6yqy - Revision history

OCA at 13:33, 24 January 2024

2024-01-24T13:33:40Z

←Older revision		Revision as of 13:33, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6yqy' size='340' side='right'caption='[[6yqy]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='6yqy' size='340' side='right'caption='[[6yqy]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqy]] is a 1 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=6YQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQY 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=6yqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqy OCA], [https://pdbe.org/6yqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqy RCSB], [https://www.ebi.ac.uk/pdbsum/6yqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqy 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]] 1.876Å</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=6yqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqy OCA], [https://pdbe.org/6yqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqy RCSB], [https://www.ebi.ac.uk/pdbsum/6yqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Fernandez-Velasco~~, D A~~]]	+	[[Category: Fernandez-Velasco DA]]
-	[[Category: Hocker, B]]	+	[[Category: Hocker B]]
-	[[Category: Kordes, S]]	+	[[Category: Kordes S]]
-	[[Category: Romero-Romero, S]]	+	[[Category: Romero-Romero S]]
-	[[Category: Shanmugaratnam, S]]	+	[[Category: Shanmugaratnam S]]
-	[[Category: Wiese~~, G J]]~~	+	[[Category: Wiese GJ]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: De novo protein design]]~~	+
-	~~[[Category: Epistasis]]~~	+
-	~~[[Category: Stability landscape]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:43, 28 July 2021

2021-07-28T10:43:15Z

←Older revision		Revision as of 10:43, 28 July 2021
Line 1:		Line 1:

	==Crystal structure of sTIM11noCys, a de novo designed TIM barrel==		==Crystal structure of sTIM11noCys, a de novo designed TIM barrel==
-	<StructureSection load='6yqy' size='340' side='right'caption='[[6yqy]]' scene=''>	+	<StructureSection load='6yqy' size='340' side='right'caption='[[6yqy]], [[Resolution\|resolution]] 1.88Å' 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=6YQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQY 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=6yqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqy OCA], [https://pdbe.org/6yqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqy RCSB], [https://www.ebi.ac.uk/pdbsum/6yqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqy 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=6yqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqy OCA], [https://pdbe.org/6yqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqy RCSB], [https://www.ebi.ac.uk/pdbsum/6yqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. Understanding and manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (beta/)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.
		+
		+	The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach.,Romero-Romero S, Costas M, Silva Manzano DA, Kordes S, Rojas-Ortega E, Tapia C, Guerra Y, Shanmugaratnam S, Rodriguez-Romero A, Baker D, Hocker B, Fernandez-Velasco DA J Mol Biol. 2021 Jul 14;433(18):167153. doi: 10.1016/j.jmb.2021.167153. PMID:34271011<ref>PMID:34271011</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yqy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fernandez-Velasco DA]]	+	[[Category: Synthetic construct sequences]]
-	[[Category: Hocker B]]	+	[[Category: Fernandez-Velasco, D A]]
-	[[Category: Kordes S]]	+	[[Category: Hocker, B]]
-	[[Category: Romero-Romero S]]	+	[[Category: Kordes, S]]
-	[[Category: Shanmugaratnam S]]	+	[[Category: Romero-Romero, S]]
-	[[Category: Wiese GJ]]	+	[[Category: Shanmugaratnam, S]]
		+	[[Category: Wiese, G J]]
		+	[[Category: De novo protein]]
		+	[[Category: De novo protein design]]
		+	[[Category: Epistasis]]
		+	[[Category: Stability landscape]]
		+	[[Category: Tim barrel]]

OCA at 08:55, 21 July 2021

2021-07-21T08:55:44Z

←Older revision		Revision as of 08:55, 21 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6yqy ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of sTIM11noCys, a de novo designed TIM barrel==
-		+	<StructureSection load='6yqy' size='340' side='right'caption='[[6yqy]]' scene=''>
-	~~Authors~~: ~~Romero~~-~~Romero, S~~., ~~Wiese, G~~.J.~~, Kordes, S~~., ~~Shanmugaratnam, S~~., ~~Fernandez-Velasco~~, D.A., ~~Hocker, B~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQY FirstGlance]. <br>
-	~~Description: Crystal structure of sTIM11noCys, a de novo designed TIM barrel~~	+	</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=6yqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqy OCA], [https://pdbe.org/6yqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqy RCSB], [https://www.ebi.ac.uk/pdbsum/6yqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Fernandez-Velasco~~, D.A~~]]	+	__TOC__
-	[[Category: ~~Shanmugaratnam, S~~]]	+	</StructureSection>
-	[[Category: ~~Hocker, B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kordes,~~ S]]	+	[[Category: Fernandez-Velasco DA]]
-	[[Category: ~~Romero-Romero,~~ S]]	+	[[Category: Hocker B]]
-	[[Category: Wiese~~, G.J~~]]	+	[[Category: Kordes S]]
		+	[[Category: Romero-Romero S]]
		+	[[Category: Shanmugaratnam S]]
		+	[[Category: Wiese GJ]]

OCA: Protected "6yqy" [edit=sysop:move=sysop]

2020-04-29T05:25:47Z

Protected "6yqy" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:25, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yqy is ON HOLD until Paper Publication Authors: Romero-Romero, S., Wiese, G.J., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B....

2020-04-29T05:25:46Z

New page: '''Unreleased structure''' The entry 6yqy is ON HOLD until Paper Publication Authors: Romero-Romero, S., Wiese, G.J., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B....

New page

'''Unreleased structure'''

The entry 6yqy is ON HOLD until Paper Publication

Authors: Romero-Romero, S., Wiese, G.J., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B.

Description: Crystal structure of sTIM11noCys, a de novo designed TIM barrel
[[Category: Unreleased Structures]]
[[Category: Fernandez-Velasco, D.A]]
[[Category: Shanmugaratnam, S]]
[[Category: Hocker, B]]
[[Category: Kordes, S]]
[[Category: Romero-Romero, S]]
[[Category: Wiese, G.J]]