2miv - Revision history

OCA at 07:00, 1 May 2024

OCA — Wed, 01 May 2024 07:00:32 GMT

←Older revision		Revision as of 07:00, 1 May 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [https://pdbe.org/2miv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [https://www.ebi.ac.uk/pdbsum/2miv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [https://pdbe.org/2miv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [https://www.ebi.ac.uk/pdbsum/2miv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The dimensions and arrangements of aromatic rings (topology) in adducts derived from the reactions of polycyclic aromatic hydrocarbon (PAH) diol epoxide metabolites with DNA influence the distortions and stabilities of double-stranded DNA, and hence their recognition and processing by the human nucleotide excision repair (NER) system. Dibenzo[a,l]pyrene (DB[a,l]P) is a highly tumorigenic six-ring PAH, which contains a nonplanar and aromatic fjord region that is absent in the structurally related bay region five-ring PAH benzo[a]pyrene (B[a]P). The PAH diol epoxide-DNA adducts formed include the stereoisomeric 14S and 14R trans-anti-DB[a,l]P-N(2)-dG and the stereochemically analogous 10S- and 10R-B[a]P-N(2)-dG (B[a]P-dG) guanine adducts. However, nuclear magnetic resonance (NMR) solution studies of the 14S-DB[a,l]P-N(2)-dG adduct in DNA have not yet been presented. Here we have investigated the 14S-DB[a,l]P-N(2)-dG adduct in two different sequence contexts using NMR methods with distance-restrained molecular dynamics simulations. In duplexes with dC opposite the adduct deleted, a well-resolved base-displaced intercalative adduct conformation can be observed. In full duplexes, in contrast to the intercalated 14R stereoisomeric adduct, the bulky DB[a,l]P residue in the 14S adduct is positioned in a greatly widened and distorted minor groove, with significant disruptions and distortions of base pairing at the lesion site and two 5'-side adjacent base pairs. These unique structural features are significantly different from those of the stereochemically analogous but smaller B[a]P-dG adduct. The greater size and different topology of the DB[a,l]P aromatic ring system lead to greater structurally destabilizing DNA distortions that are partially compensated by stabilizing DB[a,l]P-DNA van der Waals interactions, whose combined effects impact the NER response to the adduct. These structural results broaden our understanding of the structure-function relationship in NER.
-
-	Nuclear Magnetic Resonance Studies of an N(2)-Guanine Adduct Derived from the Tumorigen Dibenzo[a,l]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations.,Rodriguez FA, Liu Z, Lin CH, Ding S, Cai Y, Kolbanovskiy A, Kolbanovskiy M, Amin S, Broyde S, Geacintov NE Biochemistry. 2014 Mar 25;53(11):1827-41. doi: 10.1021/bi4017044. Epub 2014 Mar, 11. PMID:24617538<ref>PMID:24617538</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2miv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:56, 22 November 2023

OCA — Wed, 22 Nov 2023 11:56:33 GMT

←Older revision		Revision as of 11:56, 22 November 2023
Line 1:		Line 1:

	==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==		==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==
-	<StructureSection load='2miv' size='340' side='right'caption='[[2miv~~]], [[NMR_Ensembles_of_Models \| 5 NMR models~~]]' scene=''>	+	<StructureSection load='2miv' size='340' side='right'caption='[[2miv]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MIV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene>~~</td></tr>	+	</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2miw\|2miw]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [https://pdbe.org/2miv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [https://www.ebi.ac.uk/pdbsum/2miv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [https://pdbe.org/2miv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [https://www.ebi.ac.uk/pdbsum/2miv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Amin, S]]	+	[[Category: Amin S]]
-	[[Category: Broyde, S]]	+	[[Category: Broyde S]]
-	[[Category: Cai, Y]]	+	[[Category: Cai Y]]
-	[[Category: Ding, S]]	+	[[Category: Ding S]]
-	[[Category: Geacintov~~, N E~~]]	+	[[Category: Geacintov NE]]
-	[[Category: Kolbanovskiy, A]]	+	[[Category: Kolbanovskiy A]]
-	[[Category: Kolbanovskiy, M]]	+	[[Category: Kolbanovskiy M]]
-	[[Category: Lin~~, C H~~]]	+	[[Category: Lin CH]]
-	[[Category: Liu, Z]]	+	[[Category: Liu Z]]
-	[[Category: Rodriguez~~, F A]]~~	+	[[Category: Rodriguez FA]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna adduct~~]]	+

