Cooperative and directional folding of the preQ1 riboswitch aptamer domain

Journal of the American Chemical Society

Volumn 133, Issue 12, 2011, Pages 4196-4199

  Feng, Jun ^a   Walter, Nils G ^a   Brooks, Charles L ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMERS; CELLULAR LEVELS; CLASS I; FOLDING MECHANISM; FOLDING PATHWAY; INTRACELLULAR CONCENTRATION; LIGAND BINDING; MODEL SIMULATION; PSEUDOKNOT; REGULATORY MECHANISM; RIBOSWITCHES; SINGLE DOMAINS; STRUCTURAL REARRANGEMENT;

BIOCHEMISTRY; COMPUTER SIMULATION; METABOLISM; METABOLITES; NUCLEIC ACIDS; RNA;

GENE EXPRESSION;

APTAMER; BACTERIAL RNA; QUEUOSINE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACILLUS SUBTILIS; BIOSYNTHESIS; GENE EXPRESSION REGULATION; OPERON; PROTEIN FOLDING; RIBOSWITCH; THERMODYNAMICS;

APTAMERS, NUCLEOTIDE; BACILLUS SUBTILIS; KINETICS; NUCLEIC ACID CONFORMATION; NUCLEOSIDE Q; RIBOSWITCH;

EID: 79953060592     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja110411m     Document Type: Article

References (36)

1. Winkler, W.; Nahvi, A.; Breaker, R. R. Nature 2002, 419, 952
2. Nudler, E.; Mironov, A. S. Trends Biochem. Sci. 2004, 29, 11
3. Garst, A. D.; Batey, R. T. Biochim. Biophys. Acta, Gene Regul. Mech. 2009, 1789, 584
4. Roth, A.; Breaker, R. R. Annu. Rev. Biochem. 2009, 78, 305
5. Roth, A.; Winkler, W. C.; Regulski, E. E.; Lee, B. W.; Lim, J.; Jona, I.; Barrick, J. E.; Ritwik, A.; Kim, J. N.; Welz, R.; Iwata-Reuyl, D.; Breaker, R. R. Nat. Struct. Mol. Biol. 2007, 14, 308
6. Kang, M.; Peterson, R.; Feigon, J. Mol. Cell 2009, 33, 784
7. Pleij, C. W. A. Curr. Opin. Struct. Biol. 1994, 4, 337
8. Klein, D. J.; Edwards, T. E.; Ferre-D'Amare, A. R. Nat. Struct. Mol. Biol. 2009, 16, 343
9. Rieder, U.; Kreutz, C.; Micura, R. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 10804
10. Darty, K.; Denise, A.; Ponty, Y. Bioinformatics 2009, 25, 1974
11. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins: Struct., Funct., Genet. 1995, 21, 167
12. Brooks, C. L.; Onuchic, J. N.; Wales, D. J. Science 2001, 293, 612
13. Ueda, Y.; Taketomi, H.; Go, N. Biopolymers 1978, 17, 1531
14. Hills, R. D.; Brooks, C. L. Int. J. Mol. Sci. 2009, 10, 889
15. Whitford, P. C.; Noel, J. K.; Gosavi, S.; Schug, A.; Sanbonmatsu, K. Y.; Onuchic, J. N. Proteins: Struct., Funct., Bioinf. 2009, 75, 430
16. Whitford, P. C.; Schug, A.; Saunders, J.; Hennelly, S. P.; Onuchic, J. N.; Sanbonmatsu, K. Y. Biophys. J. 2009, 96, L7
17. Shimada, J.; Shakhnovich, E. I. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11175
18. Hyeon, C.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S. A. 2005, 102, 6789
19. Lin, J. C.; Thirumalai, D. J. Am. Chem. Soc. 2008, 130, 14080
20. Klimov, D. K.; Thirumalai, D. Fold. Des. 1998, 3, 127
21. Gosavi, S.; Chavez, L. L.; Jennings, P. A.; Onuchic, J. N. J. Mol. Biol. 2006, 357, 986
22. Rieder, U.; Lang, K.; Kreutz, C.; Polacek, N.; Micura, R. ChemBioChem 2009, 10, 1141
23. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1339
24. Thirumalai, D.; Lee, N.; Woodson, S. A.; Klimov, D. K. Annu. Rev. Phys. Chem. 2001, 52, 751
25. Tinoco, I.; Bustamante, C. J. Mol. Biol. 1999, 293, 271
26. Zwanzig, R. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9801
27. Jackson, S. E. Fold. Des. 1998, 3, R81
28. Plaxco, K. W.; Simons, K. T.; Ruczinski, I.; David, B. Biochemistry 2000, 39, 11177
29. Nixon, P. L.; Giedroc, D. P. Biochemistry 1998, 37, 16116
30. Theimer, C. A.; Giedroc, D. P. RNA 2000, 6, 409
31. Chen, G.; Wen, J. D.; Tinoco, I. RNA 2007, 13, 2175
32. Green, L.; Kim, C. H.; Bustamante, C.; Tinoco, I. J. Mol. Biol. 2008, 375, 511
33. Cho, S. S.; Pincus, D. L.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17349
34. Wickiser, J. K.; Cheah, M. T.; Breaker, R. R.; Crothers, D. M. Biochemistry 2005, 44, 13404
35. Wickiser, J. K.; Winkler, W. C.; Breaker, R. R.; Crothers, D. M. Mol. Cell 2005, 18, 49
36. Dawson, W. K.; Fujiwara, K.; Kawai, G. PLoS One 2007, 2, e905