Fast events in protein folding: Structural volume changes accompanying the early events in the N→I transition of apomyoglobin induced by ultrafast pH jump

Biophysical Journal

Volumn 78, Issue 1, 2000, Pages 405-415

  Abbruzzetti, Stefania ^a,b   Crema, Elisa ^a   Masino, Laura ^a   Vecli, Arnaldo ^a,b   Viappiani, Cristiano ^a,b   Small, Jeanne R ^c   Libertini, Louis J ^d   Small, Enoch W ^d  

^a UNIVERSITY OF PARMA   (Italy)

^b INFM   (Italy)

^c EASTERN WASHINGTON UNIVERSITY   (United States)

^d Quantum Northwest Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOMYOGLOBIN;

ACIDIFICATION; ARTICLE; PHOTOACOUSTIC SPECTROSCOPY; PROTEIN FOLDING; PROTON TRANSPORT;

EID: 0034127327     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76603-3     Document Type: Article

References (57)

1. R.M. Ballew J. Sabelko M. Gruebele Direct observation of fast protein folding: the initial collapse of apomyoglobin Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 93 1996 5759 5764
2. R.M. Ballew J. Sabelko M. Gruebele Observation of distinct nanosecond and microsecond protein folding events Nat. Struct. Biol. 3 1996 923 926
3. D. Barrick R.L. Baldwin The molten globule intermediate of apomyoglobin and the process of protein folding Protein Sci. 2 1993 869 876
4. D. Barrick F.M. Hughson R. Baldwin Molecular mechanism of acid denaturation of apomyoglobin: the role of hystidine residues in the partial unfolding of apomyoglobin J. Mol. Biol. 237 1994 588 601
5. P.R. Bevington Data reduction and error analysis for the physical sciences 1969 McGraw-Hill New York
6. G. Bonetti A. Vecli C. Viappiani Reaction volume of water formation detected by time resolved photoacoustics: photoinduced proton transfer between o-nitrobenzaldehyde and hydroxyls in water Chem. Phys. Lett. 269 1997 268 273
7. C.D. Borsarelli S.E. Braslavsky Volume changes correlate with enthalpy changes during the photoinduced formation of the (MLCT)-M3 state of ruthenium (II) bipyridine cyano complexes in the presence of salts. A case of entropy-enthalpy compensation effect J. Phys. Chem. B 102 1998 6231 6238
8. S.E. Braslavsky G.E. Heibel Time-resolved photothermal and photoacoustics methods applied to photoinduced processes in solution Chem. Rev. 92 1992 1381 1410
9. J.B. Callis W.W. Parson M. Gouterman Fast changes of enthalpy and volume of flash excitation of chromatium chromatophores Biochim. Biophys Acta 267 1972 348 362
10. T.V. Chalikian On volume changes accompanying conformational transitions of biopolymers Biopolymers 39 1996 619 626
11. C. Chan Y. Hu S. Takahashi D.L. Rousseau W.A. Eaton J. Hofrichter Submillisecond protein folding kinetics studied by ultrarapid mixing Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 94 1997 1779 1784
12. Y. Chen M.D. Barkley Toward understanding tryptophan fluorescence in proteins Biochemistry 37 1998 9976 9982
13. X. Cheng B.P. Schoenborn Neutron diffraction study of carbonmonoxymyoglobin J. Mol. Biol. 220 1991 381 399
14. M. Cocco Y.H. Kao A. Phillips J.T.J. Lecomte Structural comparison of apomyoglobin and metaquomyoglobin: pH titration of[[page end]] histidines by NMR spectroscopy Biochemistry 31 1992 6481 6491
15. M.J. Cocco J.T.J. Lecomte Characterization of hydrophobic cores in apomyoglobin: a proton NMR spectroscopy study Biochemistry 29 1990 11067 11072
16. M.J. Cocco J.T.J. Lecomte The native state of apomyoglobin described by proton NMR spectroscopy: interaction with the paramagnetic probe HyTEMPO and fluorescent dye ANS Protein Sci. 3 1994 267 281
17. 1H nuclear magnetic resonance spectrum of the carbon monoxide complex of sperm whale myoglobin by phase-sensitive two dimensional techniques J. Mol. Biol. 194 1987 313 327
18. D. Eliezer P.A. Jennings P.E. Wright S. Doniach K.O. Hodgson H. Tsuruta The radius of gyration of an apomyoglobin folding intermediate Science 270 1995 487 488
19. D. Eliezer J. Yao H.J. Dyson P.E. Wright Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding Nat. Struct. Biol. 5 1998 148 155
20. T. Gensch S.E. Braslavsky Volume changes related to triplet formation of water-soluble porphyrins: a laser-induced optoacoustic spectroscopy (LIOAS) study J. Phys. Chem. 101 1997 101 108
21. M.V. George J.C. Scaiano Photochemistry of o-nitrobenzaldehyde and related studies J. Phys. Chem. 84 1980 492 495
22. R. Gilmanshin R.H. Callender R.B. Dyer The core of apomyoglobin E-form folds at the diffusion limit Nat. Struct. Biol. 5 1998 363 365
23. R. Gilmanshin R.B. Dyer R.H. Callender Structural heterogeneity of the various forms of apomyoglobin: implications for protein folding Protein Sci. 6 1997 2134 2142
24. R. Gilmanshin S. Williams R.H. Callender W.H. Woodruff R.B. Dyer Fast events in protein folding: relaxation dynamics of secondary structure in native apomyoglobin Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 94 1997 3709 3713
