Controlling Allosteric Networks in Proteins

Chemical Reviews

Volumn 116, Issue 11, 2016, Pages 6463-6487

  Dokholyan, Nikolay V ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINS; BIOLOGICAL SYSTEMS; COMPLEX NETWORKS; LIGANDS;

ALLOSTERIC TRANSITION; CONFORMATIONAL CHANGE; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATORS; EXPERIMENTAL APPROACHES; FUNDAMENTAL PROPERTIES; LIGAND-BINDING SITES; PAIRWISE INTERACTION; THERAPEUTIC STRATEGY;

PROTEINS;

CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; FOCAL ADHESION KINASE; LIGAND; PROTEIN;

ALLOSTERISM; BINDING SITE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN QUATERNARY STRUCTURE;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; FOCAL ADHESION PROTEIN-TYROSINE KINASES; HUMANS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, QUATERNARY; PROTEINS;

EID: 84974577224     PISSN: 00092665     EISSN: 15206890     Source Type: Journal    
DOI: 10.1021/acs.chemrev.5b00544     Document Type: Review

References (333)

1. Monod, J.; Changeux, J.; Jacob, F. Allosteric Proteins and Cellular Control Systems J. Mol. Biol. 1963, 6, 306-329 10.1016/S0022-2836(63)80091-1
2. Koshland, D. E. Application of a Theory of Enzyme Specificity to Protein Synthesis Proc. Natl. Acad. Sci. U. S. A. 1958, 44, 98-104 10.1073/pnas.44.2.98
3. Frauenfelder, H.; McMahon, B. H.; Austin, R. H.; Chu, K.; Groves, J. T. The Role of Structure, Energy Landscape, Dynamics, and Allostery in the Enzymatic Function of Myoglobin Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 2370-2374 10.1073/pnas.041614298
4. Adams, J.; Johnson, K.; Matthews, R.; Benkovic, S. J. Effects of Distal Point-site Mutations on the Binding and Catalysis of Dihydrofolate Reductase from Escherichia Coli Biochemistry 1989, 28, 6611-6618 10.1021/bi00442a012
5. Green, S. M.; Shortle, D. Patterns of Nonadditivity Between Pairs of Stability Mutations in Staphylococcal Nuclease Biochemistry 1993, 32, 10131-10139 10.1021/bi00089a032
6. Mace, J. E.; Wilk, B. J.; Agard, D. A. Functional Linkage Between the Active Site of Alpha-lytic Protease and Distant Regions of Structure: Scanning Alanine Mutagenesis of a Surface Loop Affects Activity and Substrate Specificity J. Mol. Biol. 1995, 251, 116-134 10.1006/jmbi.1995.0420
7. Olsen, D. B.; Stahlhut, M. W.; Rutkowski, C. A.; Schock, H. B.; vanOlden, A. L.; Kuo, L. C. Non-active Site Changes Elicit Broad-based Cross-resistance of the HIV-1 Protease to Inhibitors J. Biol. Chem. 1999, 274, 23699-23701 10.1074/jbc.274.34.23699
8. Meroueh, S. O.; Roblin, P.; Golemi, D.; Maveyraud, L.; Vakulenko, S. B.; Zhang, Y.; Samama, J. P.; Mobashery, S. Molecular Dynamics at the Root of Expansion of Function in the M69L Inhibitor-resistant TEM Beta-lactamase from Escherichia Coli J. Am. Chem. Soc. 2002, 124, 9422-9430 10.1021/ja026547q
9. Duke, T. A.; Le Novère, N.; Bray, D. Conformational Spread in a Ring of Proteins: a Stochastic Approach to Allostery J. Mol. Biol. 2001, 308, 541-553 10.1006/jmbi.2001.4610
10. Pasqualato, S.; Ménétrey, J.; Franco, M.; Cherfils, J. The Structural GDP/GTP Cycle of Human Arf6 EMBO Rep. 2001, 2, 234-238 10.1093/embo-reports/kve043
11. Soisson, S. M.; MacDougall-Shackleton, B.; Schleif, R.; Wolberger, C. Structural Basis for Ligand-regulated Oligomerization of AraC Science 1997, 276, 421-425 10.1126/science.276.5311.421
12. Strater, N.; Hakansson, K.; Schnappauf, G.; Braus, G.; Lipscomb, W. N. Crystal Structure of the T State of Allosteric Yeast Chorismate Mutase and Comparison with the R State Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 3330-3334 10.1073/pnas.93.8.3330
13. Oliva, G.; Fontes, M. R.; Garratt, R. C.; Altamirano, M. M.; Calcagno, M. L.; Horjales, E. Structure and Catalytic Mechanism of Glucosamine 6-phosphate Deaminase from Escherichia Coli at 2.1 A Resolution Structure 1995, 3, 1323-1332 10.1016/S0969-2126(01)00270-2
14. Wiesmann, C.; Barr, K. J.; Kung, J.; Zhu, J.; Erlanson, D. A.; Shen, W.; Fahr, B. J.; Zhong, M.; Taylor, L.; Randal, M.; McDowell, R. S.; Hansen, S. K. Allosteric Inhibition of Protein Tyrosine Phosphatase 1B Nat. Struct. Mol. Biol. 2004, 11, 730-737 10.1038/nsmb803
15. Makhlynets, O. V.; Raymond, E. A.; Korendovych, I. V. Design of Allosterically Regulated Protein Catalysts Biochemistry 2015, 54, 1444-1456 10.1021/bi5015248
16. Pauling, L. The Oxygen Equilibrium of Hemoglobin and Its Structural Interpretation Proc. Natl. Acad. Sci. U. S. A. 1935, 21, 186-191 10.1073/pnas.21.4.186
17. Gerhart, J. C.; Pardee, A. B. The Enzymology of Control by Feedback Inhibition J. Biol. Chem. 1962, 237, 891-896
18. Stadtman, E. R.; Cohen, G. N.; Lebras, G. Feedback Inhibition and Repression of Aspartokinase Activity in Escherichia Coli Ann. N. Y. Acad. Sci. 1961, 94, 952-959 10.1111/j.1749-6632.1961.tb35587.x
19. Patte, J. C.; Le Bras, G.; Loviny, T.; Cohen, G. N. Retro-inhibition and Repression of the Homoserine Dehydrogenase of Escherichia Coli Biochim. Biophys. Acta, Spec. Sect. Enzymol. Subj. 1963, 67, 16-30 10.1016/0926-6569(63)90204-9
20. Monod, J.; Wyman, J.; Changeux, J. P. On The Nature Of Allosteric Transitions: A Plausible Model J. Mol. Biol. 1965, 12, 88-118 10.1016/S0022-2836(65)80285-6
21. Cooper, A.; Dryden, D. T. Allostery Without Conformational Change. A Plausible Model Eur. Biophys. J. 1984, 11, 103-109 10.1007/BF00276625
22. Ptitsyn, O. B. Inter-domain Mobility in Proteins and Its Probable Functional Role FEBS Lett. 1978, 93, 1-4 10.1016/0014-5793(78)80791-1
23. Birktoft, J. J.; Kraut, J.; Freer, S. T. A Detailed Structural Comparison Between the Charge Relay System in Chymotrypsinogen and in Alpha-chymotrypsin Biochemistry 1976, 15, 4481-4485 10.1021/bi00665a023
24. Yonath, A.; Podjarny, A.; Honig, B.; Sielecki, A.; Traub, W. Crystallographic Studies of Protein Denaturation and Renaturation. 2. Sodium Dodecyl Sulfate Induced Structural Changes in Triclinic Lysozyme Biochemistry 1977, 16, 1418-1424 10.1021/bi00626a028
25. Levitt, M.; Warshel, A. Computer Simulation of Protein Folding Nature 1975, 253, 694-698 10.1038/253694a0
26. McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. The Hinge-bending Mode in Lysozyme Nature 1976, 262, 325-326 10.1038/262325a0
27. Honig, B.; Ray, A.; Levinthal, C. Conformational Flexibility and Protein Folding: Rigid Structural Fragments Connected by Flexible Joints in Subtilisin BPN Proc. Natl. Acad. Sci. U. S. A. 1976, 73, 1974-1978 10.1073/pnas.73.6.1974
28. Gunasekaran, K.; Ma, B.; Nussinov, R. Is Allostery an Intrinsic Property of All Dynamic Proteins? Proteins: Struct.; Funct.; Genet. 2004, 57, 433-443 10.1002/prot.20232
29. Kar, G.; Keskin, O.; Gursoy, A.; Nussinov, R. Allostery and Population Shift in Drug Discovery Curr. Opin. Pharmacol. 2010, 10, 715-722 10.1016/j.coph.2010.09.002
30. Zhuravlev, P. I.; Papoian, G. A. Protein Functional Landscapes, Dynamics, Allostery: a Tortuous Path Towards a Universal Theoretical Framework Q. Rev. Biophys. 2010, 43, 295-332 10.1017/S0033583510000119
31. Hilser, V. J.; Wrabl, J. O.; Motlagh, H. N. Structural and Energetic Basis of Allostery Annu. Rev. Biophys. 2012, 41, 585-609 10.1146/annurev-biophys-050511-102319
32. Motlagh, H. N.; Wrabl, J. O.; Li, J.; Hilser, V. J. The Ensemble Nature of Allostery Nature 2014, 508, 331-339 10.1038/nature13001
33. Volkman, B. F.; Lipson, D.; Wemmer, D. E.; Kern, D. Two-state Allosteric Behavior in a Single-domain Signaling Protein Science 2001, 291, 2429-2433 10.1126/science.291.5512.2429
34. Popovych, N.; Sun, S.; Ebright, R. H.; Kalodimos, C. G. Dynamically Driven Protein Allostery Nat. Struct. Mol. Biol. 2006, 13, 831-838 10.1038/nsmb1132
35. Gsponer, J.; Christodoulou, J.; Cavalli, A.; Bui, J. M.; Richter, B.; Dobson, C. M.; Vendruscolo, M. A Coupled Equilibrium Shift Mechanism in Calmodulin-mediated Signal Transduction Structure 2008, 16, 736-746 10.1016/j.str.2008.02.017
36. Tzeng, S. R.; Kalodimos, C. G. Protein Dynamics and Allostery: An NMR View Curr. Opin. Struct. Biol. 2011, 21, 62-67 10.1016/j.sbi.2010.10.007
37. Tzeng, S. R.; Kalodimos, C. G. Dynamic Activation of an Allosteric Regulatory Protein Nature 2009, 462, 368-372 10.1038/nature08560
