Protein function and allostery: A dynamic relationship

Annals of the New York Academy of Sciences

Volumn 1260, Issue 1, 2012, Pages 81-86

  Kalodimos, Charalampos G ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

NMR spectroscopy; Protein allostery; Protein dynamics

Indexed keywords

CYCLIC AMP BINDING PROTEIN;

ALLOSTERISM; ARTICLE; ENZYME ACTIVITY; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

EID: 84864065499     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.2011.06319.x     Document Type: Article

References (50)

1. Changeux, J. & S. Edelstein. 2005. Allosteric mechanisms of signal transduction. Science 308: 1424-1428.
2. Smock, R. & L. Gierasch. 2009. Sending signals dynamically. Science 324: 198-203.
3. Tsai, C., A. del Sol & R. Nussinov. 2008. Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 378: 1-11.
4. Brunori, M. 2011. Allostery turns 50: is the vintage yet attractive? Protein Sci. 20: 1097-1099.
5. Maksay, G. 2011. Allostery in pharmacology: thermodynamics, evolution and design. Prog. Biophys. Mol. Biol. 106: 463-473.
6. Wand, A. 2001. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8: 926-931.
7. Cooper, A. & D. Dryden. 1984. Allostery without conformational change. A plausible model. Eur. Biophys. J. 11: 103-109.
8. Kern, D. & E. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13: 748-757.
9. Tzeng, S-R. & C.G. Kalodimos. 2011. Protein dynamics and allostery: an NMR view. Curr. Opin. Struct. Biol. 21: 62-67.
10. Mittermaier, A. & L.E. Kay. 2006. New tools provide new insights in NMR studies of protein dynamics. Science 312: 224-228.
11. Palmer, A., J. Williams & A. McDermott. 1996. Nuclear magnetic resonance studies of biopolymer dynamics. J. Phys. Chem. 100: 13293-13310.
12. Yang, D. & L. Kay. 1996. 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.
13. Li, Z., S. Raychaudhuri & A. Wand. 1996. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 5: 2647-2650.
14. Korzhnev, D.M., T.L. Religa, W. Banachewicz, A.R. Fersht & L.E. Kay. 2010. A transient and low-populated protein-folding intermediate at atomic resolution. Science 329: 1312-1316.
15. Bouvignies, G., P. Vallurupalli, D.F. Hansen, et al. 2011. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477: 111-114.
16. Popovych, N., S. Sun, R.H. Ebright, & C.G. Kalodimos. 2006. Dynamically driven protein allostery. Nat. Struct. Mol. Biol. 13: 831-838.
17. Popovych, N., S-R. Tzeng, M. Tonelli, et al. 2009. Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc. Natl. Acad. Sci. U.S.A. 106: 6927-6932.
18. Tzeng, S.-R. & C.G. Kalodimos. 2009. Dynamic activation of an allosteric regulatory protein. Nature 462: 368-372.
19. Harman, J. 2001. Allosteric regulation of the cAMP receptor protein. Biochim. Biophys. Acta 1547: 1-17.
20. Lawson, C., D. Swigon, K. Murakami, et al. 2004. Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struct. Biol. 14: 10-20.
21. Schultz, S., G. Shields & T. Steitz. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253: 1001-1007.
22. Passner, J.M., S.C. Schultz & T.A. Steitz. 2000. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution. J. Mol. Biol. 304: 847-859.
23. Koshland, D. 1996. The structural basis of negative cooperativity: receptors and enzymes. Curr. Opin. Struct. Biol. 6: 757-761.
24. Stevens, S., S. Sanker, C. Kent & E. Zuiderweg. 2001. Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity. Nat. Struct. Biol. 8: 947-952.
25. Akke, M. 2002. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 12: 642-647.
26. Palmer, A. 2004. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 104: 3623-3640.
27. Mittermaier, A.K. & L.E. Kay. 2009. Observing biological dynamics at atomic resolution using NMR. Trends Biochem. Sci. 34: 601-611.
28. Jarymowycz, V. & M. Stone. 2006. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem. Rev. 106: 1624-1671.
29. Igumenova, T., K. Frederick & A. Wand. 2006. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem. Rev. 106: 1672-1699.
30. Forman-Kay, J. 1999. The "dynamics" in the thermodynamics of binding. Nat. Struct. Biol. 6: 1086-1087.
31. Cavanagh, J. & M. Akke. 2000. May the driving force be with you-whatever it is. Nat. Struct. Biol. 7: 11-13.
32. Bosshard, H. 2001. Molecular recognition by induced fit: how fit is the concept. News Physiol. Sci. 16: 171-173.
33. Kalodimos, C.G. 2011. NMR reveals novel mechanisms of protein activity regulation. Protein Sci. 20: 773-782.
34. Marlow, M.S. J. Dogan, K.K. Frederick, et al. 2010. The role of conformational entropy in molecular recognition by calmodulin. Nat. Chem. Biol. 6: 352-358.
35. Frederick, K.K., M.S. Marlow, K.G. Valentine, & A.J Wand. 2007. Conformational entropy in molecular recognition by proteins. Nature 448: 325-329.
36. Hilser, V.J. 2010. Biochemistry. An ensemble view of allostery. Science 327: 653-654.
37. Boehr, D.D., R. Nussinov & P.E. Wright. 2009. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5: 789-796.
38. Goodey, N. & S. Benkovic. 2008. Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 4: 474-482.
39. Ma, B. & R. Nussinov. 2009. Amplification of signaling via cellular allosteric relay and protein disorder. Proc. Natl. Acad. Sci. U.S.A. 106: 6887-6888.
40. Masterson, L.R. T. Yu, L. Shi, et al. 2011. cAMP-dependent protein kinase a selects the excited state of the membrane substrate phospholamban. J. Mol. Biol. 412: 155-164.
41. Masterson, L., A. Mascioni, N. Traaseth, et al. 2008. Allosteric cooperativity in protein kinase A. Proc. Natl. Acad. Sci. U.S.A. 105: 506-511.
42. Vendruscolo, M. 2011. Protein regulation: the statistical theory of allostery. Nat. Chem. Biol. 7: 411-412.
43. Killian, B.J., J.Y. Kravitz, S. Somani, et al. 2009. Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J. Mol. Biol. 389: 315-335.
44. Homans, S. 2005. Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem 6: 1585-1591.
45. Sarkar, P., C. Reichman, T. Saleh, et al. 2007. Proline cis-trans isomerization controls autoinhibition of a signaling protein. Mol. Cell. 25: 413-426.
46. Sarkar, P., T. Saleh, S-R. Tzeng, et al. 2011. Structural basis for regulation of the Crk signaling protein by a proline switch. Nat. Chem. Biol. 7: 51-57.
47. Keramisanou, D., N. Biris, I. Gelis, et al. 2006. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat. Struct. Mol. Biol. 13: 594-602.
48. Gelis, I., A.M.J.J. Bonvin, D. Keramisanou, et al. 2007. Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell 131: 756-769.
49. Religa, T.L., R. Sprangers & L.E Kay. 2010. Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR. Science 328: 98-102.
50. Henzler-Wildman, K. & D. Kern. 2007. Dynamic personalities of proteins. Nature 450: 964-972.