Binding leverage as a molecular basis for allosteric regulation

PLoS Computational Biology

Volumn 7, Issue 9, 2011, Pages

  Mitternacht, Simon ^a   Berezovsky, Igor N ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CONFORMATIONS; ENZYMES; INTELLIGENT SYSTEMS; MONTE CARLO METHODS; SINGLE CRYSTALS;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; BINDING-SITES; CONFORMATIONAL FLUCTUATIONS; CONFORMATIONAL TRANSITIONS; INTRINSIC MOTIONS; MOLECULAR BASIS; MONTE CARLO'S SIMULATION; NORMAL MODES; POTENTIAL BINDING SITES;

CRYSTAL STRUCTURE;

ADENYLATE KINASE; CYCLIC AMP DEPENDENT PROTEIN KINASE; PROTEIN;

ALLOSTERISM; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ANALYSIS; MONTE CARLO METHOD; PREDICTION; PROTEIN BINDING; PROTEIN DOMAIN; SIMULATION; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; PROTEIN CONFORMATION;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; DRUG DESIGN; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEINS;

EID: 80053440006     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002148     Document Type: Article

References (63)

1. Monod J, Wyman J, Changeux JP, (1965) On the Nature of Allosteric Transitions: A Plausible Model. J Mol Biol 12: 88-118.
2. Koshland DE Jr, Nemethy G, Filmer D, (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5: 365-385.
3. Changeux JP, Edelstein SJ, (2005) Allosteric mechanisms of signal transduction. Science 308: 1424-1428.
4. Weber G, (1972) Ligand binding and internal equilibria in proteins. Biochemistry 11: 864-878.
5. Gunasekaran K, Ma B, Nussinov R, (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57: 433-443.
6. Bahar I, Chennubhotla C, Tobi D, (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 17: 633-640.
7. Cui Q, Karplus M, (2008) Allostery and cooperativity revisited. Protein Sci 17: 1295-1307.
8. Liu T, Whitten ST, Hilser VJ, (2007) Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci U S A 104: 4347-4352.
9. Atilgan C, Atilgan AR, (2009) Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput Biol 5: e1000544.
10. Ferreiro DU, Hegler JA, Komives EA, Wolynes PG, (2011) On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A 108: 3499-3503.
11. Cooper A, Dryden DT, (1984) Allostery without conformational change. A plausible model. Eur Biophys J 11: 103-109.
12. Ming D, Wall ME, (2005) Quantifying allosteric effects in proteins. Proteins 59: 697-707.
13. Toncrova H, McLeish TC, (2010) Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP. Biophys J 98: 2317-2326.
14. Ma J, (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13: 373-380.
15. Bahar I, Rader AJ, (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15: 586-592.
16. Chennubhotla C, Bahar I, (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol 2: 36.
17. Yang LW, Bahar I, (2005) Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 13: 893-904.
18. Lockless SW, Ranganathan R, (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
19. Smock RG, Gierasch LM, (2009) Sending signals dynamically. Science 324: 198-203.
20. Tehver R, Chen J, Thirumalai D, (2009) Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle. J Mol Biol 387: 390-406.
21. del Sol A, Tsai CJ, Ma B, Nussinov R, (2009) The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 17: 1042-1050.
22. Kern D, Zuiderweg ER, (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13: 748-757.
23. Bahar I, Lezon TR, Yang LW, Eyal E, (2010) Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 39: 23-42.
24. Popovych N, Sun S, Ebright RH, Kalodimos CG, (2006) Dynamically driven protein allostery. Nat Struct Mol Biol 13: 831-838.
25. Hardy JA, Wells JA, (2004) Searching for new allosteric sites in enzymes. Curr Opin Struct Biol 14: 706-715.
26. Goodey NM, Benkovic SJ, (2008) Allosteric regulation and catalysis emerge via a common route. Nat Chem Biol 4: 474-482.
27. Miyashita O, Onuchic JN, Wolynes PG, (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A 100: 12570-12575.
28. Hammes GG, Chang YC, Oas TG, (2009) Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci U S A 106: 13737-13741.
29. Okazaki K, Takada S, (2008) Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms. Proc Natl Acad Sci U S A 105: 11182-11187.
30. Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
31. Porter CT, Bartlett GJ, Thornton JM, (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-133.
32. Slama P, Filippis I, Lappe M, (2008) Detection of protein catalytic residues at high precision using local network properties. BMC Bioinformatics 9: 517.
33. Mitternacht S, Berezovsky IN, (2011) A geometry-based generic predictor for catalytic and allosteric sites. Protein Eng Des Sel 24: 405-409.
