Multiple native states reveal persistent ruggedness of an RNA folding landscape (original) (raw)

References

  1. Anfinsen, C. B. Principles that govern the folding of protein chains. Science 181, 223–230 (1973)
    Article ADS CAS Google Scholar
  2. Bryngelson, J. D., Onuchic, J. N., Socci, N. D. & Wolynes, P. G. Funnels, pathways and the energy landscape of protein folding: a synthesis. Proteins Struct. Funct. Genet. 21, 167–195 (1995)
    Article CAS Google Scholar
  3. James, L. C. & Tawfik, D. S. Conformational diversity and protein evolution - a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361–368 (2003)
    Article CAS Google Scholar
  4. Zwanzig, R. Two-state models of protein folding kinetics. Proc. Natl Acad. Sci. USA 94, 148–150 (1997)
    Article ADS CAS Google Scholar
  5. Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10–19 (1997)
    Article CAS Google Scholar
  6. Schmid, F. X. & Blaschek, H. A. Native-like intermediate on the ribonuclease A folding pathway. Eur. J. Biochem. 114, 111–117 (1981)
    Article CAS Google Scholar
  7. Jennings, P. A., Finn, B. E., Jones, B. E. & Matthews, C. R. A reexamination of the folding mechanism of dihydrofolate reductase from Escherichia coli: verification and refinement of a four-channel model. Biochemistry 32, 3783–3789 (1993)
    Article CAS Google Scholar
  8. Kamagata, K., Sawano, Y., Tanokura, M. & Kuwajima, K. Multiple parallel-pathway folding of proline-free staphylococcal nuclease. J. Mol. Biol. 332, 1143–1153 (2003)
    Article CAS Google Scholar
  9. Dinner, A. R., Sali, A., Smith, L. J., Dobson, C. M. & Karplus, M. Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331–339 (2000)
    Article CAS Google Scholar
  10. Frieden, C. Slow transitions and hysteretic behavior in enzymes. Annu. Rev. Biochem. 48, 471–489 (1979)
    Article CAS Google Scholar
  11. Flomenbom, O. et al. Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proc. Natl Acad. Sci. USA 102, 2368–2372 (2005)
    Article ADS CAS Google Scholar
  12. Lu, H. P., Xun, L. & Xie, X. S. Single-molecule enzymatic dynamics. Science 282, 1877–1882 (1998)
    Article ADS CAS Google Scholar
  13. English, B. P. et al. Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nature Chem. Biol. 2, 87–94 (2005); erratum 2, 168 (2006)
    Article Google Scholar
  14. Herschlag, D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270, 20871–20874 (1995)
    Article CAS Google Scholar
  15. Treiber, D. K. & Williamson, J. R. Exposing the kinetic traps in RNA folding. Curr. Opin. Struct. Biol. 9, 339–345 (1999)
    Article CAS Google Scholar
  16. Chen, S.-J. & Dill, K. A. RNA folding energy landscapes. Proc. Natl Acad. Sci. USA 97, 646–651 (2000)
    Article ADS CAS Google Scholar
  17. Pan, J., Thirumalai, D. & Woodson, S. A. Folding of RNA involves parallel pathways. J. Mol. Biol. 273, 7–13 (1997)
    Article CAS Google Scholar
  18. Zhuang, X. et al. Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473–1476 (2002)
    Article ADS CAS Google Scholar
  19. Tan, E. et al. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl Acad. Sci. USA 100, 9308–9313 (2003)
    Article ADS CAS Google Scholar
  20. Herschlag, D. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry 31, 1386–1399 (1992)
    Article CAS Google Scholar
  21. Bevilacqua, P. C., Kierzek, R., Johnson, K. A. & Turner, D. H. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science 258, 1355–1358 (1992)
    Article ADS CAS Google Scholar
  22. Ditzler, M. A., Rueda, D., Mo, J., Hakansson, K. & Walter, N. G. A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res. 36, 7088–7099 (2008)
    Article CAS Google Scholar
  23. Lindahl, T., Adams, A. & Fresco, J. R. Renaturation of transfer ribonucleic acids through site binding of magnesium. Proc. Natl Acad. Sci. USA 55, 941–948 (1966)
    Article ADS CAS Google Scholar
  24. Korennykh, A. V., Plantinga, M. J., Correll, C. C. & Piccirilli, J. A. Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry 46, 12744–12756 (2007)
    Article CAS Google Scholar
  25. Levinthal, C. Are there pathways for protein folding? J. Chim. Phys. 65, 44–45 (1968)
    Article Google Scholar
  26. Russell, R. et al. Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA 99, 155–160 (2002)
    Article ADS CAS Google Scholar
  27. Zhuang, X. et al. A single-molecule study of RNA catalysis and folding. Science 288, 2048–2051 (2000)
    Article ADS CAS Google Scholar
  28. Sattin, B. D., Zhao, W., Travers, K., Chu, S. & Herschlag, D. Direct measurement of tertiary contact cooperativity in RNA folding. J. Am. Chem. Soc. 130, 6085–6087 (2008)
    Article CAS Google Scholar
  29. Russell, R. & Herschlag, D. Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway. J. Mol. Biol. 308, 839–851 (2001)
    Article CAS Google Scholar
  30. Narlikar, G. J., Bartley, L. E., Khosla, M. & Herschlag, D. Characterization of a local folding event of the Tetrahymena group I ribozyme: effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps. Biochemistry 38, 14192–14204 (1999)
    Article CAS Google Scholar

Download references