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Controlling Allosteric Networks in Proteins
Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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“DNA alkylation drugs, as the first class of drugs targeting DNA, have been clinically used for nearly 70 years to treat cancers.468”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [468]
In the citing paper
“According to the ensemble model, first described in the 1980s (Cooper, 1984; Frauenfelder et al., 1988), the allosteric behavior of a macromolecular system arises from the properties of the native free-energy landscape of the system, and how this land-scape is remodeled by various “perturbations,” such as ligand binding, protonation, or interactions with other proteins (Dokholyan, 2016; Kern and Z”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Dokholyan, 2016
In the citing paper
“Unraveling the mechanistic underpinning of this behavior should therefore lead to improved understanding of how signaling events are relayed and regulated, and enable their modulation with promising pharmaceutical avenues for targeting human disease (Dokholyan, 2016).”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Dokholyan, 2016
Citations
Cites
Collective dynamics of ‘small-world’ networks
Watts, D. J., & Strogatz, S. H. (1998) · Nature · doi:10.1038/30918 · Cited by 43,060
A note on two problems in connexion with graphs
Dijkstra, E. (1959) · Numerische Mathematik · doi:10.1007/bf01386390 · Cited by 24,351
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
Self-organized criticality: An explanation of the 1/ f noise
Bak, P., Tang, C., & Wiesenfeld, K. A. (1987) · Physical Review Letters · doi:10.1103/physrevlett.59.381 · Cited by 7,644
Error and attack tolerance of complex networks
Albert, R., Jeong, H., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35019019 · Cited by 7,534
Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA
Riordan, J. R., Rommens, J. M., Kerem, B.-S., Alon, N., Rozmahel, R., Grzelczak, Z., Zielenski, J., Lok, S., Plavsic, N., Chou, J.-L., et al. (1989) · Science · doi:10.1126/science.2475911 · Cited by 7,418
Error and attack tolerance of complex networksPreprint
Albert, R., Jeong, H., & Barabási, A.-Ĺ. (2000) · Cited by 6,554
Essential dynamics of proteins
Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170408 · Cited by 3,487
Classes of small-world networks
Amaral, L. A. N., Scala, A., Barthélémy, M., & Stanley, H. E. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.200327197 · Cited by 3,051
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
The Hsp70 and Hsp60 Chaperone Machines
Bukau, B., & Horwich, A. L. (1998) · Cell · doi:10.1016/s0092-8674(00)80928-9 · Cited by 2,837
CATH – a hierarchic classification of protein domain structures
Orengo, C., Michie, A. D., Jones, S., Jones, D., Swindells, M. B., & Thornton, J. M. (1997) · Structure · doi:10.1016/s0969-2126(97)00260-8 · Cited by 2,658
Studies in Molecular Dynamics. I. General Method
Alder, B. J., & Wainwright, T. E. (1959) · The Journal of Chemical Physics · doi:10.1063/1.1730376 · Cited by 2,524
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones
Cech, T. R., & Steitz, J. A. (2014) · Cell · doi:10.1016/j.cell.2014.03.008 · Cited by 2,524
Allosteric proteins and cellular control systems
Monod, J., Changeux, J., & Jacob, F. (1963) · Journal of Molecular Biology · doi:10.1016/s0022-2836(63)80091-1 · Cited by 2,240
Application of a Theory of Enzyme Specificity to Protein Synthesis.
