Mg2+-dependent folding of a large ribozyme without kinetic traps.
The folding kinetics of the catalytic domain of Bacillus subtilis ribonuclease P is analyzed here by fluorescence and catalytic activity. The folding pathway is apparently free of kinetic traps, as indicated by a decrease in folding rates upon the addition of urea. We apply Mg2+ and urea chevron analysis to fully describe the folding and unfolding kinetics of this ribozyme. A folding scheme containing two kinetic intermediates completely accounts for the free energy, the Mg2+ Hill coefficient and the surface buried in the equilibrium transition. At saturating Mg 2+concentrations, folding is limited by a barrier that is independent of Mg2+ and urea. These results describe the first trap-free folding pathway of a large ribozyme and indicate that kinetic traps are not an obligate feature of RNA folding.
Fang
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Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.
Pan
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Sosnick
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D000818:Animals; D001412:Bacillus subtilis / Q000201:enzymology* / Q000235:genetics; D002384:Catalysis / Q000187:drug effects; D004305:Dose-Response Relationship, Drug; D004722:Endoribonucleases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D007700:Kinetics; D008274:Magnesium / Q000494:pharmacology*; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D043262:Ribonuclease P; D013050:Spectrometry, Fluorescence; D013696:Temperature; D013816:Thermodynamics; D014508:Urea / Q000494:pharmacology
D012329:RNA, Bacterial; D016337:RNA, Catalytic; D016053:RNA, Protozoan; D014508:Urea; D004722:Endoribonucleases; D043262:Ribonuclease P; D008274:Magnesium