Direct observation of protein folding in nanoenvironments using a molecular ruler

Biophysical Chemistry

Volumn 123, Issue 1, 2006, Pages 40-48

  Sarkar, Rupa ^a   Shaw, Ajay Kumar ^a   Narayanan, S Shankara ^a   Dias, Fernando ^b   Monkman, Andy ^b   Pal, Samir Kumar ^a  

^a S N BOSE NATIONAL CENTRE FOR BASIC SCIENCES   (India)

^b DURHAM UNIVERSITY   (United Kingdom)

Author keywords

Circular dichroism spectroscopy; Cytochrome c; Micelles and reverse micelles; Picosecond dynamics; Protein folding; Time resolved fluorescence anisotropy

Indexed keywords

CYTOCHROME C; DANSYL CHLORIDE; HEME; NANOPARTICLE;

ANISOTROPY; ARTICLE; CIRCULAR DICHROISM; COVALENT BOND; ENERGY TRANSFER; FLUORESCENCE; LIGHT SCATTERING; MICELLE; NANOTECHNOLOGY; PRIORITY JOURNAL; PROTEIN FOLDING; REVERSE MICELLE;

CIRCULAR DICHROISM; FLUORESCENCE RESONANCE ENERGY TRANSFER; PROTEIN FOLDING; SCATTERING, RADIATION; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET;

EQUUS CABALLUS;

EID: 33747118682     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.04.006     Document Type: Article

References (38)