Koshland, D. (1958) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.44.2.98 · Cited by 2,140
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
Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., & Steitz, T. A. (1992) · Science · doi:10.1126/science.1377403 · Cited by 1,914
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Kuhlman, B. A., Dantas, G. A., Ireton, G. C., Varani, G., Stoddard, B. L., & Baker, D. A. (2003) · Science · doi:10.1126/science.1089427 · Cited by 1,666
Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model
Atılgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, Ö., & Bahar, İ. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)76033-x · Cited by 1,638
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
Tirion, M. M. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.1905 · Cited by 1,617
Structure of influenza haemagglutinin at the pH of membrane fusion
Bullough, P. A., Hughson, F. M., Skehel, J. J., & Wiley, D. C. (1994) · Nature · doi:10.1038/371037a0 · Cited by 1,564
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
Hamelberg, D., Mongan, J., & McCammon, J. A. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1755656 · Cited by 1,536
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
Bahar, İ., Atılgan, A. R., & Erman, B. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00024-2 · Cited by 1,377
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
Deep mutational scanning: a new style of protein science
Fowler, D. M., & Fields, S. (2014) · Nature Methods · doi:10.1038/nmeth.3027 · Cited by 1,287
The ensemble nature of allostery
Motlagh, H. N., Wrabl, J. O., Li, J., & Hilser, V. J. (2014) · Nature · doi:10.1038/nature13001 · Cited by 1,247
Clementi, C., Nymeyer, H., & Onuchic, J. N. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3693 · Cited by 1,228
De Novo Protein Design: Fully Automated Sequence Selection
Dahiyat, B. I., & Mayo, S. L. (1997) · Science · doi:10.1126/science.278.5335.82 · Cited by 1,156
Protein 3D Structure Computed from Evolutionary Sequence Variation
Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144
Doyle, D., Lee, A., Lewis, J. H., Kim, E., Sheng, M., & MacKinnon, R. (1996) · Cell · doi:10.1016/s0092-8674(00)81307-0 · Cited by 1,126
Wolynes, P., Onuchic, J., & Thirumalai, D. (1995) · Science · doi:10.1126/science.7886447 · Cited by 1,080
Computer simulation of protein folding
Levitt, M., & Warshel, A. (1975) · Nature · doi:10.1038/253694a0 · Cited by 1,051
The Enzymology of Control by Feedback Inhibition
Gerhart, J. C., & Pardee, A. B. (1962) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)60389-8 · Cited by 1,022
Fersht, A. R., Matouschek, A. T., & Serrano, L. G. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90561-w · Cited by 930
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 896
How do small single-domain proteins fold?
Jackson, S. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00033-9 · Cited by 895
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
Jackson, S., & Fersht, A. R. (1991) · Biochemistry · doi:10.1021/bi00107a010 · Cited by 888
Correlated mutations and residue contacts in proteins
Göbel, U., Sander, C., Schneider, R., & Valencia, A. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180402 · Cited by 863
Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
Süel, G. M., Lockless, S. W., Wall, M. A., & Ranganathan, R. (2002) · Nature Structural Biology · doi:10.1038/nsb881 · Cited by 816
Native protein sequences are close to optimal for their structures
Kuhlman, B. A., & Baker, D. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.19.10383 · Cited by 814
New Tools Provide New Insights in NMR Studies of Protein Dynamics
Mittermaier, A., & Kay, L. E. (2006) · Science · doi:10.1126/science.1124964 · Cited by 785
Dynamical networks in tRNA:protein complexes
Sethi, A., Eargle, J., Black, A. A., & Luthey-Schulten, Z. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810961106 · Cited by 777
Allostery in Disease and in Drug Discovery
Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769
Gaussian Dynamics of Folded Proteins
Haliloǧlu, T., Bahar, İ., & Erman, B. (1997) · Physical Review Letters · doi:10.1103/physrevlett.79.3090 · Cited by 761
Allostery without conformational change
Cooper, A., & Dryden, D. T. F. (1984) · European Biophysics Journal · doi:10.1007/bf00276625 · Cited by 740
Coarse-grained normal mode analysis in structural biology
Bahar, İ., & Rader, A. J. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.08.007 · Cited by 732
Dynamics of a small globular protein in terms of low-frequency vibrational modes.
