Polyproline and the "spectroscopic ruler" revisited with single-molecule flourescence

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 8, 2005, Pages 2754-2759

  Schuler, Benjamin ^a,c,d   Lipman, Everett A ^a,e   Steinbach, Peter J ^b   Kumkell, Michael ^c   Eaton, William A ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c UNIVERSITY OF POTSDAM   (Germany)

^d UNIVERSITY OF ZURICH   (Switzerland)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

F rster resonance energy transfer; FRET; Molecular dynamics; Polypeptide

Indexed keywords

DYE; POLYAMINOACID; POLYPEPTIDE; POLYPROLINE; PROLINE; UNCLASSIFIED DRUG;

ARTICLE; ENERGY TRANSFER; FLUORESCENCE; FORSTER RESONANCE ENERGY TRANSFER; MOLECULAR DYNAMICS; PEPTIDE ANALYSIS; PRIORITY JOURNAL; SPECTROSCOPY;

FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; PEPTIDES;

EID: 14544283620     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0408164102     Document Type: Article

References (48)

1. Stryer, L. & Haugland, R. P. (1967) Proc. Natl. Acad. Sci. USA 58, 719-726.
2. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy (Kluwer Academic/Plenum, New York).
3. Stryer, L. (1978) Annu. Rev. Biochem. 47, 819-846.
4. Haas, E., Katchalskikatzir, E. & Steinberg, I. Z. (1978) Biopolymers 17, 11-31.
5. Selvin, P. R. (2000) Nat. Struct. Biol. 7, 730-734.
6. Michalet, X., Kapanidis, A. N., Laurence, T., Pinaud, F., Doose, S., Pflughoefft, M. & Weiss, S. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 161-182.
7. Ha, T., Enderle, T., Ogletree, D. F., Chemla, D. S., Selvin, P. R. & Weiss, S. (1996) Proc. Natl. Acad. Sci. USA 93, 6264-6268.
8. Jia, Y. W., Talaga, D. S., Lau, W. L., Lu, H. S. M., DeGrado, W. F. & Hochstrasser, R. M. (1999) Chem. Phys. 247, 69-83.
9. Ishii, Y., Yoshida, T., Funatsu, T., Wazawa, T. & Yanagida, T. (1999) Chem. Phys. 247, 163-173.
10. Deniz, A. A., Laurence, T. A., Beligere, G. S., Dahan, M., Martin, A. B., Chemla, D. S., Dawson, P. E., Schultz, P. G. & Weiss, S. (2000) Proc. Natl. Acad. Sci. USA 97, 5179-5184.
11. Talaga, D. S., Lau, W. L., Roder, H., Tang, J. Y., Jia, Y. W., DeGrado, W. F. & Hochstrasser, R. M. (2000) Proc. Natl. Acad. Sci. USA 97, 13021-13026.
12. Ha, T. (2001) Methods 25, 78-86.
13. Schuler, B., Lipman, E. A. & Eaton, W. A. (2002) Nature 419, 743-747.
14. Heyduk, T. (2002) Curr. Opin. Biotechnol. 13, 292-296.
15. Borsch, M., Diez, M., Zimmermann, B., Reuter, R. & Gräber, P. (2002) FEBS Lett. 527, 147-152.
16. Lipman, E. A., Schuler, B., Bakajin, O. & Eaton, W. A. (2003) Science 301, 1233-1235.
17. Rhoades, E., Gussakovsky, E. & Haran, G. (2003) Proc. Natl. Acad. Sci. USA 100, 3197-3202.
18. Berney, C. & Danuser, G. (2003) Biophys. J. 84, 3992-4010.
19. Nguyen, V. T., Kamio, Y. & Higuchi, H. (2003) EMBO J. 22, 4968-4979.
