Contact rearrangements form coupled networks from local motions in allosteric proteins

Proteins: Structure, Function and Genetics

Volumn 71, Issue 1, 2008, Pages 455-466

  Daily, Michael D ^a   Upadhyaya, Tarak J ^b   Gray, Jeffrey J ^a,c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b USA   (United States)

^c Johns Hopkins University   (United States)

Author keywords

Allosteric mechanism; Conformational change; Graph theory; Signal propagation; Small world network

Indexed keywords

MUTANT PROTEIN; PROTEIN;

ALLOSTERISM; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; MOTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; METABOLIC NETWORKS AND PATHWAYS; MODELS, CHEMICAL; MOTION; PROTEINS;

EID: 40549084038     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21800     Document Type: Article

References (55)

1. Berg JM, Tymoczko JL, Stryer L. Biochemistry. New York: W.H. Freeman; 2002.
2. Monod J, Changeux JP, Jacob F. Allosteric proteins and cellular control systems. J Mol Biol 1963;6:306-329.
3. Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000;9:10-19.
4. Luque I, Leavitt SA, Freire E. The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu Rev Biophys Biomol Struct 2002;31:235-256.
5. Gunasekaran K, Ma B, Nussinov R. Is allostery an intrinsic property of all dynamic proteins? Proteins 2004;57:433-443.
6. Kern D, Zuiderweg ER. The role of dynamics in allosteric regulation. Curr Opin Struct Biol 2003;13:748-757.
7. Yu EW, Koshland DE, Jr. Propagating conformational changes over long (and short) distances in proteins. Proc Natl Acad Sci USA 2001;98:9517-9520.
8. Formaneck MS, Ma L, Cui Q. Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins 2006;63:846-867.
9. Jardetzky O. Protein dynamics and conformational transitions in allosteric proteins. Prog Biophys Mol Biol 1996;65:171-219.
10. Daily MD, Gray JJ. Local motions in a benchmark of allosteric proteins. Proteins 2007;67:385-399.
11. Koshland DE, Jr, Nemethy G, Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 1966;5:365-385.
12. Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 2005;102:18908-18913.
13. Zheng W, Brooks B. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J Mol Biol 2005;346:745-759.
14. Banavali NK, Roux B. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins 2007;67:1096-1112.
15. Liu T, Whitten ST, Hilser VJ. Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins 2006;62:728-738.
16. Lu G, Giroux EL, Kantrowitz ER. Importance of the dimer-dimer interface for allosteric signal transduction and AMP cooperativity of pig kidney fructose-1,6-bisphosphatase. Site-specific mutagenesis studies of Glu-192 and Asp-187 residues on the 190's loop. J Biol Chem 1997;272:5076-5081.
17. Barrick D, Ho NT, Simplaceanu V, Dahlquist FW, Ho C. A test of the role of the proximal histidines in the Perutz model for cooperativity in haemoglobin. Nat Struct Biol 1997;4:78-83.
18. Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998;393:440-442.
19. Greene LH, Higman VA. Uncovering network systems within protein structures. J Mol Biol 2003;334:781-791.
20. Vendruscolo M, Dokholyan NV, Paci E, Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys Rev E Stat Nonlin Soft Matter Phys 2002;65(6, Part 1):061910.
21. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S. Network analysis of protein structures identifies functional residues. J Mol Biol 2004;344:1135-1146.
22. Thibert B, Bredesen DE, del Rio G. Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 2005;6:213.
23. del Sol A, O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2005;58:672-682.
24. del Sol A, Fujihashi H, Amoros D, Nussinov R. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol 2006;2:2006.0019.
25. Swint-Kruse L. Using networks to identify fine structural differences between functionally distinct protein states. Biochemistry 2004;43:10886-10895.
26. Srinivasan R, Rose GD. The T-to-R transformation in hemoglobin: a reevaluation. Proc Natl Acad Sci USA 1994;91:11113-11117.
27. Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
28. Gu J, Bourne PE. Identifying allosteric fluctuation transitions between different protein conformational states as applied to cyclin dependent kinase 2. BMC Bioinformatics 2007;8:45.
29. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The protein data bank. Acta Crystallogr D Biol Crystallogr 2002;58 (Part 6):899-907.
30. Watts DJ. Small worlds: the dynamics of networks between order and randomness. Princeton, NJ: Princeton University Press; 1999. xv, 262 pp.
31. Albert R, Jeong H, Barabasi AL. Error and attack tolerance of complex networks. Nature 2000;406:378-382.
32. Erdos P, Renyi A. On the evolution of random graphs. Publ Math Inst Hung Acad Sci 1960;5:17-61.
33. Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999;286:509-512.
34. Amaral LA, Scala A, Barthelemy M, Stanley HE. Classes of small-world networks. Proc Natl Acad Sci USA 2000;97:11149-11152.
35. Gidh-Jain M, Zhang Y, van Poelje PD, Liang JY, Huang S, Kim J, Elliott JT, Erion MD, Pilkis SJ, Raafat el-Maghrabi M. The allosteric site of human liver fructose-1,6-bisphosphatase. Analysis of six AMP site mutants based on the crystal structure. J Biol Chem 1994;269:27732-27738.
36. De Staercke C, Van Vliet F, Xi XG, Rani CS, Ladjimi M, Jacobs A, Triniolles F, Herve G, Cunin R. Intramolecular transmission of the ATP regulatory signal in Escherichia coli aspartate transcarbamylase: specific involvement of a clustered set of amino acid interactions at an interface between regulatory and catalytic subunits. J Mol Biol 1995;246:132-143.
37. Kimmel JL, Reinhart GD. Reevaluation of the accepted allosteric mechanism of phosphofructokinase from Bacillus stearothermophilus. Proc Natl Acad Sci USA 2000;97:3844-3849.
38. Samuels ML, Witmer JA. Statistics for the life sciences. Upper Saddle River, NJ: Prentice Hall; 2003.
39. Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286:295-299.
40. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R. Evolutionary information for specifying a protein fold. Nature 2005;437:512-518.
41. Fuentes EJ, Der CJ, Lee AL. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J Mol Biol 2004;335:1105-1115.
42. Clarkson MW, Gilmore SA, Edgell MH, Lee AL. Dynamic coupling and allosteric behavior in a nonallosteric protein. Biochemistry 2006;45:7693-7699.
43. Ota N, Agard DA. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol 2005;351:345-354.
44. Ke HM, Lipscomb WN, Cho YJ, Honzatko RB. Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms. J Mol Biol 1988;204:725-747.
45. Barford D, Hu SH, Johnson LN. Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP. J Mol Biol 1991;218:233-260.
46. Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ. Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase. Biochemistry 2005;44:5763-5773.
47. Monod J, Wyman J, Changeux JP. On the nature of allosteric transitions: a plausible model. J Mol Biol 1965;12:88-118.
48. Chennubhotla C, Bahar I. Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol 2006;2:36.
49. Eyal E, Gerzon S, Potapov V, Edelman M, Sobolev V. The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J Mol Biol 2005;351:431-442.
50. Cormen TH. Introduction to algorithms. Cambridge, MA: MIT Press; 2001.
51. Beauchamp MA. An improved index of centrality. Behav Sci 1965;10:161-163.
52. Sabidussi G. The centrality of a graph. Psychometrika 1966;31:581-603.
53. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res 2006;34(Database Issue):D247-D251.
54. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 2003;31:3497-3500.
55. Pei J, Sadreyev R, Grishin NV. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 2003;19:427-428.