by 157 · see citing works

Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

Iversen, L., Tu, H.-L., Lin, W.-C., Christensen, S. M., Abel, S. M., Iwig, J., Wu, H.-J., Gureasko, J., Rhodes, C., Petit, R. S., et al. (2014) · Science · doi:10.1126/science.1250373 · Cited by 154 · see citing works

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

Morra, G., Verkhivker, G. M., & Colombo, G. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000323 · Cited by 148 · see citing works

Computational approaches to mapping allosteric pathways

Feher, V. A., Durrant, J. D., Wart, A. T. V., & Amaro, R. E. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.02.004 · Cited by 138 · see citing works

Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation

Symersky, J., Pagadala, V., Osowski, D., Krah, A., Meier, T. W., Faraldo‐Gómez, J. D., & Mueller, D. M. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2284 · Cited by 125 · see citing works

Unraveling structural mechanisms of allosteric drug action

Nussinov, R., & Tsai, C.-J. (2014) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2014.03.006 · Cited by 119 · see citing works

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

Hohl, M., Hürlimann, L. M., Böhm, S., Schöppe, J., Grütter, M. G., Bordignon, E., & Seeger, M. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400485111 · Cited by 118 · see citing works

Local motions in a benchmark of allosteric proteins

Daily, M. D., & Gray, J. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21300 · Cited by 113 · see citing works

NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT

Levine, M. V., & Weinstein, H. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003603 · Cited by 102 · see citing works

Disruption of Allosteric Response as an Unprecedented Mechanism of Resistance to Antibiotics

Fishovitz, J., Rojas-Altuve, A., Otero, L. H., Dawley, M. M., Carrasco‐López, C., Chang, M., Hermoso, J. A., & Mobashery, S. (2014) · Journal of the American Chemical Society · doi:10.1021/ja5030657 · Cited by 92 · see citing works

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

Blacklock, K. M., & Verkhivker, G. M. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003679 · Cited by 90 · see citing works

Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding

Sharma, H., Yu, S., Kong, J., Wang, J., & Steitz, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908380106 · Cited by 89 · see citing works

A potentiator of orthosteric ligand activity at GLP-1R acts via covalent modification

Nolte, W. M., Fortin, J.-P., Stevens, B. D., Aspnes, G. E., Griffith, D. A., Hoth, L. R., Ruggeri, R. B., Mathiowetz, A. M., Limberakis, C., Hepworth, D., et al. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1581 · Cited by 86 · see citing works

A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase

Boehr, D. D., Schnell, J. R., McElheny, D., Bae, S.-H., Duggan, B. M., Benkovic, S. J., Dyson, H. J., & Wright, P. E. (2013) · Biochemistry · doi:10.1021/bi400563c · Cited by 84 · see citing works

Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle

Tehver, R., Chen, J., & Thirumalai, D. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.032 · Cited by 78 · see citing works

Coarse-Grained Model Of Entropic Allostery

Hawkins, R. J., & McLeish, T. C. B. (2004) · Physical Review Letters · doi:10.1103/physrevlett.93.098104 · Cited by 67 · see citing works

Prepaying the entropic cost for allosteric regulation in KIX

Law, S., Gagnon, J. K., Mapp, A., & Brooks, C. (2014) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1405831111 · Cited by 62 · see citing works

Emerging computational approaches for the study of protein allostery

Collier, G., & Ortiz, V. (2013) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2013.07.025 · Cited by 60 · see citing works

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

Chiappori, F., Ivan Merelli, A., Colombo, G., Milanesi, L., & Morra, G. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002844 · Cited by 54 · see citing works

Impact of Mutations on the Allosteric Conformational Equilibrium

Weinkam, P., Chen, Y. C., Pons, J., & Šali, A. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.11.041 · Cited by 52 · see citing works

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

Korkmaz, E. N., Nussinov, R., & Haliloǧlu, T. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002420 · Cited by 40 · see citing works

Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis

Blackmore, N. J., Reichau, S., Jiao, W., Hutton, R. D., Baker, E. N., Jameson, G. B., & Parker, E. J. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.12.019 · Cited by 39 · see citing works

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

Linder, T., de Groot, B. L., & Stary‐Weinzinger, A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003058 · Cited by 39 · see citing works

The Allosteric Switch and Conformational States in Ras GTPase Affected by Small Molecules

Johnson, C. W., & Mattos, C. (2013) · The Enzymes · doi:10.1016/b978-0-12-416749-0.00003-8 · Cited by 35 · see citing works