Gō, N., Noguti, T., & Nishikawa, T. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.12.3696 · Cited by 729
Riboswitches and the RNA WorldPreprint
Breaker, R. R. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003566 · Cited by 712
Mapping the transition state and pathway of protein folding by protein engineering
Matouschek, A. T., Kellis, J. T., Serrano, L., & Fersht, A. R. (1989) · Nature · doi:10.1038/340122a0 · Cited by 703
Allosteric Modulation of G Protein–Coupled Receptors
May, L. T., Leach, K., Sexton, P. M., & Christopoulos, A. (2006) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.47.120505.105159 · Cited by 698
Protein Sectors: Evolutionary Units of Three-Dimensional Structure
Halabi, N. M., Rivoire, O., Leibler, S., & Ranganathan, R. (2009) · Cell · doi:10.1016/j.cell.2009.07.038 · Cited by 697
Allostery and cooperativity revisited
Cui, Q., & Karplus, M. (2008) · Protein Science · doi:10.1110/ps.03259908 · Cited by 684
Allosteric binding sites on cell-surface receptors: novel targets for drug discovery
Christopoulos, A. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd746 · Cited by 665
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
Karplus, M., & Weaver, D. L. (1976) · Nature · doi:10.1038/260404a0 · Cited by 629
Activation mechanism of the β 2 -adrenergic receptor
Dror, R. O., Arlow, D. H., Maragakis, P., Mildorf, T. J., Pan, A. C., Xu, H., Borhani, D. W., & Shaw, D. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110499108 · Cited by 629
Protein structure prediction from sequence variation
Marks, D. S., Hopf, T. A., & Sander, C. (2012) · Nature Biotechnology · doi:10.1038/nbt.2419 · Cited by 622
CFTR Function and Prospects for Therapy
Riordan, J. R. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.103004.142532 · Cited by 610
Two-State Allosteric Behavior in a Single-Domain Signaling Protein
Volkman, B. F., Lipson, D., Wemmer, D. E., & Kern, D. (2001) · Science · doi:10.1126/science.291.5512.2429 · Cited by 594
Li, W. (2004) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2003.10.041 · Cited by 588
The riboswitch control of bacterial metabolism
Nudler, E. (2003) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2003.11.004 · Cited by 574
Parameters for the Description of Transition States
Leffler, J. E. (1953) · Science · doi:10.1126/science.117.3039.340 · Cited by 572
Schreiber, G., & Fersht, A. R. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(95)80064-6 · Cited by 569
Protein structure determination from NMR chemical shifts
Cavalli, A., Salvatella, X., Dobson, C. M., & Vendruscolo, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610313104 · Cited by 557
Nucleation mechanisms in protein folding
Fersht, A. R. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80002-4 · Cited by 545
Protein Design: A Hierarchic Approach
Bryson, J. W., Betz, S. F., Lu, H. S. M., Suich, D. J., Zhou, H. X., O’Neil, K. T., & DeGrado, W. F. (1995) · Science · doi:10.1126/science.270.5238.935 · Cited by 530
Allosteric inhibition of protein tyrosine phosphatase 1B
Wiesmann, C., Barr, K. J., Kung, J., Zhu, J., Erlanson, D. A., Wang, S., Fahr, B. J., Zhong, M., Taylor, L., Randal, M., et al. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb803 · Cited by 528
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
Rose, P. W., Prlić, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J., Woo, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1214 · Cited by 519
Smock, R. G., & Gierasch, L. M. (2009) · Science · doi:10.1126/science.1169377 · Cited by 510
Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes
Ma, J. (2005) · Structure · doi:10.1016/j.str.2005.02.002 · Cited by 486
Understanding the transcriptome through RNA structure
Wan, Y., Kertesz, M., Spitale, R. C., Segal, E., & Chang, H. Y. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3049 · Cited by 482
Protein Design, a Minimalist Approach
DeGrado, W. F., Wasserman, Z. R., & Lear, J. D. (1989) · Science · doi:10.1126/science.2464850 · Cited by 479
Fersht, A. R. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.24.10869 · Cited by 469
Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model
Abkevich, V., Gutin, A. M., & Shakhnovich, E. I. (1994) · Biochemistry · doi:10.1021/bi00199a029 · Cited by 468
Sharp, P. A. (2009) · Cell · doi:10.1016/j.cell.2009.02.007 · Cited by 462
Transient folding intermediates characterized by protein engineering
Matouschek, A. T., Kellis, J. T., Serrano, L. G., Bycroft, M., & Fersht, A. R. (1990) · Nature · doi:10.1038/346440a0 · Cited by 451
Fold Change in Evolution of Protein Structures
Grishin, N. V. (2001) · Journal of Structural Biology · doi:10.1006/jsbi.2001.4335 · Cited by 445
Widespread genetic switches and toxicity resistance proteins for fluoride
Baker, J. L., Sudarsan, N., Weinberg, Z., Roth, A., Stockbridge, R. B., & Breaker, R. R. (2012) · Science · doi:10.1126/science.1215063 · Cited by 438
Three key residues form a critical contact network in a protein folding transition state
Vendruscolo, M., Paci, E., Dobson, C. M., & Karplus, M. (2001) · Nature · doi:10.1038/35054591 · Cited by 429
