8a09 - Revision history

OCA at 06:24, 19 June 2024

2024-06-19T06:24:24Z

← Older revision		Revision as of 06:24, 19 June 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8a09]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A09 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a09]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A09 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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]] 1.35Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=8a09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a09 OCA], [https://pdbe.org/8a09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a09 RCSB], [https://www.ebi.ac.uk/pdbsum/8a09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a09 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=8a09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a09 OCA], [https://pdbe.org/8a09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a09 RCSB], [https://www.ebi.ac.uk/pdbsum/8a09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a09 ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Differential sensing attempts to mimic the mammalian senses of smell and taste to identify analytes and complex mixtures. In place of hundreds of complex, membrane-bound G-protein coupled receptors, differential sensors employ arrays of small molecules. Here we show that arrays of computationally designed de novo peptides provide alternative synthetic receptors for differential sensing. We use self-assembling alpha-helical barrels (alphaHBs) with central channels that can be altered predictably to vary their sizes, shapes and chemistries. The channels accommodate environment-sensitive dyes that fluoresce upon binding. Challenging arrays of dye-loaded barrels with analytes causes differential fluorophore displacement. The resulting fluorimetric fingerprints are used to train machine-learning models that relate the patterns to the analytes. We show that this system discriminates between a range of biomolecules, drink, and diagnostically relevant biological samples. As alphaHBs are robust and chemically diverse, the system has potential to sense many analytes in various settings.

	Differential sensing with arrays of de novo designed peptide assemblies.,Dawson WM, Shelley KL, Fletcher JM, Scott DA, Lombardi L, Rhys GG, LaGambina TJ, Obst U, Burton AJ, Cross JA, Davies G, Martin FJO, Wiseman FJ, Brady RL, Tew D, Wood CW, Woolfson DN Nat Commun. 2023 Jan 24;14(1):383. doi: 10.1038/s41467-023-36024-y. PMID:36693847<ref>PMID:36693847</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 8a09" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:59, 8 February 2023

2023-02-08T06:59:53Z

← Older revision		Revision as of 06:59, 8 February 2023
Line 1:		Line 1:

	==A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4==		==A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4==
	<StructureSection load='8a09' size='340' side='right'caption='[[8a09]]' scene=''>		<StructureSection load='8a09' size='340' side='right'caption='[[8a09]], [[Resolution\|resolution]] 1.35Å' 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=8A09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A09 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a09]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A09 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=8a09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a09 OCA], [https://pdbe.org/8a09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a09 RCSB], [https://www.ebi.ac.uk/pdbsum/8a09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a09 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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=8a09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a09 OCA], [https://pdbe.org/8a09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a09 RCSB], [https://www.ebi.ac.uk/pdbsum/8a09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a09 ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Differential sensing attempts to mimic the mammalian senses of smell and taste to identify analytes and complex mixtures. In place of hundreds of complex, membrane-bound G-protein coupled receptors, differential sensors employ arrays of small molecules. Here we show that arrays of computationally designed de novo peptides provide alternative synthetic receptors for differential sensing. We use self-assembling alpha-helical barrels (alphaHBs) with central channels that can be altered predictably to vary their sizes, shapes and chemistries. The channels accommodate environment-sensitive dyes that fluoresce upon binding. Challenging arrays of dye-loaded barrels with analytes causes differential fluorophore displacement. The resulting fluorimetric fingerprints are used to train machine-learning models that relate the patterns to the analytes. We show that this system discriminates between a range of biomolecules, drink, and diagnostically relevant biological samples. As alphaHBs are robust and chemically diverse, the system has potential to sense many analytes in various settings.

			Differential sensing with arrays of de novo designed peptide assemblies.,Dawson WM, Shelley KL, Fletcher JM, Scott DA, Lombardi L, Rhys GG, LaGambina TJ, Obst U, Burton AJ, Cross JA, Davies G, Martin FJO, Wiseman FJ, Brady RL, Tew D, Wood CW, Woolfson DN Nat Commun. 2023 Jan 24;14(1):383. doi: 10.1038/s41467-023-36024-y. PMID:36693847<ref>PMID:36693847</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8a09" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Synthetic construct]]
	[[Category: Dawson WM]]		[[Category: Dawson WM]]
	[[Category: Martin FJO]]		[[Category: Martin FJO]]
	[[Category: Rhys GG]]		[[Category: Rhys GG]]
	[[Category: Woolfson DN]]		[[Category: Woolfson DN]]

OCA at 05:13, 15 June 2022

2022-06-15T05:13:12Z

← Older revision		Revision as of 05:13, 15 June 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 8a09 is ON HOLD until Paper Publication~~		==A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4==
			<StructureSection load='8a09' size='340' side='right'caption='[[8a09]]' scene=''>
	~~Authors: Martin, F.J.O., Rhys, G.G., Dawson, W.M., Woolfson, D.N.~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8A09 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A09 FirstGlance]. <br>
	~~Description:~~ A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4		</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=8a09 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a09 OCA], [https://pdbe.org/8a09 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a09 RCSB], [https://www.ebi.ac.uk/pdbsum/8a09 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a09 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: Dawson~~, W.M~~]]		__TOC__
	[[Category: ~~Woolfson, D.N~~]]		</StructureSection>
	[[Category: Rhys~~, G.G~~]]		[[Category: Large Structures]]
	[[Category: ~~Martin, F.J.O~~]]		[[Category: Dawson WM]]
			[[Category: Martin FJO]]
			[[Category: Rhys GG]]
			[[Category: Woolfson DN]]

OCA: Protected "8a09" [edit=sysop:move=sysop]

2022-06-08T04:20:51Z

Protected "8a09" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:20, 8 June 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8a09 is ON HOLD until Paper Publication Authors: Martin, F.J.O., Rhys, G.G., Dawson, W.M., Woolfson, D.N. Description: A hexameric barrel state of ...

2022-06-08T04:20:50Z

New page: '''Unreleased structure''' The entry 8a09 is ON HOLD until Paper Publication Authors: Martin, F.J.O., Rhys, G.G., Dawson, W.M., Woolfson, D.N. Description: A hexameric barrel state of ...

New page

'''Unreleased structure'''

The entry 8a09 is ON HOLD until Paper Publication

Authors: Martin, F.J.O., Rhys, G.G., Dawson, W.M., Woolfson, D.N.

Description: A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(QgLaId)4
[[Category: Unreleased Structures]]
[[Category: Dawson, W.M]]
[[Category: Woolfson, D.N]]
[[Category: Rhys, G.G]]
[[Category: Martin, F.J.O]]