38. Boehr, D. D.; Nussinov, R.; Wright, P. E. The Role of Dynamic Conformational Ensembles in Biomolecular Recognition Nat. Chem. Biol. 2009, 5, 789-796 10.1038/nchembio.232
39. Frantom, P. A.; Zhang, H. M.; Emmett, M. R.; Marshall, A. G.; Blanchard, J. S. Mapping of the Allosteric Network in the Regulation of Alpha-isopropylmalate Synthase from Mycobacterium Tuberculosis by the Feedback Inhibitor L-leucine: Solution-phase H/D Exchange Monitored by FT-ICR Mass Spectrometry Biochemistry 2009, 48, 7457-7464 10.1021/bi900851q
40. Cui, Q.; Karplus, M. Allostery and Cooperativity Revisited Protein Sci. 2008, 17, 1295-1307 10.1110/ps.03259908
41. Kim, S.; Broströmer, E.; Xing, D.; Jin, J.; Chong, S.; Ge, H.; Wang, S.; Gu, C.; Yang, L.; Gao, Y. Q.; Su, X. D.; Sun, Y.; Xie, X. S. Probing Allostery through DNA Science 2013, 339, 816-819 10.1126/science.1229223
42. Vitreschak, A. G.; Rodionov, D. A.; Mironov, A. A.; Gelfand, M. S. Riboswitches: The Oldest Mechanism for the Regulation of Gene Expression? Trends Genet. 2004, 20, 44-50 10.1016/j.tig.2003.11.008
43. Nudler, E.; Mironov, A. S. The Riboswitch Control of Bacterial Metabolism Trends Biochem. Sci. 2004, 29, 11-17 10.1016/j.tibs.2003.11.004
44. Henkin, T. M. Riboswitch RNAs: Using RNA to Sense Cellular Metabolism Genes Dev. 2008, 22, 3383-3390 10.1101/gad.1747308
45. Ren, A.; Rajashankar, K. R.; Patel, D. J. Fluoride Ion Encapsulation by Mg2+ Ions and Phosphates in a Fluoride Riboswitch Nature 2012, 486, 85-89 10.1038/nature11152
46. Breaker, R. R. Riboswitches and the RNA World Cold Spring Harbor Perspect. Biol. 2012, 4, a003566 10.1101/cshperspect.a003566
47. Baker, J. L.; Sudarsan, N.; Weinberg, Z.; Roth, A.; Stockbridge, R. B.; Breaker, R. R. Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride Science 2012, 335, 233-235 10.1126/science.1215063
48. Tsai, C. J.; Nussinov, R. A Unified View of "How Allostery Works PLoS Comput. Biol. 2014, 10, e1003394 10.1371/journal.pcbi.1003394
49. Christopoulos, A. Allosteric Binding Sites on Cell-surface Receptors: Novel Targets for Drug Discovery Nat. Rev. Drug. Discovery 2002, 1, 198-210 10.1038/nrd746
50. Lindsley, C. W. 2013 Philip S. Portoghese Medicinal Chemistry Lectureship: Drug Discovery Targeting Allosteric Sites J. Med. Chem. 2014, 57, 7485-7498 10.1021/jm5011786
51. Wenthur, C. J.; Gentry, P. R.; Mathews, T. P.; Lindsley, C. W. Drugs for Allosteric Sites on Receptors Annu. Rev. Pharmacol. Toxicol. 2014, 54, 165-184 10.1146/annurev-pharmtox-010611-134525
52. Szilágyi, A.; Nussinov, R.; Csermely, P. Allo-network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks Curr. Top. Med. Chem. 2013, 13, 64-77 10.2174/1568026611313010007
53. Nussinov, R.; Tsai, C. J.; Csermely, P. Allo-network Drugs: Harnessing Allostery in Cellular Networks Trends Pharmacol. Sci. 2011, 32, 686-693 10.1016/j.tips.2011.08.004
54. Dokholyan, N. V.; Shakhnovich, E. I. Understanding Hierarchical Protein Evolution from First Principles J. Mol. Biol. 2001, 312, 289-307 10.1006/jmbi.2001.4949
55. Ramachandran, S.; Vogel, L.; Strahl, B. D.; Dokholyan, N. V. Thermodynamic Stability of Histone H3 Is a Necessary but Not Sufficient Driving Force for Its Evolutionary Conservation PLoS Comput. Biol. 2011, 7, e1001042 10.1371/journal.pcbi.1001042
56. Proctor, E. A.; Kota, P.; Demarest, S. J.; Caravella, J. A.; Dokholyan, N. V. Highly Covarying Residues Have a Functional Role in Antibody Constant Domains Proteins: Struct.; Funct.; Genet. 2013, 81, 884-895 10.1002/prot.24247
57. Kannan, N.; Wu, J.; Anand, G. S.; Yooseph, S.; Neuwald, A. F.; Venter, J. C.; Taylor, S. S. Evolution of Allostery in the Cyclic Nucleotide Binding Module Genome Biol. 2007, 8, R264 10.1186/gb-2007-8-12-r264
58. Shukla, D.; Meng, Y.; Roux, B.; Pande, V. S. Activation Pathway of Src Kinase Reveals Intermediate States as Targets for Drug Design Nat. Commun. 2014, 5, 3397 10.1038/ncomms4397
59. Kohl, A.; Amstutz, P.; Parizek, P.; Binz, H. K.; Briand, C.; Capitani, G.; Forrer, P.; Plückthun, A.; Grütter, M. G. Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein Structure 2005, 13, 1131-1141 10.1016/j.str.2005.04.020
60. Yang, Z.; Májek, P.; Bahar, I. Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL PLoS Comput. Biol. 2009, 5, e1000360 10.1371/journal.pcbi.1000360
61. Csermely, P.; Palotai, R.; Nussinov, R. Induced Fit, Conformational Selection and Independent Dynamic Segments: An Extended View of Binding Events Trends Biochem. Sci. 2010, 35, 539-546 10.1016/j.tibs.2010.04.009
62. Novinec, M.; Korenč, M.; Caflisch, A.; Ranganathan, R.; Lenarčič, B.; Baici, A. A Novel Allosteric Mechanism in the Cysteine Peptidase Cathepsin K Discovered by Computational Methods Nat. Commun. 2014, 5, 3287 10.1038/ncomms4287
63. Vanatta, D. K.; Shukla, D.; Lawrenz, M.; Pande, V. S. A Network of Molecular Switches Controls the Activation of the Two-component Response Regulator NtrC Nat. Commun. 2015, 6, 7283 10.1038/ncomms8283
64. Sumbul, F.; Acuner-Ozbabacan, S. E.; Haliloglu, T. Allosteric Dynamic Control of Binding Biophys. J. 2015, 109, 1190-1201 10.1016/j.bpj.2015.08.011
65. Zhuravleva, A.; Gierasch, L. M. Allosteric Signal Transmission in the Nucleotide-binding Domain of 70-kDa Heat Shock Protein (Hsp70) Molecular Chaperones Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 6987-6992 10.1073/pnas.1014448108
66. Selvaratnam, R.; Chowdhury, S.; VanSchouwen, B.; Melacini, G. Mapping Allostery through the Covariance Analysis of NMR Chemical Shifts Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 6133-6138 10.1073/pnas.1017311108
67. Buchli, B.; Waldauer, S. A.; Walser, R.; Donten, M. L.; Pfister, R.; Blöchliger, N.; Steiner, S.; Caflisch, A.; Zerbe, O.; Hamm, P. Kinetic Response of a Photoperturbed Allosteric Protein Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 11725-11730 10.1073/pnas.1306323110
68. Henry, E. R.; Mozzarelli, A.; Viappiani, C.; Abbruzzetti, S.; Bettati, S.; Ronda, L.; Bruno, S.; Eaton, W. A. Experiments on Hemoglobin in Single Crystals and Silica Gels Distinguish Among Allosteric Models Biophys. J. 2015, 109, 1264-1272 10.1016/j.bpj.2015.04.037
69. Lockless, S. W.; Ranganathan, R. Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families Science 1999, 286, 295-299 10.1126/science.286.5438.295
70. Watts, D. J.; Strogatz, S. H. Collective Dynamics of "Small-world" Networks Nature 1998, 393, 440-442 10.1038/30918
71. Dokholyan, N. V.; Li, L.; Ding, F.; Shakhnovich, E. I. Topological Determinants of Protein Folding Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 8637-8641 10.1073/pnas.122076099
72. Vendruscolo, M.; Dokholyan, N.; Paci, E.; Karplus, M. Small-world View of the Amino Acids That Play a Key Role in Protein Folding Phys. Rev. E: Stat. Phys.; Plasmas, Fluids, Relat. Interdiscip. Top. 2002, 65, 061910 10.1103/PhysRevE.65.061910
73. Rose, P. W.; Prlić, A.; Bi, C.; Bluhm, W. F.; Christie, C. H.; Dutta, S.; Green, R. K.; Goodsell, D. S.; Westbrook, J. D.; Woo, J.; Young, J.; Zardecki, C.; Berman, H. M.; Bourne, P. E.; Burley, S. K. The RCSB Protein Data Bank: Views of Structural Biology for Basic and Applied Research and Education Nucleic Acids Res. 2015, 43, D345-D356 10.1093/nar/gku1214
74. Ding, F.; Jha, R. K.; Dokholyan, N. V. Scaling Behavior and Structure of Denatured Proteins Structure 2005, 13, 1047-1054 10.1016/j.str.2005.04.009
75. Fersht, A. R. Nucleation Mechanisms in Protein Folding Curr. Opin. Struct. Biol. 1997, 7, 3-9 10.1016/S0959-440X(97)80002-4
76. Clementi, C.; Nymeyer, H.; Onuchic, J. N. Topological and Energetic Factors: What Determines the Structural Details of the Transition State Ensemble and "En-route" Intermediates for Protein Folding? An Investigation for Small Globular Proteins J. Mol. Biol. 2000, 298, 937-953 10.1006/jmbi.2000.3693
77. Dokholyan, N. V.; Buldyrev, S. V.; Stanley, H. E.; Shakhnovich, E. I. Identifying the Protein Folding Nucleus Using Molecular Dynamics J. Mol. Biol. 2000, 296, 1183-1188 10.1006/jmbi.1999.3534
78. Ding, F.; Dokholyan, N. V.; Buldyrev, S. V.; Stanley, H. E.; Shakhnovich, E. I. Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble Biophys. J. 2002, 83, 3525-3532 10.1016/S0006-3495(02)75352-6
