7zek - Revision history

OCA at 07:26, 8 September 2022

OCA — Thu, 08 Sep 2022 07:26:41 GMT

←Older revision		Revision as of 07:26, 8 September 2022
Line 1:		Line 1:

	==Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')==		==Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')==
-	<StructureSection load='7zek' size='340' side='right'caption='[[7zek~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='7zek' size='340' side='right'caption='[[7zek]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7zek]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zek]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEK FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene>, <scene name='pdbligand=L1J:'>L1J</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene>, <scene name='pdbligand=L1J:2-azanyl-9-[(2~{R},4~{S},5~{R})-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one'>L1J</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=7zek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zek OCA], [https://pdbe.org/7zek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zek RCSB], [https://www.ebi.ac.uk/pdbsum/7zek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zek 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=7zek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zek OCA], [https://pdbe.org/7zek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zek RCSB], [https://www.ebi.ac.uk/pdbsum/7zek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zek ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
-
-	Guiding the folding of G-quadruplexes through loop residue interactions.,Jana J, Vianney YM, Schroder N, Weisz K Nucleic Acids Res. 2022 Jun 27. pii: 6618545. doi: 10.1093/nar/gkac549. PMID:35758626<ref>PMID:35758626</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7zek" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jana, J]]	+	[[Category: Synthetic construct]]
-	[[Category: Schroeder, N]]	+	[[Category: Jana J]]
-	[[Category: Vianney~~, Y M~~]]	+	[[Category: Schroeder N]]
-	[[Category: Weisz, K]]	+	[[Category: Vianney YM]]
-	~~[[Category: Dna]]~~	+	[[Category: Weisz K]]
-	~~[[Category: Hybrid g-quadruplex]]~~	+
-	~~[[Category: Snapback loop~~]]	+

OCA at 16:28, 6 July 2022

OCA — Wed, 06 Jul 2022 16:28:14 GMT

←Older revision		Revision as of 16:28, 6 July 2022
Line 1:		Line 1:

	==Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')==		==Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')==
-	<StructureSection load='7zek' size='340' side='right'caption='[[7zek]]' scene=''>	+	<StructureSection load='7zek' size='340' side='right'caption='[[7zek]], [[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=7ZEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zek]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEK 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=7zek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zek OCA], [https://pdbe.org/7zek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zek RCSB], [https://www.ebi.ac.uk/pdbsum/7zek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zek ProSAT]</span></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene>, <scene name='pdbligand=L1J:'>L1J</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=7zek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zek OCA], [https://pdbe.org/7zek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zek RCSB], [https://www.ebi.ac.uk/pdbsum/7zek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zek ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
		+
		+	Guiding the folding of G-quadruplexes through loop residue interactions.,Jana J, Vianney YM, Schroder N, Weisz K Nucleic Acids Res. 2022 Jun 27. pii: 6618545. doi: 10.1093/nar/gkac549. PMID:35758626<ref>PMID:35758626</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7zek" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jana J]]	+	[[Category: Jana, J]]
-	[[Category: Schroeder N]]	+	[[Category: Schroeder, N]]
-	[[Category: Vianney YM]]	+	[[Category: Vianney, Y M]]
-	[[Category: Weisz K]]	+	[[Category: Weisz, K]]
		+	[[Category: Dna]]
		+	[[Category: Hybrid g-quadruplex]]
		+	[[Category: Snapback loop]]

OCA at 09:48, 22 June 2022

OCA — Wed, 22 Jun 2022 09:48:08 GMT

←Older revision		Revision as of 09:48, 22 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7zek is ON HOLD until Paper Publication~~	+	==Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')==
-		+	<StructureSection load='7zek' size='340' side='right'caption='[[7zek]]' scene=''>
-	~~Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEK FirstGlance]. <br>
-	~~Description:~~ Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')	+	</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=7zek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zek OCA], [https://pdbe.org/7zek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zek RCSB], [https://www.ebi.ac.uk/pdbsum/7zek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zek ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Schroeder~~, N]]	+	__TOC__
-	[[Category: ~~Vianney, Y.M~~]]	+	</StructureSection>
-	[[Category: Jana, J]]	+	[[Category: Large Structures]]
-	[[Category: Weisz, K]]	+	[[Category: Jana J]]
		+	[[Category: Schroeder N]]
		+	[[Category: Vianney YM]]
		+	[[Category: Weisz K]]

OCA at 11:45, 4 May 2022

OCA — Wed, 04 May 2022 11:45:01 GMT

←Older revision		Revision as of 11:45, 4 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K.		Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K.

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

OCA — Wed, 06 Apr 2022 09:26:26 GMT

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

←Older revision

Revision as of 09:26, 6 April 2022

OCA: New page: '''Unreleased structure''' The entry 7zek is ON HOLD Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K. Description: Structure of a hybrid-type G-quadruplex with a snapback loo...

OCA — Wed, 06 Apr 2022 09:26:25 GMT

New page: '''Unreleased structure''' The entry 7zek is ON HOLD Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K. Description: Structure of a hybrid-type G-quadruplex with a snapback loo...

New page

'''Unreleased structure'''

The entry 7zek is ON HOLD

Authors: Jana, J., Vianney, Y.M., Schroeder, N., Weisz, K.

Description: Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R')
[[Category: Unreleased Structures]]
[[Category: Schroeder, N]]
[[Category: Vianney, Y.M]]
[[Category: Jana, J]]
[[Category: Weisz, K]]