Crystal Structure of the Thermosome, the Archaeal Chaperonin and Homolog of CCT
Ditzel, L., Löwe, J., Stock, D., Stetter, K.-O., Huber, H., Huber, R., & Steinbacher, S. (1998) · Cell · doi:10.1016/s0092-8674(00)81152-6 · Cited by 427
Elrod-Erickson, M., Rould, M. A., Nekludova, L., & Pabo, C. O. (1996) · Structure · doi:10.1016/s0969-2126(96)00125-6 · Cited by 421
Eris: an automated estimator of protein stability
Yin, S., Ding, F., & Dokholyan, N. V. (2007) · Nature Methods · doi:10.1038/nmeth0607-466 · Cited by 405
Self-citationA Unified View of “How Allostery Works”
Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003394 · Cited by 401
Small-world view of the amino acids that play a key role in protein folding
Vendruscolo, M., Dokholyan, N. V., Paci, E., & Karplus, M. (2002) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.65.061910 · Cited by 386
Self-citationDynamic activation of an allosteric regulatory protein
Tzeng, S., & Kalodimos, C. G. (2009) · Nature · doi:10.1038/nature08560 · Cited by 384
Serohijos, A. W. R., Hegedűs, T., Aleksandrov, A. A., He, L., Cui, L., Dokholyan, N. V., & Riordan, J. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800254105 · Cited by 381
Self-citationThe origin of protein interactions and allostery in colocalization
Kuriyan, J., & Eisenberg, D. S. (2007) · Nature · doi:10.1038/nature06524 · Cited by 380
The hinge-bending mode in lysozyme
McCammon, J. A., Gelin, B. R., Karplus, M., & Wolynes, P. G. (1976) · Nature · doi:10.1038/262325a0 · Cited by 379
Flexible docking using tabu search and an empirical estimate of binding affinity
Baxter, C. A., Murray, C. W., Clark, D. E., Westhead, D. R., & Eldridge, M. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19981115)33:3 · Cited by 378
Atomic accuracy in predicting and designing noncanonical RNA structure
Das, R., Karanicolas, J., & Baker, D. A. (2010) · Nature Methods · doi:10.1038/nmeth.1433 · Cited by 375
The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways
del Sol, A., Tsai, C., Ma, B., & Nussinov, R. (2009) · Structure · doi:10.1016/j.str.2009.06.008 · Cited by 367
Practical limits of function prediction
Devos, D. P., & Valencia, A. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001001)41:1 · Cited by 358
Rao, F. V., & Caflisch, A. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.063 · Cited by 357
Hot Spots for Allosteric Regulation on Protein Surfaces
Reynolds, K. A., McLaughlin, R. N., & Ranganathan, R. (2011) · Cell · doi:10.1016/j.cell.2011.10.049 · Cited by 350
The Dynamic Landscapes of RNA Architecture
Cruz, J. A., & Westhof, É. (2009) · Cell · doi:10.1016/j.cell.2009.02.003 · Cited by 349
Surface Sites for Engineering Allosteric Control in Proteins
Lee, J., Natarajan, M., Nashine, V. C., Socolich, M., Vo, T., Russ, W. P., Benkovic, S. J., & Ranganathan, R. (2008) · Science · doi:10.1126/science.1159052 · Cited by 343
Frauenfelder, H., McMahon, B. H., Austin, R. H., Chu, K., & Groves, J. T. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.041614298 · Cited by 340
The Oxygen Equilibrium of Hemoglobin and Its Structural Interpretation
Pauling, L. C. (1935) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.21.4.186 · Cited by 340
Conserved residues and the mechanism of protein folding
Shakhnovich, E. I., Abkevich, V., & Ptitsyn, O. B. (1996) · Nature · doi:10.1038/379096a0 · Cited by 339
Mapping the conformational wave of acetylcholine receptor channel gating
Grosman, C. F., Zhou, M., & Auerbach, A. L. (2000) · Nature · doi:10.1038/35001586 · Cited by 336
Activation pathway of Src kinase reveals intermediate states as targets for drug design
Shukla, D., Meng, Y., Roux, B., & Pande, V. S. (2014) · Nature Communications · doi:10.1038/ncomms4397 · Cited by 333
Searching for new allosteric sites in enzymes
Hardy, J. A., & Wells, J. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.10.009 · Cited by 326
Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics
Ding, F., Tsao, D., Nie, H., & Dokholyan, N. V. (2008) · Structure · doi:10.1016/j.str.2008.03.013 · Cited by 326
Self-citationStructural and Energetic Basis of Allostery
Hilser, V. J., Wrabl, J. O., & Motlagh, H. N. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-050511-102319 · Cited by 321
Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL
Yifrach, O., & Horovitz, A. (1995) · Biochemistry · doi:10.1021/bi00016a001 · Cited by 309
Davies, J. C., Alton, E. W. F. W., & Bush, A. (2007) · BMJ · doi:10.1136/bmj.39391.713229.ad · Cited by 306
Characterizing transition states in protein folding: an essential step in the puzzle
Fersht, A. R. (1995) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(95)80012-p · Cited by 305
Light-activated DNA binding in a designed allosteric protein
Strickland, D., Moffat, K., & Sosnick, T. R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709610105 · Cited by 302
The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT
Leitner, A., Joachimiak, Ł. A., Bracher, A., Mönkemeyer, L., Walzthoeni, T., Chen, B., Pechmann, S., Holmes, S., Cong, Y., Ma, B., et al. (2012) · Structure · doi:10.1016/j.str.2012.03.007 · Cited by 301
Riboswitches: the oldest mechanism for the regulation of gene expression?