79. Dokholyan, N. V. Studies of Folding and Misfolding Using Simplified Models Curr. Opin. Struct. Biol. 2006, 16, 79-85 10.1016/j.sbi.2006.01.001
80. Dokholyan, N. V.; Shakhnovich, B.; Shakhnovich, E. I. Expanding Protein Universe and Its Origin from the Biological Big Bang Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 14132-14136 10.1073/pnas.202497999
81. Dokholyan, N. V. What Is the Protein Design Alphabet? Proteins: Struct.; Funct.; Genet. 2004, 54, 622-628 10.1002/prot.10633
82. Shakhnovich, E. I.; Finkelstein, A. V. Theory of Cooperative Transitions in Protein Molecules. I. Why Denaturation of Globular Protein Is a First-order Phase Transition Biopolymers 1989, 28, 1667-1680 10.1002/bip.360281003
83. Jackson, S. E.; Fersht, A. R. Folding of Chymotrypsin Inhibitor 2. 1. Evidence for a Two-state Transition Biochemistry 1991, 30, 10428-10435 10.1021/bi00107a010
84. Abkevich, V. I.; Gutin, A. M.; Shakhnovich, E. I. Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model Biochemistry 1994, 33, 10026-10036 10.1021/bi00199a029
85. Fersht, A. R. Optimization of Rates of Protein Folding: The Nucleation-condensation Mechanism and Its Implications Proc. Natl. Acad. Sci. U. S. A. 1995, 92, 10869-10873 10.1073/pnas.92.24.10869
86. Wolynes, P. G.; Onuchic, J. N.; Thirumalai, D. Navigating the Folding Routes Science 1995, 267, 1619-1620 10.1126/science.7886447
87. Shakhnovich, E.; Abkevich, V.; Ptitsyn, O. Conserved Residues and the Mechanism of Protein Folding Nature 1996, 379, 96-98 10.1038/379096a0
88. Chen, Y.; Ding, F.; Nie, H.; Serohijos, A. W.; Sharma, S.; Wilcox, K. C.; Yin, S.; Dokholyan, N. V. Protein Folding: Then and Now Arch. Biochem. Biophys. 2008, 469, 4-19 10.1016/j.abb.2007.05.014
89. Reichheld, S. E.; Yu, Z.; Davidson, A. R. The Induction of Folding Cooperativity by Ligand Binding Drives the Allosteric Response of Tetracycline Repressor Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 22263-22268 10.1073/pnas.0911566106
90. Hatley, M. E.; Lockless, S. W.; Gibson, S. K.; Gilman, A. G.; Ranganathan, R. Allosteric Determinants in Guanine Nucleotide-binding Proteins Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 14445-14450 10.1073/pnas.1835919100
91. Halabi, N.; Rivoire, O.; Leibler, S.; Ranganathan, R. Protein Sectors: Evolutionary Units of Three-dimensional Structure Cell 2009, 138, 774-786 10.1016/j.cell.2009.07.038
92. Reynolds, K. A.; McLaughlin, R. N.; Ranganathan, R. Hot Spots for Allosteric Regulation on Protein Surfaces Cell 2011, 147, 1564-1575 10.1016/j.cell.2011.10.049
93. Nussinov, R.; Ma, B.; Tsai, C. J. A Broad View of Scaffolding Suggests That Scaffolding Proteins Can Actively Control Regulation and Signaling of Multienzyme Complexes through Allostery Biochim. Biophys. Acta, Proteins Proteomics 2013, 1834, 820-829 10.1016/j.bbapap.2012.12.014
94. Nussinov, R.; Ma, B.; Tsai, C. J. Multiple Conformational Selection and Induced Fit Events Take Place in Allosteric Propagation Biophys. Chem. 2014, 186, 22-30 10.1016/j.bpc.2013.10.002
95. Zhuravleva, A.; Clerico, E. M.; Gierasch, L. M. An Interdomain Energetic Tug-of-war Creates the Allosterically Active State in Hsp70 Molecular Chaperones Cell 2012, 151, 1296-1307 10.1016/j.cell.2012.11.002
96. Fersht, A. R.; Matouschek, A.; Serrano, L. The Folding of an Enzyme. I. Theory of Protein Engineering Analysis of Stability and Pathway of Protein Folding J. Mol. Biol. 1992, 224, 771-782 10.1016/0022-2836(92)90561-W
97. Nauli, S.; Kuhlman, B.; Baker, D. Computer-based Redesign of a Protein Folding Pathway Nat. Struct. Biol. 2001, 8, 602-605 10.1038/89638
98. DeGrado, W. F.; Wasserman, Z. R.; Lear, J. D. Protein Design, a Minimalist Approach Science 1989, 243, 622-628 10.1126/science.2464850
99. Bryson, J. W.; Betz, S. F.; Lu, H. S.; Suich, D. J.; Zhou, H. X.; O'Neil, K. T.; DeGrado, W. F. Protein Design: a Hierarchic Approach Science 1995, 270, 935-941 10.1126/science.270.5238.935
100. Dahiyat, B. I.; Mayo, S. L. De Novo Protein Design: Fully Automated Sequence Selection Science 1997, 278, 82-87 10.1126/science.278.5335.82
101. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Design of a Novel Globular Protein Fold with Atomic-level Accuracy Science 2003, 302, 1364-1368 10.1126/science.1089427
102. Bak, P.; Tang, C.; Wiesenfeld, K. Self-organized Criticality: An Explanation of the 1/f Noise Phys. Rev. Lett. 1987, 59, 381-384 10.1103/PhysRevLett.59.381
103. Albert, R.; Jeong, H.; Barabasi, A. L. Error and Attack Tolerance of Complex Networks Nature 2000, 406, 378-382 10.1038/35019019
104. Amaral, L. A.; Scala, A.; Barthelemy, M.; Stanley, H. E. Classes of Small-world Networks Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 11149-11152 10.1073/pnas.200327197
105. Di Paola, L.; Giuliani, A. Protein Contact Network Topology: a Natural Language for Allostery Curr. Opin. Struct. Biol. 2015, 31, 43-48 10.1016/j.sbi.2015.03.001
106. Di Paola, L.; De Ruvo, M.; Paci, P.; Santoni, D.; Giuliani, A. Protein Contact Networks: An Emerging Paradigm in Chemistry Chem. Rev. 2013, 113, 1598-1613 10.1021/cr3002356
107. Rao, F.; Caflisch, A. The Protein Folding Network J. Mol. Biol. 2004, 342, 299-306 10.1016/j.jmb.2004.06.063
108. Serohijos, A. W.; Hegedus, T.; Riordan, J. R.; Dokholyan, N. V. Diminished Self-chaperoning Activity of the DeltaF508 Mutant of CFTR Results in Protein Misfolding PLoS Comput. Biol. 2008, 4, e1000008 10.1371/journal.pcbi.1000008
109. Fersht, A. R. Characterizing Transition States in Protein Folding: An Essential Step in the Puzzle Curr. Opin. Struct. Biol. 1995, 5, 79-84 10.1016/0959-440X(95)80012-P
110. Vendruscolo, M.; Paci, E.; Dobson, C. M.; Karplus, M. Three Key Residues Form a Critical Contact Network in a Protein Folding Transition State Nature 2001, 409, 641-645 10.1038/35054591
111. Cecconi, F.; Micheletti, C.; Carloni, P.; Maritan, A. Molecular Dynamics Studies on HIV-1 Protease Drug Resistance and Folding Pathways Proteins: Struct.; Funct.; Genet. 2001, 43, 365-372 10.1002/prot.1049
112. Blacklock, K.; Verkhivker, G. M. Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications PLoS Comput. Biol. 2014, 10, e1003679 10.1371/journal.pcbi.1003679
113. Chen, J.; Dima, R. I.; Thirumalai, D. Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back J. Mol. Biol. 2007, 374, 250-266 10.1016/j.jmb.2007.08.047
114. Gasper, P. M.; Fuglestad, B.; Komives, E. A.; Markwick, P. R.; McCammon, J. A. Allosteric Networks in Thrombin Distinguish Procoagulant Vs. Anticoagulant Activities Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 21216-21222 10.1073/pnas.1218414109
115. Allain, A.; Chauvot de Beauchêne, I.; Langenfeld, F.; Guarracino, Y.; Laine, E.; Tchertanov, L. Allosteric Pathway Identification through Network Analysis: From Molecular Dynamics Simulations to Interactive 2D and 3D Graphs Faraday Discuss. 2014, 169, 303-321 10.1039/C4FD00024B
116. Proctor, E. A.; Kota, P.; Aleksandrov, A. A.; He, L.; Riordan, J. R.; Dokholyan, N. V. Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator Chem. Sci. 2015, 6, 1237-1246 10.1039/C4SC01320D
117. Chen, Y.; Dokholyan, N. V. Insights into Allosteric Control of Vinculin Function from Its Large Scale Conformational Dynamics J. Biol. Chem. 2006, 281, 29148-29154 10.1074/jbc.M605512200
118. Sharma, S.; Ding, F.; Dokholyan, N. V. Multiscale Modeling of Nucleosome Dynamics Biophys. J. 2007, 92, 1457-1470 10.1529/biophysj.106.094805
119. Teotico, D. G.; Frazier, M. L.; Ding, F.; Dokholyan, N. V.; Temple, B. R.; Redinbo, M. R. Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions PLoS Comput. Biol. 2008, 4, e1000111 10.1371/journal.pcbi.1000111
120. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Essential Dynamics of Proteins Proteins: Struct.; Funct.; Genet. 1993, 17, 412-425 10.1002/prot.340170408
121. Dokholyan, N. V.; Lee, Y.; Buldyrev, S. V.; Havlin, S.; King, P. R.; Stanley, H. E. Scaling of the Distribution of Shortest Paths in Percolation J. Stat. Phys. 1998, 93, 603-613 10.1023/B:JOSS.0000033244.13545.da
