This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2kbd
From Proteopedia
OCA (Talk | contribs)
(New page: 200px<br /> <applet load="2kbd" size="450" color="white" frame="true" align="right" spinBox="true" caption="2kbd" /> '''5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C...)
Next diff →
Revision as of 12:46, 8 November 2007
|
5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'
Overview
1H and 31P NMR spectroscopy have been used together with molecular, modelling to determine the fine structure of a non-palindromic 16 bp DNA, containing the NF-kappa B binding site. Much emphasis has been placed upon, NMR optimization of both two-dimensional 31P NMR techniques to extract, structural information defining the phosphodiester backbone conformation, and selective homonuclear 2D COSY experiments to determine sugar, conformations. NMR data show evidence for a dynamic behaviour of steps, flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII, equilibrium at these steps is demonstrated and two models for each extreme, conformation are proposed in agreement with NMR data. In the refined BII, structures, the NF-kappa B binding site exhibits an intrinsic curvature, towards the major groove that is magnified by the four flanking steps in, the BII conformation. Furthermore, the base-pairs are translated into the, major groove. Thus, we present a novel mode of dynamic intrinsic curvature, compatible with the DNA curvature observed in the X-ray structure of the, p50-DNA complex.
About this Structure
2KBD is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex., Tisne C, Hantz E, Hartmann B, Delepierre M, J Mol Biol. 1998 May 29;279(1):127-42. PMID:9636705
Page seeded by OCA on Thu Nov 8 14:52:48 2007
