Folding and stability of globular proteins and implications for function

Current Opinion in Structural Biology

Volumn 19, Issue 1, 2009, Pages 3-7

  Travaglini Allocatelli, Carlo ^a   Ivarsson, Ylva ^a   Jemth, Per ^b   Gianni, Stefano ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; REVIEW;

ANIMALS; BINDING SITES; HUMANS; PROTEIN FOLDING; PROTEINS;

EID: 60649096450     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2008.12.001     Document Type: Review

References (52)

1. van Gunsteren W.F., Bürgi R., Peter C., and Daura X. The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew Chem Int Ed Engl 40 (2001) 351-355
2. McCarney E.R., Kohn J.E., and Plaxco K.W. Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins. Crit Rev Biochem Mol Biol 40 (2005) 181-189
3. Mittag T., and Forman-Kay J.D. Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 17 (2007) 3-14
4. Sherman E., and Haran G. Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci U S A 103 (2006) 11539-11543
5. Merchant K.A., Best R.B., Louis J.M., Gopich I.V., and Eaton W.A. Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci U S A 104 (2007) 1528-1533
6. Plaxco K.W., Millett I.S., Segel D.J., Doniach S., and Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat Struct Biol 6 (1999) 554-556
7. Religa T.L., Markson J.S., Mayor U., Freund S.M., and Fersht A.R. Solution structure of a protein denatured state and folding intermediate. Nature 437 (2005) 1053-1056
8. Religa T.L., Johnson C.M., Vu D.M., Brewer S.H., Dyer R.B., and Fersht A.R. The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of engrailed homeodomain. Proc Natl Acad Sci U S A 104 (2007) 9272-9277
9. DeMarco M.L., Alonso D.O., and Daggett V. Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein. J Mol Biol 341 (2004) 1109-1124
10. Hubner I.A., Deeds E.J., and Shakhnovich E.I. Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A 103 (2006) 17747-17752
11. Mayor U., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M.V., Alonso D.O.V., Daggett V., and Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421 (2003) 863-867
12. Mok K.H., Kuhn L.T., Goez M., Day I.J., Lin J.C., Andersen N.H., and Hore P.J. A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein. Nature 447 (2007) 106-109
13. Fierz B., Joder K., Krieger F., and Kiefhaber T. Using triplet-triplet energy transfer to measure conformational dynamics in polypeptide chains. Methods Mol Biol 350 (2007) 169-187
14. Fierz B., and Kiefhaber T. End-to-end vs interior loop formation kinetics in unfolded polypeptide chains. J Am Chem Soc 129 (2007) 672-679
15. Fierz B., Satzger H., Root C., Gilch P., Zinth W., and Kiefhaber T. Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale. Proc Natl Acad Sci U S A 104 (2007) 2163-2168
16. Bashford D., Cohen F.E., Karplus M., Kuntz I.D., and Weaver D.L. Diffusion-collision model for the folding kinetics of myoglobin. Proteins 4 (1988) 211-227
17. Nishimura C., Prytulla S., Dyson J.H., and Wright P.E. Conservation of folding pathways in evolutionarily distant globin sequences. Nat Struct Biol 7 (2000) 679-686
18. Wong K.B., Clarke J., Bond C.J., Neira J.L., Freund S.M., Fersht A.R., and Daggett V. Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J Mol Biol 296 (2000) 1257-1282
19. Myers J.K., and Oas T.G. Contribution of a buried hydrogen bond to lambda repressor folding kinetics. Biochemistry 38 (1999) 6761-6768
20. Karplus M., and Weaver D.L. Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci 3 (1994) 650-668
21. Itzhaki L.S., Otzen D.E., and Fersht A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 254 (1995) 260-288
22. Abkevich V.I., Gutin A.M., and Shakhnovich E.I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33 (1994) 10026-10036
23. Gianni S., Guydosh N.R., Khan F., Caldas T.D., Mayor U., White G.W., DeMarco M.L., Daggett V., and Fersht A.R. Unifying features in protein-folding mechanisms. Proc Natl Acad Sci U S A 100 (2003) 13286-13291
24. White G.W., Gianni S., Grossmann J.G., Jemth P., Fersht A.R., and Daggett V. Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding. J Mol Biol 350 (2005) 757-775
25. Mayor U., Grossmann J.G., Foster N.W., Freund S.M., and Fersht A.R. The denatured state of engrailed homeodomain under denaturing and native conditions. J Mol Biol 333 (2003) 977-991
