Circular dichroism and UV resonance raman study of the impact of alcohols on the gibbs free energy landscape of an α-helical peptide

Biochemistry

Volumn 49, Issue 15, 2010, Pages 3336-3342

  Xiong, Kan ^a   Asher, Sanford A ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM; CONFORMATIONAL EQUILIBRIUM; HELICAL PEPTIDE; PURE WATER; TRIFLUOROETHANOL; UV RESONANCE RAMAN; UV-RESONANCE RAMAN SPECTROSCOPY;

CONFORMATIONS; DICHROISM; FREE ENERGY; GIBBS FREE ENERGY; METHANOL; PEPTIDES; RAMAN SPECTROSCOPY; RESONANCE;

ETHANOL;

ALCOHOL; ALCOHOL DERIVATIVE; METHANOL; PEPTIDE DERIVATIVE; TRIFLUOROETHANOL;

ALPHA HELIX; ARTICLE; CIRCULAR DICHROISM; ENERGY; HUMAN; HYDROPHOBICITY; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; RAMAN SPECTROMETRY; ULTRAVIOLET SPECTROSCOPY;

ALCOHOLS; AMINO ACID SEQUENCE; CIRCULAR DICHROISM; ETHANOL; INDICATORS AND REAGENTS; METHANOL; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; SPECTROPHOTOMETRY, ULTRAVIOLET; SPECTRUM ANALYSIS, RAMAN; THERMODYNAMICS; WATER;

EID: 77950949985     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100176a     Document Type: Article

References (47)

