5vh8 - Revision history

OCA at 07:28, 1 May 2024

OCA — Wed, 01 May 2024 07:28:36 GMT

←Older revision		Revision as of 07:28, 1 May 2024
Line 1:		Line 1:

	==Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1==		==Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1==
-	<StructureSection load='5vh8' size='340' side='right'caption='[[5vh8~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5vh8' size='340' side='right'caption='[[5vh8]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vh8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VH8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VH8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vh8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VH8 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5vh7\|5vh7]]~~</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='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=5vh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vh8 OCA], [~~http~~://pdbe.org/5vh8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vh8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vh8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vh8 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=5vh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vh8 OCA], [https://pdbe.org/5vh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vh8 RCSB], [https://www.ebi.ac.uk/pdbsum/5vh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vh8 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 x 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3xCAG)] or r(CUG) [r(3xCUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 x 1 internal loops of r(3xCAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3xCUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.
-
-	Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.,Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD Biochemistry. 2017 Jul 11;56(27):3463-3474. doi: 10.1021/acs.biochem.7b00252., Epub 2017 Jun 29. PMID:28617590<ref>PMID:28617590</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5vh8" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, J L~~]]	+	[[Category: Chen JL]]
-	[[Category: Disney~~, M D~~]]	+	[[Category: Disney MD]]
-	[[Category: Fountain~~, M A~~]]	+	[[Category: Fountain MA]]
-	[[Category: VanEtten~~, D M~~]]	+	[[Category: VanEtten DM]]
-	[[Category: Yildirim, I]]	+	[[Category: Yildirim I]]
-	~~[[Category: Cug repeat]]~~	+
-	~~[[Category: Myotonic dystrophy]]~~	+
-	~~[[Category: Repeat expansion]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Triplet repeat]]~~	+
-	~~[[Category: Uu pair~~]]	+

OCA at 09:09, 18 December 2019

OCA — Wed, 18 Dec 2019 09:09:01 GMT

←Older revision		Revision as of 09:09, 18 December 2019
Line 1:		Line 1:

	==Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1==		==Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1==
-	<StructureSection load='5vh8' size='340' side='right' caption='[[5vh8]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5vh8' size='340' side='right'caption='[[5vh8]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vh8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VH8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vh8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VH8 FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chen, J L]]		[[Category: Chen, J L]]
	[[Category: Disney, M D]]		[[Category: Disney, M D]]

OCA at 04:36, 21 September 2017

OCA — Thu, 21 Sep 2017 04:36:14 GMT

←Older revision		Revision as of 04:36, 21 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vh8 is ~~ON HOLD until Paper~~ Publication	+	==Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1==
		+	<StructureSection load='5vh8' size='340' side='right' caption='[[5vh8]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vh8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VH8 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vh7\|5vh7]]</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=5vh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vh8 OCA], [http://pdbe.org/5vh8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vh8 RCSB], [http://www.ebi.ac.uk/pdbsum/5vh8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vh8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 x 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3xCAG)] or r(CUG) [r(3xCUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 x 1 internal loops of r(3xCAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3xCUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

-	~~Authors:~~ Chen~~, J.L.~~, VanEtten~~, D.M.~~, Fountain~~, M.A.~~, Yildirim, I., Disney, ~~M.D~~.	+	Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.,Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD Biochemistry. 2017 Jul 11;56(27):3463-3474. doi: 10.1021/acs.biochem.7b00252., Epub 2017 Jun 29. PMID:28617590<ref>PMID:28617590</ref>

-	~~Description: Structure and dynamics~~ of ~~RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Disney, M.D]]	+	<div class="pdbe-citations 5vh8" style="background-color:#fffaf0;"></div>
-	~~[[Category: Chen, J.L~~]]	+	== References ==
-	[[Category: Fountain, M.A]]	+	<references/>
-	[[Category: ~~Vanetten~~, D.M]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, J L]]
		+	[[Category: Disney, M D]]
		+	[[Category: Fountain, M A]]
		+	[[Category: VanEtten, D M]]
	[[Category: Yildirim, I]]		[[Category: Yildirim, I]]
		+	[[Category: Cug repeat]]
		+	[[Category: Myotonic dystrophy]]
		+	[[Category: Repeat expansion]]
		+	[[Category: Rna]]
		+	[[Category: Triplet repeat]]
		+	[[Category: Uu pair]]

OCA at 11:19, 4 May 2017

OCA — Thu, 04 May 2017 11:19:08 GMT

←Older revision		Revision as of 11:19, 4 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vh8 is ON HOLD	+	The entry 5vh8 is ON HOLD until Paper Publication

	Authors: Chen, J.L., VanEtten, D.M., Fountain, M.A., Yildirim, I., Disney, M.D.		Authors: Chen, J.L., VanEtten, D.M., Fountain, M.A., Yildirim, I., Disney, M.D.

OCA: Protected "5vh8" [edit=sysop:move=sysop]

OCA — Wed, 19 Apr 2017 11:27:13 GMT

Protected "5vh8" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:27, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vh8 is ON HOLD Authors: Chen, J.L., VanEtten, D.M., Fountain, M.A., Yildirim, I., Disney, M.D. Description: Structure and dynamics of RNA repeat e...

OCA — Wed, 19 Apr 2017 11:27:12 GMT

New page: '''Unreleased structure''' The entry 5vh8 is ON HOLD Authors: Chen, J.L., VanEtten, D.M., Fountain, M.A., Yildirim, I., Disney, M.D. Description: Structure and dynamics of RNA repeat e...

New page

'''Unreleased structure'''

The entry 5vh8 is ON HOLD

Authors: Chen, J.L., VanEtten, D.M., Fountain, M.A., Yildirim, I., Disney, M.D.

Description: Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1
[[Category: Unreleased Structures]]
[[Category: Disney, M.D]]
[[Category: Chen, J.L]]
[[Category: Fountain, M.A]]
[[Category: Vanetten, D.M]]
[[Category: Yildirim, I]]