10 gaines cs york dm ribozyme catalysis with a twist

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10. Gaines, C.S. & York, D.M. Ribozyme catalysis with a twist: active state of the twister ribozyme in solution predicted from molecular simulation. J. Am. Chem. Soc. 138 , 3058–3065 (2016). 11. Zhang, S. et al. Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. J. Am. Chem. Soc. 137 , 784–798 (2015). 12. Gebetsberger, J. & Micura, R. Unwinding the twister ribozyme: from structure to mechanism. Wiley Interdiscip. Rev. RNA 8 (2017). 13. Vušurović, N., Altman, R.B., Terry, D.S., Micura, R. & Blanchard, S.C. Pseudoknot formation seeds the twister ribozyme cleavage reaction coordinate. J. Am. Chem. Soc. 139 , 8186–8193 (2017). 14. Košutić, M. et al. A mini-twister variant and impact of residues/cations on the phosphodiester cleavage of this ribozyme class. Angew. Chem. Int. Edn. Engl. 54 , 15128–15133 (2015). 15. Ucisik, M.N., Bevilacqua, P.C. & Hammes-Schiffer, S. Molecular dynamics study of twister ribozyme: role of Mg 2+ ions and the hydrogen-bonding network in the active site. Biochemistry 55 , 3834–3846 (2016). 16. Alatossava, T., Jütte, H., Kuhn, A. & Kellenberger, E. Manipulation of intracellular magnesium content in polymyxin B nonapeptide-sensitized Escherichia coli by ionophore A23187. J. Bacteriol. 162 , 413–419 (1985). 17. Froschauer, E.M., Kolisek, M., Dieterich, F., Schweigel, M. & Schweyen, R.J. Fluorescence measurements of free [Mg 2+ ] by use of mag-fura 2 in Salmonella enterica. FEMS Microbiol. Lett. 237 , 49–55 (2004). 18. Zhong, W., Schobert, C. & Komor, E. Transport of magnesium ions in the phloem of Ricinus communis L. seedlings. Planta 190 , 114–119 (1993). 19. Ha, T. et al. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl. Acad. Sci. USA 93 , 6264–6268 (1996). 20. Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5 , 507–516 (2008). 21. Kilburn, D., Roh, J.H., Guo, L., Briber, R.M. & Woodson, S.A. Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J. Am. Chem. Soc. 132 , 8690–8696 (2010). 22. Paudel, B.P. & Rueda, D. Molecular crowding accelerates ribozyme docking and catalysis. J. Am. Chem. Soc. 136 , 16700–16703 (2014). 23. Dupuis, N.F., Holmstrom, E.D. & Nesbitt, D.J. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics. Proc. Natl. Acad. Sci. USA 111 , 8464–8469 (2014). 24. Bokinsky, G. et al. Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA 100 , 9302–9307 (2003). 25. Leffler, J.E. Parameters for the description of transition states. Science 117 , 340–341 (1953). 26. Tanford, C. Protein denaturation. C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24 , 1–95 (1970). 27. Jackson, S.E. & Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30 , 10428–10435 (1991). 28. Koculi, E., Thirumalai, D. & Woodson, S.A. Counterion charge density determines the position and plasticity of RNA folding transition states. J. Mol. Biol. 359 , 446–454 (2006). 29. Sosnick, T.R. Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci. 17 , 1308–1318 (2008).
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  • Spring '13
  • Nelson
  • RNA, Wind, Ribozyme, Hammerhead Ribozyme, Osa twister

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