Intermediacy of Poly(L-proline) II and β-strand conformations in poly(L-lysine) β-sheet formation probed by temperature-jump/UV resonance Raman spectroscopy

Biochemistry

Volumn 45, Issue 1, 2006, Pages 34-41

  Jiji, Renee D ^a,b   Balakrishnan, Gurusamy ^a   Hu, Ying ^a,c   Spiro, Thomas G ^a  

^a PRINCETON UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; RAMAN SPECTROSCOPY; RESONANCE; SIGNAL PROCESSING; SPECTRUM ANALYSIS; TEMPERATURE CONTROL; ULTRAVIOLET RADIATION;

CONFORMATIONAL TRANSITION; POLYPEPTIDE; SAPPHIRE LASER; ULTRAVIOLET RESONANCE RAMAN SPECTROSCOPY (UVRR);

LASER APPLICATIONS;

POLYLYSINE; POLYMER; POLYPROLINE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMYLOIDOSIS; ARTICLE; BETA SHEET; HYDROGEN BOND; IONIZATION; MELTING POINT; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RAMAN SPECTROMETRY; SPECTRUM; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE; TEMPERATURE JUMP; ULTRAVIOLET RESONANCE RAMAN SPECTROSCOPY;

AMYLOID; PEPTIDES; POLYLYSINE; PROTEIN STRUCTURE, SECONDARY; SPECTROPHOTOMETRY, ULTRAVIOLET; SPECTRUM ANALYSIS, RAMAN; TEMPERATURE;

EID: 30144436601     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051507v     Document Type: Article

References (54)

