Time-resolved events on the reaction pathway of transcript initiation by a single-subunit RNA polymerase: Raman crystallographic evidence

Journal of the American Chemical Society

Volumn 133, Issue 32, 2011, Pages 12544-12555

  Chen, Yuanyuan ^a   Basu, Ritwika ^b   Gleghorn, Michael L ^b,c   Murakami, Katsuhiko S ^b   Carey, Paul R ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; COMPLEX CRYSTALS; CONFORMATIONAL CHANGE; DIVALENT CATION; DIVALENT METALS; DNA COMPLEX; DNA CONFORMATIONS; ISOTOPICALLY LABELED; PHOSPHODIESTER BONDS; RAMAN MICROSCOPY; REACTION PATHWAYS; REAL TIME; RNA POLYMERASE; SUBSTRATE BINDING; TIME-RESOLVED; TRANSFER REACTION; TRIPHOSPHATE; X RAY CRYSTAL STRUCTURES;

CONFORMATIONS; DIFFRACTIVE OPTICS; DNA; ESTERS; METALS; RAMAN SCATTERING; RAMAN SPECTROSCOPY; REACTION INTERMEDIATES; REACTION KINETICS; RNA; SINGLE CRYSTALS; SPECTROSCOPIC ANALYSIS;

SUBSTRATES;

DNA BASE; ISOTOPE; NUCLEOSIDE TRIPHOSPHATE; NUCLEOTIDYLTRANSFERASE; PHOSPHODIESTERASE; PROTEIN SUBUNIT; RNA POLYMERASE;

ARTICLE; CATALYSIS; CHEMICAL BOND; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; METAL BINDING; RAMAN SPECTROMETRY; TRANSCRIPTION INITIATION; VIRION; X RAY CRYSTALLOGRAPHY;

ADENOSINE TRIPHOSPHATE; BACTERIOPHAGE N4; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA, VIRAL; DNA-DIRECTED RNA POLYMERASES; GUANOSINE TRIPHOSPHATE; KINETICS; METALS; MODELS, MOLECULAR; SPECTRUM ANALYSIS, RAMAN; TRANSCRIPTION, GENETIC;

EID: 80051601456     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja201557w     Document Type: Article

References (19)

1. Gleghorn, M. L.; Davydova, E. K.; Basu, R.; Rothman-Denes, L. B.; Murakami, K. S. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3566
2. Gleghorn, M. L.; Davydova, E. K.; Rothman-Denes, L. B.; Murakami, K. S. Mol. Cell 2008, 32, 707
3. Carey, P. R. Annu. Rev. Phys. Chem. 2006, 57, 527
4. Gong, B.; Chen, J. H.; Yajima, R.; Chen, Y.; Chase, E.; Chadalavada, D. M.; Golden, B. L.; Carey, P. R.; Bevilacqua, P. C. Methods 2009, 49, 101
5. Carey, P. R.; Chen, Y.; Gong, B.; Kalp, M. Biochim. Biophys. Acta 2010, 1814, 742
6. Harada, I.; Takeuchi, H. In Spectroscopy of Biological Systems; Clark, R. J. H.; Hester, R. E., Eds.; John Wiley & Sons Ltd.: New York, 1986; p 113.
7. Raso, S. W.; Clark, P. L.; Haase-Pettingell, C.; King, J.; Thomas, G. J., Jr. J. Mol. Biol. 2001, 307, 899
8. Chen, Y.; Eldho, N. V.; Dayie, T. K.; Carey, P. R. Biochemistry 2010, 49, 3427
9. Duguid, J.; Bloomfield, V. A.; Benevides, J.; Thomas, G. J., Jr. Biophys. J. 1993, 65, 1916
10. Nakamoto, K. John Wiley & Sons, Inc.: New York, 1997; Vol. III-8.
11. Takeuchi, H.; Murata, H.; Harada, I. J. Am. Chem. Soc. 1988, 110, 392
12. Carey, P. R. Biochemical Applications of Raman and Resonance Raman Spectroscopies; Academic Press: New York, 1982.
13. Frushour, B. G.; Koenig, J. L. Biopolymers 1974, 13, 1809
14. Pézolet, M.; Pigeon, M.; Ménard, D.; Caillé, J. P. Biophys. J. 1988, 53, 319
15. Tsuboi, M.; Suzuki, M.; Overman, S. A.; Thomas, G. J., Jr. Biochemistry 2000, 39, 2677
16. Zheng, X.; Rivera-Hainaj, R. E.; Zheng, Y.; Pusztai-Carey, M.; Hall, P. R.; Yee, V. C.; Carey, P. R. Biochemistry 2002, 41, 10741
17. Leulliot, N.; Baumruk, V.; Abdelkafi, M.; Turpin, P. Y.; Namane, A.; Gouyette, C.; Huynh-Dinh, T.; Ghomi, M. Nucleic Acids Res. 1999, 27, 1398
18. Baumruk, V.; Gouyette, C.; Huynh-Dinh, T.; Sun, J. S.; Ghomi, M. Nucleic Acids Res. 2001, 29, 4089
19. Bermek, O.; Grindley, N. D.; Joyce, C. M. J. Biol. Chem. 2010, 286, 3755