122. Lee, Y.; Andrade, J. S.; Buldyrev, S. V.; Dokholyan, N. V.; Havlin, S.; King, P. R.; Paul, G.; Stanley, H. E. Traveling Time and Traveling Length in Critical Percolation Clusters Phys. Rev. E: Stat. Phys.; Plasmas, Fluids, Relat. Interdiscip. Top. 1999, 60, 3425-3428 10.1103/PhysRevE.60.3425
123. Dijkstra, E. W. A Note on Two Problems in Connexion with Graphs Numerische Mathematik 1959, 1, 269-271 10.1007/BF01386390
124. Sethi, A.; Eargle, J.; Black, A. A.; Luthey-Schulten, Z. Dynamical Networks in tRNA:protein Complexes Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 6620-6625 10.1073/pnas.0810961106
125. Bhattacharya, S.; Vaidehi, N. Differences in Allosteric Communication Pipelines in the Inactive and Active States of a GPCR Biophys. J. 2014, 107, 422-434 10.1016/j.bpj.2014.06.015
126. Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated Molecular Dynamics: a Promising and Efficient Simulation Method for Biomolecules J. Chem. Phys. 2004, 120, 11919-11929 10.1063/1.1755656
127. Markwick, P. R.; McCammon, J. A. Studying Functional Dynamics in Bio-molecules Using Accelerated Molecular Dynamics Phys. Chem. Chem. Phys. 2011, 13, 20053-20065 10.1039/c1cp22100k
128. Krammer, A.; Lu, H.; Isralewitz, B.; Schulten, K.; Vogel, V. Forced Unfolding of the Fibronectin Type III Module Reveals a Tensile Molecular Recognition Switch Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 1351-1356 10.1073/pnas.96.4.1351
129. Gao, M.; Craig, D.; Lequin, O.; Campbell, I. D.; Vogel, V.; Schulten, K. Structure and Functional Significance of Mechanically Unfolded Fibronectin Type III1 Intermediates Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 14784-14789 10.1073/pnas.2334390100
130. Autenrieth, F.; Tajkhorshid, E.; Schulten, K.; Luthey-Schulten, Z. Role of Water in Transient Cytochrome c2 Docking J. Phys. Chem. B 2004, 108, 20376-20387 10.1021/jp047994q
131. Aksimentiev, A.; Balabin, I. A.; Fillingame, R. H.; Schulten, K. Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase Biophys. J. 2004, 86, 1332-1344 10.1016/S0006-3495(04)74205-8
132. Amaro, R. E.; Sethi, A.; Myers, R. S.; Davisson, V. J.; Luthey-Schulten, Z. A. A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase Biochemistry 2007, 46, 2156-2173 10.1021/bi061708e
133. Dokholyan, N. V.; Buldyrev, S. V.; Stanley, H. E.; Shakhnovich, E. I. Discrete Molecular Dynamics Studies of the Folding of a Protein-like Model Folding Des. 1998, 3, 577-587 10.1016/S1359-0278(98)00072-8
134. Shirvanyants, D.; Ding, F.; Tsao, D.; Ramachandran, S.; Dokholyan, N. V. Discrete Molecular Dynamics: An Efficient and Versatile Simulation Method for Fine Protein Characterization J. Phys. Chem. B 2012, 116, 8375-8382 10.1021/jp2114576
135. Proctor, E.; Ding, F.; Dokholyan, N. Discrete Molecular Dynamics Comput. Mol. Sci. 2011, 1, 80-92 10.1002/wcms.4
136. Alder, B. J.; Wainwright, T. E. Studies in Molecular Dynamics. I. General Method J. Chem. Phys. 1959, 31, 459 10.1063/1.1730376
137. Zhou, Y.; Karplus, M. Folding Thermodynamics of a Model Three-helix-bundle Protein Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 14429-14432 10.1073/pnas.94.26.14429
138. Zhou, Y.; Karplus, M.; Wichert, J. M.; Hall, C. K. Equilibrium Thermodynamics of Homopolymers and Clusters: Molecular Dynamics and Monte Carlo Simulations of Systems with Square-well Interactions J. Chem. Phys. 1997, 107, 10691 10.1063/1.474186
139. Sfriso, P.; Emperador, A.; Gelpi, J. L.; Orozco, M. Discrete Molecular Dynamics: Foundations and Biomolecular Applications. Computational Approaches to Protein Dynamics; CRC Press: Boca Raton, FL, 2015; pp 339-362.
140. Sfriso, P.; Hospital, A.; Emperador, A.; Orozco, M. Exploration of Conformational Transition Pathways from Coarse-grained Simulations Bioinformatics 2013, 29, 1980-1986 10.1093/bioinformatics/btt324
141. Ding, F.; Buldyrev, S. V.; Dokholyan, N. V. Folding Trp-cage to NMR Resolution Native Structure Using a Coarse-grained Protein Model Biophys. J. 2005, 88, 147-155 10.1529/biophysj.104.046375
142. Ding, F.; Tsao, D.; Nie, H.; Dokholyan, N. V. Ab Initio Folding of Proteins with All-atom Discrete Molecular Dynamics Structure 2008, 16, 1010-1018 10.1016/j.str.2008.03.013
143. Kota, P.; Summers, D. W.; Ren, H. Y.; Cyr, D. M.; Dokholyan, N. V. Identification of a Consensus Motif in Substrates Bound by a Type I Hsp40 Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 11073-11078 10.1073/pnas.0900746106
144. Dagliyan, O.; Proctor, E. A.; D'Auria, K. M.; Ding, F.; Dokholyan, N. V. Structural and Dynamic Determinants of Protein-peptide Recognition Structure 2011, 19, 1837-1845 10.1016/j.str.2011.09.014
145. Kota, P.; García-Caballero, A.; Dang, H.; Gentzsch, M.; Stutts, M. J.; Dokholyan, N. V. Energetic and Structural Basis for Activation of the Epithelial Sodium Channel by Matriptase Biochemistry 2012, 51, 3460-3469 10.1021/bi2014773
146. Emperador, A.; Solernou, A.; Sfriso, P.; Pons, C.; Gelpi, J. L.; Fernandez-Recio, J.; Orozco, M. Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations J. Chem. Theory Comput. 2013, 9, 1222-1229 10.1021/ct301039e
147. Aleksandrov, A. A.; Kota, P.; Aleksandrov, L. A.; He, L.; Jensen, T.; Cui, L.; Gentzsch, M.; Dokholyan, N. V.; Riordan, J. R. Regulatory Insertion Removal Restores Maturation, Stability and Function of DeltaF508 CFTR J. Mol. Biol. 2010, 401, 194-210 10.1016/j.jmb.2010.06.019
148. Serohijos, A. W.; Chen, Y.; Ding, F.; Elston, T. C.; Dokholyan, N. V. A Structural Model Reveals Energy Transduction in Dynein Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 18540-18545 10.1073/pnas.0602867103
149. Serohijos, A. W.; Yin, S.; Ding, F.; Gauthier, J.; Gibson, D. G.; Maixner, W.; Dokholyan, N. V.; Diatchenko, L. Structural Basis for μ-Opioid Receptor Binding and Activation Structure 2011, 19, 1683-1690 10.1016/j.str.2011.08.003
150. Kota, P.; Buchner, G.; Chakraborty, H.; Dang, Y. L.; He, H.; Garcia, G. J.; Kubelka, J.; Gentzsch, M.; Stutts, M. J.; Dokholyan, N. V. The N-terminal Domain Allosterically Regulates Cleavage and Activation of the Epithelial Sodium Channel J. Biol. Chem. 2014, 289, 23029-23042 10.1074/jbc.M114.570952
151. Tasumi, M.; Takeuchi, H.; Ataka, S.; Dwivedi, A. M.; Krimm, S. Normal Vibrations of Proteins: Glucagon Biopolymers 1982, 21, 711-714 10.1002/bip.360210318
152. Levitt, M.; Sander, C.; Stern, P. S. The Normal Modes of a Protein: Native Bovine Pancreatic Trypsin Inhibitor Int. J. Quantum Chem. 1983, 24, 181-199 10.1002/qua.560240721
153. Go, N.; Noguti, T.; Nishikawa, T. Dynamics of a Small Globular Protein in Terms of Low-frequency Vibrational Modes Proc. Natl. Acad. Sci. U. S. A. 1983, 80, 3696-3700 10.1073/pnas.80.12.3696
154. Bahar, I.; Rader, A. J. Coarse-grained Normal Mode Analysis in Structural Biology Curr. Opin. Struct. Biol. 2005, 15, 586-592 10.1016/j.sbi.2005.08.007
155. Skjaerven, L.; Hollup, S. M.; Reuter, N. Normal Mode Analysis for Proteins J. Mol. Struct.: THEOCHEM 2009, 898, 42-48 10.1016/j.theochem.2008.09.024
156. Ma, J. Usefulness and Limitations of Normal Mode Analysis in Modeling Dynamics of Biomolecular Complexes Structure 2005, 13, 373-380 10.1016/j.str.2005.02.002
157. Rueda, M.; Chacón, P.; Orozco, M. Thorough Validation of Protein Normal Mode Analysis: a Comparative Study with Essential Dynamics Structure 2007, 15, 565-575 10.1016/j.str.2007.03.013
158. Mouawad, L.; Perahia, D. Diagonalization in a Mixed Basis: A Method to Compute Low-frequency Normal Modes for Large Macromolecules Biopolymers 1993, 33, 599-611 10.1002/bip.360330409
159. Marques, O.; Sanejouand, Y. H. Hinge-bending Motion in Citrate Synthase Arising from Normal Mode Calculations Proteins: Struct.; Funct.; Genet. 1995, 23, 557-560 10.1002/prot.340230410
160. Durand, P.; Trinquier, G.; Sanejouand, Y. A New Approach for Determining Low-Frequency Normal Modes in Macromolecules Biopolymers 1994, 34, 759-771 10.1002/bip.360340608
161. Tama, F.; Gadea, F. X.; Marques, O.; Sanejouand, Y. H. Building-block Approach for Determining Low-frequency Normal Modes of Macromolecules Proteins: Struct.; Funct.; Genet. 2000, 41, 1-7 10.1002/1097-0134(20001001)41:1<1::AID-PROT10>3.0.CO;2-P
162. Tirion, M. M. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis Phys. Rev. Lett. 1996, 77, 1905-1908 10.1103/PhysRevLett.77.1905