Free Energy Diagrams for Protein Function

Nussinov, R., & Tsai, C. (2014) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.12.015 · Cited by 31 · see citing works

A Mechanistic View of the Role of E3 in Sumoylation

Tozluoǧlu, M., Karaca, E., Nussinov, R., & Haliloǧlu, T. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000913 · Cited by 29 · see citing works

Discovery of Inter-Domain Stabilizers—A Novel Assay System for Allosteric Akt Inhibitors

Fang, Z., Simard, J. R., Plenker, D., Nguyen, H. D., Phan, T. T. P., Wolle, P., Baumeister, S., & Rauh, D. (2014) · ACS Chemical Biology · doi:10.1021/cb500355c · Cited by 27 · see citing works

An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis

Palmai, Z., Seifert, C., Gräter, F., & Balog, E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003444 · Cited by 22 · see citing works

The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions

Zhu, L., Bolhuis, P. G., & Vreede, J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002913 · Cited by 18 · see citing works

The N-terminal Domain Allosterically Regulates Cleavage and Activation of the Epithelial Sodium Channel

Kota, P. B., Buchner, G. S., Chakraborty, H., Dang, Y. L., He, H. X., Garcia, G. J. M., Kubelka, J., Gentzsch, M., Stutts, M. J., & Dokholyan, N. V. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.570952 · Cited by 16 · see citing works

Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity

Nazmi, A. R., Schofield, L. R., Dobson, R. C. J., Jameson, G. B., & Parker, E. J. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.11.008 · Cited by 16 · see citing works

Frequency Response of a Protein to Local Conformational Perturbations

Eren, D., & Alakent, B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003238 · Cited by 9 · see citing works

Structure of catabolite activator protein with cobalt(II) and sulfate

Rao, R. R., & Lawson, C. L. (2014) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x14005366 · Cited by 5 · see citing works

Protein Allostery and Conformational Dynamics

Guo, J., & Zhou, H.-X. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00590 · Cited by 484 · see citing works

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

Papaleo, E., Saladino, G., Lambrughi, M., Lindorff‐Larsen, K., Gervasio, F. L., & Nussinov, R. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00623 · Cited by 426 · see citing works

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 · see citing works

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 · see citing works

AlphaFold, Artificial Intelligence (AI), and Allostery

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

Melo, M. C. R., Bernardi, R. C., de la Fuente‐Núñez, C., & Luthey-Schulten, Z. A. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0018980 · Cited by 149 · see citing works

Kinetic trapping – a strategy for directing the self-assembly of unique functional nanostructures

Yan, Y., Huang, J., & Tang, B. Z. (2016) · Chemical Communications · doi:10.1039/c6cc03620a · Cited by 148 · see citing works

Time-resolved crystallography reveals allosteric communication aligned with molecular breathing

Mehrabi, P., Schulz, E. C., Dsouza, R., Müller‐Werkmeister, H. M., Tellkamp, F., Miller, R. J. D., & PAI, E. F. (2019) · Science · doi:10.1126/science.aaw9904 · Cited by 140 · see citing works

Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation

Berlow, R. B., Dyson, H. J., & Wright, P. E. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.04.003 · Cited by 129 · see citing works

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 129 · see citing works

Solution NMR Spectroscopy for the Study of Enzyme Allostery

Lisi, G. P., & Loria, J. P. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00541 · Cited by 127 · see citing works

Integrated Computational Approaches and Tools for Allosteric Drug Discovery

Amamuddy, O. S., Veldman, W., Manyumwa, C. V., Khairallah, A., Agajanian, S., Odeyemi, O., Verkhivker, G. M., & Bishop, Ö. T. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21030847 · Cited by 105 · see citing works

Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines

Thirumalai, D., Hyeon, C., Zhuravlev, P. I., & Lorimer, G. H. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00760 · Cited by 105 · see citing works

Hidden electrostatic basis of dynamic allostery in a PDZ domain

Kumawat, A., & Chakrabarty, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705311114 · Cited by 97 · see citing works

Entropy redistribution controls allostery in a metalloregulatory protein

Capdevila, D. A., Braymer, J. J., Edmonds, K. A., Wu, H., & Giedroc, D. P. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620665114 · Cited by 96 · see citing works

Advances in NMR Methods To Map Allosteric Sites: From Models to Translation

Boulton, S., & Melacini, G. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00718 · Cited by 89 · see citing works