26. Gianni S., Calosci N., Aelen J.M., Vuister G.W., Brunori M., and Travaglini-Allocatelli C. Kinetic folding mechanism of PDZ2 from PTP-BL. Prot Eng Des Sel 18 (2005) 389-395
27. Ivarsson Y., Travaglini-Allocatelli C., Jemth P., Malatesta F., Brunori M., and Gianni S. An on-pathway intermediate in the folding of a PDZ domain. J Biol Chem 282 (2007) 8568-8572
28. Gianni S., Geierhaas C.D., Calosci N., Jemth P., Vuister G.W., Travaglini-Allocatelli C., Vendruscolo M., and Brunori M. A PDZ domain recapitulates a unifying mechanism for protein folding. Proc Natl Acad Sci U S A 104 (2007) 128-133
29. Joerger A.C., and Fersht A.R. Structure-function-rescue: the diverse nature of common p53 cancer mutants. Oncogene 26 (2007) 2226-2242
30. Bullock A.N., and Fersht A.R. Rescuing the function of mutant p53. Nat Rev Cancer 1 (2001) 68-76
31. Mayer S., Rüdiger S., Ang H.C., Joerger A.C., and Fersht A.R. Correlation of levels of folded recombinant p53 in Escherichia coli with thermodynamic stability in vitro. J Mol Biol 372 (2007) 268-276
32. Friedler A., Hansson L.O., Veprintsev D.B., Freund S.M., Rippin T.M., Nikolova P.V., Proctor M.R., Rüdiger S., and Fersht A.R. A peptide that binds and stabilizes p53 core domain: chaperone strategy for rescue of oncogenic mutants. Proc Natl Acad Sci U S A 99 (2002) 937-942
33. Boeckler F.M., Joerger A.C., Jaggi G., Rutherford T.J., Veprintsev D.B., and Fersht A.R. Targeted rescue of a destabilized mutant of p53 by an in silico screened drug. Proc Natl Acad Sci U S A 105 (2008) 10360-10365
34. Koshland D.E.J., Némethy G., and Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5 (1966) 365-385
35. Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J Mol Biol 12 (1965) 88-118
36. Gunasekaran K., Ma B., and Nussinov R. Is allostery an intrinsic property of all dynamic proteins?. Proteins 57 (2004) 433-443
37. Pan H., Lee J.C., and Hilser V.J. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc Natl Acad Sci U S A 97 (2000) 12020-12025
38. Cooper A., and Dryden D.T. Allostery without conformational change. A plausible model. Eur Biophys J 11 (1984) 103-109
39. Tsai C.J., del Sol A., and Nussinov R. Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol 378 (2008) 1-11
40. Lee A.L., Kinnear S.A., and Wand A.J. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat Struct Biol 7 (2000) 72-77
41. Mittermaier A., and Kay L.E. New tools provide new insights in NMR studies of protein dynamics. Science 312 (2006) 224-228
42. Akke M., Skelton N.J., Kördel J., Palmer A.G.r., and Chazin W.J. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation. Biochemistry 32 (1993) 9832-9844
43. Popovych N., Sun S., Ebright R.H., and Kalodimos C.G. Dynamically driven protein allostery. Nat Struct Mol Biol 13 (2006) 831-838
44. Ferreiro D.U., Hegler J.A., Komives E.A., and Wolynes P.G. Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci U S A 104 (2007) 19819-19824
45. Sutto L., Lätzer J., Hegler J.A., Ferreiro D.U., and Wolynes P.G. Consequences of localized frustration for the folding mechanism of the IM7 protein. Proc Natl Acad Sci U S A 104 (2007) 19825-19830
46. Gianni S., Engstrom A., Larsson M., Calosci N., Malatesta F., Eklund L., Ngang C., Travaglini-Allocatelli C., and Jemth P. The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism. J Biol Chem 280 (2005) 34805-34812
47. Gianni S., Walma T., Arcovito A., Calosci N., Bellelli A., Engström A., Travaglini-Allocatelli C., Brunori M., Jemth P., and Vuister G.W. Demonstration of long-range interactions in a PDZ domain by NMR, kinetics and protein engineering. Structure 14 (2006) 1801-1809
48. Jemth P., and Gianni S. PDZ domains: folding and binding. Biochemistry 46 (2007) 8701-8708
49. Di Nardo A.A., Larson S.M., and Davidson A.R. The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core. J Mol Biol 333 (2003) 641-655
50. Chi C.N., Elfström L., Shi Y., Snäll T., Engström A., and Jemth P. Reassessing a sparse energetic network within a single protein domain. Proc Natl Acad Sci U S A 105 (2008) 4679-4684
51. Chi C.N., Engström A., Gianni S., Larsson M., and Jemth P. Two conserved residues govern the salt and pH dependencies of the binding reaction of a PDZ domain. J Biol Chem 281 (2006) 36811-36818
52. Uversky V.N., Oldfield C.J., and Dunker A.K. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu Rev Biophys 37 (2008) 215-246