163. Hinsen, K. Analysis of Domain Motions by Approximate Normal Mode Calculations Proteins: Struct.; Funct.; Genet. 1998, 33, 417-429 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
164. Bahar, I.; Atilgan, A. R.; Erman, B. Direct Evaluation of Thermal Fluctuations in Proteins Using a Single-parameter Harmonic Potential Folding Des. 1997, 2, 173-181 10.1016/S1359-0278(97)00024-2
165. Haliloglu, T.; Bahar, I.; Erman, B. Gaussian Dynamics of Folded Proteins Phys. Rev. Lett. 1997, 79, 3090-3093 10.1103/PhysRevLett.79.3090
166. Atilgan, A. R.; Durell, S. R.; Jernigan, R. L.; Demirel, M. C.; Keskin, O.; Bahar, I. Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model Biophys. J. 2001, 80, 505-515 10.1016/S0006-3495(01)76033-X
167. Gur, M.; Zomot, E.; Bahar, I. Global Motions Exhibited by Proteins in Micro- to Milliseconds Simulations Concur with Anisotropic Network Model Predictions J. Chem. Phys. 2013, 139, 121912 10.1063/1.4816375
168. Vanwart, A. T.; Eargle, J.; Luthey-Schulten, Z.; Amaro, R. E. Exploring Residue Component Contributions to Dynamical Network Models of Allostery J. Chem. Theory Comput. 2012, 8, 2949-2961 10.1021/ct300377a
169. Su, J. G.; Qi, L. S.; Li, C. H.; Zhu, Y. Y.; Du, H. J.; Hou, Y. X.; Hao, R.; Wang, J. H. Prediction of Allosteric Sites on Protein Surfaces with an Elastic-network-model-based Thermodynamic Method Phys. Rev. E 2014, 90, 022719 10.1103/PhysRevE.90.022719
170. Chennubhotla, C.; Bahar, I. Markov Propagation of Allosteric Effects in Biomolecular Systems: Application to GroEL-GroES Mol. Syst. Biol. 2006, 2, 36 10.1038/msb4100075
171. Zheng, W.; Brooks, B. R.; Thirumalai, D. Low-frequency Normal Modes That Describe Allosteric Transitions in Biological Nanomachines Are Robust to Sequence Variations Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 7664-7669 10.1073/pnas.0510426103
172. Fenton, W. A.; Horwich, A. L. Chaperonin-mediated Protein Folding: Fate of Substrate Polypeptide Q. Rev. Biophys. 2003, 36, 229-256 10.1017/S0033583503003883
173. Saibil, H. R.; Ranson, N. A. The Chaperonin Folding Machine Trends Biochem. Sci. 2002, 27, 627-632 10.1016/S0968-0004(02)02211-9
174. Bukau, B.; Horwich, A. L. The Hsp70 and Hsp60 Chaperone Machines Cell 1998, 92, 351-366 10.1016/S0092-8674(00)80928-9
175. Chaudhry, C.; Farr, G. W.; Todd, M. J.; Rye, H. S.; Brunger, A. T.; Adams, P. D.; Horwich, A. L.; Sigler, P. B. Role of the Gamma-phosphate of ATP in Triggering Protein Folding by GroEL-GroES: Function, Structure and Energetics EMBO J. 2003, 22, 4877-4887 10.1093/emboj/cdg477
176. Yifrach, O.; Horovitz, A. Nested Cooperativity in the ATPase Activity of the Oligomeric Chaperonin GroEL Biochemistry 1995, 34, 5303-5308 10.1021/bi00016a001
177. Yifrach, O.; Horovitz, A. Mapping the Transition State of the Allosteric Pathway of GroEL by Protein Engineering J. Am. Chem. Soc. 1998, 120, 13262-13263 10.1021/ja983136u
178. Ma, J.; Karplus, M. The Allosteric Mechanism of the Chaperonin GroEL: a Dynamic Analysis Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 8502-8507 10.1073/pnas.95.15.8502
179. Ditzel, L.; Löwe, J.; Stock, D.; Stetter, K. O.; Huber, H.; Huber, R.; Steinbacher, S. Crystal Structure of the Thermosome, the Archaeal Chaperonin and Homolog of CCT Cell 1998, 93, 125-138 10.1016/S0092-8674(00)81152-6
180. Leitner, A.; Joachimiak, L. A.; Bracher, A.; Mönkemeyer, L.; Walzthoeni, T.; Chen, B.; Pechmann, S.; Holmes, S.; Cong, Y.; Ma, B.; Ludtke, S.; Chiu, W.; Hartl, F. U.; Aebersold, R.; Frydman, J. The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT Structure 2012, 20, 814-825 10.1016/j.str.2012.03.007
181. Dekker, C.; Roe, S. M.; McCormack, E. A.; Beuron, F.; Pearl, L. H.; Willison, K. R. The Crystal Structure of Yeast CCT Reveals Intrinsic Asymmetry of Eukaryotic Cytosolic Chaperonins EMBO J. 2011, 30, 3078-3090 10.1038/emboj.2011.208
182. Rivenzon-Segal, D.; Wolf, S. G.; Shimon, L.; Willison, K. R.; Horovitz, A. Sequential ATP-induced Allosteric Transitions of the Cytoplasmic Chaperonin Containing TCP-1 Revealed by EM Analysis Nat. Struct. Mol. Biol. 2005, 12, 233-237 10.1038/nsmb901
183. Koshland, D. E.; Némethy, G.; Filmer, D. Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits Biochemistry 1966, 5, 365-385 10.1021/bi00865a047
184. Keskin, O.; Bahar, I.; Flatow, D.; Covell, D. G.; Jernigan, R. L. Molecular Mechanisms of Chaperonin GroEL-GroES Function Biochemistry 2002, 41, 491-501 10.1021/bi011393x
185. Zheng, W.; Brooks, B. R.; Thirumalai, D. Allosteric Transitions in the Chaperonin GroEL Are Captured by a Dominant Normal Mode That Is Most Robust to Sequence Variations Biophys. J. 2007, 93, 2289-2299 10.1529/biophysj.107.105270
186. Chennubhotla, C.; Yang, Z.; Bahar, I. Coupling Between Global Dynamics and Signal Transduction Pathways: a Mechanism of Allostery for Chaperonin GroEL Mol. BioSyst. 2008, 4, 287-292 10.1039/b717819k
187. Tehver, R.; Chen, J.; Thirumalai, D. Allostery Wiring Diagrams in the Transitions That Drive the GroEL Reaction Cycle J. Mol. Biol. 2009, 387, 390-406 10.1016/j.jmb.2008.12.032
188. Jayasinghe, M.; Shrestha, P.; Wu, X.; Tehver, R.; Stan, G. Weak Intra-ring Allosteric Communications of the Archaeal Chaperonin Thermosome Revealed by Normal Mode Analysis Biophys. J. 2012, 103, 1285-1295 10.1016/j.bpj.2012.07.049
189. Doyle, D. A.; Lee, A.; Lewis, J.; Kim, E.; Sheng, M.; MacKinnon, R. Crystal Structures of a Complexed and Peptide-free Membrane Protein-binding Domain: Molecular Basis of Peptide Recognition by PDZ Cell 1996, 85, 1067-1076 10.1016/S0092-8674(00)81307-0
190. Süel, G. M.; Lockless, S. W.; Wall, M. A.; Ranganathan, R. Evolutionarily Conserved Networks of Residues Mediate Allosteric Communication in Proteins Nat. Struct. Biol. 2003, 10, 59-69 10.1038/nsb881
191. Dima, R. I.; Thirumalai, D. Determination of Network of Residues That Regulate Allostery in Protein Families Using Sequence Analysis Protein Sci. 2006, 15, 258-268 10.1110/ps.051767306
192. Fodor, A. A.; Aldrich, R. W. Influence of Conservation on Calculations of Amino Acid Covariance in Multiple Sequence Alignments Proteins: Struct.; Funct.; Genet. 2004, 56, 211-221 10.1002/prot.20098
193. Kass, I.; Horovitz, A. Mapping Pathways of Allosteric Communication in GroEL by Analysis of Correlated Mutations Proteins: Struct.; Funct.; Genet. 2002, 48, 611-617 10.1002/prot.10180
194. Atchley, W. R.; Wollenberg, K. R.; Fitch, W. M.; Terhalle, W.; Dress, A. W. Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis Mol. Biol. Evol. 2000, 17, 164-178 10.1093/oxfordjournals.molbev.a026229
195. Göbel, U.; Sander, C.; Schneider, R.; Valencia, A. Correlated Mutations and Residue Contacts in Proteins Proteins: Struct.; Funct.; Genet. 1994, 18, 309-317 10.1002/prot.340180402
196. Olmea, O.; Rost, B.; Valencia, A. Effective Use of Sequence Correlation and Conservation in Fold Recognition J. Mol. Biol. 1999, 293, 1221-1239 10.1006/jmbi.1999.3208
197. Fodor, A. A.; Aldrich, R. W. On Evolutionary Conservation of Thermodynamic Coupling in Proteins J. Biol. Chem. 2004, 279, 19046-19050 10.1074/jbc.M402560200
198. Marks, D. S.; Hopf, T. A.; Sander, C. Protein Structure Prediction from Sequence Variation Nat. Biotechnol. 2012, 30, 1072-1080 10.1038/nbt.2419
199. Marks, D. S.; Colwell, L. J.; Sheridan, R.; Hopf, T. A.; Pagnani, A.; Zecchina, R.; Sander, C. Protein 3D Structure Computed from Evolutionary Sequence Variation PLoS One 2011, 6, e28766 10.1371/journal.pone.0028766
200. Sukowska, J. I.; Morcos, F.; Weigt, M.; Hwa, T.; Onuchic, J. N. Genomics-aided Structure Prediction Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 10340-10345 10.1073/pnas.1207864109
201. Nugent, T.; Jones, D. T. Accurate de Novo Structure Prediction of Large Transmembrane Protein Domains Using Fragment-assembly and Correlated Mutation Analysis Proc. Natl. Acad. Sci. U. S. A. 2012, 109, E1540-E1547 10.1073/pnas.1120036109
202. Wollenberg, K. R.; Atchley, W. R. Separation of Phylogenetic and Functional Associations in Biological Sequences by Using the Parametric Bootstrap Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 3288-3291 10.1073/pnas.97.7.3288
