7nwd - Revision history

OCA at 05:55, 6 October 2021

OCA — Wed, 06 Oct 2021 05:55:38 GMT

←Older revision		Revision as of 05:55, 6 October 2021
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	==Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate==		==Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate==
-	<StructureSection load='7nwd' size='340' side='right'caption='[[7nwd]]' scene=''>	+	<StructureSection load='7nwd' size='340' side='right'caption='[[7nwd]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nwd]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWD FirstGlance]. <br>
-	</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=7nwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwd OCA], [https://pdbe.org/7nwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwd RCSB], [https://www.ebi.ac.uk/pdbsum/7nwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwd ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UTB:'>UTB</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=7nwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwd OCA], [https://pdbe.org/7nwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwd RCSB], [https://www.ebi.ac.uk/pdbsum/7nwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from pi-pi stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
		+
		+	c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry.,Peterkova K, Durnik I, Marek R, Plavec J, Podbevsek P Nucleic Acids Res. 2021 Sep 7;49(15):8947-8960. doi: 10.1093/nar/gkab659. PMID:34365512<ref>PMID:34365512</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7nwd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Durnik I]]	+	[[Category: Durnik, I]]
-	[[Category: Marek R]]	+	[[Category: Marek, R]]
-	[[Category: Peterkova K]]	+	[[Category: Peterkova, K]]
-	[[Category: Plavec J]]	+	[[Category: Plavec, J]]
-	[[Category: Podbevsek P]]	+	[[Category: Podbevsek, P]]
		+	[[Category: C-kit2]]
		+	[[Category: Dna]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Pyrene]]

OCA at 10:20, 4 August 2021

OCA — Wed, 04 Aug 2021 10:20:50 GMT

←Older revision		Revision as of 10:20, 4 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7nwd is ~~ON HOLD~~	+	==Three-quartet c-kit2 G-quadruplex stabilized by a pyrene conjugate==
-		+	<StructureSection load='7nwd' size='340' side='right'caption='[[7nwd]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NWD FirstGlance]. <br>
-	~~Description~~:	+	</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=7nwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nwd OCA], [https://pdbe.org/7nwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nwd RCSB], [https://www.ebi.ac.uk/pdbsum/7nwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nwd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Durnik I]]
		+	[[Category: Marek R]]
		+	[[Category: Peterkova K]]
		+	[[Category: Plavec J]]
		+	[[Category: Podbevsek P]]

OCA at 07:52, 21 July 2021

OCA — Wed, 21 Jul 2021 07:52:04 GMT

←Older revision		Revision as of 07:52, 21 July 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7nwd is ON HOLD ~~until Paper Publication~~	+	The entry 7nwd is ON HOLD

	Authors:		Authors:

OCA at 06:30, 21 April 2021

OCA — Wed, 21 Apr 2021 06:30:11 GMT

←Older revision		Revision as of 06:30, 21 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7nwd is ON HOLD	+	The entry 7nwd is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 09:31, 31 March 2021

OCA — Wed, 31 Mar 2021 09:31:34 GMT

←Older revision		Revision as of 09:31, 31 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7nwd is ON HOLD ~~until sometime in the future~~	+	The entry 7nwd is ON HOLD

	Authors:		Authors:

OCA: Protected "7nwd" [edit=sysop:move=sysop]

OCA — Wed, 24 Mar 2021 05:41:26 GMT

Protected "7nwd" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 24 March 2021

OCA: New page: '''Unreleased structure''' The entry 7nwd is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Mar 2021 05:41:25 GMT

New page: '''Unreleased structure''' The entry 7nwd is ON HOLD until sometime in the future Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7nwd is ON HOLD until sometime in the future

Authors:

Description:
[[Category: Unreleased Structures]]