Dynamically driven protein allostery

Nature Structural and Molecular Biology

Volumn 13, Issue 9, 2006, Pages 831-838

  Popovych, Nataliya ^a   Sun, Shangjin ^a   Ebright, Richard H ^b   Kalodimos, Charalampos G ^a  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP; CYCLIC AMP BINDING PROTEIN;

ALLOSTERISM; ARTICLE; ENTROPY; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; THERMODYNAMICS;

ALLOSTERIC REGULATION; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; ENTROPY; ESCHERICHIA COLI; MODELS, BIOLOGICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS;

EID: 33748363077     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1132     Document Type: Article

References (47)

1. Hardy, J.A. & Wells, J.A. Searching for new allosteric sites in enzymes. Curr. Opin. Struct. Biol. 14, 706-715 (2004).
2. Gao, Z.G. & Jacobson, K.A. Allosterism in membrane receptors. Drug Discov. Today 11, 191-202 (2006).
3. Swain, J.F. & Gierasch, L.M. The changing landscape of protein allostery. Curr. Opin. Struct. Biol. 16, 102-108 (2006).
4. Suel, G.M., Lockless, S.W., Wall, M.A. & Ranganathan, R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59-69 (2003).
5. Koshland, D.E., Jr. Conformational changes: how small is big enough? Nat. Med. 4, 1112-1114 (1998).
6. Changeux, J.P. & Edelstein, S.J. Allosteric mechanisms of signal transduction. Science 308, 1424-1428 (2005).
7. Bray, D. & Duke, T. Conformational spread: the propagation of allosteric states in large multiprotein complexes. Annu. Rev. Biophys. Biomol. Struct. 33, 53-73 (2004).
8. Wand, A.J. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8, 926-931 (2001).
9. Homans, S.W. Probing the binding entropy of ligand-protein interactions by NMR. ChemBioChem 6, 1585-1591 (2005).
10. Cooper, A. & Dryden, D.T. Allostery without conformational change. A plausible model. Eur. Biophys. J. 11, 103-109 (1984).
11. Freire, E. The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc. Natl. Acad. Sci. USA 96, 10118-10122 (1999).
12. Pan, H., Lee, J.C. & Hilser, V.J. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc. Natl. Acad. Sci. USA 97, 12020-12025 (2000).
13. Kern, D. & Zuiderweg, E.R. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13, 748-757 (2003).
14. Stevens, S.Y., Sanker, S., Kent, C. & Zuiderweg, E.R. Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity. Nat. Struct. Biol. 8, 947-952 (2001).
15. Maler, L., Blankenship, J., Rance, M. & Chazin, W.J. Site-site communication in the EF-hand Ca2+-binding protein calbindin D9k. Nat. Struct. Biol. 7, 245-250 (2000).
16. Lee, A.L., Kinnear, S.A. & Wand, A.J. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat. Struct. Biol. 7, 72-77 (2000).
17. Fuentes, E.J., Der, C.J. & Lee, A.L. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol. 335, 1105-1115 (2004).
18. Koshland, D.E., Jr. The structural basis of negative cooperativity: receptors and enzymes. Curr. Opin. Struct. Biol. 6, 757-761 (1996).
19. Brown, A.M. & Crothers, D.M. Modulation of the stability of a gene-regulatory protein dimer by DNA and cAMP. Proc. Natl. Acad. Sci. USA 86, 7387-7391 (1989).
20. Harman, J.G. Allosteric regulation of the cAMP receptor protein. Biochim. Biophys. Acta 1547, 1-17 (2001).
21. Passner, J.M., Schultz, S.C. & Steitz, T.A. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution. J. Mol. Biol. 304, 847-859 (2000).
22. Heyduk, E., Heyduk, T. & Lee, J.C. Intersubunit communications in Escherichia coli cyclic AMP receptor protein: studies of the ligand binding domain. Biochemistry 31, 3682-3688 (1992).
23. Akke, M. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 12, 642-647 (2002).