203. Noivirt, O.; Eisenstein, M.; Horovitz, A. Detection and Reduction of Evolutionary Noise in Correlated Mutation Analysis Protein Eng.; Des. Sel. 2005, 18, 247-253 10.1093/protein/gzi029
204. Pei, J.; Dokholyan, N. V.; Shakhnovich, E. I.; Grishin, N. V. Using Protein Design for Homology Detection and Active Site Searches Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 11361-11366 10.1073/pnas.2034878100
205. Hudson, J. W.; Golding, G. B.; Crerar, M. M. Evolution of Allosteric Control in Glycogen Phosphorylase J. Mol. Biol. 1993, 234, 700-721 10.1006/jmbi.1993.1621
206. Jensen, A. A.; Spalding, T. A. Allosteric Modulation of G-protein Coupled Receptors Eur. J. Pharm. Sci. 2004, 21, 407-420 10.1016/j.ejps.2003.11.007
207. May, L. T.; Leach, K.; Sexton, P. M.; Christopoulos, A. Allosteric Modulation of G Protein-coupled Receptors Annu. Rev. Pharmacol. Toxicol. 2007, 47, 1-51 10.1146/annurev.pharmtox.47.120505.105159
208. Convertino, M.; Samoshkin, A.; Viet, C. T.; Gauthier, J.; Li Fraine, S. P.; Sharif-Naeini, R.; Schmidt, B. L.; Maixner, W.; Diatchenko, L.; Dokholyan, N. V. Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation PLoS One 2015, 10, e0142826 10.1371/journal.pone.0142826
209. Samoshkin, A.; Convertino, M.; Viet, C. T.; Wieskopf, J. S.; Kambur, O.; Marcovitz, J.; Patel, P.; Stone, L. S.; Kalso, E.; Mogil, J. S.; Schmidt, B. L.; Maixner, W.; Dokholyan, N. V.; Diatchenko, L. Structural and Functional Interactions Between Six-transmembrane M-opioid Receptors and B2-adrenoreceptors Modulate Opioid Signaling Sci. Rep. 2015, 5, 18198 10.1038/srep18198
210. Livesay, D. R.; Kreth, K. E.; Fodor, A. A. A Critical Evaluation of Correlated Mutation Algorithms and Coevolution Within Allosteric Mechanisms Methods Mol. Biol. 2012, 796, 385-398 10.1007/978-1-61779-334-9-21
211. Royer, W. E.; Knapp, J. E.; Strand, K.; Heaslet, H. A. Cooperative Hemoglobins: Conserved Fold, Diverse Quaternary Assemblies and Allosteric Mechanisms Trends Biochem. Sci. 2001, 26, 297-304 10.1016/S0968-0004(01)01811-4
212. Royer, W. E.; Zhu, H.; Gorr, T. A.; Flores, J. F.; Knapp, J. E. Allosteric Hemoglobin Assembly: Diversity and Similarity J. Biol. Chem. 2005, 280, 27477-27480 10.1074/jbc.R500006200
213. Kuriyan, J.; Eisenberg, D. The Origin of Protein Interactions and Allostery in Colocalization Nature 2007, 450, 983-990 10.1038/nature06524
214. Del Sol, A.; Tsai, C. J.; Ma, B.; Nussinov, R. The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways Structure 2009, 17, 1042-1050 10.1016/j.str.2009.06.008
215. Formaneck, M. S.; Ma, L.; Cui, Q. Reconciling the "Old" and "New" Views of Protein Allostery: a Molecular Simulation Study of Chemotaxis Y Protein (CheY) Proteins: Struct.; Funct.; Genet. 2006, 63, 846-867 10.1002/prot.20893
216. Liu, Z.; Chen, J.; Thirumalai, D. On the Accuracy of Inferring Energetic Coupling Between Distant Sites in Protein Families from Evolutionary Imprints: Illustrations Using Lattice Model Proteins: Struct.; Funct.; Genet. 2009, 77, 823-831 10.1002/prot.22498
217. Tang, S.; Liao, J. C.; Dunn, A. R.; Altman, R. B.; Spudich, J. A.; Schmidt, J. P. Predicting Allosteric Communication in Myosin via a Pathway of Conserved Residues J. Mol. Biol. 2007, 373, 1361-1373 10.1016/j.jmb.2007.08.059
218. Mittermaier, A.; Kay, L. E. New Tools Provide New Insights in NMR Studies of Protein Dynamics Science 2006, 312, 224-228 10.1126/science.1124964
219. Smock, R. G.; Gierasch, L. M. Sending Signals Dynamically Science 2009, 324, 198-203 10.1126/science.1169377
220. Nussinov, R.; Tsai, C. J. Allostery in Disease and in Drug Discovery Cell 2013, 153, 293-305 10.1016/j.cell.2013.03.034
221. Das, R.; Esposito, V.; Abu-Abed, M.; Anand, G. S.; Taylor, S. S.; Melacini, G. cAMP Activation of PKA Defines an Ancient Signaling Mechanism Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 93-98 10.1073/pnas.0609033103
222. Manley, G.; Loria, J. P. NMR Insights into Protein Allostery Arch. Biochem. Biophys. 2012, 519, 223-231 10.1016/j.abb.2011.10.023
223. Masterson, L. R.; Mascioni, A.; Traaseth, N. J.; Taylor, S. S.; Veglia, G. Allosteric Cooperativity in Protein Kinase A Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 506-511 10.1073/pnas.0709214104
224. Tzeng, S. R.; Kalodimos, C. G. Allosteric Inhibition through Suppression of Transient Conformational States Nat. Chem. Biol. 2013, 9, 462-465 10.1038/nchembio.1250
225. Shi, L.; Kay, L. E. Tracing an Allosteric Pathway Regulating the Activity of the HslV Protease Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 2140-2145 10.1073/pnas.1318476111
226. Clarkson, M. W.; Gilmore, S. A.; Edgell, M. H.; Lee, A. L. Dynamic Coupling and Allosteric Behavior in a Nonallosteric Protein Biochemistry 2006, 45, 7693-7699 10.1021/bi060652l
227. Fuentes, E. J.; Gilmore, S. A.; Mauldin, R. V.; Lee, A. L. Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein J. Mol. Biol. 2006, 364, 337-351 10.1016/j.jmb.2006.08.076
228. Cavalli, A.; Salvatella, X.; Dobson, C. M.; Vendruscolo, M. Protein Structure Determination from NMR Chemical Shifts Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9615-9620 10.1073/pnas.0610313104
229. Camilloni, C.; Robustelli, P.; De Simone, A.; Cavalli, A.; Vendruscolo, M. Characterization of the Conformational Equilibrium Between the Two Major Substates of RNase A Using NMR Chemical Shifts J. Am. Chem. Soc. 2012, 134, 3968-3971 10.1021/ja210951z
230. Robustelli, P.; Kohlhoff, K.; Cavalli, A.; Vendruscolo, M. Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins Structure 2010, 18, 923-933 10.1016/j.str.2010.04.016
231. Camilloni, C.; Cavalli, A.; Vendruscolo, M. Assessment of the Use of NMR Chemical Shifts as Replica-averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins J. Phys. Chem. B 2013, 117, 1838-1843 10.1021/jp3106666
232. De Simone, A.; Montalvao, R. W.; Dobson, C. M.; Vendruscolo, M. Characterization of the Interdomain Motions in Hen Lysozyme Using Residual Dipolar Couplings as Replica-averaged Structural Restraints in Molecular Dynamics Simulations Biochemistry 2013, 52, 6480-6486 10.1021/bi4007513
233. Best, R. B.; Vendruscolo, M. Structural Interpretation of Hydrogen Exchange Protection Factors in Proteins: Characterization of the Native State Fluctuations of CI2 Structure 2006, 14, 97-106 10.1016/j.str.2005.09.012
234. Dixon, R. D.; Chen, Y.; Ding, F.; Khare, S. D.; Prutzman, K. C.; Schaller, M. D.; Campbell, S. L.; Dokholyan, N. V. New Insights into FAK Signaling and Localization Based on Detection of a FAT Domain Folding Intermediate Structure 2004, 12, 2161-2171 10.1016/j.str.2004.09.011
235. Chen, Y.; Campbell, S. L.; Dokholyan, N. V. Deciphering Protein Dynamics from NMR Data Using Explicit Structure Sampling and Selection Biophys. J. 2007, 93, 2300-2306 10.1529/biophysj.107.104174
236. Grosman, C.; Zhou, M.; Auerbach, A. Mapping the Conformational Wave of Acetylcholine Receptor Channel Gating Nature 2000, 403, 773-776 10.1038/35001586
237. Mitra, A.; Tascione, R.; Auerbach, A.; Licht, S. Plasticity of Acetylcholine Receptor Gating Motions via Rate-energy Relationships Biophys. J. 2005, 89, 3071-3078 10.1529/biophysj.105.068783
238. Leffler, J. E. Parameters for the Description of Transition States Science 1953, 117, 340-341 10.1126/science.117.3039.340
239. Oliveberg, M.; Tan, Y. J.; Silow, M.; Fersht, A. R. The Changing Nature of the Protein Folding Transition State: Implications for the Shape of the Free-energy Profile for Folding J. Mol. Biol. 1998, 277, 933-943 10.1006/jmbi.1997.1612
240. Jackson, S. E. How Do Small Single-domain Proteins Fold? Folding Des. 1998, 3, R81-R91 10.1016/S1359-0278(98)00033-9
241. Salvatella, X.; Dobson, C. M.; Fersht, A. R.; Vendruscolo, M. Determination of the Folding Transition States of Barnase by Using PhiI-value-restrained Simulations Validated by Double Mutant PhiIJ-values Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 12389-12394 10.1073/pnas.0408226102
242. Hubner, I. A.; Edmonds, K. A.; Shakhnovich, E. I. Nucleation and the Transition State of the SH3 Domain J. Mol. Biol. 2005, 349, 424-434 10.1016/j.jmb.2005.03.050