OCA at 11:36, 16 February 2022

OCA — Wed, 16 Feb 2022 11:36:20 GMT

←Older revision		Revision as of 11:36, 16 February 2022
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	<StructureSection load='2miv' size='340' side='right'caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>		<StructureSection load='2miv' size='340' side='right'caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2MIV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MIV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2miw\|2miw]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [~~http~~://pdbe.org/2miv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2miv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [https://pdbe.org/2miv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [https://www.ebi.ac.uk/pdbsum/2miv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:24, 13 May 2020

OCA — Wed, 13 May 2020 06:24:22 GMT

←Older revision		Revision as of 06:24, 13 May 2020
Line 1:		Line 1:

	==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==		==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==
-	<StructureSection load='2miv' size='340' side='right' caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>	+	<StructureSection load='2miv' size='340' side='right'caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2MIV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2MIV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://pdbe.org/2miv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://pdbe.org/2miv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Amin, S]]		[[Category: Amin, S]]
	[[Category: Broyde, S]]		[[Category: Broyde, S]]

OCA at 22:54, 9 August 2018

OCA — Thu, 09 Aug 2018 22:54:07 GMT

←Older revision		Revision as of 22:54, 9 August 2018
Line 1:		Line 1:
		+
	==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==		==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==
	<StructureSection load='2miv' size='340' side='right' caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>		<StructureSection load='2miv' size='340' side='right' caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://pdbe.org/2miv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://pdbe.org/2miv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2miv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:07, 10 September 2015

OCA — Thu, 10 Sep 2015 07:07:58 GMT

←Older revision		Revision as of 07:07, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://pdbe.org/2miv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2miv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:46, 19 January 2015

OCA — Mon, 19 Jan 2015 13:46:14 GMT

←Older revision		Revision as of 13:46, 19 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_2miv\| PDB=2miv \| SCENE= }}~~	+	==NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations==
-	===NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations===	+	<StructureSection load='2miv' size='340' side='right' caption='[[2miv]], [[NMR_Ensembles_of_Models \| 5 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_24617538}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MIV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2QL:(11R,12R,13R)-11,12,13,14-TETRAHYDRONAPHTHO[1,2,3,4-PQR]TETRAPHENE-11,12,13-TRIOL'>2QL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2miw\|2miw]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2miv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2miv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2miv RCSB], [http://www.ebi.ac.uk/pdbsum/2miv PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The dimensions and arrangements of aromatic rings (topology) in adducts derived from the reactions of polycyclic aromatic hydrocarbon (PAH) diol epoxide metabolites with DNA influence the distortions and stabilities of double-stranded DNA, and hence their recognition and processing by the human nucleotide excision repair (NER) system. Dibenzo[a,l]pyrene (DB[a,l]P) is a highly tumorigenic six-ring PAH, which contains a nonplanar and aromatic fjord region that is absent in the structurally related bay region five-ring PAH benzo[a]pyrene (B[a]P). The PAH diol epoxide-DNA adducts formed include the stereoisomeric 14S and 14R trans-anti-DB[a,l]P-N(2)-dG and the stereochemically analogous 10S- and 10R-B[a]P-N(2)-dG (B[a]P-dG) guanine adducts. However, nuclear magnetic resonance (NMR) solution studies of the 14S-DB[a,l]P-N(2)-dG adduct in DNA have not yet been presented. Here we have investigated the 14S-DB[a,l]P-N(2)-dG adduct in two different sequence contexts using NMR methods with distance-restrained molecular dynamics simulations. In duplexes with dC opposite the adduct deleted, a well-resolved base-displaced intercalative adduct conformation can be observed. In full duplexes, in contrast to the intercalated 14R stereoisomeric adduct, the bulky DB[a,l]P residue in the 14S adduct is positioned in a greatly widened and distorted minor groove, with significant disruptions and distortions of base pairing at the lesion site and two 5'-side adjacent base pairs. These unique structural features are significantly different from those of the stereochemically analogous but smaller B[a]P-dG adduct. The greater size and different topology of the DB[a,l]P aromatic ring system lead to greater structurally destabilizing DNA distortions that are partially compensated by stabilizing DB[a,l]P-DNA van der Waals interactions, whose combined effects impact the NER response to the adduct. These structural results broaden our understanding of the structure-function relationship in NER.

