The TAR hairpin is an important part of the 5' long terminal repeat of HIV-1 and appears to be recognized by a cellular protein. A 14-base model of the native TAR hairpin 5'-GAGC[CUGGGA]-GCUC-3' (loop bases in square brackets) has been studied by proton, phosphorus, and natural abundance carbon NMR; these results are compared to other published NMR studies of the TAR hairpin. Assignments of all nonexchangeable protons and of all the stem-exchangeable protons have been made, as well as all phosphorus and many carbon resonances. Large J1'2' and J3'4' proton-proton coupling in the C5, G8, and G9 sugars indicate an equilibrium between C2'- and C3'-endo forms; these data show a dynamic loop structure. We see three broad imino resonances that have not been reported before; these resonances are in the right region for unbonded loop imino protons. These peaks suggest the protons are protected from fast exchange with the solvent by the structure of the hairpin loop. Simulated annealing and molecular dynamics with 148 distance constraints, 11 hydrogen bonds, and 84 torsion angle constraints showed a wide variety of structures. Certain trends are evident, such as continuation of the A-form helix on the 3' side of the hairpin loop. The ensemble of calculated structures agree with most chemical modification data.
[NMR paper] Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dy
Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR.
Related Articles Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR.
Biophys J. 2000 Aug;79(2):656-69
Authors: Derreumaux S, Fermandjian S
DNA bending is assumed to play a crucial role during recognition of the cAMP-responsive element (CRE) by transcription factors. However, diverging results have been obtained for the bending direction of the unbound double helix. The...
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[NMR paper] Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1
Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Related Articles Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Biochemistry. 2000 May 16;39(19):5630-41
Authors: Lacourciere KA, Stivers JT, Marino JP
Rev is an essential HIV-1 regulatory protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome and is involved in transport of...
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Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cry
Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography.
Related Articles Structure of a Conserved Retroviral RNA Packaging Element by NMR Spectroscopy and Cryo-Electron Tomography.
J Mol Biol. 2010 Oct 6;
Authors: Miyazaki Y, Irobalieva RN, Tolbert B, Smalls-Mantey A, Iyalla K, Loeliger K, D'Souza V, Khant H, Schmid MF, Garcia E, Telesnitsky A, Chiu W, Summers MF
The 5'-untranslated regions (5'-UTRs) of all gammaretroviruses contain a conserved "double hairpin motif" (?(CD)) that is required for...
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10-12-2010 02:52 PM
[NMR paper] An NMR study on the beta-hairpin region of barnase.
An NMR study on the beta-hairpin region of barnase.
Related Articles An NMR study on the beta-hairpin region of barnase.
Fold Des. 1996;1(3):231-41
Authors: Neira JL, Fersht AR
BACKGROUND: The beta-hairpin of barnase (residues Ser92-Leu95) has been proposed in theoretical and protein engineering studies to be an initiation site for folding . There is evidence for residual structure in this region from NMR studies of the denatured protein under different denaturing conditions . A more detailed analysis is possible by NMR studies of isolated...
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[NMR paper] A model of the iron responsive element RNA hairpin loop structure determined from NMR
A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data.
Biochemistry. 1996 Oct 22;35(42):13586-96
Authors: Laing LG, Hall KB
The iron responsive element (IRE) is a conserved RNA structure that is found in the 5' UTR of ferritin mRNA and in the 3' UTR of transferrin receptor mRNA....
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[NMR paper] Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using
Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR.
Related Articles Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR.
J Biomol NMR. 1995 Dec;6(4):375-89
Authors: Battiste JL, Tan R, Frankel AD, Williamson JR
The Rev Response Element (RRE) RNA-Rev protein interaction is important for regulation of gene expression in the human immunodeficiency virus. A model system for this interaction, which includes stem IIB of the RRE RNA and an...
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[NMR paper] The importance of a single G in the hairpin loop of the iron responsive element (IRE)
The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.
Nucleic Acids Res. 1995 Jan 11;23(1):146-53
Authors: Sierzputowska-Gracz H, McKenzie RA, Theil EC
Noncoding sequences...
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[NMR paper] An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA fo
An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies.
Eur J Biochem. 1999 Feb;259(3):877-86
Authors: Chaoui M, Derreumaux S, Mauffret O, Fermandjian S
The...
An NMR study of the HIV-1 TAR element hairpin.
Linear Mode
