Structural characterization of the transition state for folding of muscle acylphosphatase

Journal of Molecular Biology

Volumn 283, Issue 4, 1998, Pages 893-903

  Chiti, Fabrizio ^a   Taddei, Niccolo' ^b   Van Nuland, Nico A J ^a   Magherini, Francesca ^b   Stefani, Massimo ^b   Ramponi, Giampietro ^b   Dobson, Christopher M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF FLORENCE   (Italy)

Author keywords

Acylphosphatase; Folding transition state; Protein folding; Sugars; Trifluoroethanol

Indexed keywords

2 PROPANOL; ACYLPHOSPHATASE; ALCOHOL DERIVATIVE; ENZYME INHIBITOR; MUSCLE ENZYME; SOLVENT; TRIFLUOROETHANOL; UREA;

ARTICLE; BINDING AFFINITY; COMPETITIVE INHIBITION; CONFORMATIONAL TRANSITION; ENZYME CONFORMATION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING;

EID: 0032491469     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2010     Document Type: Article

References (54)

1. Adler E., Wolfenden R. Inhibitor binding in the transition state for unfolding of adenosine deaminase. Bioorg. Chem. 22:1994;216-225
2. Baldwin R.L. Pieces of the folding puzzle. Nature. 346:1990;409-410
3. Buck M., Radford S.E., Dobson C.M. A partially folded state of HEWL in TFE structural characterisation and implications for protein folding. Biochemistry. 32:1993;669-678
4. Burton R.E., Huang G.S., Daugherty M.A., Calderone T.L., Oas T.G. The energy landscape of a fast folding protein mapped by Ala → Gly substitutions. Nature Struct. Biol. 4:1997;305-310
5. Chen B.L., Baase W.A., Schellman J.A. Low-temperature unfolding of a mutant of phage T4 lysozyme. Biochemistry. 28:1989;691-699
6. Chiti F., van Nuland N.A.J., Taddei N., Magherini F., Stefani M., Ramponi G., Dobson C.M. Conformational stability of muscle acylphosphatase. The role of temperature, denaturant concentration and pH. Biochemistry. 37:1998;1447-1455
7. Dobson C.M., Sali A., Karplus M. Protein folding a perspective from theory and experiment. Angew. Chem. Int. Ed. 37:1998;868-893
8. Dyson H.J., Merutka G., Waltho J.P., Lerner R.A., Wright P.E. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding I. Myohemerythrin. J. Mol. Biol. 226:1992;795-817
9. Fersht A.R. Enzyme Structure and Mechanism. 2nd edit. :1985;47-49 Freeman, New York
10. Fersht A.R. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7:1997;3-9
11. Frye K.J., Royer C.A. The kinetic basis for the stabilization of staphylococcal nuclease by xylose. Protein Sci. 6:1997;789-793
12. Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:1983;183-210
13. Hibbard L.S., Tulinsky A. Expression of functionality of alpha-chymotrypsin. Effects of guanidine hydrochloride and urea in the onset of denaturation. Biochemistry. 17:1978;5460-5468
14. Itzhaki L.S., Otzen D.E., 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
15. Jackson S.E., Fersht A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry. 30:1991;10428-10435
16. Jackson S.E., elMasry N., Fersht A.R. Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2 a critical test of the protein engineering method of analysis. Biochemistry. 32:1993;11270-11278
17. Kamatari Y.O., Konno T., Kataoka M., Akasaka K. The methanol-induced globular and expanded denatured states of cytochrome c a study by CD, fluorescence, NMR and small angle X-ray scattering. J. Mol. Biol. 259:1996;512-523
18. Karplus M., Weaver D.L. Protein folding dynamics the diffusion-collision model and experimental data. Protein Sci. 3:1994;650-668
19. Kramers H.A. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. 7:1940;284-304
20. Kraut J. How do enzymes work? Science. 242:1988;533-540
21. Kuwajima K. Stopped-flow circular dichroism. Fasman G.D. Circular Dichroism and the Conformational Stability of Biomolecules. 1996;159-181 Plenum Press, New York
22. Kuwajima K., Sakuraoka A., Fueki S., Yoneyama M., Sugai S. Folding of carp parvalbumin studied by equilibrium and kinetic circular dichroism spectra. Biochemistry. 27:1988;7419-7428
23. 2+ binding on the folding kinetics of α-lactalbumin. J. Mol. Biol. 206:1989;547-561
24. Livingstone J.R., Spolar R.S., Record M.T. Contribution to the thermodynamics of protein folding from the reduction in water-accessible surface area. Biochemistry. 30:1991;4237-4244
25. Lopez-Hernandez E., Serrano L. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. Fold Des. 1:1996;43-55
26. Lu H., Buck M., Radford S.E., Dobson C.M. Acceleration of the folding of hen lysozyme by trifluoroethanol. J. Mol. Biol. 265:1997;112-117