1. Goldbeck R.A., Thomas Y.G., Chen E., Esquerra R.M., and Kliger D.S. Multiple pathways on a protein-folding energy landscape: kinetic evidence. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 2782-2787
2. Russell B.S., Melenkivitz R., and Bren K.L. NMR investigation of ferricytochrome c unfolding: detection of an equilibrium unfolding intermediate and residual structure in the denatured state. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 8312-8317
3. Lefebvre B.G., Liu W., Peterson R.W., Valentine K.G., and Wand A.J. NMR spectroscopy of proteins encapsulated in a positively charged surfactant. J. Magn. Reson. 175 (2005) 158-162
4. Peterson R.W., Anbalagan K., Tommos C., and Wand A.J. Forced folding and structural analysis of metastable proteins. J. Am. Chem. Soc. 126 (2004) 9498-9499
5. Akiyama S., Kimura T., Ishimori K., and Morishima I. Conformational landscape of cytochrome c folding studied by microsecond-resolved small angle X-ray scattering. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 1329-1334
6. Flanagan M., Kataoka M., and Shortle D. Truncated staphylococcal nuclease is compact but disordered. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 748-752
7. Xu Q., and Keiderling T.A. Effect of sodium dodecyl sulfate on folding and thermal stability of acid denatured cytochrome c: a spectroscopic approach. Protein Sci. 13 (2004) 2949-2959
8. Naoe K., Noda K., Kawagoe M., and Imai M. Higher order structure of proteins solubilized in AOT reverse micelle. Colloids Surf., B Biointerfaces 38 (2004) 179-185
9. Elove G.A., Chaffotte A.F., Roder H., and Goldberg M.E. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry 31 (1992) 6876-6883
10. Vincent M., Bronchon J.-C., Merola F., Jordi W., and Gallay J. Nanosecond dynamics of horse heart apocytochrome c in aqueous solution as studied by time-resolved fluorescence of the single tryptophan residue (Trp-59). Biochemistry 27 (1988) 8752-8761
11. Shastry M.C.R., and Eftink M.R. Reversible thermal unfolding of ribonuclease T1 in reverse micelles. Biochemistry 35 (1996) 4094-4101
12. Dong A., and Lam T. Equilibrium titrations of acid induced unfolding-refolding and salt-induced molten globule of cytochrome c by FT-IR spectroscopy. Arch. Biochem. Biophys. 436 (2005) 154-160
13. Kotting C., and Gerwert K. Time-resolved FTIR studies provide activation free energy, activation enthalpy and activation entropy for GTPase reactions. Chem. Phys. Lett. 307 (2004) 227-232
14. Kotting C., and Gerwert K. Proteins in action monitored by time-resolved FTIR spectroscopy. ChemPhysChem 6 (2005) 881-888
15. Shaw A.K., Sarkar R., and Pal S.K. Direct observation of DNA condensation in a nano-cage by using a molecular ruler. Chem. Phys. Lett. 408 (2005) 366-370
16. Yun C.S., Javier A., Jennings T., Fisher M., Hira S., Peterson S., Hopkins B., Reich N.O., and Strouse G.F. Nanometal surface energy transfer in optical rulers, breaking the FRET barrier. J. Am. Chem. Soc. 127 (2005) 3115-3119
17. Tsong T.Y. Ferricytochrome c chain folding measured by the energy transfer of tryptophan 59 to the heme group. Biochemistry 15 (1976) 5467-5473
18. Shen X.H., and Knutson J. Subpicosecond fluorescence spectra of tryptophan in water. J. Phys. Chem., B 105 (2001) 6260-6265
19. Pal S.K., and Zewail A.H. Dynamics of water in biological recognition. Chem. Rev. 104 (2004) 2099-2123
20. Dale R.E., Eisinger J., and Blumberg W.E. The orientational freedom of molecular probes. The orientation factor in intramolecular energy transfer. Biophys. J. 26 (1979) 161-193
21. Dale R.E., and Eisinger J. Intramolecular distances determined by energy transfer. Dependence of orientational freedom of donor and acceptor. Biopolymers 13 (1974) 1573-1605
22. Lakowicz J.R. Principles of Fluorescence Spectroscopy (1999), Kluwer Academic/Plenum, New York
23. Majumder P., Sarkar R., Shaw A.K., Chakraborty A., and Pal S.K. Ultrafast dynamics in a nanocage of enzymes: solvation and fluorescence resonance energy transfer in reverse micelles. J. Colloid Interface Sci. 290 (2005) 462-474
24. Pletneva E.V., Gray H.B., and Winkler J.R. Many faces of the unfolded state: conformational heterogeneity in denatured yeast cytochrome c. J. Mol. Biol. 345 (2005) 855-867
25. Haugland R.P. Handbook of Fluorescent Probes and Research Chemicals (1996), Molecular Probes, Eugene, OR
26. Zhong D., Pal S.K., and Zewail A.H. Femtosecond studies of protein-DNA binding and dynamics: histone I. ChemPhysChem 2 (2001) 219-227
27. Pal S.K., Peon J., and Zewail A.H. Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 1763-1768
28. Sarkar R., Ghosh M., Shaw A.K., and Pal S.K. Ultrafast surface solvation dynamics and functionality of an enzyme chymotrypsin upon interfacial binding to a cationic micelle. J. Photochem. Photobiol., B Biol. 79 (2005) 67-78
29. Andrade A.A., Barbosa Neto N.M., Misoguti L., De Boni L., Zilio S.C., and Mendonca C.R. Two-photon absorption investigation in reduced and oxidized cytochrome c solutions. Chem. Phys. Lett. 390 (2004) 506-510
30. Biswas R., and Pal S.K. Caging enzyme function: α-chymotrypsin in reverse micelle. Chem. Phys. Lett. 387 (2004) 221-226
31. Johnson W.C. Analyzing protein circular dichorism spectra for accurate secondary structures. Proteins Struct. Funct. Genet. 35 (1999) 307-312
32. O'Connor D.V., and Philips D. Time Correlated Single Photon Counting (1984), Academic Press, London
33. Sarkar R., Ghosh M., and Pal S.K. Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface. J. Photochem. Photobiol., B Biol. 78 (2005) 93-98
34. Banci L., Bertini I., Gray H.B., Luchinat C., Reddig T., Rosato A., and Turano P. Solution structure of oxidized horse heart cytochrome C, NMR, minimized average structure. Biochemistry 36 (1997) 9867-9877
35. Shortle D., and Ackerman M.S. Persistance of native like topology in a denatured protein in 8 M urea. Science 293 (2001) 487-489
36. Pileni M.P., Zemb T., and Petit C. Solubilization by reverse micelles: solute localization and structure perturbation. Chem. Phys. Lett. 118 (1985) 414-420
37. Celej M.S., D'Adrea M.G., Campana P.T., Fidelio G.D., and Bianconi M.L. Superactivity and conformational changes on α-chymotrypsin upon interfacial binding to cationic micelles. Biochem. J. 378 (2004) 1059-1066
38. Sakono M., Goto M., and Furusaki S. Refolding of cytochrome c using reversed micelles. J. Biosci. Bioeng. 89 (2000) 458-462