Vitreschak, A. G. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.11.008 · Cited by 297
Kim, S., Broströmer, E., Xing, D., Jin, J., Chong, S., Ge, H., Wang, S., Gu, C., Yang, L., Gao, Y. Q., et al. (2013) · Science · doi:10.1126/science.1229223 · Cited by 297
Discrete molecular dynamics studies of the folding of a protein-like model
Dokholyan, N. V., Buldyrev, S. V., Stanley, E., & Shakhnovich, E. I. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00072-8 · Cited by 296
Self-citationTopological determinants of protein folding
Dokholyan, N. V., Li, L., Ding, F., & Shakhnovich, E. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122076099 · Cited by 287
Self-citationShakhnovich, E. I., & Finkelstein, A. V. (1989) · Biopolymers · doi:10.1002/bip.360281003 · Cited by 285
Riboswitch RNAs: using RNA to sense cellular metabolismPreprint
Henkin, T. M. (2008) · Genes & Development · doi:10.1101/gad.1747308 · Cited by 285
Drugs for Allosteric Sites on Receptors
Wenthur, C. J., Gentry, P. R., Mathews, T. P., & Lindsley, C. W. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134525 · Cited by 285
Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch
Krammer, A., Lu, H. J., Isralewitz, B., Schulten, K. J., & Viola Vogel, B. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1351 · Cited by 278
Protein Contact Networks: An Emerging Paradigm in Chemistry
Paola, L. D., Ruvo, M. D., Paci, P., Santoni, D., & Giuliani, A. (2012) · Chemical Reviews · doi:10.1021/cr3002356 · Cited by 270
Zheng, W., Brooks, B. R., & Thirumalai, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510426103 · Cited by 261
Protein dynamics and allostery: an NMR view
Tzeng, S., & Kalodimos, C. G. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.10.007 · Cited by 258
Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis
Atchley, W. R., Wollenberg, K. R., Fitch, W. M., Terhalle, W. F., & Dress, A. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026229 · Cited by 256
Zhuravleva, A., Clerico, E. M., & Gierasch, L. (2012) · Cell · doi:10.1016/j.cell.2012.11.002 · Cited by 253
Conformational spread in a ring of proteins: a stochastic approach to allostery
Duke, T. A. J., Novère, N. L., & Bray, D. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4610 · Cited by 241
Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
Fodor, A. A., & Aldrich, R. W. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20098 · Cited by 238
Discovery of an allosteric site in the caspases
Hardy, J. A., Lam, J. W., Nguyen, J. T., O'Brien, T., & Wells, J. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404781101 · Cited by 236
Computer-based redesign of a protein folding pathway.
Nauli, S., Kuhlman, B. A., & Baker, D. A. (2001) · Nature Structural Biology · doi:10.1038/89638 · Cited by 229
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
Genomics-aided structure prediction
Sulkowska, J. I., Morcos, F., Weigt, M., Terence Hwa, B., & Onuchic, J. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207864109 · Cited by 226
Activation and dynamic network of the M2 muscarinic receptor
Miao, Y., Nichols, S. E., Gasper, P. M., Metzger, V. T., & McCammon, J. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309755110 · Cited by 224
Protein structure modeling for structural genomics.