Structure-based prediction of protein allostery

Greener, J. G., & Sternberg, M. J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.002 · Cited by 91 · see citing works

NMR Methods to Study Dynamic Allostery

Grutsch, S., Brüschweiler, S., & Tollinger, M. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004620 · Cited by 78 · see citing works

Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning

Verkhivker, G. M., Agajanian, S., Hu, G., & Tao, P. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00136 · Cited by 76 · see citing works

β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates

Sun, Y., Ge, X., Xing, Y., Wang, B., & Ding, F. (2018) · Scientific Reports · doi:10.1038/s41598-018-28649-7 · Cited by 76 · see citing works

Tuning the “violin” of protein kinases: The role of dynamics‐based allostery

Ahuja, L. G., Taylor, S. S., & Kornev, A. P. (2019) · IUBMB Life · doi:10.1002/iub.2057 · Cited by 73 · see citing works

Real-time observation of ligand-induced allosteric transitions in a PDZ domain

Božović, O., Zanobini, C., Gulzar, A., Janković, B. G., Buhrke, D., Post, M., Wolf, S., Stock, G., & Hamm, P. M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2012999117 · Cited by 70 · see citing works

Ancient origins of allosteric activation in a Ser-Thr kinase

Hadzipasic, A., Wilson, C., Nguyen, V., Kern, N., Kim, C., Pitsawong, W., Villali, J., Zheng, Y., & Kern, D. (2020) · Science · doi:10.1126/science.aay9959 · Cited by 65 · see citing works

High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning

Unke, O. T., Koner, D., Patra, S., Käser, S., & Meuwly, M. (2020) · Machine Learning Science and Technology · doi:10.1088/2632-2153/ab5922 · Cited by 62 · see citing works

Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches

Verkhivker, G. M., & Paola, L. D. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c10637 · Cited by 56 · see citing works

A General Mechanism for the Propagation of Mutational Effects in Proteins

Rajasekaran, N., Suresh, S., Gopi, S., Raman, K., & Naganathan, A. N. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00798 · Cited by 62 · see citing works

Altering the allosteric pathway in IGPS suppresses millisecond motions and catalytic activity

Lisi, G. P., East, K. W., Batista, V. S., & Loria, J. P. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700448114 · Cited by 61 · see citing works

Intrinsic protein disorder in oncogenic KRAS signaling

Nussinov, R., Jang, H., Tsai, C., Liao, T.-J., Li, S., Fushman, D., & Zhang, J. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2564-3 · Cited by 57 · see citing works

Selection on protein structure, interaction, and sequence

Chi, P. B., & Liberles, D. A. (2016) · Protein Science · doi:10.1002/pro.2886 · Cited by 56 · see citing works

Computational approaches to detect allosteric pathways in transmembrane molecular machines

Stolzenberg, S., Michino, M., Levine, M. V., Weinstein, H., & Shi, L. (2016) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2016.01.010 · Cited by 56 · see citing works

Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Calvó‐Tusell, C., Maria‐Solano, M. A., Osuna, S., & Feixas, F. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.1c12629 · Cited by 54 · see citing works

Conformational diversity analysis reveals three functional mechanisms in proteins

Monzón, A. M., Zea, D. J., Fornasari, M. S., Saldaño, T. E., Fernández-Alberti, S., Tosatto, S. C. E., & Parisi, G. D. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005398 · Cited by 55 · see citing works

Allosteric control of metal-responsive transcriptional regulators in bacteria

Baksh, K. A., & Zamble, D. B. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.011444 · Cited by 54 · see citing works

Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants: Interaction Patterns in Ras Oncogenic Mutants

Sayyed-Ahmad, A., Prakash, P., & Gorfe, A. A. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25317 · Cited by 54 · see citing works

Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

Thayer, K. M., Lakhani, B., & Beveridge, D. L. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b02083 · Cited by 54 · see citing works

How do disordered regions achieve comparable functions to structured domains?

Latysheva, N. S., Flock, T., Weatheritt, R. J., Chavali, S., & Babu, M. M. (2015) · Protein Science · doi:10.1002/pro.2674 · Cited by 50 · see citing works

Does Ras Activate Raf and PI3K Allosterically?