1. Klibanov, A. M. (2001) Improving enzymes by using them in organic solvents Nature 409 (6817) 241 - 246
2. Carrea, G. and Riva, S. (2000) Properties and synthetic applications of enzymes in organic solvents Angew. Chem., Int. Ed. 39 (13) 2226 - 2254
3. Scharnagl, C., Reif, M., and Friedrich, J. (2005) Stability of proteins: Temperature, pressure and the role of the solvent Biochim. Biophys. Acta 1749 (2) 187 - 213
4. Kony, D. B., Hunenberger, P. H., and van Gunsteren, W. F. (2007) Molecular dynamics simulations of the native and partially folded states of ubiquitin: Influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics Protein Sci. 16 (6) 1101 - 1118
5. Waterhous, D. V. and Johnson, W. C. (1994) Importance of Environment in Determining Secondary Structure in Proteins Biochemistry 33 (8) 2121 - 2128
6. Roccatano, D. (2008) Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions Curr. Protein Pept. Sci. 9 (4) 407 - 426
7. Pace, C. N., Trevino, S., Prabhakaran, E., and Scholtz, J. M. (2004) Protein structure, stability and solubility in water and other solvents Philos. Trans. R. Soc. London, Ser. B 359 (1448) 1225 - 1234
8. Hirota, N., Mizuno, K., and Goto, Y. (1998) Group additive contributions to the alcohol-induced α-helix formation of melittin: Implication for the mechanism of the alcohol effects on proteins J. Mol. Biol. 275 (2) 365 - 378
9. Buck, M. (1998) Trifluoroethanol and colleagues: Cosolvents come of age. Recent studies with peptides and proteins Q. Rev. Biophys. 31 (3) 297 - 355
10. Fioroni, M., Diaz, M. D., Burger, K., and Berger, S. (2002) Solvation phenomena of a tetrapeptide in water/trifluoroethanol and water/ethanol mixtures: A diffusion NMR, intermolecular NOE, and molecular dynamics study J. Am. Chem. Soc. 124 (26) 7737 - 7744
11. Luo, P. Z. and Baldwin, R. L. (1997) Mechanism of helix induction by trifluoroethanol: A framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water Biochemistry 36 (27) 8413 - 8421
12. Kinoshita, M., Okamoto, Y., and Hirata, F. (2000) Peptide conformations in alcohol and water: Analyses by the reference interaction site model theory J. Am. Chem. Soc. 122 (12) 2773 - 2779
13. Roccatano, D., Colombo, G., Fioroni, M., and Mark, A. E. (2002) Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study Proc. Natl. Acad. Sci. U.S.A. 99 (19) 12179 - 12184
14. Walgers, R., Lee, T. C., and Cammers-Goodwin, A. (1998) An Indirect Chaotropic Mechanism for the Stabilization of Helix Conformation of Peptides in Aqueous Trifluoroethanol and Hexafluoro-2-propanol J. Am. Chem. Soc. 120, 5073 - 5079
15. Reiersen, H. and Rees, A. R. (2000) Trifluoroethanol may form a solvent matrix for assisted hydrophobic interactions between peptide side chains Protein Eng. 13 (11) 739 - 743
16. Roccatano, D., Fioroni, M., Zacharias, M., and Colombo, G. (2005) Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study Protein Sci. 14 (10) 2582 - 2589
17. Olivella, M., Deupi, X., Govaerts, C., and Pardo, L. (2002) Influence of the environment in the conformation of α-helices studied by protein database search and molecular dynamics simulations Biophys. J. 82 (6) 3207 - 3213
18. Liu, H. L. and Hsu, C. M. (2003) The effects of solvent and temperature on the structural integrity of monomeric melittin by molecular dynamics simulations Chem. Phys. Lett. 375 (1-2) 119 - 125
19. Bykov, S., Lednev, I., Ianoul, A., Mikhonin, A., Munro, C., and Asher, S. A. (2005) Steady-state and transient ultraviolet resonance Raman spectrometer for the 193-270 nm spectral region Appl. Spectrosc. 59 (12) 1541 - 1552
20. Manning, M. C. and Woody, R. W. (1991) Theoretical CD studies of polypeptide helices: Examination of important electronic and geometric factors Biopolymers 31, 569 - 586
21. Asher, S., Mikhonin, A., and Bykov, S. (2004) UV Raman demonstrates that α-helical polyalanine peptides melt to polyproline II conformations J. Am. Chem. Soc. 126 (27) 8433 - 8440
22. Lednev, I. K., Karnoup, A. S., Sparrow, M. C., and Asher, S. A. (1999) α-Helix peptide folding and unfolding activation barriers: A nanosecond UV resonance Raman study J. Am. Chem. Soc. 121 (35) 8074 - 8086
23. Myshakina, N. S., Ahmed, Z., and Asher, S. A. (2008) Dependence of amide vibrations on hydrogen bonding J. Phys. Chem. B 112 (38) 11873 - 11877
