Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins

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

Volumn 102, Issue 48, 2005, Pages 17348-17353

  Laurence, Ted A ^a   Kong, Xiangxu ^b   Jäger, Marcus ^b   Weiss, Shimon ^b,c  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Conformational dynamics; Fluorescence resonance energy transfer; Nucleic acid structure; Protein folding; Single molecule fluorescence spectroscopy

Indexed keywords

ACYL COENZYME A BINDING PROTEIN; BINDING PROTEIN; CHYMOTRYPSIN INHIBITOR; DOUBLE STRANDED DNA; NUCLEIC ACID; POLYTHYMIDYLIC ACID; UNCLASSIFIED DRUG;

ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DIFFUSION; ELECTRICITY; FLUORESCENCE RESONANCE ENERGY TRANSFER; IONIC STRENGTH; MOLECULAR DYNAMICS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

DIAZEPAM BINDING INHIBITOR; FLUORESCENCE RESONANCE ENERGY TRANSFER; LASERS; MODELS, MOLECULAR; NUCLEIC ACIDS; PEPTIDES; PLANT PROTEINS; POLYMERS; PROTEIN DENATURATION; PROTEINS;

EID: 28444431959     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0508584102     Document Type: Article

References (39)

1. de Gennes, P. G. (1979) Nature 282, 367-370.
2. Barrat, J.-L. & Joanny, J.-F. (1996) in Advances in Chemical Physics, eds. Prigogine, I. & Rice, S. A. (Wiley, New York), Vol. 94, pp. 1-65.
3. Dill, K. A. & Chan, H. S. (1997) Nat. Struct. Biol. 4, 10-19.
4. Eaton, W. A., Munoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R. & Hofrichter, J. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 327-359.
5. Cannavacciuolo, L. & Pedersen, J. (2002) J. Chem. Phys. 117, 8973-8982.
6. 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.
7. Schuler, B., Lipman, E. A. & Eaton, W. A. (2002) Nature 419, 743-747.
8. Lipman, E. A., Schuler, B., Bakajin, O. & Eaton, W. A. (2003) Science 301, 1233-1235.
9. Haas, E., Wilchek, M., Katchalski-Katzir, E. & Steinberg, I. Z. (1975) Proc. Natl. Acad. Sci. USA 72, 1807-1811.
10. Lindorff-Larsen, K., Kristjansdottir, S., Teilum, K., Fieber, W., Dobson, C. M., Poulsen, F. M. & Vendruscolo, M. (2004) J. Am. Chem. Soc. 126, 3291-3299.
11. Teilum, K., Kragelund, B. B. & Poulsen, F. M. (2002) J. Mol. Biol. 324, 349-357.
12. Kapanidis, A. N., Lee, N. K., Laurence, T. A., Doose, S., Margeat, E. & Weiss, S. (2004) Proc. Natl. Acad. Sci. USA 101, 8936-8941.
13. Fries, J. R., Brand, L., Eggeling, C., Kollner, M. & Seidel, C. A. M. (1998) J. Phys. Chem. A 102, 6601-6613.
14. Deniz, A. A., Laurence, T. A., Dahan, M., Chemla, D. S., Schultz, P. G. & Weiss, S. (2001) Annu. Rev. Phys. Chem. 52, 233-253.
15. Doi, M. & Edwards, S. F. (1986) The Theory of Polymer Dynamics (Clarendon/Oxford Univ. Press, Oxford).
16. Hagerman, P. J. & Zimm, B. H. (1981) Biopolymers 20, 1481-1502.
17. Lapidus, L. J., Steinbach, P. J., Eaton, W. A., Szabo, A. & Hofrichter, J. (2002) J. Phys. Chem. B 106, 11628-11640.
18. Dale, R. E., Eisinger, J. & Blumberg, W. E. (1979) Biophys. J. 26, 161-193.
19. dos Remedios, C. G. & Moens, P. D. (1995) J. Struct. Biol. 115, 175-185.
20. Beechem, J. M. & Haas, E. (1989) Biophys. J. 55, 1225-1236.
21. Lakshmikanth, G. S., Sridevi, K., Krishnamoorthy, G. & Udgaonkar, J. B. (2001) Nat. Struct. Biol. 8, 799-804.
22. Istratov, A. A. & Vyvenko, O. F. (1999) Rev. Sci. Instrum. 70, 1233-1257.
23. Lee, N. K., Kapanidis, A. N., Wang, Y., Michalet, X., Mukhopadhyay, J., Ebright, R. H. & Weiss, S. (2005) Biophys. J. 88, 2939-2953.
24. Hochstrasser, R. A., Chen, S. M. & Millar, D. P. (1992) Biophys. Chem. 45, 133-141.
25. Parkhurst, K. M. & Parkhurst, L. J. (1995) Biochemistry 34, 293-300.
26. Patel, D. J. & Hilbers, C. W. (1975) Biochemistry 14, 2651-2656.
27. Zandi, R., Rudnick, J. & Golestanian, R. (2002) Eur. Phys. J. E 9, 41-46.
28. Murphy, M. C., Rasnik, I., Cheng, W., Lohman, T. M. & Ha, T. (2004) Biophys. J. 86, 2530-2537.
29. Mills, J. B., Vacano, E. & Hagerman, P. J. (1999) J. Mol. Biol. 285, 245-257.
30. Hingerty, B. E., Broyde, S. B. & Olson, W. K. (1982) Biopolymers 21, 1167-1188.
31. Rivetti, C., Walker, C. & Bustamante, C. (1998) J. Mol. Biol. 280, 41-59.
32. Smith, S. B., Cui, Y. & Bustamante, C. (1996) Science 271, 795-799.
33. Tinland, B., Pluen, A., Sturm, J. & Weill, G. (1997) Macromolecules 30, 5763-5765.
34. Everaers, R., Milchev, A. & Yamakov, V. (2002) Eur. Phys. J. E 8, 3-14.
35. Khokhlov, A. & Khachaturian, K. (1982) Polymer 23, 1742-1750.
36. Barrat, J. & Joanny, J. (1993) Europhys. Lett. 24, 333-338.
37. Ha, B. & Thirumalai, D. (1995) Macromolecules 28, 577-581.
38. Kazmirski, S. L., Wong, K. B., Freund, S. M., Tan, Y. J., Fersht, A. R. & Daggett, V. (2001) Proc. Natl. Acad. Sci. USA 98, 4349-4354.
39. Fitzkee, N. C. & Rose, G. D. (2004) Proc. Natl. Acad. Sci. USA 101, 12497-12502.