Nussinov, R., Tsai, C., & Jang, H. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.01231 · Cited by 50 · see citing works

Allosteric communication and signal transduction in proteins

Wu, N., Barahona, M., & Yaliraki, S. N. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102737 · Cited by 49 · see citing works

Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites

Tong, M., Pelton, J., Gill, M. L., Zhang, W., Picart, F., & Seeliger, M. A. (2017) · Nature Communications · doi:10.1038/s41467-017-02240-6 · Cited by 48 · see citing works

Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα

Akimoto, M., McNicholl, E. T., Ramkissoon, A., Moleschi, K., Taylor, S. S., & Melacini, G. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002305 · Cited by 43 · see citing works

Remote electrochemical modulation of pK a in a rotaxane by co-conformational allostery

Ragazzon, G., Schäfer, C., Franchi, P., Silvi, S., Colasson, B., Lucarini, M., & Credi, A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1712783115 · Cited by 43 · see citing works

Oncogenic mutations weaken the interactions that stabilize the p110α‐p85α heterodimer in phosphatidylinositol 3‐kinase α

Echeverria, I., Liu, Y., Gabelli, S. B., & Amzel, L. M. (2015) · FEBS Journal · doi:10.1111/febs.13365 · Cited by 41 · see citing works

Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor

Bartuzi, D., Kaczor, A. A., & Matosiuk, D. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00705 · Cited by 40 · see citing works

Energetic redistribution in allostery to execute protein function

Liu, J., & Nussinov, R. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1709071114 · Cited by 40 · see citing works

Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1

Lee, Y. M., & Liou, Y. (2018) · Frontiers in Oncology · doi:10.3389/fonc.2018.00469 · Cited by 40 · see citing works

What is allosteric regulation? Exploring the exceptions that prove the rule!

McCullagh, M., Zeczycki, T. N., Kariyawasam, C. S., Durie, C. L., Halkidis, K., Fitzkee, N. C., Holt, J. M., & Fenton, A. W. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.105672 · Cited by 40 · see citing works

Conformational Dynamics and Allostery in Pyruvate Kinase

Donovan, K. A., Zhu, S., Liuni, P., Peng, F., Kessans, S. A., Wilson, D. J., & Dobson, R. C. J. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.676270 · Cited by 39 · see citing works

Allosteric regulation of Arf GTPases and their GEFs at the membrane interface

Nawrotek, A., Zeghouf, M., & Cherfils, J. (2016) · Small GTPases · doi:10.1080/21541248.2016.1215778 · Cited by 39 · see citing works

Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism

Medina‐Carmona, E., Neira, J. L., SALIDO, E. C., Fuchs, J. E., Palomino‐Morales, R., Timson, D. J., & Pey, A. L. (2017) · Scientific Reports · doi:10.1038/srep44532 · Cited by 37 · see citing works

Recognition 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 · see citing works

Double Mutant Cycles as a Tool to Address Folding, Binding, and Allostery

Pagano, L., Toto, A., Malagrinò, F., Visconti, L., Jemth, P., & Gianni, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020828 · Cited by 36 · see citing works

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 · see citing works

Sensing the allosteric force

Božović, O., Janković, B. G., & Hamm, P. M. (2020) · Nature Communications · doi:10.1038/s41467-020-19689-7 · Cited by 35 · see citing works

Engineering an Allosteric Control of Protein Function

Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33 · see citing works

Computational methods for studying G protein-coupled receptors (GPCRs)

Kaczor, A. A., Rutkowska, E. E., Bartuzi, D., Targowska‐Duda, K. M., Matosiuk, D., & Selent, J. (2015) · Methods in cell biology · doi:10.1016/bs.mcb.2015.11.002 · Cited by 34 · see citing works

Allosteric DNA nanoswitches for controlled release of a molecular cargo triggered by biological inputs

Rossetti, M., Ranallo, S., Idili, A., Palleschi, G., Porchetta, A., & Ricci, F. (2016) · Chemical Science · doi:10.1039/c6sc03404g · Cited by 34 · see citing works

Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp

Burschowsky, D., Thorbjørnsrud, H. V., Heim, J. B., Fahrig‐Kamarauskaitė, J., Würth-Roderer, K., Kast, P., & Krengel, U. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b01018 · Cited by 34 · see citing works

Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation

Ge, X., Sun, Y., & Ding, F. (2018) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2018.03.011 · Cited by 34 · see citing works

Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator

Kromann-Hansen, T., Lange, E. L., Sørensen, H. P., Hassanzadeh‐Ghassabeh, G., Huang, M., Jensen, J. K., Muyldermans, S., Declerck, P. J., Komives, E. A., & Andreasen, P. A. (2017) · Scientific Reports · doi:10.1038/s41598-017-03457-7 · Cited by 33 · see citing works

Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System

Capdevila, D. A., Edmonds, K. A., Campanello, G. C., Wu, H., González-Gutiérrez, G., & Giedroc, D. P. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b02129 · Cited by 33 · see citing works

An engineered photoswitchable mammalian pyruvate kinase

Gehrig, S. M., Macpherson, J. A., Driscoll, P. C., Symon, A., Martin, S. R., MacRae, J. I., Kleinjung, J., Fraternali, F., & Anastasiou, D. (2017) · FEBS Journal · doi:10.1111/febs.14175 · Cited by 32 · see citing works

Seeking allosteric networks in PDZ domains

Gautier, C., Laursen, L. V., Jemth, P., & Gianni, S. (2018) · Protein Engineering Design and Selection · doi:10.1093/protein/gzy033 · Cited by 31 · see citing works

Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery

Pfleger, C., Minges, A., Boehm, M., McClendon, C. L., Torella, R., & Gohlke, H. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00529 · Cited by 32 · see citing works

Beyond active site residues: overall structural dynamics control catalysis in flavin-containing and heme-containing monooxygenases

Fürst, M. J. L. J., Fiorentini, F., & Fraaije, M. W. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.01.019 · Cited by 31 · see citing works

Autism Linked to Increased Oncogene Mutations but Decreased Cancer Rate

Darbro, B. W., Singh, R., Zimmerman, M. B., Mahajan, V. B., & Bassuk, A. G. (2016) · PLoS ONE · doi:10.1371/journal.pone.0149041 · Cited by 31 · see citing works

Implications of short time scale dynamics on long time processes

Hage, K. E., Brickel, S., Hermelin, S., Gaulier, G., Schmidt, C., Bonacina, L., van Keulen, S. C., Bhattacharyya, S., Chergui, M., Hamm, P. M., et al. (2017) · Structural Dynamics · doi:10.1063/1.4996448 · Cited by 31 · see citing works

Mechanism of activation and the rewired network: New drug design concepts

Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30 · see citing works

Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 M pro and its evolutionary mutations as a case study

Amamuddy, O. S., Boateng, R. A., Barozi, V., Nyamai, D. W., & Bishop, Ö. T. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.11.016 · Cited by 29 · see citing works

Mechanistic insights into thrombin's switch between “slow” and “fast” forms

Xiao, J., Melvin, R. L., & Salsbury, F. R. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp03671j · Cited by 28 · see citing works

Controlling protein conformation with light

Dağliyan, O., & Hahn, K. M. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.01.012 · Cited by 28 · see citing works

Allostery Frustrates the Experimentalist

Gianni, S., & Jemth, P. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167934 · Cited by 25 · see citing works

Combining structural and coevolution information to unveil allosteric sites

Sala, G. L., Pfleger, C., Käck, H., Wissler, L., Nevin, P., Böhm, K., Janet, J. P., Schimpl, M., Stubbs, C. J., Vivo, M. D., et al. (2023) · Chemical Science · doi:10.1039/d2sc06272k · Cited by 23 · see citing works

Mapping the allosteric network within a SH3 domain

Malagrinò, F., Troilo, F., Bonetti, D., Toto, A., & Gianni, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-44656-8 · Cited by 24 · see citing works

Norovirus, glycans and attachment

Taube, S., Mallagaray, Á., & Peters, T. (2018) · Current Opinion in Virology · doi:10.1016/j.coviro.2018.04.007 · Cited by 22 · see citing works

The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization

Roche, J., Girard, É., Mas, C., & Madern, D. (2019) · Journal of Structural Biology · doi:10.1016/j.jsb.2019.07.006 · Cited by 23 · see citing works

The “violin model”: Looking at community networks for dynamic allostery

Madan, L. K., Welsh, C. L., Kornev, A. P., & Taylor, S. S. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0138175 · Cited by 23 · see citing works

Allosteric Dynamic Control of Binding

Sumbul, F., Acuner, S. E., & Haliloǧlu, T. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.08.011 · Cited by 23 · see citing works

Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach

Alvarez, L. H., Gomes, D. E. B., González, J. E. H., & Pascutti, P. G. (2019) · PLoS ONE · doi:10.1371/journal.pone.0211227 · Cited by 23 · see citing works

Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks

Astl, L., & Verkhivker, G. M. (2019) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2019.07.008 · Cited by 21 · see citing works

Chemical shift imprint of intersubunit communication in a symmetric homodimer

Falk, B. T., Sapienza, P. J., & Lee, A. L. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604748113 · Cited by 21 · see citing works

