Nanosecond temperature jump relaxation dynamics of cyclic β-hairpin peptides

Biophysical Journal

Volumn 84, Issue 6, 2003, Pages 3874-3882

  Maness, Shelia J ^a   Franzen, Stefan ^a   Gibbs, Alan C ^b   Causgrove, Timothy P ^c   Dyer, R Brian ^d  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

^c MISSISSIPPI UNIVERSITY FOR WOMEN   (United States)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE DERIVATIVE;

ARTICLE; BETA SHEET; ENERGY; ENTROPY; INFRARED SPECTROSCOPY; KINETICS; LASER; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

ARRHENIUS;

EID: 0038778497     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75115-7     Document Type: Article

References (41)

1. Arrondo, J. L. R., F. J. Blanco, L. Serrano, and F. M. Goni. 1996. Infrared evidence of a β-hairpin peptide structure in solution. FEBS Lett. 384: 35-37.
2. Callender, R. H., R. B. Dyer, R. Gilmanshin, and W. H. Woodruff. 1998. Fast events in protein folding: the time evolution of primary processes. Annu. Rev. Phys. Chem. 49:173-202.
3. Chen, B. L., W. A. Baase, and J. A. Schellman. 1989. Low-temperature unfolding of a mutant of phage-T4 lysozyme.2. Kinetic investigations. Biochemistry. 28:691-699.
4. Colley, C. S., S. R. Griffiths-Jones, M. W. George, and M. S. Searle. 2000. Do interstrand hydrogen bonds contribute to b-hairpin peptide stability in solution? IR analysis of peptide folding in water. Chemical Communications: 593-594.
5. 2+ by polypyridine complexes of iron(III): Evidence for multiple paths for outer-sphere electron-transfer. Inorg. Chem. 13:1250-1252.
6. Dinner, A., T. Lazaridis, and M. Karplus. 1999. Understanding beta-hairpin formation. Proc. Natl. Acad. Sci. USA. 96:9068-9073.
7. Dyer, R. B., F. Gai, W. H. Woodruff, R. Gilmanshin, and R. H. Callender. 1998. Infrared studies of fast events in protein folding. Acc. Chem. Res. 31:709-716.
8. Eaton, W. A., V. Munoz, P. A. Thompson, E. R. Henry, and J. Hofrichter. 1998. Kinetics and dynamics of loops, alpha-helices, beta-hairpins, and fast-folding proteins. Acc. Chem. Res. 31:745-753.
9. Espinosa, J. F., and S. H. Gellman. 2000. A designed beta-hairpin containing a natural hydrophobic cluster. Angew. Chem. Int. Ed. 39 (13):2330-2333.
10. Fernandez-Lopez, S., H. S. Kim, E. C. Choi, M. Delgado, J. R. Granja, A. Khasanov, K. Kraehenbuehl, G. Long, D. A. Weinberger, K. M. Wilcoxen, and M. R. Ghadiri. 2001. Antibacterial agents based on the cyclic D,L-alpha-peptide architecture. Nature. 412:452-455.
11. Gibbs, A. C., T. C. Bjorndahl, R. S. Hodges, and D. S. Wishart. 2002. Probing the structural determinants of type II′ beta-turn formation in peptides and proteins. J. Am. Chem. Soc. 124:1203-1213.
12. Gibbs, A. C., L. H. Kondejewski, W. Gronwald, A. M. Nip, R. S. Hodges, B. D. Sykes, and D. S. Wishart. 1998. Unusual beta-sheet periodicity in small cyclic peptides. Nat. Struct. Biol. 5:284-288.
13. Gilmanshin, R., S. Williams, R. H. Callender, W. H. Woodruff, and R. B. Dyer. 1997. Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Proc. Natl. Acad. Sci. USA. 94:3709-3713.
14. Griffiths-Jones, S. R., A. J. Maynard, and M. S. Searle, 1999. Dissecting the stability of a β-hairpin peptide that folds in water. J. Mol. Biol. 292:1051-1069.
15. Hagerman, P. J., and R. L. Baldwin. 1976. Quantitative treatment of kinetics of folding transition of ribonuclease-A. Biochemistry. 15:1462-1473.
16. Jäger, M., H. Nguyen, J. C. Crane, J. W. Kelly, and M. Gruebele. 2001. The folding mechanism of a β-sheet: the WW domain. J. Mol. Biol. 311: 373-393.
17. Jelokhani-Niaraki, M., L. H. Kondejewski, S. W. Farmer, R. E. W. Hancock, C. M. Kay, and R. S. Hodges. 2000. Diastereoisomeric analogues of gramicidin S: structure, biological activity and interaction with lipid bilayers. Biochem. J. 349:747-755.
18. Jelokhani-Niaraki, M., E. J. Prenner, L. H. Kondejewski, C. M. Kay, R. N. McElhaney, and R. S. Hodges. 2001. Conformation and other biophysical properties of cyclic antimicrobial peptides in aqueous solutions. J. Pept. Res. 58:293-306.
