204d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:31, 13 December 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:204d.png|left|200px]]
 
-
<!--
+
==THE SOLUTION STRUCTURES OF PSORALEN MONOADDUCTED AND CROSSLINKED DNA OLIGOMERS BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS==
-
The line below this paragraph, containing "STRUCTURE_204d", creates the "Structure Box" on the page.
+
<StructureSection load='204d' size='340' side='right'caption='[[204d]]' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[204d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=204D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=204D FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PSO:4-HYDROXYMETHYL-4,5,8-TRIMETHYLPSORALEN'>PSO</scene></td></tr>
-
{{STRUCTURE_204d| PDB=204d | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=204d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=204d OCA], [https://pdbe.org/204d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=204d RCSB], [https://www.ebi.ac.uk/pdbsum/204d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=204d ProSAT]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We have used two-dimensional 1H NMR spectroscopy to determine the solution structures of the 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) furanside monoadducted (MAf) and the photoisomeric HMT interstrand cross-linked (XL) DNA oligonucleotide d(5'-GCGTACGC-3')2. The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for both the MAf and XL from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviations of the coordinates for the 40 structures for the MAf and XL were 1.12 and 1.10 A, respectively. The rmsd of the MAf with respect to the XL is 2.20 A. The local DNA structure is distorted in both adducts, with the helix unwound by 34 degrees and 25 degrees for the MAf and XL, respectively, and an overall helical repeat of 11 base pairs, caused by intercalation of the HMT. The MAf is a photochemical intermediate on the path to interstrand XL. Considerable local structural distortion is induced by both adducts, but the DNA returns to B-form structure within three base pairs of the damage site. There is no significant bend in the helix axis of either the MAf or the XL. We have evaluated the accuracy of the two major methods of converting NOESY data into interproton distances, the isolated spin-pair approximation (ISPA) and the complete relaxation rate matrix analysis (RMA). Both methods were evaluated by comparing the resulting calculated interproton distances generated to known covalently fixed distances in the HMT. The overall structures were evaluated by checking their agreement with biophysical evidence from non-NMR techniques. Only the modified RMA method gave correct interproton distances.
-
===THE SOLUTION STRUCTURES OF PSORALEN MONOADDUCTED AND CROSSLINKED DNA OLIGOMERS BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS===
+
Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics.,Spielmann HP, Dwyer TJ, Hearst JE, Wemmer DE Biochemistry. 1995 Oct 10;34(40):12937-53. PMID:7548052<ref>PMID:7548052</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_7548052}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 204d" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 7548052 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_7548052}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=204D OCA].
+
[[Category: Dwyer TJ]]
-
 
+
[[Category: Hearst JE]]
-
==Reference==
+
[[Category: Spielmann HP]]
-
Solution structures of psoralen monoadducted and cross-linked DNA oligomers by NMR spectroscopy and restrained molecular dynamics., Spielmann HP, Dwyer TJ, Hearst JE, Wemmer DE, Biochemistry. 1995 Oct 10;34(40):12937-53. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7548052 7548052]
+
[[Category: Wemmer DE]]
-
[[Category: Dwyer, T J.]]
+
-
[[Category: Hearst, J E.]]
+
-
[[Category: Spielmann, H P.]]
+
-
[[Category: Wemmer, D E.]]
+
-
[[Category: Dna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:39:19 2008''
+

Current revision

THE SOLUTION STRUCTURES OF PSORALEN MONOADDUCTED AND CROSSLINKED DNA OLIGOMERS BY NMR SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS

PDB ID 204d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/204d"
Personal tools