34. Bruschweiler R, (1995) Collective Protein Dynamics and Nuclear-Spin Relaxation. Journal of Chemical Physics 102: 3396-3403.
35. Miles EW, Rhee S, Davies DR, (1999) The molecular basis of substrate channeling. J Biol Chem 274: 12193-12196.
36. Barends TR, Dunn MF, Schlichting I, (2008) Tryptophan synthase, an allosteric molecular factory. Curr Opin Chem Biol 12: 593-600.
37. Spraggon G, Kim C, Nguyen-Huu X, Yee MC, Yanofsky C, et al. (2001) The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Proc Natl Acad Sci U S A 98: 6021-6026.
38. Mouilleron S, Golinelli-Pimpaneau B, (2007) Conformational changes in ammonia-channeling glutamine amidotransferases. Curr Opin Struct Biol 17: 653-664.
39. Arora K, Brooks CL 3rd, (2007) Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A 104: 18496-18501.
40. Taylor SS, Yang J, Wu J, Haste NM, Radzio-Andzelm E, et al. (2004) PKA: a portrait of protein kinase dynamics. Biochim Biophys Acta 1697: 259-269.
41. Masterson LR, Mascioni A, Traaseth NJ, Taylor SS, Veglia G, (2008) Allosteric cooperativity in protein kinase A. Proc Natl Acad Sci U S A 105: 506-511.
42. Wolf-Watz M, Thai V, Henzler-Wildman K, Hadjipavlou G, Eisenmesser EZ, et al. (2004) Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat Struct Mol Biol 11: 945-949.
43. Hanson JA, Duderstadt K, Watkins LP, Bhattacharyya S, Brokaw J, et al. (2007) Illuminating the mechanistic roles of enzyme conformational dynamics. Proc Natl Acad Sci U S A 104: 18055-18060.
44. Daily MD, Phillips GN Jr, Cui Q, (2010) Many local motions cooperate to produce the adenylate kinase conformational transition. J Mol Biol 400: 618-631.
45. Whitford PC, Gosavi S, Onuchic JN, (2008) Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. J Biol Chem 283: 2042-2048.
46. Masterson LR, Cheng C, Yu T, Tonelli M, Kornev A, et al. (2010) Dynamics connect substrate recognition to catalysis in protein kinase A. Nat Chem Biol 6: 821-828.
47. Tama F, Sanejouand YH, (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14: 1-6.
48. Wiesmann C, Barr KJ, Kung J, Zhu J, Erlanson DA, et al. (2004) Allosteric inhibition of protein tyrosine phosphatase 1B. Nat Struct Mol Biol 11: 730-737.
49. Curien G, Job D, Douce R, Dumas R, (1998) Allosteric activation of Arabidopsis threonine synthase by S-adenosylmethionine. Biochemistry 37: 13212-13221.
50. Mas-Droux C, Biou V, Dumas R, (2006) Allosteric threonine synthase. Reorganization of the pyridoxal phosphate site upon asymmetric activation through S-adenosylmethionine binding to a novel site. J Biol Chem 281: 5188-5196.
51. Smith TJ, Stanley CA, (2008) Untangling the glutamate dehydrogenase allosteric nightmare. Trends Biochem Sci 33: 557-564.
52. Singh N, Maniscalco SJ, Fisher HF, (1993) The real-time resolution of proton-related transient-state steps in an enzymatic reaction. The early steps in the oxidative deamination reaction of bovine liver glutamate dehydrogenase. J Biol Chem 268: 21-28.
53. Banerjee S, Schmidt T, Fang J, Stanley CA, Smith TJ, (2003) Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation. Biochemistry 42: 3446-3456.
54. Smith TJ, Schmidt T, Fang J, Wu J, Siuzdak G, et al. (2002) The structure of apo human glutamate dehydrogenase details subunit communication and allostery. J Mol Biol 318: 765-777.
55. Li M, Smith CJ, Walker MT, Smith TJ, (2009) Novel inhibitors complexed with glutamate dehydrogenase: allosteric regulation by control of protein dynamics. J Biol Chem 284: 22988-23000.
56. Schirmer T, Evans PR, (1990) Structural basis of the allosteric behaviour of phosphofructokinase. Nature 343: 140-145.
57. Valdez BC, French BA, Younathan ES, Chang SH, (1989) Site-directed mutagenesis in Bacillus stearothermophilus fructose-6-phosphate 1-kinase. Mutation at the substrate-binding site affects allosteric behavior. J Biol Chem 264: 131-135.
58. Evans PR, Farrants GW, Hudson PJ, (1981) Phosphofructokinase: structure and control. Philos Trans R Soc Lond B Biol Sci 293: 53-62.
59. Harman JG, (2001) Allosteric regulation of the cAMP receptor protein. Biochim Biophys Acta 1547: 1-17.
60. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E, (1953) Equation of State Calculations by Fast Computing Machines. J Chem Phys 21: 1087-1092.
61. Hinsen K, (2000) The molecular modeling toolkit: A new approach to molecular simulations. J Comput Chem 21: 79-85.
62. Sanejouand Y, (2006) Functional information from slow mode shapes. In: Cui Q, Bahar I, editors. Normal mode analysis: Theory and applications to biological and chemical systems London Chapman & Hall/CRC pp. 91-110.
63. Daily MD, Gray JJ, (2007) Local motions in a benchmark of allosteric proteins. Proteins 67: 385-399.