Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy

Biochemistry

Volumn 42, Issue 4, 2003, Pages 940-950

  Tsuboi, Masamichi ^a,b   Kubo, Yoshiko ^a,c   Ikeda, Teruki ^c   Overman, Stacy A ^a   Osman, Olivia ^a   Thomas Jr , George J ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^b IWAKI MEISEI UNIVERSITY   (Japan)

^c Hachioji shi   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DNA; GENES; POLARIZATION; RAMAN SPECTROSCOPY; VIRUSES;

NUCLEOTIDES;

PROTEINS;

ALPHA HELIX; ARTICLE; COLIPHAGE; CONFORMATIONAL TRANSITION; CRYSTALLIZATION; ENZYME ACTIVE SITE; FOURIER TRANSFORMATION; NONHUMAN; POLARIZATION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; RESIDUE ANALYSIS; STRUCTURE ANALYSIS; VIRUS GENOME; X RAY DIFFRACTION;

ALANINE; AMIDES; ARGININE; BACTERIOPHAGE PF1; CAPSID; DNA, SINGLE-STRANDED; DNA, VIRAL; GENOME, VIRAL; MICROSPECTROPHOTOMETRY; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SPECTRUM ANALYSIS, RAMAN; TYROSINE; VIRAL PROTEINS; VIRION; VIRUS ASSEMBLY;

BACTERIA (MICROORGANISMS); MIRIDAE; PSEUDOMONAS; PSEUDOMONAS PHAGE PF1;

EID: 0037417751     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi020566v     Document Type: Article

References (68)