24. Volkman, B.F., Lipson, D., Wemmer, D.E. & Kern, D. Two-state allosteric behavior in a single-domain signaling protein. Science 291, 2429-2433 (2001).
25. Kalodimos, C.G. et al. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305, 386-389 (2004).
26. Keramisanou, D. et al. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat. Struct. Mol. Biol. 13, 594-602 (2006).
27. Mulder, F.A., Mittermaier, A., Hon, B., Dahlquist, F.W. & Kay, L.E. Studying excited states of proteins by NMR spectroscopy. Nat. Struct. Biol. 8, 932-935 (2001).
28. Forman-Kay, J.D. The 'dynamics' in the thermodynamics of binding. Nat. Struct. Biol. 6, 1086-1087 (1999).
29. Cavanagh, J. & Akke, M. May the driving force be with you-whatever it is. Nat. Struct. Biol. 7, 11-13 (2000).
30. Zidek, L., Novotny, M.V. & Stone, M.J. Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nat. Struct. Biol. 6, 1118-1121 (1999).
31. Stone, M.J. NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding. Acc. Chem. Res. 34, 379-388 (2001).
32. Igumenova, T.I., Frederick, K.K. & Wand, A.J. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem. Rev. 106, 1672-1699 (2006).
33. Hilser, V.J., Garcia-Moreno, E.B., Oas, T.G., Kapp, G. & Whitten, S.T. A statistical thermodynamic model of the protein ensemble. Chem. Rev. 106, 1545-1558 (2006).
34. Gekko, K., Obu, N., Li, J. & Lee, J.C. A linear correlation between the energetics of allosteric communication and protein flexibility in the Escherichia coli cyclic AMP receptor protein revealed by mutation-induced changes in compressibility and amide hydrogen-deuterium exchange. Biochemistry 43, 3844-3852 (2004).
35. Englander, J.J., Louie, G., McKinnie, R.E. & Englander, S.W. Energetic components of the allosteric machinery in hemoglobin measured by hydrogen exchange. J. Mol. Biol. 284, 1695-1706 (1998).
36. Yang, D. & Kay, L.E. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J. Mol. Biol. 263, 369-382 (1996).
37. Bracken, C., Carr, P.A., Cavanagh, J. & Palmer, A.G., III Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J. Mol. Biol. 285, 2133-2146 (1999).
38. Gunasekaran, K., Ma, B. & Nussinov, R. Is allostery an intrinsic property of all dynamic proteins? Proteins 57, 433-443 (2004).
39. Anderson, A.C., O'Neil, R.H., DeLano, W.L. & Stroud, R.M. The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits. Biochemistry 38, 13829-13836 (1999).
40. Leslie, A.G. & Wonacott, A.J. Structural evidence for ligand-induced sequential conformational changes in glyceraldehyde 3-phosphate dehydrogenase. J. Mol. Biol. 178, 743-772 (1984).
41. Hampele, I.C. et al. Structure and function of the dihydropteroate synthase from Staphylococcus aureus. J. Mol. Biol. 268, 21-30 (1997).
42. Lee, A.L. & Wand, A.J. Microscopic origins of entropy, heat capacity and the glass transition in proteins. Nature 411, 501-504 (2001).
43. Evenas, J. et al. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J. Mol. Biol. 309, 961-974 (2001).
44. Korzhnev, D.M., Skrynnikov, N.R., Millet, O., Torchia, D.A. & Kay, L.E. An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J. Am. Chem. Soc. 124, 10743-10753 (2002).
45. 15N relaxation data exclusively. J. Biomol. NMR 6, 153-162 (1995).
46. Lefevre, J.F., Dayie, K.T., Peng, J.W. & Wagner, G. Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. Biochemistry 35, 2674-2686 (1996).
47. Krizova, H., Zidek, L., Stone, M.J., Novotny, M.V. & Sklenar, V. Temperature-dependent spectral density analysis applied to monitoring backbone dynamics of major urinary protein-I complexed with the pheromone 2-sec-butyl-4,5-dihydrothiazole. J. Biomol. NMR 28, 369-384 (2004).