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 Probing the details of the HIV-1 Rev-Rev-responsive element interaction: effects of modified nucleotides on protein affinity and conformational changes during complex formation

1995 ◽  
Vol 308 (2) ◽  
pp. 447-453 ◽  
Author(s):  
S B Renwick ◽  
A D Critchley ◽  
C J Adams ◽  
S M Kelly ◽  
N C Price ◽  
...  
Keyword(s):  
Complex Formation ◽  
Conformational Changes ◽  
Solution Structure ◽  
Cd Spectroscopy ◽  
Sequence Information ◽  
Stem Loop ◽  
Contact Points ◽  
Responsive Element ◽  
Hiv 1 ◽  
Rev Protein

The solution structure of the human immunodeficiency virus type 1 (HIV-1) Rev-responsive element (RRE) has been investigated by enzymic and chemical structural probing of a 71 nt RRE transcript. The minimum sequence information required to maintain recognition by the Rev protein has previously been mapped to a 29 nt stem-loop structure, known as minSLIIB. The key recognition target is a single-stranded RNA bubble at the base of the RNA stem. The fine details of RNA recognition have been probed using chemically synthesized minSLIIBs containing variant base or sugar residues at sites within the bubble. These have been analysed by gel retardation assays and their relative affinities for Rev protein determined. Complex formation between the wild-type minSLIIB RRE and Rev protein was also monitored using CD spectroscopy, which suggests a change in RNA conformation upon Rev binding. The spectral change is consistent with localized melting of RNA, leading to a decrease in the level of base stacking and/or a change in base tilting, during formation of the complex. Deoxynucleotide substitutions on just one side, the 5′ side, of the bubble inhibit the conformational change detected by CD. The data are consistent with a dynamic interaction between Rev and its target site. The contact points between Rev and the RRE were probed directly using photo-cross-linking with either ribo-5-bromouridine- or ribo-4-thiouridine-substituted minSLIIBs. The data are consistent with protein-RNA contacts at the bottom of the bubble.

scholarly journals Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽  
2013 ◽  
Vol 3 (11) ◽  
pp. 130100 ◽  
Author(s):  
Zhisheng Lu ◽  
Julien R. C. Bergeron ◽  
R. Andrew Atkinson ◽  
Torsten Schaller ◽  
Dennis A. Veselkov ◽  
...  
Keyword(s):  
Solution Structure ◽  
Hydrophobic Interactions ◽  
Dynamic Information ◽  
Ubiquitin Ligase Complex ◽  
Biophysical Studies ◽  
Viral Infectivity Factor ◽  
Β Sheet ◽  
Socs Box ◽  
Insight Into ◽  
Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

scholarly journals Solution Structure of Calmodulin Bound to the Binding Domain of the HIV-1 Matrix Protein

2014 ◽  
Vol 289 (12) ◽  
pp. 8697-8705 ◽  
Author(s):  
Jiri Vlach ◽  
Alexandra B. Samal ◽  
Jamil S. Saad
Keyword(s):  
Solution Structure ◽  
Matrix Protein ◽  
Binding Domain ◽  
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.

scholarly journals mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis inArabidopsis thaliana

2020 ◽  
Vol 117 (35) ◽  
pp. 21785-21795 ◽  
Author(s):  
Susheel Sagar Bhat ◽  
Dawid Bielewicz ◽  
Tomasz Gulanicz ◽  
Zsuzsanna Bodi ◽  
Xiang Yu ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Structure ◽  
Methylation Status ◽  
Mirna Biogenesis ◽  
Stem Loop ◽  
Structure Probing ◽  
Plant Transcriptome ◽  
Loop Regions

InArabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introducesN6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem–loop regions of these transcripts inmtamutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA inmtamutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes ofmtamutant plants.

scholarly journals Solution structure of the His 12 → Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium

1998 ◽  
Vol 7 (12) ◽  
pp. 2669-2674 ◽  
Author(s):  
Mengli Cai ◽  
Michael Caffrey ◽  
G. Marius Clore ◽  
Angela M. Gronenborn ◽  
Ying Huang ◽  
...  
Keyword(s):  
Solution Structure ◽  
Binding Domain ◽  
Zinc Binding ◽  
Zinc Binding Domain ◽  
Hiv 1
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