Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backbone

Journal of the American Chemical Society

Volumn 132, Issue 22, 2010, Pages 7769-7775

  Abramavicius, Darius ^a   Jiang, Jun ^a   Bulheller, Benjamin M ^b   Hirst, Jonathan D ^b   Mukamel, Shaul ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM; ELECTRONIC TRANSITION; FIBRILLAR PROTEINS; PROTEIN BACKBONE; PROTEIN STRUCTURES; SECONDARY STRUCTURES; SIMULATED SIGNALS; SIMULATION STUDIES; SPECTROSCOPIC SIGNATURES; STRUCTURAL MOTIFS; STRUCTURE CHARACTERIZATION; TWO-DIMENSION; ULTRA-VIOLET; ULTRAFAST LASER; UV PHOTONS;

AMIDES; DICHROISM; PHOTONS; TWO DIMENSIONAL; ULTRAVIOLET SPECTROSCOPY;

PROTEINS;

FIBRILLAR PROTEIN; GLOBULAR PROTEIN; MUSCLE PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CHIRALITY; CIRCULAR DICHROISM; CONTROLLED STUDY; CROSS LINKING; ELECTRONICS; PARTICLE SIZE; PHOTON; POLARIZATION; PROTEIN ANALYSIS; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SIGNAL PROCESSING; SIMULATION; TWO DIMENSIONAL ULTRAVIOLET SPECTROSCOPY; ULTRAVIOLET SPECTROSCOPY;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; HUMANS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 77953105004     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja101968g     Document Type: Article

References (45)

1. Whitford, D. Proteins: Structure and function; Wiley: New York, 2005.
2. Mukamel, S., Tanimura, Y., and Hamm, P., Eds. Accounts of Chemical Research: Special Issue on Coherent Multidimensional Optical Spectroscopy; American Chemical Society: Washington, DC, 2009; Vol. 42.
3. Mukamel, S., Abramavicius, D., Yang, L., Zhuang, W., Schweigert, I. V., and Voronine, D. Acc. Chem. Res. 2009, 42, 553-562
4. Zanni, M. T., Ge, N.-H., Kim, Y. S., and Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11265-11270
5. Sul, S., Karaiskaj, D., Jiang, Y., and Ge, N. H. J. Phys. Chem. B 2006, 110, 19891-19905
6. Engel, G. S., Calhoun, T. R., Read, E. L., Ahn, T. K., Mançal, T., Cheng, Y. C., Blankenship, R. E., and Fleming, G. R. Nature 2007, 446, 782-786
7. Read, E. L., Engel, G. S., Calhoun, T. R., Mançal, T., Ahn, T. K., Blankenship, R. E., and Fleming, G. R. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14203-14208
8. Chung, H., Khalil, M., Smith, A. W., Ganim, Z., and Tokmakoff, A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 612-617
9. Cho, M. Chem. Rev. 2008, 108, 1331-1418
10. Milota, F., Sperling, J., Nemeth, A., Abramavicius, D., Mukamel, S., and Kauffmann, H. F. J. Chem. Phys. 2009, 131 054510
11. Stone, K. W., Gundogdu, K., Turner, D. B., Li, X., Cundiff, S. T., and Nelson, K. A. Science 2009, 324, 1169-1173
12. Li, Z., Abramavicius, D., and Mukamel, S. J. Am. Chem. Soc. 2008, 130, 3509-3515
13. Mukamel, S. Annu. Rev. Phys. Chem. 2000, 51, 691-729
14. Zhuang, W., Hayashi, T., and Mukamel, S. Angew. Chem. 2009, 48, 3750-3781
15. Abramavicius, D., Palmieri, B., Voronine, D. V., S'anda, F., and Mukamel, S. Chem. Rev. 2009, 109, 2350-2408
16. Berova, N., Nakanishi, K., and Woody, R. W., Eds. Circular Dichroism. Principles and Applications, 2nd ed.; John Wiley & Sons, Inc.: New York, 2000.
17. Barron, L. D. Molecular Light Scattering and Optical Activity, 2nd ed.; Cambridge University Press: Cambridge, U.K., 2004.
18. Bulheller, B. M., Rodger, A., and Hirst, J. D. Phys. Chem. Chem. Phys. 2007, 9, 2020-2035
19. Greenfield, N. J. Anal. Biochem. 1996, 235, 1-10
20. Greenfield, N. J. Methods Enzymol. 2004, 383, 282-317
21. Whitmore, L. and Wallace, B. A. Nucleic Acids Res. 2004, 32, W668-W673
22. Whitmore, L. and Wallace, B. A. Biopolymers 2008, 89, 392-400
23. Woody, R. W. Monatsh. Chem. 2005, 136, 347-366
24. Besley, N. A. and Hirst, J. D. J. Am. Chem. Soc. 1999, 121, 9636-9644
25. Phillips, J., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R., Kale, L., and Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
26. MacKerell, A. D., Jr. J. Phys. Chem. B 1998, 102, 3586-3616
27. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
28. Darden, T., York, D., and Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
29. Li, Z., Abramavicius, D., Zhuang, W., and Mukamel, S. Chem. Phys. 2007, 341, 29-36
30. Jiang, J., Abramavicius, D., Bulheller, B. M., Hirst, J. D., and Mukamel, S. J. Phys. Chem. B 2010, in press.
31. Corkum, P., De Silvestri, S., Nelson, K., Riedle, E., and Schoenlein, R., Eds. Ultrafast Phenomena XVI; Springer: Berlin, 2009.
32. Bressler, C. and Chergui, M. Chem. Rev. 2004, 104, 1781-1812
33. Kapteyn, H., Cohen, O., Christov, I., and Murnane, M. Science 2007, 317, 775-778
34. http://ssrl.slac.stanford.edu/lcls.
35. Krausz, F. and Ivanov, M. Rev. Mod. Phys. 2009, 81, 163-234
36. Cho, M. Two-Dimensional Optical Spectroscopy; CRC Press: Boca Raton, FL, 2009.
37. Bulheller, B. M. and Hirst, J. D. Bioinformatics 2009, 25, 539-540
38. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
39. Wagersreiter, T. and Mukamel, S. J. Chem. Phys. 1996, 105, 7995
40. Read, E. L., Schlau-Cohen, G. S., Engel, G. S., Wen, J., Blankenship, R. E., and Fleming, G. R. Biophys. J. 2008, 95, 847-856
41. Abramavicius, D., Voronine, D. V., and Mukamel, S. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8525
42. Stone, K. W., Gundogdu, K., Turner, D. B., Li, X., Cundiff, S. T., and Nelson, K. A. Science 2009, 324, 1169-1173
43. Oakley, M. T. and Hirst, J. D. J. Am. Chem. Soc. 2006, 128, 12414-12415
44. Bulheller, B. M., Miles, A. J., Wallace, B. A., and Hirst, J. D. J. Phys. Chem. B 2008, 112, 1866-1874
45. Eaves, J. D., Tokmakoff, A., and Geissler, P. L. J. Phys. Chem. A 2005, 109, 9424-9436