Helical Junctions as Determinants for RNA Folding:  Origin of Tertiary Structure Stability of the Hairpin Ribozyme†

Biochemistry ◽  
2000 ◽  
Vol 39 (42) ◽  
pp. 12970-12978 ◽  
Author(s):  
Dagmar Klostermeier ◽  
David P. Millar
Keyword(s):  
Rna Folding ◽  
Tertiary Structure ◽  
Structure Stability ◽  
Hairpin Ribozyme

Tertiary Structure Stability of the Hairpin Ribozyme in Its Natural and Minimal Forms:  Different Energetic Contributions from a Ribose Zipper Motif†

Biochemistry ◽  
2001 ◽  
Vol 40 (37) ◽  
pp. 11211-11218 ◽  
Author(s):  
Dagmar Klostermeier ◽  
David P. Millar
Keyword(s):  
Tertiary Structure ◽  
Structure Stability ◽  
Hairpin Ribozyme

scholarly journals Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization

Biochemistry ◽  
2017 ◽  
Vol 56 (27) ◽  
pp. 3422-3433 ◽  
Author(s):  
Kathleen A. Leamy ◽  
Neela H. Yennawar ◽  
Philip C. Bevilacqua
Keyword(s):  
Secondary Structure ◽  
Rna Folding ◽  
Tertiary Structure ◽  
Structure Stabilization

An RNA folding motif: GNRA tetraloop–receptor interactions

2013 ◽  
Vol 46 (3) ◽  
pp. 223-264 ◽  
Author(s):  
Julie L. Fiore ◽  
David J. Nesbitt
Keyword(s):  
Rna Structure ◽  
Rna Folding ◽  
Tertiary Structure ◽  
Quantitative Prediction ◽  
Biophysical Characterization ◽  
Receptor Interactions ◽  
Structural Assembly ◽  
Rna Tertiary Structure ◽  
Free Energy Landscapes

AbstractNearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.

scholarly journals Multiple binding of thallium and rubidium to potassium-activated yeast aldehyde dehydrogenase. Influences on tertiary structure, stability and catalytic activity

1982 ◽  
Vol 207 (1) ◽  
pp. 73-80 ◽  
Author(s):  
K A Bostian ◽  
G F Betts ◽  
W K Man ◽  
M N Hughes
Keyword(s):  
Steady State ◽  
Aldehyde Dehydrogenase ◽  
Binding Sites ◽  
Tertiary Structure ◽  
Equilibrium Dialysis ◽  
Structure Stability ◽  
Conformation Changes ◽  
Steady State Kinetic ◽  
Multiple Binding ◽  
Inhibitory Site

Univalent cation activators of aldehyde dehydrogenase have dual effects, both interpreted as cation-induced or -stabilized conformation changes. These two processes are differentiated by the time scales of their associated changes in activity. Using Tl+ as an activator, under certain conditions, the slower change in activity saturates at a Tl+ concentration which is only 0.1 Ks for the faster change. This, together with evidence for cation-induced rather than cation-stabilized conformation changes, is used to propose separate binding sites for cations responsible for the two activation processes. Equilibrium dialysis indicates 4 binding sites per active site for Rb+ or 6 sites for Tl+. At least one of the additional sites for Tl+ is an inhibitory site which has been differentiated from the activator sites on the basis of steady-state and pre-steady-state kinetic data.

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