243. Levy, Y.; Cho, S. S.; Onuchic, J. N.; Wolynes, P. G. A Survey of Flexible Protein Binding Mechanisms and Their Transition States Using Native Topology Based Energy Landscapes J. Mol. Biol. 2005, 346, 1121-1145 10.1016/j.jmb.2004.12.021
244. Matouschek, A.; Kellis, J. T.; Serrano, L.; Fersht, A. R. Mapping the Transition State and Pathway of Protein Folding by Protein Engineering Nature 1989, 340, 122-126 10.1038/340122a0
245. Matouschek, A.; Kellis, J. T.; Serrano, L.; Bycroft, M.; Fersht, A. R. Transient Folding Intermediates Characterized by Protein Engineering Nature 1990, 346, 440-445 10.1038/346440a0
246. Horovitz, A.; Amir, A.; Danziger, O.; Kafri, G. Phi Value Analysis of Heterogeneity in Pathways of Allosteric Transitions: Evidence for Parallel Pathways of ATP-induced Conformational Changes in a GroEL Ring Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 14095-14097 10.1073/pnas.222303299
247. Serohijos, A. W.; Hegedus, T.; Aleksandrov, A. A.; He, L.; Cui, L.; Dokholyan, N. V.; Riordan, J. R. Phenylalanine-508 Mediates a Cytoplasmic-membrane Domain Contact in the CFTR 3D Structure Crucial to Assembly and Channel Function Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 3256-3261 10.1073/pnas.0800254105
248. Hultqvist, G.; Haq, S. R.; Punekar, A. S.; Chi, C. N.; Engström, Å.; Bach, A.; Strømgaard, K.; Selmer, M.; Gianni, S.; Jemth, P. Energetic Pathway Sampling in a Protein Interaction Domain Structure 2013, 21, 1193-1202 10.1016/j.str.2013.05.010
249. Schreiber, G.; Fersht, A. R. Energetics of Protein-protein Interactions: Analysis of the Barnase-barstar Interface by Single Mutations and Double Mutant Cycles J. Mol. Biol. 1995, 248, 478-486 10.1016/S0022-2836(95)80064-6
250. Kohlstaedt, L. A.; Wang, J.; Friedman, J. M.; Rice, P. A.; Steitz, T. A. Crystal Structure at 3.5 A Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor Science 1992, 256, 1783-1790 10.1126/science.1377403
251. Oikonomakos, N. G.; Skamnaki, V. T.; Tsitsanou, K. E.; Gavalas, N. G.; Johnson, L. N. A New Allosteric Site in Glycogen Phosphorylase b as a Target for Drug Interactions Structure 2000, 8, 575-584 10.1016/S0969-2126(00)00144-1
252. Rath, V. L.; Ammirati, M.; Danley, D. E.; Ekstrom, J. L.; Gibbs, E. M.; Hynes, T. R.; Mathiowetz, A. M.; McPherson, R. K.; Olson, T. V.; Treadway, J. L.; Hoover, D. J. Human Liver Glycogen Phosphorylase Inhibitors Bind at a New Allosteric Site Chem. Biol. 2000, 7, 677-682 10.1016/S1074-5521(00)00004-1
253. Hardy, J. A.; Wells, J. A. Searching for New Allosteric Sites in Enzymes Curr. Opin. Struct. Biol. 2004, 14, 706-715 10.1016/j.sbi.2004.10.009
254. Hardy, J. A.; Lam, J.; Nguyen, J. T.; O'Brien, T.; Wells, J. A. Discovery of an Allosteric Site in the Caspases Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 12461-12466 10.1073/pnas.0404781101
255. Radley, T. L.; Markowska, A. I.; Bettinger, B. T.; Ha, J. H.; Loh, S. N. Allosteric Switching by Mutually Exclusive Folding of Protein Domains J. Mol. Biol. 2003, 332, 529-536 10.1016/S0022-2836(03)00925-2
256. Ha, J. H.; Butler, J. S.; Mitrea, D. M.; Loh, S. N. Modular Enzyme Design: Regulation by Mutually Exclusive Protein Folding J. Mol. Biol. 2006, 357, 1058-1062 10.1016/j.jmb.2006.01.073
257. Guntas, G.; Mitchell, S. F.; Ostermeier, M. A Molecular Switch Created by in Vitro Recombination of Nonhomologous Genes Chem. Biol. 2004, 11, 1483-1487 10.1016/j.chembiol.2004.08.020
258. Guntas, G.; Ostermeier, M. Creation of an Allosteric Enzyme by Domain Insertion J. Mol. Biol. 2004, 336, 263-273 10.1016/j.jmb.2003.12.016
259. Guntas, G.; Mansell, T. J.; Kim, J. R.; Ostermeier, M. Directed Evolution of Protein Switches and Their Application to the Creation of Ligand-binding Proteins Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 11224-11229 10.1073/pnas.0502673102
260. Choi, J. H.; Laurent, A. H.; Hilser, V. J.; Ostermeier, M. Design of Protein Switches Based on an Ensemble Model of Allostery Nat. Commun. 2015, 6, 6968 10.1038/ncomms7968
261. Tucker, C. L.; Fields, S. A Yeast Sensor of Ligand Binding Nat. Biotechnol. 2001, 19, 1042-1046 10.1038/nbt1101-1042
262. Karginov, A. V.; Zou, Y.; Shirvanyants, D.; Kota, P.; Dokholyan, N. V.; Young, D. D.; Hahn, K. M.; Deiters, A. Light Regulation of Protein Dimerization and Kinase Activity in Living Cells Using Photocaged Rapamycin and Engineered FKBP J. Am. Chem. Soc. 2011, 133, 420-423 10.1021/ja109630v
263. Liang, J.; Choi, J.; Clardy, J. Refined Structure of the FKBP12-rapamycin-FRB Ternary Complex at 2.2 A Resolution Acta Crystallogr.; Sect. D: Biol. Crystallogr. 1999, 55, 736-744 10.1107/S0907444998014747
264. Karginov, A. V.; Ding, F.; Kota, P.; Dokholyan, N. V.; Hahn, K. M. Engineered Allosteric Activation of Kinases in Living Cells Nat. Biotechnol. 2010, 28, 743-747 10.1038/nbt.1639
265. Chu, P. H.; Tsygankov, D.; Berginski, M. E.; Dagliyan, O.; Gomez, S. M.; Elston, T. C.; Karginov, A. V.; Hahn, K. M. Engineered Kinase Activation Reveals Unique Morphodynamic Phenotypes and Associated Trafficking for Src Family Isoforms Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 12420-12425 10.1073/pnas.1404487111
266. Brown, K. A.; Zou, Y.; Shirvanyants, D.; Zhang, J.; Samanta, S.; Mantravadi, P. K.; Dokholyan, N. V.; Deiters, A. Light-cleavable Rapamycin Dimer as an Optical Trigger for Protein Dimerization Chem. Commun. 2015, 51, 5702-5705 10.1039/C4CC09442E
267. Dagliyan, O.; Shirvanyants, D.; Karginov, A. V.; Ding, F.; Fee, L.; Chandrasekaran, S. N.; Freisinger, C. M.; Smolen, G. A.; Huttenlocher, A.; Hahn, K. M.; Dokholyan, N. V. Rational Design of a Ligand-controlled Protein Conformational Switch Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 6800-6804 10.1073/pnas.1218319110
268. Ding, F.; Dokholyan, N. V. Emergence of Protein Fold Families through Rational Design PLoS Comput. Biol. 2006, 2, e85 10.1371/journal.pcbi.0020085
269. Yin, S.; Ding, F.; Dokholyan, N. V. Modeling Backbone Flexibility Improves Protein Stability Estimation Structure 2007, 15, 1567-1576 10.1016/j.str.2007.09.024
270. Yin, S.; Ding, F.; Dokholyan, N. Eris: An Automated Estimator of Protein Stability Nat. Methods 2007, 4, 466-467 10.1038/nmeth0607-466
271. Holm, L. Unification of Protein Families Curr. Opin. Struct. Biol. 1998, 8, 372-379 10.1016/S0959-440X(98)80072-9
272. Holmes, K. C.; Sander, C.; Valencia, A. A New ATP-binding Fold in Actin, Hexokinase and Hsc70 Trends Cell Biol. 1993, 3, 53-59 10.1016/0962-8924(93)90161-S
273. Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. CATH - a Hierarchic Classification of Protein Domain Structures Structure 1997, 5, 1093-1108 10.1016/S0969-2126(97)00260-8
274. Dodge, C.; Schneider, R.; Sander, C. The HSSP Database of Protein Structure-sequence Alignments and Family Profiles Nucleic Acids Res. 1998, 26, 313-315 10.1093/nar/26.1.313
275. Sánchez, R.; Pieper, U.; Melo, F.; Eswar, N.; Martí-Renom, M. A.; Madhusudhan, M. S.; Mirković, N.; Sali, A. Protein Structure Modeling for Structural Genomics Nat. Struct. Biol. 2000, 7, 986-990 10.1038/80776
276. Pearl, F. M.; Lee, D.; Bray, J. E.; Sillitoe, I.; Todd, A. E.; Harrison, A. P.; Thornton, J. M.; Orengo, C. A. Assigning Genomic Sequences to CATH Nucleic Acids Res. 2000, 28, 277-282 10.1093/nar/28.1.277
277. Dalal, S.; Regan, L. Understanding the Sequence Determinants of Conformational Switching Using Protein Design Protein Sci. 2000, 9, 1651-1659 10.1110/ps.9.9.1651
278. Cordes, M. H.; Burton, R. E.; Walsh, N. P.; McKnight, C. J.; Sauer, R. T. An Evolutionary Bridge to a New Protein Fold Nat. Struct. Biol. 2000, 7, 1129-1132 10.1038/81985
279. Cordes, M. H.; Walsh, N. P.; McKnight, C. J.; Sauer, R. T. Evolution of a Protein Fold in Vitro Science 1999, 284, 325-327 10.1126/science.284.5412.325
280. Dokholyan, N. V. The Architecture of the Protein Domain Universe Gene 2005, 347, 199-206 10.1016/j.gene.2004.12.020
281. LeFevre, K. R.; Cordes, M. H. Retroevolution of Lambda Cro Toward a Stable Monomer Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 2345-2350 10.1073/pnas.0537925100
282. Dokholyan, N. V. Protein Designability and Engineering. In Structural Bioinformatics; Bourne, P. E.; Gu, J.; Eds.; Wiley & Sons: Hoboken, NJ, 2008; pp 961-982.