1. Dobson, C. M. (2001) The structural basis of protein folding and its links with human disease, Philos. Trans. R. Soc. London, Ser. B: Biol. Sci. 356, 133-145.
2. Tycko, R. (2004) Progress towards a molecular-level structural understanding of amyloid fibrils, Curr. Opin. Struct. Biol. 14, 96-103.
3. Fezoui, Y., and Teplow, D. B. (2002) Kinetic studies of amyloid β-protein fibril assembly-Differential effects of α-helix stabilization, J. Biol. Chem. 277, 36948-36954.
4. Morillas, M., Vanik, D. L., and Surewicz, W. K. (2001) On the mechanism of α-helix to β-sheet transition in the recombinant prion protein, Biochemistry 40, 6982-6987.
5. Fandrich, M., Fletcher, M. A., and Dobson, C. M. (2001) Amyloid fibrils from muscle myoglobin, Nature 410, 165-166.
6. Fandrich, M., Forge, V., Buder, K., Kittler, M., Dobson, C. M., and Diekmann, S. (2003) Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments, Proc. Natl. Acad. Sci. U.S.A.100, 15463-15468.
7. (1-28) fragment of the amyloid peptide predominantly adopts a polyproline II conformation in an acidic solution, Biochemistry 43, 6893-6898.
8. 1H NMR of Aβ amyloid peptide congeners in water solution. Conformational-changes correlate with plaque competence, Biochemistry 34, 5191-5200.
9. Kirkitadze, M. D., Condron, M. M., and Teplow, D. B. (2001) Identification and characterization of key kinetic intermediates in amyloids-protein fibrillogenesis, J. Mol. Biol. 312, 1103-1119.
10. Blanch, E. W., Morozova-Roche, L. A., Cochran, D. A. E., Doig, A. J., Hecht, L., and Barren, L. D. (2000) Is polyproline II helix the killer conformation? A Raman optical activity study of the amyloidogenic prefibrillar intermediate of human lysozyme, J. Mol. Biol. 301, 553-563.
11. Tiffany, M. L., and Krimm, S. (1968) New chain conformations of poly(glutamic acid) and polylysine, Biopolymers 6, 1379-1382.
12. Danielsson, J., Jarvet, J., Damberg, P., and Graslund, A. (2005) The Alzheimer β-peptide shows temperature-dependent transitions between left-handed 31-helix, β-strand and random coil secondary structures, FEBS J. 272, 3938-3949.
13. McColl, L. H., Blanch, E. W., Gill, A. C., Rhie, A. G. O., Ritchie, M. A., Hecht, L., Nielsen, K., and Barren, L. D. (2003) A new perspective on β-sheet structures using vibrational Raman optical activity: From poly(L-lysine) to the prion protein, J. Am. Chem. Soc. 125, 10019-10026.
14. Wilson, G., Hecht, L., and Barren, L. D. (1996) Residual structure in unfolded proteins revealed by Raman optical activity, Biochemistry 35, 12518-12525.
15. Shi, Z., Olson, C. A., Rose, G. D., Baldwin, R. L., and Kallenbach, N. R. (2002) Polyproline II structure in a sequence of seven alanine residues, Proc. Natl. Acad. Sci. U.S.A. 99, 9190-9195.
16. Eker, F., Griebenow, K., Cao, X., Nafie, L. A., and Schweitzer-Stenner, R. (2004) Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution, Proc. Natl. Acad. Sci. U.S.A. 101, 10054-10059.
17. Asher, S. A., Mikhonin, A. V., and Bykov, S. (2004) UV Raman demonstrates that α-helical polyalanine peptides melt to polyproline II conformations, J. Am. Chem. Soc. 126, 8433-8440.
18. McColl, I. H., Blanch, E. W., Hecht, L., Kallenbach, N. R., and Barren, L. D. (2004) Vibrational Raman optical activity characterization of poly(L-proline) II helix in alanine oligopeptides, J. Am. Chem. Soc. 126, 5076-5077.
19. Davidson, B., and Fasman, G. D. (1967) Conformational transitions of uncharged poly-L-lysine. α-Helix-random coil-β structure, Biochemistry 6, 1616-1629.
20. Chi, Z., Chen, X. G., Holtz, J. S. W., and Asher, S. A. (1998) UV resonance Raman: Selective amide vibrational enhancement: Quantitative methodology for determining protein secondary structure, Biochemistry 37, 2854-2864.
21. Wang, Y., Purrello, R., and Spiro, T. G. (1989) UV photoisomerization of N-methylacetamide and resonance Raman enhancement of a new conformation: sensitive amide mode, J. Am. Chem. Soc. 111, 8274-8276.
22. Song, S. H., and Asher, S. A. (1989) UV resonance Raman studies of peptide conformation in poly(L-lysine), poly(L-glutamic acid), and model complexes: the basis for protein secondary structure determinations, J. Am. Chem. Soc. 111, 4295-4305.
23. Balakrishnan, G., Hu, Y., Nielsen, S. B., and Spiro, T. G. (2005) Tunable kHz deep ultraviolet (193-210 nm) laser for Raman applications, Appl. Spectrosc. 59, 776-781.
24. Balakrishnan, G., Hu, Y., and Spiro, T. G. (2005) (manuscript in preparation).
25. Phillips, C. M., Mizutani, Y., and Hochstrasser, R. M. (1995) Ultrafast thermally induced unfolding of RNAse-A, Proc. Natl. Acad. Sci. U.S.A. 92, 7292-7296.
26. 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, 8074-8086.
27. Wang, Y., Purrello, R., Georgiou, S., and Spiro, T. G. (1991) UVRR spectroscopy of the peptide-bond. 2. Carbonyl H-bond effects on the ground-state and excited-state structures of N-methylacetamide, J. Am. Chem. Soc. 113, 6368-6377.