27. Matouschek A., Serrano L., Fersht A.R. The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure. J. Mol. Biol. 224:1992;819-835
28. Miranker A.D., Dobson C.M. Collapse and cooperativity in protein folding. Curr. Opin. Struct. Biol. 6:1996;31-42
29. Modesti A., Taddei N., Bucciantini M., Stefani M., Colombini B., Raugei G., Ramponi G. Expression, purification and characterization of acylphosphatase muscular isoenzyme as fusion protein with glutathione S-transferase. Protein Express. Purif. 6:1995;799-805
30. Murphy K.P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Advan. Protein Chem. 43:1992;313-361
31. Myers J.K., Pace C.N., Scholtz J.M. Denaturant m values and heat capacity changes relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:1995;2138-2148
32. Nozaki Y., Tanford C. The solubility of amino acids and related compounds in aqueous urea solutions. J. Biol. Chem. 238:1963;4074-4081
33. Pace C.N., Laurents D.V., Erickson R.E. Urea denaturation of barnase. pH dependence and characterization of the unfolded state. Biochemistry. 31:1992;2728-2734
34. Plaxco K.W., Simons K.T., Baker D. Contact order, transition state placement and the folding kinetics of single domain proteins. J. Mol. Biol. 277:1998;985-994
35. Radford S.E., Dobson C.M., Evans P.A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature. 358:1992;302-307
36. Roder H., Elove G.A., Englander S.W. Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR. Nature. 335:1988;700-704
37. Sancho J., Meiering E.M., Fersht A.R. Mapping transition states of protein unfolding by protein engineering of ligand-binding sites. J. Mol. Biol. 221:1991;1007-1014
38. Santoro M.M., Bolen D.W. Unfolding free-energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry. 27:1988;8063-8068
39. Scalley M.L., Baker D. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proc. Natl Acad. Sci. USA. 94:1997;10636-10640
40. Segawa S.-I., Kume K. Comparison between the unfolding rate and structural fluctuations in native lysozyme - effects of denaturants, ligand binding, and intrachain cross-linking on hydrogen exchange and unfolding kinetics. Biopolymers. 25:1986;1981-1996
41. Shortle D. Staphylococcal nuclease a showcase of m-value effects. Advan. Protein Chem. 46:1995;217-247
42. Taddei N., Buck M., Broadhurst R.W., Stefani M., Ramponi G., Dobson C.M. Equilibrium unfolding studies of horse muscle acylphosphatase. Eur. J. Biochem. 225:1994;811-817
43. Taddei N., Stefani M., Vecchi M., Modesti A., Raugei G., Bucciantini M., Magherini F., Ramponi G. Arginine-23 is involved in the catalytic site of muscle acylphosphatase. Biochim. Biophys. Acta. 1208:1994;75-80
44. Taddei N., Stefani M., Magherini F., Chiti F., Modesti A., Raugei G., Ramponi G. Looking for residues involved in the muscle acylphosphatase catalytic mechanism and structural stabilization role of Asn41, Thr42 and Thr46. Biochemistry. 35:1996;7077-7083
45. Taddei N., Chiti F., Magherini F., Stefani M., Thunnissen M.M.G.M., Nordlund P., Ramponi G. Structural and kinetic investigations on the 15-21 and 42-45 loops of muscle acylphosphatase evidence for their involvment in enzyme catalysis and conformational stabilization. Biochemistry. 36:1997;7217-7224
46. Tanford C. Protein denaturation. Advan. Protein Chem. 24:1970;1-95
47. Thomas P.D., Dill K.A. Local and non local interactions in globular proteins and mechanism of alcohol denaturation. Protein Sci. 2:1993;2050-2065
48. Thunnissen M.M.G.M., Taddei N., Liguri G., Ramponi G., Nordlund P. Crystal structure of common type acylphosphatase from bovine testis. Structure. 5:1997;69-79
49. Timasheff S.N. The control of protein stability and association by weak interactions with water how do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22:1993;67-97
50. Udgaonkar J.B., Baldwin R.L. NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature. 335:1988;694-699
51. Udgaonkar J.B., Baldwin R.L. Nature of the early folding intermediate of ribonuclease A. Biochemistry. 34:1995;4088-4096
52. van Nuland N.A.J., Chiti F., Taddei N., Raugei G., Ramponi G., Dobson C.M. Slow folding of muscle acylphosphatase in the absence of intermediates. J. Mol. Biol. 283:1998;883-891
53. Viguera A.R., Serrano L., Wilmanns M. Different folding transition-states may result in the same native structure. Nature Struct. Biol. 3:1996;874-880
54. Viguera A.R., Villegas V., Aviles F.X., Serrano L. Favourable native-like helical local interactions can accelerate protein folding. Fold. Des. 2:1997;23-33