Sánchez, R., Pieper, U., Melo, F., Eswar, N., Martı́-Renom, M. A., Madhusudhan, M. S., Mirković, N., & Šali, A. (2000) · Nature Structural Biology · doi:10.1038/80776 · Cited by 216
Automated and fast building of three-dimensional RNA structures
Zhao, Y., Huang, Y., Gong, Z., Wang, Y., Man, J., & Xiao, Y. (2012) · Scientific Reports · doi:10.1038/srep00734 · Cited by 216
Guntas, G., Mansell, T. J., Kim, J. R., & Ostermeier, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502673102 · Cited by 215
Levy, Y., Cho, S. S., Onuchic, J. N., & Wolynes, P. G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.12.021 · Cited by 213
An optomechanical transducer in the blue light receptor phototropin from Avena sativa
Salomon, M., Eisenreich, W., Dürr, H., Schleicher, E., Knieb, E., Massey, V., Rüdiger, W., Müller, F., Bacher, A., & Richter, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.221455298 · Cited by 212
Shirvanyants, D. G., Ding, F., Tsao, D., Ramachandran, S., & Dokholyan, N. V. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp2114576 · Cited by 209
Self-citationStructural Basis for Ligand-Regulated Oligomerization of AraC
Soisson, S. M., MacDougall-Shackleton, B., Schleif, R. F., & Wolberger, C. (1997) · Science · doi:10.1126/science.276.5311.421 · Cited by 208
Dietrich, J. A., Shis, D. L., Alikhani, A., & Keasling, J. D. (2012) · ACS Synthetic Biology · doi:10.1021/sb300091d · Cited by 206
Engineered allosteric activation of kinases in living cells
Karginov, A. V., Ding, F., Kota, P. B., Dokholyan, N. V., & Hahn, K. M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1639 · Cited by 203
Self-citationAmbroggio, X. I., & Kuhlman, B. (2006) · Journal of the American Chemical Society · doi:10.1021/ja054718w · Cited by 200
The HSSP database of protein structure-sequence alignments and family profiles
Dodge, C. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.313 · Cited by 197
Emergence of Protein Fold Families through Rational Design
Ding, F., & Dokholyan, N. V. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020085 · Cited by 197
Self-citationCystic Fibrosis: Lessons from the Sweat Gland
Quinton, P. (2007) · Physiology · doi:10.1152/physiol.00041.2006 · Cited by 196
Structure and functional significance of mechanically unfolded fibronectin type III 1 intermediates
Gao, M., Craig, D. W., Lequin, O., Campbell, I. D., Viola Vogel, B., & Schulten, K. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2334390100 · Cited by 195
Assigning genomic sequences to CATH
Pearl, F. M. G. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.277 · Cited by 191
Allostery and population shift in drug discovery
Kar, G., Keskin, Ö., Gürsoy, A., & Nussinov, R. (2010) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2010.09.002 · Cited by 190
Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch
Ren, A., Rajashankar, K. R., & Patel, D. J. (2012) · Nature · doi:10.1038/nature11152 · Cited by 189
Hinge‐bending motion in citrate synthase arising from normal mode calculations
Marques, O., & Sanejouand, Y. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230410 · Cited by 188
Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
Kass, I., & Horovitz, A. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10180 · Cited by 187
Zhou, Y., Karplus, M., Wichert, J. M., & Hall, C. K. (1997) · The Journal of Chemical Physics · doi:10.1063/1.474186 · Cited by 186
The allosteric mechanism of the chaperonin GroEL: A dynamic analysis
Ma, J., & Karplus, M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.15.8502 · Cited by 185
Expanding protein universe and its origin from the biological Big Bang
Dokholyan, N., Shakhnovich, B. E., & Shakhnovich, E. (2002) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.202497999 · Cited by 183
Self-citationYura, K., Shionyu, M., & Toh, H. (2008) · Springer eBooks · doi:10.1007/978-3-540-38918-7_6791 · Cited by 178
A new approach for determining low‐frequency normal modes in macromolecules
Durand, P., Trinquier, G., & Sanejouand, Y. (1994) · Biopolymers · doi:10.1002/bip.360340608 · Cited by 177
Nugent, T., & Jones, D. T. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120036109 · Cited by 177
Studying functional dynamics in bio-molecules using accelerated molecular dynamics
Markwick, P. R. L., & McCammon, J. A. (2011) · Physical Chemistry Chemical Physics · doi:10.1039/c1cp22100k · Cited by 173
Exploring Residue Component Contributions to Dynamical Network Models of Allostery
VanWart, A. T., Eargle, J., Luthey-Schulten, Z. A., & Amaro, R. E. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300377a · Cited by 171
Allosteric cooperativity in protein kinase A