24. Wang, Y., Purrello, R., Jordan, T., and Spiro, T. G. (1991) UVRR spectroscopy of the peptide bond. 1. Amide S, a nonhelical structure marker, is a CαH bending mode J. Am. Chem. Soc. 113, 6359 - 6368
25. Mikhonin, A. V., Bykov, S. V., Myshakina, N. S., and Asher, S. A. (2006) Peptide secondary structure folding reaction coordinate: Correlation between UV Raman amide III frequency, φ Ramachandran angle, and hydrogen bonding J. Phys. Chem. B 110 (4) 1928 - 1943
26. 10-helix and π-bulge premelting during α-helix unfolding J. Am. Chem. Soc. 128 (42) 13789 - 13795
27. Xiong, K., Asciutto, E. K., Madura, J. D., and Asher, S. A. (2009) Salt Dependence of α-Helical Peptide Folding Energy Landscapes Biochemistry 48, 10818 - 10826
28. Ma, L., Ahmed, Z., Mikhonin, A. V., and Asher, S. A. (2007) UV resonance Raman measurements of poly- l -lysine's conformational energy landscapes: Dependence on perchlorate concentration and temperature J. Phys. Chem. B 111 (26) 7675 - 7680
29. Liu, Z. G., Chen, K., Ng, A., Shi, Z. S., Woody, R. W., and Kallenbach, N. R. (2004) Solvent dependence of PII conformation in model alanine peptides J. Am. Chem. Soc. 126 (46) 15141 - 15150
30. Dwyer, D. S. (1999) Molecular simulation of the effects of alcohols on peptide structure Biopolymers 49 (7) 635 - 645
31. Deshpande, A., Nimsadkar, S., and Mande, S. C. (2005) Effect of alcohols on protein hydration: Crystallographic analysis of hen egg-white lysozyme in the presence of alcohols Acta Crystallogr. 61, 1005 - 1008
32. Starzyk, A., Barber-Armstrong, W., Sridharan, M., and Decatur, S. M. (2005) Spectroscopic evidence for backbone desolvation of helical peptides by 2,2,2-trifluoroethanol: An isotope-edited FTIR study Biochemistry 44 (1) 369 - 376
33. Sorin, E. J., Rhee, Y. M., Shirts, M. R., and Pande, V. S. (2006) The solvation interface is a determining factor in peptide conformational preferences J. Mol. Biol. 356 (1) 248 - 256
34. 10-helix and α-helix in Ala-rich peptides: A hydrogen exchange and high field NMR study J. Mol. Biol. 267 (4) 963 - 974
35. Balakrishnan, G., Hu, Y., Bender, G. M., Getahun, Z., DeGrado, W. F., and Spiro, T. G. (2007) Enthalpic and entropic stages in α-helical peptide unfolding, from laser T-Jump/UV raman spectroscopy J. Am. Chem. Soc. 129 (42) 12801 - 12808
36. Ozdemir, A., Lednev, I. K., and Asher, S. A. (2002) Comparison between UV Raman and circular dichroism detection of short α helices in Bombolitin III Biochemistry 41 (6) 1893 - 1896
37. Ianoul, A., Mikhonin, A., Lednev, I. K., and Asher, S. A. (2002) UV resonance Raman study of the spatial dependence of α-helix unfolding J. Phys. Chem. A 106 (14) 3621 - 3624
38. Woddy, R. W. (1996) Circular Dichroism and the Conformational Analysis of Biomolecules, pp 25 - 68, Plenum Press, New York.
39. Chen, Y.-H., Yang, J. T., and Chau, K. H. (1974) Determination of the helix and β-form of proteins in aqueous solution by circular dichroism Biochemistry 13, 3350 - 3359
40. Mikhonin, A. V. and Asher, S. A. (2005) Uncoupled peptide bond vibrations in α-helical and polyproline II conformations of polyalanine peptides J. Phys. Chem. B 109 (7) 3047 - 3052
41. Myshakina, N. S. and Asher, S. A. (2007) Peptide bond vibrational coupling J. Phys. Chem. B 111 (16) 4271 - 4279
42. Gerig, J. T. (2004) Structure and solvation of melittin in 1,1,1,3,3,3-hexafluoro-2-propanol/water Biophys. J. 86 (5) 3166 - 3175
43. Diaz, M. D. and Berger, S. (2001) Preferential solvation of a tetrapeptide by trifluoroethanol as studied by intermolecular NOE Magn. Reson. Chem. 39 (7) 369 - 373
44. Hong, Q. and Schellman, J. A. (1992) Helix-Coil Theories: A Comparative-Study for Finite Length Polypeptides J. Phys. Chem. 96 (10) 3987 - 3994
45. Doig, A. J. (2002) Recent advances in helix-coil theory Biophys. Chem. 101, 281 - 293
46. Yang, J. X., Zhao, K., Gong, Y. X., Vologodskii, A., and Kallenbach, N. R. (1998) α-Helix nucleation constant in copolypeptides of alanine and ornithine or lysine J. Am. Chem. Soc. 120 (41) 10646 - 10652
47. Scholtz, J. M., Qian, H., York, E. J., Stewart, J. M., and Baldwin, R. L. (1991) Parameters of helix-coil transition theory for alanine-based peptides of varying chain length in water Biopolymers 31, 1463 - 1470