Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κb site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco

Tisné, Carine; Hantz, Edith; Hartmann, Brigitte; Delepierre, Muriel

doi:10.1006/jmbi.1998.1757

Cited by 63 publications

(88 citation statements)

References 51 publications

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“…The scattering factor of P is about twice as large as those of C, O and N. This is probably why alternative locations of P atoms are more often detected than those of other atoms. As shown using NMR and MD, phosphate backbones equilibrate with different conformations in solution (Tisné et al, 1998;Wecker et al, 2002;Djuranovic & Hartmann, 2005;Robertson & Cheatham, 2015). Thus, it was interpreted that the peaks found here most probably correspond to different backbone conformations.…”

Section: Distribution Of Peaks In M|f O | à D|f C | Mapssupporting

confidence: 60%

“…Several studies have been performed to analyse the DNA deformability from this aspect, as exemplified in the following. NMR data revealed evidence for a BI-BII equilibrium in steps flanking the NF-B binding site and a curvature of the DNA duplex induced by the equilibrium (Tisné et al, 1998;Wecker et al, 2002). A mutation study showed that the distribution of BI-BII conformational equilibria had a critical effect on the binding affinity (Tisné et al, 1999).…”

Section: Introductionmentioning

confidence: 99%

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DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

Sunami

Chatake

Kono

2017

Acta Cryst Sect D Struct Biol

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Edited by G. J. Kleywegt, EMBL-EBI, Hinxton, EnglandKeywords: crystallographic heterogeneity; DNA; flexibility of phosphate backbone; Z-DNA; ZI/ZII transition. Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|F o | À D|F c | electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|F o | À D|F c | peaks indicated that some of these unassigned densities correspond to ZI $ ZII or A/B ! BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.

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Section: Distribution Of Peaks In M|f O | à D|f C | Mapssupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

Sunami

Chatake

Kono

2017

Acta Cryst Sect D Struct Biol

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“…(However, in vivo studies do not distinguish between direct DNA-binding events and protein-protein interaction-mediated promoter association by NF-kB). X-ray crystal structures of several kB DNA sequences are known both in free and NF-kB-bound states (Tisne et al, 1998(Tisne et al, , 1999Berkowitz et al, 2002;Chen-Park et al, 2002;Huang et al, 2005a). The conformations of the kB DNA sites exhibit global structural likeness in their protein-bound forms.…”

Section: Dna Target Sites Of Nf-kb Dimersmentioning

confidence: 99%

Transcriptional regulation via the NF-κB signaling module

2006

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Stimulus-induced nuclear factor-jB (NF-jB) activity, the central mediator of inflammatory responses and immune function, comprises a family of dimeric transcription factors that regulate diverse gene expression programs consisting of hundreds of genes. A family of inhibitor of jB (IjB) proteins controls NF-jB DNA-binding activity and nuclear localization. IjB protein metabolism is intricately regulated through stimulus-induced degradation and feedback re-synthesis, which allows for dynamic control of NF-jB activity. This network of interactions has been termed the NF-jB signaling module. Here, we summarize the current understanding of the molecular structures and biochemical mechanisms that determine NF-jB dimer formation and the signal-processing characteristics of the signaling module. We identify NF-jB-jB site interaction specificities and dynamic control of NF-jB activity as mechanisms that generate specificity in transcriptional regulation. We discuss examples of gene regulation that illustrate how these mechanisms may interface with other transcription regulators and promoter-associated events, and how these mechanisms suggest regulatory principles for NF-jB-mediated gene activation.

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“…NMR studies have been done on the HIV-1 LTR 5'-GGGACTTTC-3' and a mutated kB DNA sequence (Tisne et al, 1998(Tisne et al, , 1999. The wildtype kB site exists in an equilibrium between being inherently straight or bent 208 towards the major groove while the mutations, biochemically observed to abrogate protein binding (Nabel and Baltimore, 1987), e ect a pronounced kink that precludes protein binding (Tisne et al, 1999).…”

Section: Dna Sequence Variationsmentioning

confidence: 99%

Regulation of DNA binding by Rel/NF-κB transcription factors: structural views

1999

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Rel/NF-kB transcription factors form homo-and heterodimers with di erent DNA binding site speci®cities and DNA binding a nities. Several intracellular pathways evoked by a wide range of biological factors and environmental conditions can lead to the activation of Rel/NF-kB dimers by signaling degradation of the inhibitory IkB protein. In the nucleus Rel/NF-kB dimers modulate the expression of a variety of genes including those encoding cytokines, growth factors, acute phase response proteins, immunoreceptors, other transcription factors, cell adhesion molecules, viral proteins and regulators of apoptosis. The primary focus of this review is on structural and functional aspects of Rel/NFkB:DNA complexes and their formation. The salient features of the Rel/NF-kB dimer:DNA structure are described, as are modes of transcriptional regulation by phosphorylation, altered DNA binding properties, varying protein conformations, and interactions with IkB proteins.

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Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κb site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco

Cited by 63 publications

References 51 publications

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

Transcriptional regulation via the NF-κB signaling module

Regulation of DNA binding by Rel/NF-κB transcription factors: structural views

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Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 κb site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex 1 1Edited by I. Tinoco

Cited by 63 publications

References 51 publications

DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps

DNA conformational transitions inferred from re-evaluation ofm|Fo| −D|Fc| electron-density maps

Transcriptional regulation via the NF-κB signaling module

Regulation of DNA binding by Rel/NF-κB transcription factors: structural views

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Product

Resources

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DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps

DNA conformational transitions inferred from re-evaluation ofm|F_o| −D|F_c| electron-density maps