Masterson, L. R., Mascioni, A., Traaseth, N. J., Taylor, S. S., & Veglia, G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709214104 · Cited by 171
Protein contact network topology: a natural language for allostery
Paola, L. D., & Giuliani, A. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.03.001 · Cited by 169
Olmea, O., Rost, B., & Valencia, A. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3208 · Cited by 169
Exploring amyloid formation by a de novo design
Kammerer, R. A., Kostrewa, D., Zurdo, J., Detken, A., Garcı́a-Echeverrı́a, C., Green, J. D., Müller, S. A., Meier, B. H., Winkler, F. K., Dobson, C. M., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306786101 · Cited by 165
Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton
Dokholyan, N. V., & Shakhnovich, E. I. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4949 · Cited by 165
Self-citationUsing NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins
Robustelli, P., Kohlhoff, K., Cavalli, A., & Vendruscolo, M. (2010) · Structure · doi:10.1016/j.str.2010.04.016 · Cited by 164
Folding thermodynamics of a model three-helix-bundle protein
Zhou, Y., & Karplus, M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.26.14429 · Cited by 163
Modeling Backbone Flexibility Improves Protein Stability Estimation
Yin, S., Ding, F., & Dokholyan, N. V. (2007) · Structure · doi:10.1016/j.str.2007.09.024 · Cited by 160
Self-citationZhuravleva, A., & Gierasch, L. (2011) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1014448108 · Cited by 157
Molecular Mechanisms of Chaperonin GroEL−GroES Function
Keskin, Ö., Bahar, İ., Flatow, D. T., Covell, D. G., & Jernigan, R. L. (2001) · Biochemistry · doi:10.1021/bi011393x · Cited by 157
Chaperonin-mediated protein folding: fate of substrate polypeptide
Fenton, W. A., & Horwich, A. L. (2003) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583503003883 · Cited by 155
Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics
Rueda, M., Chacón, P., & Orozco, M. (2007) · Structure · doi:10.1016/j.str.2007.03.013 · Cited by 154
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities
Gasper, P. M., Fuglestad, B., Komives, E. A., Markwick, P. R. L., & McCammon, J. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218414109 · Cited by 154
Engineering of a light-gated potassium channel
Cosentino, C., Alberio, L., Gazzarrini, S., Aquila, M., Romano, E., Cermenati, S., Zuccolini, P., Petersen, J., Beltrame, M., Etten, J. L. V., et al. (2015) · Science · doi:10.1126/science.aaa2787 · Cited by 151
Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES
Chennubhotla, C., & Bahar, İ. (2006) · Molecular Systems Biology · doi:10.1038/msb4100075 · Cited by 151
Refined structure of the FKBP12–rapamycin–FRB ternary complex at 2.2 Å resolution
Liang, J., Choi, J., & Clardy, J. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998014747 · Cited by 148
Conformational behavior of ionic self‐complementary peptides
Altman, M. D., Lee, P., Rich, A., & Zhang, S. (2000) · Protein Science · doi:10.1110/ps.9.6.1095 · Cited by 148
Creation of an Allosteric Enzyme by Domain Insertion
Guntas, G., & Ostermeier, M. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.016 · Cited by 147
Karginov, A. V., Zou, Y., Shirvanyants, D. G., Kota, P. B., Dokholyan, N. V., Young, D. D., Hahn, K. M., & Deiters, A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja109630v · Cited by 146
Self-citationAllo-network drugs: harnessing allostery in cellular networks
Nussinov, R., Tsai, C., & Csermely, P. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.08.004 · Cited by 144
Identifying the protein folding nucleus using molecular dynamics
Dokholyan, N. V., Buldyrev, S. V., Stanley, E., & Shakhnovich, E. I. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3534 · Cited by 142
Self-citationNormal mode analysis for proteins
Skjærven, L., Hollup, S. M., & Reuter, N. (2008) · Journal of Molecular Structure THEOCHEM · doi:10.1016/j.theochem.2008.09.024 · Cited by 138
Zhuravlev, P. I., & Papoian, G. A. (2010) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583510000119 · Cited by 138
Chaudhry, C., Farr, G. W., Todd, M. J., Rye, H. S., Brünger, A. T., Adams, P. D., Horwich, A. L., & Sigler, P. B. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg477 · Cited by 137
Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model
Ding, F., Buldyrev, S. V., & Dokholyan, N. V. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.046375 · Cited by 137
Self-citationYang, Z., Májek, P., & Bahar, İ. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000360 · Cited by 136
The structural GDP/GTP cycle of human Arf6
Pasqualato, S., Ménétrey, J., Franco, M., & Cherfils, J. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve043 · Cited by 136