1. Day, L. A., Marzec, C. J., Reisberg, S. A., and Casadevall, A. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 509-539.
2. Welsh, L. C., Symmons, M. F., and Marvin, D. A. (2000) Acta Crystallogr., Sect. D: Biol. Crystallogr. 56 (Pt. 2), 137-150.
3. Welsh, L. C., Marvin, D. A., and Perham, R. N. (1998) J. Mol. Biol. 284, 1265-1271.
4. Zweckstetter, M., and Bax, A. (2001) J. Biomol. NMR 20, 365-377.
5. Zweckstetter, M., and Bax, A. (2001) J. Am. Chem. Soc. 123, 9490-9491.
6. Torbet, J., and Maret, G. (1979) J. Mol. Biol. 134, 843-845.
7. Thomas, G. J., Jr., Prescott, B., and Day, L. A. (1983) J. Mol. Biol. 165, 321-356.
8. Cross, T. A., Tsang, P., and Opella, S. J. (1983) Biochemistry 22, 721-726.
9. Fritzsche, H., Tsang, P., Opella, S. J., and Kallenbach, N. R. (1986) Stud. Biophys. 116, 175-180.
10. Thomas, G. J., Jr., Prescott, B., Opella, S. J., and Day, L. A. (1988) Biochemistry 27, 4350-4357.
11. Day, L. A., Casadevall, A., Prescott, B., and Thomas, G. J., Jr. (1988) Biochemistry 27, 706-711.
12. Nambudripad, R., Stark, W., and Makowski, L. (1991) J. Mol. Biol. 220, 359-379.
13. Nambudripad, R., Stark, W., Opella, S. J., and Makowski, L. (1991) Science 252, 1305-1308.
14. Clack, B. A., and Gray, D. M. (1992) Biopolymers 32, 795-810.
15. Kostrikis, L. G., Liu, D. J., and Day, L. A. (1994) Biochemistry 33, 1694-1703.
16. Liu, D. J., and Day, L. A. (1994) Science 265, 671-674.
17. Wen, Z. Q., Armstrong, A., and Thomas, G. J., Jr. (1999) Biochemistry 38, 3148-3156.
18. Blanch, E. W., Bell, A. F., Hecht, L., Day, L. A., and Barron, L. D. (1999) J. Mol. Biol. 290, 1-7.
19. Tsuboi, M., Suzuki, M., Overman, S. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 2677-2684.
20. Day, L. A., Wiseman, R. L., and Marzec, C. J. (1979) Nucleic Acids Res. 7, 1393-1403.
21. Marzec, C. J., and Day, L. A. (1983) Biophys. J. 42, 171-180.
22. Allemand, J. F., Bensimon, D., Lavery, R., and Croquette, V. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 14152-14157.
23. Bustamante, C., Smith, S. B., Liphardt, J., and Smith, D. (2000) Curr. Opin. Struct. Biol. 10, 279-285.
24. Tsuboi, M., Overman, S. A., and Thomas, G. J., Jr. (1996) Biochemistry 35, 10403-10410.
25. Overman, S. A., Tsuboi, M., and Thomas, G. J., Jr. (1996) J. Mol. Biol. 259, 331-336.
26. Takeuchi, H., Matsuno, M., Overman, S. A., and Thomas, G. J., Jr. (1996) J. Am. Chem. Soc. 118, 3498-3507.
27. Matsuno, M., Takeuchi, H., Overman, S. A., and Thomas, G. J., Jr. (1998) Biophys. J. 74, 3217-3225.
28. Tsuboi, M., Ushizawa, K., Nakamura, K., Benevides, J. M., Overman, S. A., and Thomas, G. J., Jr. (2001) Biochemistry 40, 1238-1247.
29. Tsuboi, M., and Thomas, G. J., Jr. (1997) Appl. Spectrosc. Rev. 32, 263-299.
30. Tuma, R., and Thomas, G. J., Jr. (2002) Applications in Life, Pharmaceutical, and Natural Sciences, in Handbook of Vibrational Spectroscopy 5 (Chalmers, J. M., and Griffiths, P. R., Eds.) pp 3519-3535, John Wiley & Sons, Chichester, U.K.
31. Fritzsche, H., Cross, T. A., Opella, S. J., and Kallenbach, N. R. (1981) Biophys. Chem. 14, 283-291.
32. Aubrey, K. L., and Thomas, G. J., Jr. (1991) Biophys. J. 61, 1337-1349.
33. Overman, S. A., and Thomas, G. J., Jr. (1995) Biochemistry 34, 5440-5451.
34. Overman, S. A., and Thomas, G. J., Jr. (1998) Biochemistry 37, 5654-5665.
35. Overman, S. A., and Thomas, G. J., Jr. (1999) Biochemistry 38, 4018-4027.
36. Arp, Z., Autrey, D., Laane, J., Overman, S. A., and Thomas, G. J., Jr. (2001) Biochemistry 40, 2522-2529.
37. Berkowitz, S. A., and Day, L. A. (1976) J. Mol. Biol. 102, 531-547.
38. Sutherland, G. B. B. M., and Tsuboi, M. (2001) Proc. R. Soc. London, Ser. A 239, 446-463.
39. Wilser, W. T., and Fitchen, D. B. (1975) J. Chem. Phys. 62, 720-724.
40. Benevides, J. M., Tsuboi, M., Wang, A. H. J., and Thomas, G. J., Jr. (1993) J. Am. Chem. Soc. 115, 5351-5359.
41. Higgs, P. W. (1953) Proc. R. Soc. London, Ser. A 220, 472-485.
42. Zbinden, R. (1964) Infrared Spectroscopy of High Polymers Academic Press, New York.
43. Thomas, G. J., Jr., and Murphy, P. (1975) Science 188, 1205-1207.
44. Bandekar, J. (1992) Biochim. Biophys. Acta 1120, 123-143.
45. Thomas, G. J., Jr. (1985) Spectrochim. Acta 41A, 217-221.
46. Lee, S.-H., and Krimm, S. (1998) Biopolymers 46, 283-317.
47. Siamwiza, M. N., Lord, R. C., Chen, M. C., Takamatsu, T., Harada, I., Matsuura, H., and Shimanouchi, T. (1975) Biochemistry 14, 4870-4876.
48. Takeuchi, H., Watanabe, N., and Harada, I. (1988) Spectrochim. Acta 44A, 749-761.
49. Tsuboi, M., Ezaki, Y., Aida, M., Suzuki, M., Yimit, A., Ushizawa, K., and Ueda, T. (1998) Biospectroscopy 4, 61-71.
50. Lord, R. C., and Thomas, G. J., Jr. (1967) Spectrochim. Acta 23A, 2551-2591.
51. Benevides, J. M., and Thomas, G. J., Jr. (1983) Nucleic Acids Res. 11, 5747-5761.
52. Nishimura, Y., Tsuboi, M., and Sato, T. (1984) Nucleic Acids Res. 12, 6901-6908.
53. Thomas, G. J., Jr. (1986) in Spectroscopy of Biological Systems (Clark, R. J. H., and Hester, R. E., Eds.) pp 233-309, John Wiley and Sons, London.
54. Benevides, J. M., Wang, A. H. J., van der Marel, G. A., van Boom, J. H., and Thomas, G. J., Jr. (1988) Biochemistry 27, 931-938.
55. Thomas, G. J., Jr., and Tsuboi, M. (1993) in Advances in Biophysical Chemistry, 3 (Bush, C. A., Ed.) pp 1-70, JAI Press Inc., Greenwich, CT.
56. Thomas, G. J., Jr., and Benevides, J. M. (1985) Biopolymers 24, 1101-1105.
57. Tsuboi, M. (1962) J. Polymer Sci. 59, 139-153.
58. Miyazawa, T. (1960) J. Chem. Phys. 32, 1647-1652.
59. Tsuboi, M., Ikeda, T., and Ueda, T. (1991) J. Raman Spectrosc. 22, 619-626.
60. Marvin, D. A., Bryan, R. K., and Nave, C. (1987) J. Mol. Biol. 193, 315-343.
61. Gonzalez, A., Nave, C., and Marvin, D. A. (1995) Acta Crystallogr., Sect. D: Biol. Crystallogr. 51, 792-804.
62. Shon, K. J., Kim, Y., Colnago, L. A., and Opella, S. J. (1991) Science 252, 1303-1305.
63. Ueda, T., Ushizawa, K., and Tsuboi, M. (1996) J. Mol. Struct. 319, 171-187.
64. Wen, Z. Q., and Thomas, G. J., Jr. (2000) Biochemistry 39, 146-152.
65. Wen, Z. Q., Overman, S. A., Bondre, P., and Thomas, G. J., Jr. (2001) Biochemistry 40, 449-458.
66. Overman, S. A., Aubrey, K. L., Vispo, N. S., Cesareni, G., and Thomas, G. J., Jr. (1994) Biochemistry 33, 1037-1042.
67. Thomas, G. J., Jr., Benevides, J. M., Overman, S. A., Ueda, T., Ushizawa, K., Saitoh, M., and Tsuboi, M. (1995) Biophys. J. 68, 1073-1088.
68. Tsuboi, M., Ueda, T., Ushizawa, K., Ezaki, Y., Overman, S. A., and Thomas, G. J., Jr. (1996) J. Mol. Struct. 379, 43-50.