25. Y.V. Griko P.L. Privalov S.Y. Venyaminov Thermodynamic study of apomyoglobin structure J. Mol. Biol. 202 1988 127 138
26. M. Gutman E. Nachliel The dynamic aspects of proton transfer processes Biochim. Biophys Acta 1015 1990 391 414
27. S.C. Harrison R. Blout Reversible conformational changes of myoglobin and apomyoglobin J. Biol. Chem. 240 1965 299 303
28. L.G. Hepler Entropy and volume changes on ionization of aqueous acids J. Phys. Chem. 69 1965 965
29. F.M. Hughson D. Barrick R.L. Baldwin Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis Biochemistry 30 1991 4113 4118
30. F.M. Hughson P.E. Wright R.L. Baldwin Structural characterization of a partly folded apomyoglobin intermediate Science 249 1990 1544 1548
31. P.A. Jennings P.E. Wright Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin Science 262 1993 892 896
32. R.S. Johnson K.A. Walsh Mass spectrometric measurement of protein amide hydrogen exchange rates of apo- and holo- myoglobin Protein Sci. 3 1994 2411 2418
33. C.M. Jones E.R. Henry Y. Hu C. Chan S.D. Luck A. Bhuyan H. Roder J. Hofrichter W.A. Eaton Fast events in protein folding initiated by nanosecond laser photolysis Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 90 1993 11860 11864
34. K.J. Laidler Chemical Kinetics 1987 HarperCollins Publishers New York
35. A. Losi C. Viappiani Reaction volume and rate constants for the excited state proton transfer in aqueous solutions of naphthols Chem. Phys. Lett. 289 1998 500 506
36. V. Muñoz P.A. Thompson J. Hofrichter W.A. Eaton Folding dynamics and mechanism of β -hairpin formation Nature 390 1997 196 199
37. P. Pelagatti M. Carcelli C. Viappiani Determination of the pKa of the aci-nitro intermediate in o-nitrobenzyl systems Israel J. Chem. 38 1998 213 221
38. K.S. Peters G.J. Snyder Time-resolved photoacoustic calorimetry: probing the energetics and dynamics of fast chemical and biochemical reactions Science 241 1988 1053 1057
39. C.M. Phillips Y. Mizutani R.M. Hochstrasser Ultrafast thermally induced unfolding of RNase A Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 92 1995 7292 7296
40. P.L. Privalov Intermediate states in protein folding J. Mol. Biol. 258 1996 707 725
41. M.C. Ramachandra Shastry S.D. Luck H. Roder A continuous-flow capillary mixing method to monitor reactions on the microsecond time scale Biophys. J. 74 1998 2714 2721
42. J. Rasper W. Kauzmann Volume changes in protein reactions. I. Ionization reactions of proteins J. Am. Chem. Soc. 84 1962 1771 1777
43. J. Rasper W. Kauzmann Volume changes in protein reactions. II. Comparison of ionization reactions in proteins and small molecules J. Am. Chem. Soc. 84 1962 1777 1788
44. A. Rossi Fanelli E. Antonini A. Caputo Biochim. Biophys Acta 30 1958 608 615
45. J.E. Rudzki J.L. Goodman K.S. Peters Simultaneous determination of photoreaction dynamics and energetics using pulsed, time-resolved photoacoustic calorimetry J. Am. Chem. Soc. 107 1985 7849 7854
46. J.R. Small Deconvolution analysis for pulsed-laser photoacoustics L. Brand M.L. Johnson Numerical Computer Methods 1992 Academic Press San Diego 505 521
47. J.R. Small E. Kurian Volumetric photoacoustics: listening to more than just heat Spectroscopy 10 1995 27 33
48. J.R. Small L.J. Libertini E.W. Small Analysis of photoacoustic waveforms using the nonlinear least squares method Biophys. Chem. 42 1992 24 48
49. T.R. Sosnick M.D. Shtilerman L. Mayne S.W. Englander Ultrafast signals in protein folding and the polypeptide contracted state Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 94 1997 8545 8550
50. P.A. Thompson W.A. Eaton J. Hofrichter Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a ‘kinetic zipper’ model Biochemistry 36 1997 9200 9210
51. R. VanEldick T. Asano W.J. Le Noble Activation and reaction volumes in solution 2. Chem. Rev. 89 1989 549 688
52. C. Viappiani S. Abbruzzetti J.R. Small L.J. Libertini E.W. Small An experimental methodology for measuring volume changes in proton transfer reactions in aqueous solutions Biophys. Chem. 73 1998 13 22
53. C. Viappiani G. Bonetti M. Carcelli F. Ferrari A. Sternieri Study of proton transfer processes in solution using the laser induced pH-jump: a new experimental setup and an improved data analysis based on genetic algorithms Rev. Sci. Instrum. 69 1998 270 276
54. J.P. Waltho V.A. Feher G. Merutka H.J. Dyson P.E. Wright Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G-helix and H-helix of myoglobin Biochemistry 32 1993 6337 6347
55. R.C. Weast CRC Handbook of Biochemistry 1968 CRC Press Boca Raton, FL
56. R.C. Weast CRC Handbook of Chemistry and Physics. 1971 CRC Press Boca Raton, FL
57. S. Williams T.P. Causgrove R. Gilmanshin K.S. Fang R.H. Callender W.H. Woodruff R.B. Dyer Fast events in protein folding: helix melting and formation in a small peptide Biochemistry 35 1996 691 697