Saturation transfer difference nuclear magnetic resonance titrations reveal complex multistep-binding of l-fucose to norovirus particles

Mallagaray, Á., Rademacher, C., Parra, F., Hansman, G. S., & Peters, T. (2016) · Glycobiology · doi:10.1093/glycob/cww070 · Cited by 21 · see citing works

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps

Hayatshahi, H. S., Ahuactzin-Garcia, E., Tao, P., Wang, S., & Liu, J. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00447 · Cited by 20 · see citing works

HDX‐MS reveals orthosteric and allosteric changes in apolipoprotein‐D structural dynamics upon binding of progesterone

Kielkopf, C. S., Ghosh, M., Anand, G. S., & Brown, S. H. J. (2018) · Protein Science · doi:10.1002/pro.3534 · Cited by 20 · see citing works

Biased Allostery

Edelstein, S. J., & Changeux, J. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.07.044 · Cited by 20 · see citing works

All over or overall – Do we understand allostery?

Hofmann, H. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102724 · Cited by 20 · see citing works

Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks

Astl, L., Tse, A., & Verkhivker, G. M. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_9 · Cited by 18 · see citing works

Protonation-Induced Dynamic Allostery in PDZ Domain: Evidence of Perturbation-Independent Universal Response Network

Kumawat, A., & Chakrabarty, S. (2020) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.0c02885 · Cited by 20 · see citing works

Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments

Fata, F., Silvestri, I., Ardini, M., Ippoliti, R., Leandro, L. D., Demitri, N., Polentarutti, M., Matteo, A. D., Lyu, H., Thatcher, G. R. J., et al. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.0c00909 · Cited by 20 · see citing works

Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases

Movilla, S., Roca, M., Moliner, V., & Magistrato, A. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c11980 · Cited by 19 · see citing works

Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression

Anandapadamanaban, M., Pilstål, R., Andrésen, C., Trewhella, J., Moche, M., Wallner, B., & Sunnerhagen, M. (2016) · Structure · doi:10.1016/j.str.2016.06.008 · Cited by 19 · see citing works

Advances in the Computational Identification of Allosteric Sites and Pathways in Proteins

Daura, X. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_7 · Cited by 19 · see citing works

Calculated pKa Variations Expose Dynamic Allosteric Communication Networks

Lang, E. J. M., Heyes, L. C., Jameson, G. B., & Parker, E. J. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.5b13134 · Cited by 19 · see citing works

Dynamic 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 · see citing works

An allosteric site enables fine‐tuning of cathepsin K by diverse effectors

Novinec, M., Rebernik, M., & Lenar≷cic̆, B. (2016) · FEBS Letters · doi:10.1002/1873-3468.12495 · Cited by 18 · see citing works

Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions

Frezza, E., & Lavery, R. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b11913 · Cited by 18 · see citing works

Computational analysis of long-range allosteric communications in CFTR

Ayca, E., Altintel, B., Levanon, N. L., Ben‐Tal, N., Haliloǧlu, T., & Lewinson, O. (2023) · eLife · doi:10.7554/elife.88659.3 · Cited by 17 · see citing works

Allostery in molecular self-assemblies: metal ions triggered self-assembly and emissions of terthiophene

Liu, S., Zhao, L., Xiao, Y., Huang, T., Li, J., Huang, J., & Yan, Y. (2016) · Chemical Communications · doi:10.1039/c6cc00492j · Cited by 17 · see citing works

Conditionally disordered proteins: bringing the environment back into the fold

Hausrath, A. C., & Kingston, R. L. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2558-1 · Cited by 17 · see citing works

Computational investigation of conformational variability and allostery in cathepsin K and other related peptidases

Novinec, M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182387 · Cited by 17 · see citing works

Allostery without conformation change: modelling protein dynamics at multiple scales

McLeish, T. C. B., Rodgers, T. L., & Wilson, M. R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/5/056004 · Cited by 72 · see citing works

The role of dynamics in allosteric regulation

Kern, D., & Zuiderweg, E. R. P. (2003) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2003.10.008 · Cited by 653 · see citing works

Evidence of allosteric conformational

Oda, M., Kozono, H., Morii, H., & Azuma, T. (2014)

Protein Allostery and Conformational Dynamics

Guo, J., & Zhou, H.-X. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00590 · Cited by 484 · see citing works

Structural aspects of allostery

Evans, P. R. (1991) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(91)90178-v · Cited by 15 · see citing works