28. Austin, J. C., Jordan, T., and Spiro, T. G. (1993) Ultraviolet resonance Raman studies of proteins and related model compounds, in Biomolecular Spectroscopy (Clark, R. J. H., and Hester, R. E., Eds.) pp 55-127, Wiley & Sons Ltd., New York.
29. Krimm, S., and Bandekar, J. (1986) Vibrational spectroscopy and conformation of peptides, polypeptides and proteins, in Advances in Protein Chemistry (Anfinson, C. B., Edsall, J. T., and Richards, F. M., Eds.) pp 181-365, Academic Press, New York.
30. αH bending mode, J. Am. Chem. Soc. 113, 6359-6368.
31. Asher, S. A., Ianoul, A., Mix, G., Boyden, M. N., Karnoup, A., Diem, M., and Schweitzer-Stenner, R. (2001) Dihedral ψ angle dependence of the amide III vibration: A uniquely sensitive UV resonance Raman secondary structural probe, J. Am. Chem. Soc. 123, 11775-11781.
32. Abe, Y., and Krimm, S. (1972) Normal vibrations of polyglycine-II, Biopolymers 11, 1841-1853.
33. Abe, Y., and Krimm, S. (1972) Normal vibrations of crystalline polyglycine-I, Biopolymers 11, 1817-1839.
34. Dwivedi, A. M., and Krimm, S. (1982) Vibrational analysis of peptides, polypeptides, and proteins. XV. Crystalline polyglycine-II, Biopolymers 21, 2377-2397.
35. Moore, W. H., and Krimm, S. (1976) Vibrational analysis of peptides, polypeptides, and proteins. I. polyglycine I, Biopolymers 15, 2439-2464.
36. Snell, C. R., and Fasman, G. D. (1973) Kinetics and thermodynamics of α-helix D β transconformation of poly(L-lysine) and L-leucine copolymers. A compensation phenomenon, Biochemistry 12, 1017-1025.
37. Sugawara, Y., Harada, I., Matsuura, H., and Shimanouchi, T. (1978) Preresonance Raman studies of poly(L-lysine), poly(L-glutamic acid), and deuterated N-methylacetamides, Biopolymers 17, 1405-1421.
38. Yu, T. J., Lippert, J. L., and Peticola, WI. (1973) Laser Raman studies of conformational variations of poly-L-lysine, Biopolymers 12, 2161-2176.
39. Kundu, A., and Kishore, N. (2004) Interaction of 2,2,2-trifluoroethanol with proteins: calorimetric, densimetric and surface tension approach, Biophys. Chem. 109, 427-442.
40. 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, 8413-8421.
41. Kentsis, A., and Sosnick, T. R. (1998) Trifluoroethanol promotes helix formation by destabilizing backbone exposure: Desolvation rather than native hydrogen bonding defines the kinetic pathway of dimeric coiled coil folding, Biochemistry 37, 14613-14622.
42. Jackson, M., Haris, P. I., and Chapman, D. (1989) Conformational transitions in poly(L-lysine): studies using Fourier transform infrared spectroscopy, Biochim. Biophys. Acta 998, 75-79.
43. Tu, A. T. (1986) Peptide backbone conformation and microenvironment of protein side-chains, in Spectroscopy of Biological Systems (Clark, R. J. H., and Hester, R. E., Eds.) pp 47-111, Wiley & Sons Ltd., New York.
44. 1-helix, and β-sheet ψ angle energy landscape in poly-L-lysine and poly-L-glutamic acid, J. Am. Chem. Soc. 127, 7712-7720.
45. Tiffany, M. L., and Krimm, S. (1968) Circular dichroism of poly-L-proline in an unordered conformation, Biopolymers 6, 1767-1770.
46. Measey, T., and Schweitzer-Stenner, R. (2005) Simulation of amide Ãband profiles of trans polyproline based on an excitonic coupling model, Chem. Phys. Lett. 408, 123-127.
47. Wooley, S. Y. C., and Holzwart, G. (1970) Intramolecular β-pleated-sheet formation by poly-L-lysine in solution, Biochemistry 9, 3604-3608.
48. Greenfield N., Davidson, B., and Fasman, G. D. (1967) Use of computed optical rotatory dispersion curves for evaluation of protein conformation, Biochemistry 6, 1630-1637.
49. Copeland, R. A., and Spiro, T. G. (1986) Ultraviolet Raman hypochromism of the tropomyosin amide modes: A new method for estimating α-helical content in proteins, J. Am. Chem. Soc. 108, 1281-1285.
50. Huang, C. Y., Klemke, J. W., Getahun, Z., DeGrado, W. F., and Gai, F. (2001) Temperature-dependent helix-coil transition of an alanine based peptide, J. Am. Chem. Soc. 123, 9235-9238.
51. Lednev, I. K., Karnoup, A. S., Sparrow, M. C., and Asher, S. A. (2001) Transient UV Raman spectroscopy finds no crossing barrier between the peptide α-helix and fully random coil conformation, J. Am. Chem. Soc. 123, 2388-2392.
52. Syme, C. D., Blanch, E. W., Holt, C., Jakes, R., Goedert, M., Hecht, L., and Barron, L. D. (2002) A Raman optical activity study of rheomorphism in caseins, synucleins and tau: New insight into the structure and behaviour of natively unfolded proteins, Eur. J. Biochem. 269, 148-156.
53. Jordan, T., and Spiro, T. G. (1995) UV resonance Raman spectroscopy of cis-amides, J. Raman Spectrosc. 26, 867-876.
54. Blondelle, S. E., Forood, B., Houghten, R. A., and Perez-Paya, E. (1997) Polyalanine-based peptides as models for self-associated β-pleated-sheet complexes, Biochemistry 36, 8393-8400.