283. Dado, G. P.; Gellman, S. H. Redox Control of Secondary Structure in a Designed Peptide J. Am. Chem. Soc. 1993, 115, 12609-12610 10.1021/ja00079a060
284. Altman, M.; Lee, P.; Rich, A.; Zhang, S. Conformational Behavior of Ionic Self-complementary Peptides Protein Sci. 2000, 9, 1095-1105 10.1110/ps.9.6.1095
285. Cerpa, R.; Cohen, F. E.; Kuntz, I. D. Conformational Switching in Designed Peptides: The Helix/sheet Transition Folding Des. 1996, 1, 91-101 10.1016/S1359-0278(96)00018-1
286. Fezoui, Y.; Hartley, D. M.; Walsh, D. M.; Selkoe, D. J.; Osterhout, J. J.; Teplow, D. B. A de Novo Designed Helix-turn-helix Peptide Forms Nontoxic Amyloid Fibrils Nat. Struct. Biol. 2000, 7, 1095-1099 10.1038/81937
287. Grishin, N. V. Fold Change in Evolution of Protein Structures J. Struct. Biol. 2001, 134, 167-185 10.1006/jsbi.2001.4335
288. Lee, H. M.; Chmielewski, J. Liposomal Cargo Unloading Induced by pH-sensitive Peptides J. Pept. Res. 2005, 65, 355-363 10.1111/j.1399-3011.2005.00229.x
289. Li, W.; Nicol, F.; Szoka, F. C. GALA: a Designed Synthetic pH-responsive Amphipathic Peptide with Applications in Drug and Gene Delivery Adv. Drug Delivery Rev. 2004, 56, 967-985 10.1016/j.addr.2003.10.041
290. Mutter, M.; Gassmann, R.; Buttkus, U.; Altmann, K.-H. Switch Peptides: pH-Inducedα-Helix toβ-Sheet Transitions of Bis-amphiphilic Oligopeptides Angew. Chem.; Int. Ed. Engl. 1991, 30, 1514-1516 10.1002/anie.199115141
291. Ciani, B.; Hutchinson, E. G.; Sessions, R. B.; Woolfson, D. N. A Designed System for Assessing How Sequence Affects Alpha to Beta Conformational Transitions in Proteins J. Biol. Chem. 2002, 277, 10150-10155 10.1074/jbc.M107663200
292. Kammerer, R. A.; Kostrewa, D.; Zurdo, J.; Detken, A.; García-Echeverría, C.; Green, J. D.; Müller, S. A.; Meier, B. H.; Winkler, F. K.; Dobson, C. M.; Steinmetz, M. O. Exploring Amyloid Formation by a de Novo Design Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 4435-4440 10.1073/pnas.0306786101
293. Pagel, K.; Vagt, T.; Kohajda, T.; Koksch, B. From Alpha-helix to Beta-sheet - a Reversible Metal Ion Induced Peptide Secondary Structure Switch Org. Biomol. Chem. 2005, 3, 2500-2502 10.1039/b505979h
294. Cerasoli, E.; Sharpe, B. K.; Woolfson, D. N. ZiCo: a Peptide Designed to Switch Folded State Upon Binding Zinc J. Am. Chem. Soc. 2005, 127, 15008-15009 10.1021/ja0543604
295. Ambroggio, X. I.; Kuhlman, B. Computational Design of a Single Amino Acid Sequence That Can Switch Between Two Distinct Protein Folds J. Am. Chem. Soc. 2006, 128, 1154-1161 10.1021/ja054718w
296. Bullough, P. A.; Hughson, F. M.; Skehel, J. J.; Wiley, D. C. Structure of Influenza Haemagglutinin at the pH of Membrane Fusion Nature 1994, 371, 37-43 10.1038/371037a0
297. Elrod-Erickson, M.; Rould, M. A.; Nekludova, L.; Pabo, C. O. Zif268 protein-DNA Complex Refined at 1.6 A: a Model System for Understanding Zinc finger-DNA Interactions Structure 1996, 4, 1171-1180 10.1016/S0969-2126(96)00125-6
298. Kuhlman, B.; Baker, D. Native Protein Sequences Are Close to Optimal for Their Structures Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 10383-10388 10.1073/pnas.97.19.10383
299. Ambroggio, X. I.; Kuhlman, B. Design of Protein Conformational Switches Curr. Opin. Struct. Biol. 2006, 16, 525-530 10.1016/j.sbi.2006.05.014
300. Wright, C. M.; Heins, R. A.; Ostermeier, M. As Easy as Flipping a Switch? Curr. Opin. Chem. Biol. 2007, 11, 342-346 10.1016/j.cbpa.2007.04.011
301. Cross, P. J.; Allison, T. M.; Dobson, R. C.; Jameson, G. B.; Parker, E. J. Engineering Allosteric Control to an Unregulated Enzyme by Transfer of a Regulatory Domain Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 2111-2116 10.1073/pnas.1217923110
302. Curien, G.; Biou, V.; Mas-Droux, C.; Robert-Genthon, M.; Ferrer, J. L.; Dumas, R. Amino Acid Biosynthesis: New Architectures in Allosteric Enzymes Plant Physiol. Biochem. 2008, 46, 325-339 10.1016/j.plaphy.2007.12.006
303. Raman, S.; Taylor, N.; Genuth, N.; Fields, S.; Church, G. M. Engineering Allostery Trends Genet. 2014, 30, 521-528 10.1016/j.tig.2014.09.004
304. Dietrich, J. A.; Shis, D. L.; Alikhani, A.; Keasling, J. D. Transcription Factor-based Screens and Synthetic Selections for Microbial Small-molecule Biosynthesis ACS Synth. Biol. 2013, 2, 47-58 10.1021/sb300091d
305. Fowler, D. M.; Fields, S. Deep Mutational Scanning: a New Style of Protein Science Nat. Methods 2014, 11, 801-807 10.1038/nmeth.3027
306. Strickland, D.; Moffat, K.; Sosnick, T. R. Light-activated DNA Binding in a Designed Allosteric Protein Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 10709-10714 10.1073/pnas.0709610105
307. Salomon, M.; Eisenreich, W.; Dürr, H.; Schleicher, E.; Knieb, E.; Massey, V.; Rüdiger, W.; Müller, F.; Bacher, A.; Richter, G. An Optomechanical Transducer in the Blue Light Receptor Phototropin from Avena Sativa Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 12357-12361 10.1073/pnas.221455298
308. Cosentino, C.; Alberio, L.; Gazzarrini, S.; Aquila, M.; Romano, E.; Cermenati, S.; Zuccolini, P.; Petersen, J.; Beltrame, M.; Van Etten, J. L.; Christie, J. M.; Thiel, G.; Moroni, A. Optogenetics. Engineering of a Light-gated Potassium Channel Science 2015, 348, 707-710 10.1126/science.aaa2787
309. Lee, J.; Natarajan, M.; Nashine, V. C.; Socolich, M.; Vo, T.; Russ, W. P.; Benkovic, S. J.; Ranganathan, R. Surface Sites for Engineering Allosteric Control in Proteins Science 2008, 322, 438-442 10.1126/science.1159052
310. Riordan, J. R.; Rommens, J. M.; Kerem, B.; Alon, N.; Rozmahel, R.; Grzelczak, Z.; Zielenski, J.; Lok, S.; Plavsic, N.; Chou, J. L. et al. Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA Science 1989, 245, 1066-1073 10.1126/science.2475911
311. Quinton, P. M. Cystic Fibrosis: Lessons from the Sweat Gland Physiology 2007, 22, 212-225 10.1152/physiol.00041.2006
312. Davies, J. C.; Alton, E. W.; Bush, A. Cystic Fibrosis Br. Med. J. 2007, 335, 1255-1259 10.1136/bmj.39391.713229.AD
313. Riordan, J. R. CFTR Function and Prospects for Therapy Annu. Rev. Biochem. 2008, 77, 701-726 10.1146/annurev.biochem.75.103004.142532
314. Chong, P. A.; Kota, P.; Dokholyan, N. V.; Forman-Kay, J. D. Dynamics Intrinsic to Cystic Fibrosis Transmembrane Conductance Regulator Function and Stability Cold Spring Harbor Perspect. Med. 2013, 3, a009522 10.1101/cshperspect.a009522
315. He, L.; Aleksandrov, A. A.; An, J.; Cui, L.; Yang, Z.; Brouillette, C. G.; Riordan, J. R. Restoration of NBD1 Thermal Stability Is Necessary and Sufficient to Correct F508 CFTR Folding and Assembly J. Mol. Biol. 2015, 427, 106-120 10.1016/j.jmb.2014.07.026
316. Ding, F.; Dokholyan, N. V. Simple but Predictive Protein Models Trends Biotechnol. 2005, 23, 450-455 10.1016/j.tibtech.2005.07.001
317. Aleksandrov, A. A.; Kota, P.; Cui, L.; Jensen, T.; Alekseev, A. E.; Reyes, S.; He, L.; Gentzsch, M.; Aleksandrov, L. A.; Dokholyan, N. V.; Riordan, J. R. Allosteric Modulation Balances Thermodynamic Stability and Restores Function of F508 CFTR J. Mol. Biol. 2012, 419, 41-60 10.1016/j.jmb.2012.03.001
318. Nilsen, T. W. RNA 1997-2007: a Remarkable Decade of Discovery Mol. Cell 2007, 28, 715-720 10.1016/j.molcel.2007.11.017
319. Cruz, J. A.; Westhof, E. The Dynamic Landscapes of RNA Architecture Cell 2009, 136, 604-609 10.1016/j.cell.2009.02.003
320. Sharp, P. A. The Centrality of RNA Cell 2009, 136, 577-580 10.1016/j.cell.2009.02.007
321. Wan, Y.; Kertesz, M.; Spitale, R. C.; Segal, E.; Chang, H. Y. Understanding the Transcriptome through RNA Structure Nat. Rev. Genet. 2011, 12, 641-655 10.1038/nrg3049
322. Cech, T. R.; Steitz, J. A. The Noncoding RNA Revolution-trashing Old Rules to Forge New Ones Cell 2014, 157, 77-94 10.1016/j.cell.2014.03.008
323. Sharma, S.; Ding, F.; Nie, H.; Watson, D.; Unnithan, A.; Lopp, J.; Pozefsky, D.; Dokholyan, N. V. iFold: a Platform for Interactive Folding Simulations of Proteins Bioinformatics 2006, 22, 2693-2694 10.1093/bioinformatics/btl460
324. Gherghe, C. M.; Leonard, C. W.; Ding, F.; Dokholyan, N. V.; Weeks, K. M. Native-like RNA Tertiary Structures Using a Sequence-encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics J. Am. Chem. Soc. 2009, 131, 2541-2546 10.1021/ja805460e
325. Das, R.; Karanicolas, J.; Baker, D. Atomic Accuracy in Predicting and Designing Noncanonical RNA Structure Nat. Methods 2010, 7, 291-294 10.1038/nmeth.1433
326. Kladwang, W.; VanLang, C. C.; Cordero, P.; Das, R. A Two-dimensional Mutate-and-map Strategy for Non-coding RNA Structure Nat. Chem. 2011, 3, 954-962 10.1038/nchem.1176
327. Ding, F.; Lavender, C. A.; Weeks, K. M.; Dokholyan, N. V. Three-dimensional RNA Structure Refinement by Hydroxyl Radical Probing Nat. Methods 2012, 9, 603-608 10.1038/nmeth.1976
328. Zhao, Y.; Huang, Y.; Gong, Z.; Wang, Y.; Man, J.; Xiao, Y. Automated and Fast Building of Three-dimensional RNA Structures Sci. Rep. 2012, 2, 734 10.1038/srep00734
329. Sim, A. Y.; Minary, P.; Levitt, M. Modeling Nucleic Acids Curr. Opin. Struct. Biol. 2012, 22, 273-278 10.1016/j.sbi.2012.03.012
330. Karplus, M.; Weaver, D. L. Protein-folding Dynamics Nature 1976, 260, 404-406 10.1038/260404a0
331. Serohijos, A. W. R.; Yin, S. Y.; Ding, F.; Gauthier, J.; Gibson, D. G.; Maixner, W.; Dokholyan, N. V.; Diatchenko, L. Structural Basis for mu-Opioid Receptor Binding and Activation Structure 2011, 19, 1683-1690 10.1016/j.str.2011.08.003
332. Miao, Y.; Nichols, S. E.; Gasper, P. M.; Metzger, V. T.; McCammon, J. A. Activation and Dynamic Network of the M2Muscarinic Receptor Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 10982-10987 10.1073/pnas.1309755110
333. Dror, R. O.; Arlow, D. H.; Maragakis, P.; Mildorf, T. J.; Pan, A. C.; Xu, H.; Borhani, D. W.; Shaw, D. E. Activation Mechanism of the B2-adrenergic Receptor Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 18684-18689 10.1073/pnas.1110499108