Oliveberg, M., Tan, Y., Silow, M., & Fersht, A. R. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1612 · Cited by 135
Dynamic Coupling and Allosteric Behavior in a Nonallosteric Protein
Clarkson, M. W., Gilmore, S., Edgell, M. H., & Lee, A. L. (2006) · Biochemistry · doi:10.1021/bi060652l · Cited by 134
A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
Gsponer, J. A., Christodoulou, J. C., Cavalli, A., Bui, J. M., Richter, B., Dobson, C. M., & Vendruscolo, M. (2008) · Structure · doi:10.1016/j.str.2008.02.017 · Cited by 134
Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase
Aksimentiev, A., Balabin, I. A., Fillingame, R. H., & Schulten, K. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74205-8 · Cited by 134
Best, R. B., & Vendruscolo, M. (2006) · Structure · doi:10.1016/j.str.2005.09.012 · Cited by 133
Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble
Ding, F., Dokholyan, N. V., Buldyrev, S. V., Stanley, E., & Shakhnovich, E. I. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75352-6 · Cited by 133
Self-citationA new allosteric site in glycogen phosphorylase b as a target for drug interactions
Oikonomakos, N. G., Skamnaki, V. T., Tsitsanou, K. E., Gavalas, N. G., & Johnson, L. N. (2000) · Structure · doi:10.1016/s0969-2126(00)00144-1 · Cited by 132
Multiple conformational selection and induced fit events take place in allosteric propagation
Nussinov, R., Ma, B., & Tsai, C. (2013) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.002 · Cited by 132
Allosteric determinants in guanine nucleotide-binding proteins
Hatley, M. E., Lockless, S. W., Gibson, S. K., Gilman, A. G., & Ranganathan, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1835919100 · Cited by 130
cAMP activation of PKA defines an ancient signaling mechanism
Das, R., Esposito, V., Abu-Abed, M., Anand, G. S., Taylor, S. S., & Melacini, G. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609033103 · Cited by 130
Zheng, W., Brooks, B. R., & Thirumalai, D. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.105270 · Cited by 129
Evolution of Allosteric Control in Glycogen Phosphorylase
Hudson, J. W., Golding, G. B., & Crerar, M. M. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1621 · Cited by 128
Rational design of a ligand-controlled protein conformational switch
Dağliyan, O., Shirvanyants, D. G., Karginov, A. V., Ding, F., Fee, L. R., Chandrasekaran, S. N., Freisinger, C. M., Smolen, G. A., Anna Huttenlocher, A., Hahn, K. M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218319110 · Cited by 128
Self-citationThe chaperonin folding machine
Saibil, H. R., & Ranson, N. A. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02211-9 · Cited by 127
Human liver glycogen phosphorylase inhibitors bind at a new allosteric site
Rath, V. L., Ammirati, M. J., Danley, D. E., Ekstrom, J. L., Gibbs, E. M., Hynes, T. R., Mathiowetz, A. M., McPherson, R. K., Olson, T. V., Treadway, J. L., et al. (2000) · Chemistry & Biology · doi:10.1016/s1074-5521(00)00004-1 · Cited by 126
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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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“Although much work has focused on identifying, understanding, and controlling preexisting allosteric properties, the question of how to introduce new allosteric functions is relatively unexplored (21).”
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Self-citation
Metadata
- Authors
- Dokholyan, N. V.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Dokholyan, Nikolay V.
- Venue
- Chemical Reviews
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-02-19
- Volume
- 116
- Issue
- 11
- Pages
- 6463-6487
- ISSN
- 0009-2665 (ISSN-L)
- 1520-6890
- OpenAlex
- W2283716387
- Cited by
- 260
- References
- 333
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 24 · 2023: 48 · 2022: 23 · 2021: 31 · 2020: 27 · 2019: 28 · 2018: 21 · 2017: 18 · 2016: 7
- FWCI
- 2.23
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Chemical Reviews (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases (R01 AI102732)
- National Institute of General Medical Sciences (5 R01 GM080742)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Hemoglobin structure and function
- Keywords
- protein allostery, allosteric networks, allosteric pathways, ligand-induced conformational change, protein regulation, protein engineering, cystic fibrosis transmembrane conductance regulator, CFTR, protein misfolding, drug discovery
- MeSH terms
- Allosteric Regulation, Allosteric Site, Humans, Ligands, Proteins, Cystic Fibrosis Transmembrane Conductance Regulator, Protein Structure, Quaternary, Focal Adhesion Protein-Tyrosine Kinases, Molecular Dynamics Simulation
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