Related ArticlesAn 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 cAMP-responsive element (CRE, 5'-TGACGTCA-3') is essential to the transcriptional function of numerous gene promoters in eukaryotic cells. We carried out NMR restrained molecular mechanics studies using two different force fields (Flex and "AMBER94") on a hexadecanucleotide d(GAGATGACGTCATCTC) containing CRE. Results indicated that free CRE is a B-DNA that is intrinsically curved towards the minor groove. To our knowledge, NMR restraints have not previously been useful in accounting for a global DNA curvature. In order to validate the bend in CRE, we applied a new strategy in which DNA structures displaying different curvatures were generated and then compared with NMR data. Conformations of CRE curved towards the minor groove provided the best agreement with NMR data. Our results contrast with previous results obtained from NMR restrained modelling and gel methods; these suggested conformations that were straight or curved towards the major groove, respectively. The curve in free CRE is spread along the DNA helix: several kinks are repeated in phase within the helical turn, although they are centred mainly on CpG in between the TGA half-sites, thus slightly increasing their spacing within the major groove. Comparison with the crystal structure of CRE complexed to general control protein 4 showed that the curve orientation is reversed from the minor to the major groove upon protein binding, due to a helix distortion concentrated mainly on CpG.
[NMR paper] Micelle-induced curvature in a water-insoluble HIV-1 Env peptide revealed by NMR dipo
Micelle-induced curvature in a water-insoluble HIV-1 Env peptide revealed by NMR dipolar coupling measurement in stretched polyacrylamide gel.
Related Articles Micelle-induced curvature in a water-insoluble HIV-1 Env peptide revealed by NMR dipolar coupling measurement in stretched polyacrylamide gel.
J Am Chem Soc. 2002 Mar 20;124(11):2450-1
Authors: Chou JJ, Kaufman JD, Stahl SJ, Wingfield PT, Bax A
The structure of a water-insoluble fragment encompassing residues 282-304 of the HIV envelope protein gp41 is studied when solubilized by...
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[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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[NMR paper] Oxidation of guanines in the iron-responsive element RNA: similar structures from che
Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.
Related Articles Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.
Chem Biol. 1998 Dec;5(12):679-87
Authors: Ciftan SA, Theil EC, Thorp HH
BACKGROUND: The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins...
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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] 1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding pept
1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding peptide from the HMG-I protein.
Related Articles 1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding peptide from the HMG-I protein.
Int J Pept Protein Res. 1995 Jun;45(6):554-60
Authors: Evans JN, Zajicek J, Nissen MS, Munske G, Smith V, Reeves R
The HMG-I subfamily of high mobility group (HMG) chromatin proteins consists of DNA-binding proteins that preferentially bind to stretches of A.T-rich sequence both in vitro and in vivo....
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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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Major groove width variations in RNA structures determined by NMR and impact of 13C r
Abstract Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1Hâ?? 1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of...
An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA fo
Linear Mode
