4qtr - Revision history

OCA at 17:38, 20 September 2023

OCA — Wed, 20 Sep 2023 17:38:11 GMT

←Older revision		Revision as of 17:38, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QTR 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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [https://pdbe.org/4qtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [https://www.ebi.ac.uk/pdbsum/4qtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qtr ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.2Å</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [https://pdbe.org/4qtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [https://www.ebi.ac.uk/pdbsum/4qtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qtr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:52, 22 February 2023

OCA — Wed, 22 Feb 2023 13:52:11 GMT

←Older revision		Revision as of 13:52, 22 February 2023
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	<StructureSection load='4qtr' size='340' side='right'caption='[[4qtr]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='4qtr' size='340' side='right'caption='[[4qtr]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QTR FirstGlance]. <br>
-	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [~~http~~://pdbe.org/4qtr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qtr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qtr ProSAT]</span></td></tr>	+	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [https://pdbe.org/4qtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [https://www.ebi.ac.uk/pdbsum/4qtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qtr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mayo~~, S L~~]]	+	[[Category: Mayo SL]]
-	[[Category: Mou, Y]]	+	[[Category: Mou Y]]
-	~~[[Category: De novo design-dna complex]]~~	+
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Double-stranded dna]]~~	+
-	~~[[Category: Helix-turn-helix~~]]	+

OCA at 09:34, 24 April 2019

OCA — Wed, 24 Apr 2019 09:34:07 GMT

←Older revision		Revision as of 09:34, 24 April 2019
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		+
	==Computational design of co-assembling protein-DNA nanowires==		==Computational design of co-assembling protein-DNA nanowires==
-	<StructureSection load='4qtr' size='340' side='right' caption='[[4qtr]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='4qtr' size='340' side='right'caption='[[4qtr]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QTR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QTR FirstGlance]. <br>
-	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [http://pdbe.org/4qtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [http://www.ebi.ac.uk/pdbsum/4qtr PDBsum]</span></td></tr>	+	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [http://pdbe.org/4qtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [http://www.ebi.ac.uk/pdbsum/4qtr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qtr ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
		+	[[Category: Large Structures]]
	[[Category: Mayo, S L]]		[[Category: Mayo, S L]]
	[[Category: Mou, Y]]		[[Category: Mou, Y]]

OCA at 07:58, 30 September 2015

OCA — Wed, 30 Sep 2015 07:58:38 GMT

←Older revision		Revision as of 07:58, 30 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QTR FirstGlance]. <br>
-	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [http://www.ebi.ac.uk/pdbsum/4qtr PDBsum]</span></td></tr>	+	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [http://pdbe.org/4qtr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [http://www.ebi.ac.uk/pdbsum/4qtr PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein-DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein-DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein-DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein-DNA framework presented here.
		+
		+	Computational design of co-assembling protein-DNA nanowires.,Mou Y, Yu JY, Wannier TM, Guo CL, Mayo SL Nature. 2015 Sep 10;525(7568):230-3. doi: 10.1038/nature14874. Epub 2015 Sep 2. PMID:26331548<ref>PMID:26331548</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4qtr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:46, 29 July 2015

OCA — Wed, 29 Jul 2015 14:46:54 GMT

←Older revision		Revision as of 14:46, 29 July 2015
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-	'''~~Unreleased structure~~'''	+	==Computational design of co-assembling protein-DNA nanowires==
-		+	<StructureSection load='4qtr' size='340' side='right' caption='[[4qtr]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~The entry~~ 4qtr is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qtr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QTR FirstGlance]. <br>
-	~~Authors~~: ~~Mou, Y~~.~~, Mayo, S~~.L.	+	</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=4qtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qtr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qtr RCSB], [http://www.ebi.ac.uk/pdbsum/4qtr PDBsum]</span></td></tr>
-		+	</table>
-	~~Description~~: ~~Computational design of co~~-~~assembling protein-DNA nanowires~~	+	__TOC__
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</StructureSection>
-	[[Category: Mayo, S.L]]	+	[[Category: Mayo, S L]]
	[[Category: Mou, Y]]		[[Category: Mou, Y]]
		+	[[Category: De novo design-dna complex]]
		+	[[Category: Dna-binding protein]]
		+	[[Category: Double-stranded dna]]
		+	[[Category: Helix-turn-helix]]

OCA at 16:07, 24 December 2014

OCA — Wed, 24 Dec 2014 16:07:02 GMT

←Older revision		Revision as of 16:07, 24 December 2014
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	Description: Computational design of co-assembling protein-DNA nanowires		Description: Computational design of co-assembling protein-DNA nanowires
		+	[[Category: Unreleased Structures]]
		+	[[Category: Mayo, S.L]]
		+	[[Category: Mou, Y]]

OCA at 08:15, 24 September 2014

OCA — Wed, 24 Sep 2014 08:15:53 GMT

←Older revision		Revision as of 08:15, 24 September 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4qtr is ON HOLD	+	The entry 4qtr is ON HOLD until Paper Publication

-	Authors: Mou, Y, Mayo, S.L.	+	Authors: Mou, Y., Mayo, S.L.

	Description: Computational design of co-assembling protein-DNA nanowires		Description: Computational design of co-assembling protein-DNA nanowires

OCA: Protected "4qtr" [edit=sysop:move=sysop]

OCA — Wed, 16 Jul 2014 09:49:27 GMT

Protected "4qtr" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:49, 16 July 2014

OCA: New page: '''Unreleased structure''' The entry 4qtr is ON HOLD Authors: Mou, Y, Mayo, S.L. Description: Computational design of co-assembling protein-DNA nanowires

OCA — Wed, 16 Jul 2014 09:49:26 GMT

New page: '''Unreleased structure''' The entry 4qtr is ON HOLD Authors: Mou, Y, Mayo, S.L. Description: Computational design of co-assembling protein-DNA nanowires

New page

'''Unreleased structure'''

The entry 4qtr is ON HOLD

Authors: Mou, Y, Mayo, S.L.

Description: Computational design of co-assembling protein-DNA nanowires