-	~~==About this Structure==~~	+	Nuclear Magnetic Resonance Studies of an N(2)-Guanine Adduct Derived from the Tumorigen Dibenzo[a,l]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations.,Rodriguez FA, Liu Z, Lin CH, Ding S, Cai Y, Kolbanovskiy A, Kolbanovskiy M, Amin S, Broyde S, Geacintov NE Biochemistry. 2014 Mar 25;53(11):1827-41. doi: 10.1021/bi4017044. Epub 2014 Mar, 11. PMID:24617538<ref>PMID:24617538</ref>
-	~~[[2miv]] is a~~ 2 ~~chain structure. Full experimental information is available~~ from [~~http~~:~~//oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id=2MIV OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024617538</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Amin, S.]]	+	== References ==
-	[[Category: Broyde, S.]]	+	<references/>
-	[[Category: Cai, Y.]]	+	__TOC__
-	[[Category: Ding, S.]]	+	</StructureSection>
-	[[Category: Geacintov, N E.]]	+	[[Category: Amin, S]]
-	[[Category: Kolbanovskiy, A.]]	+	[[Category: Broyde, S]]
-	[[Category: Kolbanovskiy, M.]]	+	[[Category: Cai, Y]]
-	[[Category: Lin, C H.]]	+	[[Category: Ding, S]]
-	[[Category: Liu, Z.]]	+	[[Category: Geacintov, N E]]
-	[[Category: Rodriguez, F A.]]	+	[[Category: Kolbanovskiy, A]]
		+	[[Category: Kolbanovskiy, M]]
		+	[[Category: Lin, C H]]
		+	[[Category: Liu, Z]]
		+	[[Category: Rodriguez, F A]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna adduct]]		[[Category: Dna adduct]]

OCA at 08:59, 2 April 2014

OCA — Wed, 02 Apr 2014 08:59:38 GMT

←Older revision		Revision as of 08:59, 2 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_2miv\| PDB=2miv \| SCENE= }}
		+	===NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations===
		+	{{ABSTRACT_PUBMED_24617538}}

-	~~The entry~~ 2miv is ~~ON HOLD~~	+	==About this Structure==
		+	[[2miv]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MIV OCA].

-	~~Authors~~: ~~Rodriguez~~, ~~F.A~~., ~~Liu, Z~~., ~~Lin, C~~.~~H.,~~ Ding, S., ~~Cai, Y~~., Kolbanovskiy, A., Kolbanovskiy, M., ~~Amin, S~~., ~~Broyde, S~~., ~~Geacintov, N~~.E.	+	==Reference==
-		+	<ref group="xtra">PMID:024617538</ref><references group="xtra"/><references/>
-	~~Description: NMR studies of N2-guanine adducts derived from the tumorigen dibenzo~~[~~a,l~~]~~pyrene in DNA~~: ~~Impact of~~ adduct ~~stereochemistry, size, and local DNA structure on solution conformations~~	+	[[Category: Amin, S.]]
		+	[[Category: Broyde, S.]]
		+	[[Category: Cai, Y.]]
		+	[[Category: Ding, S.]]
		+	[[Category: Geacintov, N E.]]
		+	[[Category: Kolbanovskiy, A.]]
		+	[[Category: Kolbanovskiy, M.]]
		+	[[Category: Lin, C H.]]
		+	[[Category: Liu, Z.]]
		+	[[Category: Rodriguez, F A.]]
		+	[[Category: Dna]]
		+	[[Category: Dna adduct]]

OCA: Protected "2miv" [edit=sysop:move=sysop]

OCA — Wed, 08 Jan 2014 08:35:22 GMT

Protected "2miv" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:35, 8 January 2014

OCA: New page: '''Unreleased structure''' The entry 2miv is ON HOLD Authors: Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov...

OCA — Wed, 08 Jan 2014 08:35:20 GMT

New page: '''Unreleased structure''' The entry 2miv is ON HOLD Authors: Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov...

New page

'''Unreleased structure'''

The entry 2miv is ON HOLD

Authors: Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov, N.E.

Description: NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations