Coherent conformational degrees of freedom as a structural basis for allosteric communication

PLoS Computational Biology

Volumn 7, Issue 12, 2011, Pages

  Mitternacht, Simon ^a   Berezovsky, Igor N ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; DEGREES OF FREEDOM (MECHANICS); LIGANDS;

ALLOSTERIC COMMUNICATION; ALLOSTERIC REGULATION; BINDING-SITES; CONFORMATIONAL CHANGE; CONFORMATIONAL DEGREES OF FREEDOM; CONFORMATIONAL EQUILIBRIUM; LIGAND BINDING; MOTION VECTORS; POST-TRANSLATIONAL MODIFICATIONS; STRUCTURAL BASIS;

PROTEINS;

CHAPERONE; ENZYME; PROTEIN;

ALLOSTERISM; ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; LIGAND BINDING; MATHEMATICAL MODEL; METAL BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; BINDING SITES; ENZYMES; MODELS, MOLECULAR; MOLECULAR CHAPERONES; MOLECULAR CONFORMATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS;

EID: 84855283469     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002301     Document Type: Article

References (42)

1. Pauling L, (1935) The Oxygen Equilibrium of Hemoglobin and Its Structural Interpretation. Proc Natl Acad Sci U S A 21: 186-191.
2. Monod J, Jacob F, (1961) Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb Symp Quant Biol 26: 389-401.
3. Monod J, Wyman J, Changeux JP, (1965) On the Nature of Allosteric Transitions: A Plausible Model. J Mol Biol 12: 88-118.
4. Koshland DE Jr, Nemethy G, Filmer D, (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5: 365-385.
5. Smock RG, Gierasch LM, (2009) Sending signals dynamically. Science 324: 198-203.
6. Hilser VJ, (2010) Biochemistry. An ensemble view of allostery. Science 327: 653-654.
7. Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450: 913-916.
8. Henzler-Wildman K, Kern D, (2007) Dynamic personalities of proteins. Nature 450: 964-972.
9. Cui Q, Karplus M, (2008) Allostery and cooperativity revisited. Protein Sci 17: 1295-1307.
10. Cecchini M, Houdusse A, Karplus M, (2008) Allosteric communication in myosin V: from small conformational changes to large directed movements. PLoS Comput Biol 4: e1000129.
11. Chennubhotla C, Bahar I, (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol 2: 36.
12. Skjaerven L, Grant B, Muga A, Teigen K, McCammon JA, et al. (2011) Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations. PLoS Comput Biol 7: e1002004.
13. Weber G, (1972) Ligand binding and internal equilibria in proteins. Biochemistry 11: 864-878.
14. 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.
15. Mitternacht S, Berezovsky IN, (2011) Binding leverage as a molecular basis for allosteric regulation. PLoS Comput Biol 7: e1002148.
16. Changeux JP, Edelstein SJ, (2005) Allosteric mechanisms of signal transduction. Science 308: 1424-1428.
17. Bahar I, Rader AJ, (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 15: 586-592.
18. Ma J, (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13: 373-380.
19. Mitternacht S, Berezovsky IN, (2011) A geometry-based generic predictor for catalytic and allosteric sites. Protein Eng Des Sel 24: 405-409.
20. Yoneyama T, Brewer JM, Hatakeyama K, (1997) GTP cyclohydrolase I feedback regulatory protein is a pentamer of identical subunits. Purification, cDNA cloning, and bacterial expression. J Biol Chem 272: 9690-9696.
21. Yoneyama T, Hatakeyama K, (1998) Decameric GTP cyclohydrolase I forms complexes with two pentameric GTP cyclohydrolase I feedback regulatory proteins in the presence of phenylalanine or of a combination of tetrahydrobiopterin and GTP. J Biol Chem 273: 20102-20108.
22. Johnson LN, (1992) Glycogen phosphorylase: control by phosphorylation and allosteric effectors. FASEB J 6: 2274-2282.
23. Di Cera E, Page MJ, Bah A, Bush-Pelc LA, Garvey LC, (2007) Thrombin allostery. Phys Chem Chem Phys 9: 1291-1306.
24. Horwich AL, Fenton WA, Chapman E, Farr GW, (2007) Two families of chaperonin: physiology and mechanism. Annu Rev Cell Dev Biol 23: 115-145.
25. 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.
26. 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.
27. Johnson LN, Barford D, (1993) The effects of phosphorylation on the structure and function of proteins. Annu Rev Biophys Biomol Struct 22: 199-232.
28. Johnson LN, Oreilly M, (1996) Control by phosphorylation. Curr Opin Struct Biol 6: 762-769.
29. Chaudhry C, Horwich AL, Brunger AT, Adams PD, (2004) Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol 342: 229-245.
30. Gray TE, Fersht AR, (1991) Cooperativity in ATP hydrolysis by GroEL is increased by GroES. FEBS Lett 292: 254-258.
31. Ranson NA, Clare DK, Farr GW, Houldershaw D, Horwich AL, et al. (2006) Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Nat Struct Mol Biol 13: 147-152.
32. Weissman JS, Rye HS, Fenton WA, Beechem JM, Horwich AL, (1996) Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction. Cell 84: 481-490.
33. Rye HS, Burston SG, Fenton WA, Beechem JM, Xu Z, et al. (1997) Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature 388: 792-798.
34. Rye HS, Roseman AM, Chen S, Furtak K, Fenton WA, et al. (1999) GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings. Cell 97: 325-338.
35. Ranson NA, Farr GW, Roseman AM, Gowen B, Fenton WA, et al. (2001) ATP-bound states of GroEL captured by cryo-electron microscopy. Cell 107: 869-879.
36. Sewell BT, Best RB, Chen S, Roseman AM, Farr GW, et al. (2004) A mutant chaperonin with rearranged inter-ring electrostatic contacts and temperature-sensitive dissociation. Nat Struct Mol Biol 11: 1128-1133.
37. Rivenzon-Segal D, Wolf SG, Shimon L, Willison KR, Horovitz A, (2005) Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis. Nat Struct Mol Biol 12: 233-237.
38. Yebenes H, Mesa P, Munoz IG, Montoya G, Valpuesta JM, (2011) Chaperonins: two rings for folding. Trends Biochem Sci 36: 424-432.
39. Ma J, Sigler PB, Xu Z, Karplus M, (2000) A dynamic model for the allosteric mechanism of GroEL. J Mol Biol 302: 303-313.
40. Chennubhotla C, Yang Z, Bahar I, (2008) Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol Biosyst 4: 287-292.
41. Hinsen K, (2000) The molecular modeling toolkit: A new approach to molecular simulations. J Comput Chem 21: 79-85.
42. Hinsen K, (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33: 417-429.