20. Margittai, M., Widengren, J., Schweinberger, E., Schröder, G. F., Felekyan, S., Haustein, E., König, M., Fasshauer, D., Grubmüller, H., Jahn, R., et al. (2003) Proc. Natl. Acad. Sci. USA 100, 15516-15521.
21. Rasnik, I., Myong, S., Cheng, W., Lohman, T. M. & Ha, T. (2004) J. Mol. Biol. 336, 395-408.
22. Klostermeier, D., Sears, P., Wong, C. H., Millar, D. P. & Williamson, J. R. (2004) Nucleic Acids Res. 32, 2707-2715.
23. Slaughter, B. D., Allen, M. W., Unruh, J. R., Urbauer, R. J. B. & Johnson, C. K. (2004) J. Phys. Chem. B 108, 10388-10397.
24. Rhoades, E., Cohan, M., Schuler, B. & Haran, G. (2004) J. Am. Chem. Soc. 126, 14686-14687.
25. Van Der Meer, B. W., Coker, G., III, & Chen, S. Y. S. (1994) Resonance Energy Transfer: Theory and Data (VCH, New York).
26. Förster, T. (1948) Ann. Phys. 6, 55-75.
27. Panchuk-Voloshina, N., Haugland, R. P., Bishop-Stewart, J., Bhalgat, M. K., Millard, P. J., Mao, F. & Leung, W. Y. (1999) J. Histochem. Cytochem. 47, 1179-1188.
28. Cowan, P. M. & McGavin, S. (1955) Nature 176, 501-503.
29. Lazaridis, T. & Karplus, M. (1999) Proteins 35, 133-152.
30. Lazaridis, T. & Karplus, M. (1999) J. Mol. Biol. 288, 477-487.
31. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
32. Steinbach, P. J. (2004) Proteins 57, 665-677.
33. Deniz, A. A., Laurence, T. A., Dahan, M., Chemla, D. S., Schultz, P. G. & Weiss, S. (2001) Annu. Rev. Phys. Chem. 52, 233-253.
34. Thirumalai, D. & Ha, B. Y. (1988) in Theoretical and Mathematical Models in Polymer Research, ed. Grosberg, A. (Academia, New York), pp. 1-35.
35. Gopich, I. V. & Szabo, A. (2003) J. Phys. Chem. B 107, 5058-5063.
36. Gopich, I. V. & Szabo, A. (2005) J. Chem. Phys. 122, 014707-1-014707-18.
37. Schimmel, P. R. & Flory, P. J. (1967) Proc. Natl. Acad. Sci. USA 58, 52-59.
38. Scholes, G. D. (2003) Annu. Rev. Phys. Chem. 54, 57-87.
39. Wong, K. F., Bagchi, B. & Rossky, P. J. (2004) J. Phys. Chem. 108, 5752-5763.
40. Scholes, G. D. & Fleming, G. R. (2005) Adv. Chem. Phys., in press.
41. Henry, E. R. & Hochstrasser, R. M. (1987) Proc. Natl. Acad. Sci. USA 84, 6142-6146.
42. Cantor, C. R. & Schimmel, P. R. (1980) Biophysical Chemistry (Freeman, San Francisco).
43. Deniz, A. A., Dahan, M., Grunwell, J. R., Ha, T. J., Faulhaber, A. E., Chemla, D. S., Weiss, S. & Schultz, P. G. (1999) Proc. Natl. Acad. Sci. USA 96, 3670-3675.
44. Kapanidis, A. N., Lee, N. K., Laurence, T. A., Doose, S., Margeat, E. & Weiss, S. (2004) Proc. Natl. Acad. Sci. USA 101, 8936-8941.
45. Hillisch, A., Lorenz, M. & Diekmann, S. (2001) Curr. Opin. Struct. Biol. 11, 201-207.
46. Clegg, R. M., Murchie, A. I., Zechel, A. & Lilley, D. M. (1993) Proc. Natl. Acad. Sci. USA 90, 2994-2998.
47. Dale, R. E., Eisinger, J. & Blumberg, W. E. (1979) Biophys. J. 26, 161-193.
48. Alexiev, U., Rimke, I. & Pohlmann, T. (2003) J. Mol. Biol. 328, 705-719.