scholarly journals U1A protein-stem loop 2 RNA recognition: Prediction of structural differences from protein mutations

Biopolymers ◽  
2011 ◽  
Vol 95 (9) ◽  
pp. 591-606 ◽  
Author(s):  
Bethany L. Kormos ◽  
Susan N. Pieniazek ◽  
David L. Beveridge ◽  
Anne M. Baranger
Keyword(s):  
Rna Recognition ◽  
Stem Loop ◽  
Structural Differences ◽  
Protein Mutations ◽  
U1a Protein ◽  
Loop 2

Changes in sidechain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein

2000 ◽  
Vol 298 (1) ◽  
pp. 163 ◽  
Author(s):  
A. Mittermaier ◽  
L. Varani ◽  
D.R. Muhandiram ◽  
L.E. Kay ◽  
G. Varani
Keyword(s):  
Backbone Dynamics ◽  
Rna Recognition ◽  
U1a Protein

scholarly journals Mouse Hepatitis Virus Stem-Loop 2 Adopts a uYNMG(U)a-Like Tetraloop Structure That Is Highly Functionally Tolerant of Base Substitutions

2009 ◽  
Vol 83 (23) ◽  
pp. 12084-12093 ◽  
Author(s):  
Pinghua Liu ◽  
Lichun Li ◽  
Sarah C. Keane ◽  
Dong Yang ◽  
Julian L. Leibowitz ◽  
...  
Keyword(s):  
Hepatitis Virus ◽  
Mouse Hepatitis Virus ◽  
Point Mutations ◽  
Wild Type Virus ◽  
Wild Type ◽  
Site Mutation ◽  
Structural Element ◽  
Nucleotide Substitutions ◽  
Stem Loop ◽  
Loop 2

ABSTRACT Stem-loop 2 (SL2) of the 5′-untranslated region of the mouse hepatitis virus (MHV) contains a highly conserved pentaloop (C47-U48-U49-G50-U51) stacked on a 5-bp stem. Solution nuclear magnetic resonance experiments are consistent with a 5′-uYNMG(U)a or uCUYG(U)a tetraloop conformation characterized by an anti-C47-syn-G50 base-pairing interaction, with U51 flipped out into solution and G50 stacked on A52. Previous studies showed that U48C and U48A substitutions in MHV SL2 were lethal, while a U48G substitution was viable. Here, we characterize viruses harboring all remaining single-nucleotide substitutions in the pentaloop of MHV SL2 and also investigate the degree to which the sequence context of key pentaloop point mutations influences the MHV replication phenotype. U49 or U51 substitution mutants all are viable; C47 substitution mutants also are viable but produce slightly smaller plaques than wild-type virus. In contrast, G50A and G50C viruses are severely crippled and form much smaller plaques. Virus could not be recovered from G50U-containing mutants; rather, only true wild-type revertants or a virus, G50U/C47A, containing a second site mutation were recovered. These functional data suggest that the Watson-Crick edges of C47 and G50 (or A47 and U50 in the G50U/C47A mutant) are in close enough proximity to a hydrogen bond with U51 flipped out of the hairpin. Remarkably, increasing the helical stem stability rescues the previously lethal mutants U48C and G50U. These studies suggest that SL2 functions as an important, but rather plastic, structural element in stimulating subgenomic RNA synthesis in coronaviruses.

scholarly journals Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

Science ◽  
2010 ◽  
Vol 329 (5997) ◽  
pp. 1355-1358 ◽  
Author(s):  
Rachel E. Haurwitz ◽  
Martin Jinek ◽  
Blake Wiedenheft ◽  
Kaihong Zhou ◽  
Jennifer A. Doudna
Keyword(s):  
Rna Processing ◽  
Active Site ◽  
Large Family ◽  
Rna Recognition ◽  
Specific Interactions ◽  
Major Groove ◽  
Recognition Mechanism ◽  
Stem Loop ◽  
Crispr Locus ◽  
Phosphate Backbone

Many bacteria and archaea contain clustered regularly interspaced short palindromic repeats (CRISPRs) that confer resistance to invasive genetic elements. Central to this immune system is the production of CRISPR-derived RNAs (crRNAs) after transcription of the CRISPR locus. Here, we identify the endoribonuclease (Csy4) responsible for CRISPR transcript (pre-crRNA) processing in Pseudomonas aeruginosa. A 1.8 angstrom crystal structure of Csy4 bound to its cognate RNA reveals that Csy4 makes sequence-specific interactions in the major groove of the crRNA repeat stem-loop. Together with electrostatic contacts to the phosphate backbone, these enable Csy4 to bind selectively and cleave pre-crRNAs using phylogenetically conserved serine and histidine residues in the active site. The RNA recognition mechanism identified here explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases.

scholarly journals Correlated Motions in the U1 snRNA Stem/Loop 2:U1A RBD1 Complex

2005 ◽  
Vol 89 (3) ◽  
pp. 2046-2058 ◽  
Author(s):  
Scott A. Showalter ◽  
Kathleen B. Hall
Keyword(s):  
Stem Loop ◽  
Correlated Motions ◽  
U1 Snrna ◽  
Loop 2

scholarly journals Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops

2020 ◽  
Vol 21 (17) ◽  
pp. 6188
Author(s):  
Christina Bergonzo ◽  
Andrea L. Szakal
Keyword(s):  
Molecular Dynamics ◽  
Rna Structure ◽  
Untranslated Region ◽  
Conformational Equilibrium ◽  
3D Structure ◽  
Dimethyl Sulfate ◽  
Stem Loop ◽  
Dynamics Simulations ◽  
Loop 2 ◽  
Sampling Times

A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. To this end, we have combined molecular dynamics simulations with previous Nuclear Magnetic Resonance measurements for stem loop 2 of SARS-CoV-1 to refine 3D structure predictions of that stem loop. We find that relatively short sampling times allow for loop rearrangement from predicted structures determined in absence of water or ions, to structures better aligned with experimental data. We then use molecular dynamics to predict the refined structure of the transcription regulatory leader sequence (TRS-L) region which includes stem loop 3, and show that arrangement of the loop around exchangeable monovalent potassium can interpret the conformational equilibrium determined by in-cell dimethyl sulfate (DMS) data.

scholarly journals A novel occluded RNA recognition motif in Prp24 unwinds the U6 RNA internal stem loop

2011 ◽  
Vol 39 (17) ◽  
pp. 7837-7847 ◽  
Author(s):  
Stephen Martin-Tumasz ◽  
Ashley C. Richie ◽  
Lawrence J. Clos ◽  
David A. Brow ◽  
Samuel E. Butcher
Keyword(s):  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Stem Loop ◽  
Recognition Motif ◽  
U6 Rna
Sign in / Sign up

Export Citation Format

Share Document