title: Mapping the kinetic barriers of a Large RNA molecule's folding landscape.
abstract: The folding of linear polymers into discrete three-dimensional structures is often required for biological function. The formation of long-lived intermediates is a hallmark of the folding of large RNA molecules due to the ruggedness of their energy landscapes. The precise thermodynamic nature of the barriers (whether enthalpic or entropic) that leads to intermediate formation is still poorly characterized in large structured RNA molecules. A classic approach to analyzing kinetic barriers are temperature dependent studies analyzed with Eyring's transition state theory. We applied Eyring's theory to time-resolved hydroxyl radical (•OH) footprinting kinetics progress curves collected at eight temperature from 21.5 °C to 51 °C to characterize the thermodynamic nature of folding intermediate formation for the Mg(2+)-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast) transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. Eyring analysis reveals that the primary transitions are moderate in magnitude and primarily enthalpic in nature. In contrast, the secondary transitions are daunting in magnitude and entropic in nature. The entropic character of the secondary transitions is consistent with structural rearrangement of the intermediate species to the final folded form. This segregation of kinetic control reveals distinctly different molecular mechanisms during the two stages of RNA folding and documents the importance of entropic barriers to defining rugged RNA folding landscapes.
authors.affiliation: Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Jörg C
authors.initials: JC
authors.lastname: Schlatterer
authors.affiliation: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America ; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Martin
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
authors.forename: Alain
authors.initials: A
authors.lastname: Laederach
authors.affiliation: Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Brenowitz
mesh_terms: D001483:Base Sequence; D017665:Hydroxyl Radical / Q000378:metabolism; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059370:RNA Folding / Q000235:genetics*; D016337:RNA, Catalytic / Q000235:genetics / Q000378:metabolism; D016053:RNA, Protozoan / Q000235:genetics; D013696:Temperature; D016808:Tetrahymena thermophila / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
chemical_list: C116167:GIR1 ribozyme; D016337:RNA, Catalytic; D016053:RNA, Protozoan; D017665:Hydroxyl Radical; D008274:Magnesium