Enzymatic activity in disordered states of proteins

Current Opinion in Chemical Biology

Volumn 14, Issue 5, 2010, Pages 671-675

  Vendruscolo, Michele ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL REACTION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME MECHANISM; PROTEIN CONFORMATION; PROTEIN METABOLISM; PROTEIN STRUCTURE; REVIEW; SIGNAL TRANSDUCTION;

BIOCATALYSIS; CATALYTIC DOMAIN; ENZYMES; HUMANS; PROTEINS;

EID: 77957750160     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2010.08.022     Document Type: Review

References (50)

1. Frauenfelder H., Sligar S.G., Wolynes P.G. The energy landscapes and motions of proteins. Science 1991, 254:1598-1603.
2. Fersht A.R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding 1999, W.H. Freeman, New York.
3. Karplus M., Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci U S A 2005, 102:6679-6685.
4. Vendruscolo M., Dobson C.M. Dynamic visions of enzymatic reactions. Science 2006, 313:1586-1587.
5. Mittermaier A.K., Kay L.E. Observing biological dynamics at atomic resolution using nmr. TiBS 2009, 34:601-611.
6. Boehr D.D., Nussinov R., Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009, 5:789-796.
7. Tokuriki N., Tawfik D.S. Protein dynamism and evolvability. Science 2009, 324:203-207.
8. Dyson H.J., Wright P.E. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005, 6:197-208.
9. Tompa P. The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 2005, 579:3346-3354.
10. Dunker A.K., Silman I., Uversky V.N., Sussman J.L. Function and structure of inherently disordered proteins. Curr Opin Struct Biol 2008, 18:756-764.
11. Uversky V.N., Dunker A.K. Understanding protein non-folding. Biochim Biophys Acta 2010, 1804:1231-1264.
12. Kumar S., Ma B.Y., Tsai C.J., Sinha N., Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000, 9:10-19.
13. Papoian G.A. Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm. Proc Natl Acad Sci U S A 2008, 105:14237-14238.
14. Gsponer J., Christodoulou J., Cavalli A., Bui J.M., Richter B., Dobson C.M., Vendruscolo M. A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure 2008, 16:736-746.
15. Lange O.F., Lakomek N.A., Fares C., Schroder G.F., Walter K.F.A., Becker S., Meiler J., Grubmuller H., Griesinger C., de Groot B.L. Recognition dynamics up to microseconds revealed from an rdc-derived ubiquitin ensemble in solution. Science 2008, 320:1471-1475.
16. Bakan A., Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 2009, 106:14349-14354.
17. Wright P.E., Dyson H.J. Linking folding and binding. Curr Opin Struct Biol 2009, 19:31-38.
18. Mittag T., Kay L.E., Forman-Kay J.D. Protein dynamics and conformational disorder in molecular recognition. J Mol Rec 2009, 23:105-116.
19. Tompa P., Fuxreiter M., Oldfield C.J., Simon I., Dunker A.K., Uversky V.N. Close encounters of the third kind: disordered domains and the interactions of proteins. Bioessays 2009, 31:328-335.
20. Wlodarski T., Zagrovic B. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc Natl Acad Sci U S A 2009, 106:19346-19351.
21. Tzeng S.R., Kalodimos C.G. Dynamic activation of an allosteric regulatory protein. Nature 2009, 462. pp. 368-U139.
22. Trizac E., Levy Y., Wolynes P.G. Capillarity theory for the fly-casting mechanism. Proc Natl Acad Sci U S A 2010, 107:2746-2750.
23. Wolfenden R., Snider M.J. The depth of chemical time and the power of enzymes as catalysts. Acc Chem Res 2001, 34:938-945.
24. Benkovic S.J., Hammes-Schiffer S. A perspective on enzyme catalysis. Science 2003, 301:1196-1202.
25. Garcia-Viloca M., Gao J., Karplus M., Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 2004, 303:186-195.
26. Warshel A., Sharma P.K., Kato M., Xiang Y., Liu H.B., Olsson M.H.M. Electrostatic basis for enzyme catalysis. Chem Rev 2006, 106:3210-3235.
