scholarly journals Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing–duplex structural transition

2007 ◽  
Vol 35 (5) ◽  
pp. 1698-1713 ◽  
Author(s):  
Xiaoyan Sun ◽  
Qi Zhang ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Structural Transition ◽  
Stem Loop ◽  
Internal Loop ◽  
Slow Motions ◽  
Fast And Slow Motions ◽  
Hiv 1

scholarly journals 1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2

2021 ◽  
Author(s):  
Christian Richter ◽  
Katharina F. Hohmann ◽  
Sabrina Toews ◽  
Daniel Mathieu ◽  
Nadide Altincekic ◽  
...  
Keyword(s):  
Life Cycle ◽  
Chemical Shift ◽  
Base Pair ◽  
Chemical Shift Assignment ◽  
Potential Functions ◽  
Regulatory Rna ◽  
Structural Element ◽  
Stem Loop ◽  
Internal Loop ◽  
Shift Assignment

AbstractThe stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7–33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

Modeling and solution structure probing of the HIV-1 TAR stem-loop

1993 ◽  
Vol 11 (2) ◽  
pp. 92-97 ◽  
Author(s):  
Andrew D. Critchley ◽  
I. Haneef ◽  
Diane J. Cousens ◽  
Peter G. Stockley
Keyword(s):  
Solution Structure ◽  
Stem Loop ◽  
Structure Probing ◽  
Hiv 1

scholarly journals A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription

2019 ◽  
Vol 47 (21) ◽  
pp. 11057-11068 ◽  
Author(s):  
Emanuela Ruggiero ◽  
Sara Lago ◽  
Primož Šket ◽  
Matteo Nadai ◽  
Ilaria Frasson ◽  
...  
Keyword(s):  
Long Terminal Repeat ◽  
Antiviral Drug ◽  
Cellular Protein ◽  
Terminal Repeat ◽  
Proviral Genome ◽  
Stem Loop ◽  
Hnrnp K ◽  
Induced Folding ◽  
Ltr Promoter ◽  
Hiv 1

Abstract I-motifs are non-canonical nucleic acids structures characterized by intercalated H-bonds between hemi-protonated cytosines. Evidence on the involvement of i-motif structures in the regulation of cellular processes in human cells has been consistently growing in the recent years. However, i-motifs within non-human genomes have never been investigated. Here, we report the characterization of i-motifs within the long terminal repeat (LTR) promoter of the HIV-1 proviral genome. Biophysical and biochemical analysis revealed formation of a predominant i-motif with an unprecedented loop composition. One-dimensional nuclear magnetic resonance investigation demonstrated formation of three G-C H-bonds in the long loop, which likely improve the structure overall stability. Pull-down experiments combined with mass spectrometry and protein crosslinking analysis showed that the LTR i-motif is recognized by the cellular protein hnRNP K, which induced folding at physiological conditions. In addition, hnRNP K silencing resulted in an increased LTR promoter activity, confirming the ability of the protein to stabilize the i-motif-forming sequence, which in turn regulates the LTR-mediated HIV-1 transcription. These findings provide new insights into the complexity of the HIV-1 virus and lay the basis for innovative antiviral drug design, based on the possibility to selectively recognize and target the HIV-1 LTR i-motif.

Technical stability of a system with fast and slow motions

1981 ◽  
Vol 17 (11) ◽  
pp. 1029-1036
Author(s):  
A. A. Martynyuk ◽  
A. Karimzhanov
Keyword(s):  
Technical Stability ◽  
Slow Motions ◽  
Fast And Slow Motions

Stem of SL1 RNA in HIV-1:  Structure and Nucleocapsid Protein Binding for a 1 × 3 Internal Loop†,‡

Biochemistry ◽  
2003 ◽  
Vol 42 (18) ◽  
pp. 5259-5269 ◽  
Author(s):  
YiQiong Yuan ◽  
Deborah J. Kerwood ◽  
Andrew C. Paoletti ◽  
Michael F. Shubsda ◽  
Philip N. Borer
Keyword(s):  
Protein Binding ◽  
Nucleocapsid Protein ◽  
Internal Loop ◽  
Hiv 1

scholarly journals Proline Residues within Spacer Peptide p1 Are Important for Human Immunodeficiency Virus Type 1 Infectivity, Protein Processing, and Genomic RNA Dimer Stability

2002 ◽  
Vol 76 (22) ◽  
pp. 11245-11253 ◽  
Author(s):  
Melissa K. Hill ◽  
Miranda Shehu-Xhilaga ◽  
Suzanne M. Crowe ◽  
Johnson Mak
Keyword(s):  
Protein Processing ◽  
Viral Infectivity ◽  
Genomic Rna ◽  
Stem Loop ◽  
Altered Protein ◽  
Immunodeficiency Virus ◽  
Rna Dimer ◽  
Hiv 1

ABSTRACT The full-length human immunodeficiency virus type 1 (HIV-1) mRNA encodes two precursor polyproteins, Gag and GagProPol. An infrequent ribosomal frameshifting event allows these proteins to be synthesized from the same mRNA in a predetermined ratio of 20 Gag proteins for each GagProPol. The RNA frameshift signal consists of a slippery sequence and a hairpin stem-loop whose thermodynamic stability has been shown in in vitro translation systems to be critical to frameshifting efficiency. In this study we examined the frameshift region of HIV-1, investigating the effects of altering stem-loop stability in the context of the complete viral genome and assessing the role of the Gag spacer peptide p1 and the GagProPol transframe (TF) protein that are encoded in this region. By creating a series of frameshift region mutants that systematically altered the stability of the frameshift stem-loop and the protein sequences of the p1 spacer peptide and TF protein, we have demonstrated the importance of stem-loop thermodynamic stability in frameshifting efficiency and viral infectivity. Multiple changes to the amino acid sequence of p1 resulted in altered protein processing, reduced genomic RNA dimer stability, and abolished viral infectivity. The role of the two highly conserved proline residues in p1 (position 7 and 13) was also investigated. Replacement of the two proline residues by leucines resulted in mutants with altered protein processing and reduced genomic RNA dimer stability that were also noninfectious. The unique ability of proline to confer conformational constraints on a peptide suggests that the correct folding of p1 may be important for viral function.

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