19. Klimov, D. K., and D. Thirumalai. 2000. Mechanisms and kinetics of betahairpin formation. Proc. Natl. Acad. Sci. USA. 97:2544-2549.
20. Kondejewski, L. H., D. L. Lee, M. Jelokhani-Niaraki, S. W. Farmer, R. E. W. Hancock, and R. S. Hodges. 2002. Optimization of microbial specificity in cyclic peptides by modulation of hydrophobicity within a defined structural framework. J. Biol. Chem. 277:67-74.
21. Kortemme, T., M. Ramírez-Alvarado, and L. Serrano. 1998. Design of a 20-amino acid, three-stranded β-sheet protein. Science. 281:253-256.
22. Krantz, B. A., L. B. Moran, A. Kentsis, and T. R. Sosnick. 2000. D/H amide kinetic isotope effects reveal when hydrogen bonds form during protein folding. Nat. Struct. Biol. 7:62-71.
23. Lapidus, L. J., W. A. Eaton, and J. Hofrichter. 2000. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl. Acad. Sci. USA. 97:7220-7225.
24. Lednev, I. K., A. S. Karnoup, M. C. Sparrow, and S. A. Asher. 1999. Alpha-helix peptide folding and unfolding activation barriers: a nanosecond UV resonance raman study. J. Am. Chem. Soc. 121:8074-8086.
25. Lewis, R. N. A. H., E. J. Prenner, L. H. Kondejewski, C. R. Flach, R. Mendelsohn, R. S. Hodges, and R. N. McElhaney. 1999. Fourier transform infrared spectroscopic studies of the interaction of the antimicrobial peptide gramicidin S with lipid micelles and with lipid monolayer and bilayer membranes. Biochemistry. 38:15193-15203.
26. Marcus, R. A., and N. Sutin. 1975. Electron-transfer reactions with unusual activation parameters. A treatment of reactions accompanied by large entropy decreases. Inorg. Chem. 14:213-216.
27. McInnes, C., L. H. Kondejewski, R. S. Hodges, and B. D. Sykes. 2000. Development of the structural basis for antimicrobial and hemolytic activities of peptides based on gramicidin S and design of novel analogs using NMR spectroscopy. J. Biol. Chem. 275:14287-14294.
28. Muñoz, V., E. Henry, J. Hofrichter, and W. Eaton. 1998. A statistical mechanical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. USA. 95:5872-5879.
29. Muñoz, V., P. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:196-199.
30. Oliveberg, M., Y.-J. Tan, and A. R. Fersht. 1995. Negative activation enthalpies in the kinetics of protein folding. Proc. Natl. Acad. Sci. USA. 92:8926-8929.
31. Pande, V. S., and D. S. Rokhsar. 1999. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA. 96:9062-9067.
32. Phillips, C. M., Y. Mizutani, and R. M. Hochstrasser. 1995. Ultrafast thermally induced unfolding of RNase A. Proc. Natl. Acad. Sci. USA. 92:7292-7296.
33. Ramirez-Alvarado, M., T. Kortemme, F. J. Blanco, and L. Serrano. 1999, Beta-hairpin and beta-sheet formation in designed linear peptides. Bioorg. Med. Chem. 7:93-103.
34. Schenck, H. L., and S. H. Gellman. 1998. Use of a designed triple-stranded antiparallel β-sheet to probe β-sheet cooperativity in aqueous solution. J. Am. Chem. Soc. 120:4869-4870.
35. Smith, C. K., and L. Regan. 1997. Construction and design of β-sheets. Acc. Chem. Res. 30:153-161.
36. Susi, H., and D. M. Byler. 1986. Resolution enhanced Fourier transform infrared spectroscopy of enzymes. Methods Enzymol. 130:290-311.
37. Syud, F. A., H. E. Stanger, and S. H. Gellman. 2001. Interstrand side chain-side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings. J. Am. Chem. Soc. 123:8667-8677.
38. Werner, J. H., R. B. Dyer, R. M. Fesinmeyer, and N. H. Andersen. 2002. Dynamics of the primary processes of protein folding: helix nucleation. J. Phys. Chem. B. 106:487-494.
39. Williams, S., T. P. Causgrove, R. Gilmanshin, K. S. Fang, R. H. Callender, W. H. Woodruff, and R. B. Dyer. 1996. Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry. 35:691-697.
40. Wray, W. O., T. Aida, and R. B. Dyer. 2002. Photoacoustic cavitation and heat transfer effects in the laser-induced temperature jump in water. Appl. Phys. B. 74:57-66.
41. Zurdo, J., J. I. Guijarro, J. L. Jimenez, H. R. Saibil, and C. M. Dobson. 2001. Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain. J. Mol. Biol. 311:325-340.