27. Kamerlin S.C.L., Warshel A. At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis?. Proteins 2010, 78:1339-1375.
28. Aumuller T., Fischer G. Bioactivity of folding intermediates studied by the recovery of enzymatic activity during refolding. J Mol Biol 2008, 376:1478-1492.
29. Bemporad F., Gsponer J., Hopearuoho H.I., Plakoutsi G., Stati G., Stefani M., Taddei N., Vendruscolo M., Chiti F. Biological function in a non-native partially folded state of a protein. EMBO J 2008, 27:1525-1535.
30. Kiefhaber T., Schmid F.X., Willaert K., Engelborghs Y., Chaffotte A. Structure of a rapidly formed intermediate in ribonuclease-t1 folding. Protein Sci 1992, 1:1162-1172.
31. Li Y.H., Jing G.Z. Double point mutant f34w/w140f of staphylococcal nuclease is in a molten globule state but highly competent to fold into a functional conformation. J Biochem 2000, 128:739-744.
32. Morillas M., Eberl H., Allain F.H.T., Glockshuber R., Kuennemann E. Novel enzymatic activity derived from the semliki forest virus capsid protein. J Mol Biol 2008, 376:721-735.
33. Pervushin K., Vamvaca K., Vogeli B., Hilvert D. Structure and dynamics of a molten globular enzyme. Nat Struct Mol Biol 2007, 14:1202-1206.
34. Punchihewa C., Dai J.X., Carver M., Yang D.Z. Human topoisomerase IC-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex. J Struct Biol 2007, 159:111-121.
35. Vamvaca K., Jelesarov I., Hilvert D. Kinetics and thermodynamics of ligand binding to a molten globular enzyme and its native counterpart. J Mol Biol 2008, 382:971-977.
36. Vamvaca K., Voegeli B., Kast P., Pervushin K., Hilvert D. Enzymatic catalysis: taking 'induced fit' to extremes. Protein Sci 2004, 13:170.
37. Vamvaca K., Vogeli B., Kast P., Pervushin K., Hilvert D. An enzymatic molten globule: efficient coupling of folding and catalysis. Proc Natl Acad Sci U S A 2004, 101:12860-12864.
38. Woycechowsky K.J., Choutko A., Vamvaca K., Hilvert D. Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation. Biochemistry 2008, 47:13489-13496.
39. Jackson C.J., Foo J.L., Tokuriki N., Afriat L., Carr P.D., Kim H.K., Schenk G., Tawfik D.S., Ollis D.L. Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. Proc Natl Acad Sci U S A 2009, 106:21631-21636.
40. Uversky V.N., Kutyshenko V.P., Protasova N.Y., Rogov V.V., Vassilenko K.S., Gudkov A.T. Circularly permuted dihydrofolate reductase possesses all the properties of the molten globule state, but can resume functional tertiary structure by interaction with its ligands. Protein Sci 1996, 5:1844-1851.
41. MacBeath G., Kast P., Hilvert D. Redesigning enzyme topology by directed evolution. Science 1998, 279:1958-1961.
42. Roca M., Messer B., Hilvert D., Warshel A. On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Natl Acad Sci U S A 2008, 105:13877-13882.
43. Vendruscolo M., Paci E., Dobson C.M., Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature 2001, 409:641-645.
44. Pisliakov A.V., Cao J., Kamerlin S.C.L., Warshel A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci U S A 2009, 106:17359-17364.
45. Kjaergaard M., Teilum K., Poulsen F.M. Conformational selection in the molten globule state of the nuclear coactivator binding domain of cbp. Proc Natl Acad Sci U S A 2010, 107:12535-12540.
46. Baldwin A.J., Kay L.E. Nmr spectroscopy brings invisible protein states into focus. Nat Chem Biol 2009, 5:808-814.
47. O'Brien P.J., Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem Biol 1999, 6:R91-R105.
48. Khersonsky O., Tawfik D.S. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 2010, 79:471-505.
49. Babtie A., Tokuriki N., Hollfelder F. What makes an enzyme promiscuous?. Curr Opin Chem Biol 2010, 14:200-207.
50. Nobeli I., Favia A.D., Thornton J.M. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 2009, 27:157-167.