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

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

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.

scholarly journals Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation

2019 ◽  
Vol 116 (34) ◽  
pp. 16847-16855 ◽  
Author(s):  
Joseph D. Yesselman ◽  
Sarah K. Denny ◽  
Namita Bisaria ◽  
Daniel Herschlag ◽  
William J. Greenleaf ◽  
...  
Keyword(s):  
Structure Formation ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Protein Translation ◽  
Detailed Comparison ◽  
Structure Stability ◽  
Control Of Gene Expression ◽  
Conformational Preferences ◽  
Rna Tertiary Structure ◽  
Length Changes

Structured RNAs and RNA complexes underlie biological processes ranging from control of gene expression to protein translation. Approximately 50% of nucleotides within known structured RNAs are folded into Watson–Crick (WC) base pairs, and sequence changes that preserve these pairs are typically assumed to preserve higher-order RNA structure and binding of macromolecule partners. Here, we report that indirect effects of the helix sequence on RNA tertiary stability are, in fact, significant but are nevertheless predictable from a simple computational model called RNAMake-∆∆G. When tested through the RNA on a massively parallel array (RNA-MaP) experimental platform, blind predictions for >1500 variants of the tectoRNA heterodimer model system achieve high accuracy (rmsd 0.34 and 0.77 kcal/mol for sequence and length changes, respectively). Detailed comparison of predictions to experiments support a microscopic picture of how helix sequence changes subtly modulate conformational fluctuations at each base-pair step, which accumulate to impact RNA tertiary structure stability. Our study reveals a previously overlooked phenomenon in RNA structure formation and provides a framework of computation and experiment for understanding helix conformational preferences and their impact across biological RNA and RNA-protein assemblies.

Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation†

Biochemistry ◽  
1999 ◽  
Vol 38 (34) ◽  
pp. 11040-11050 ◽  
Author(s):  
Martha J. Fedor
Keyword(s):  
Tertiary Structure ◽  
Hairpin Ribozyme ◽  
Structure Stabilization
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