6yqx - Revision history

OCA at 07:40, 1 May 2024

OCA — Wed, 01 May 2024 07:40:09 GMT

←Older revision		Revision as of 07:40, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6yqx' size='340' side='right'caption='[[6yqx]], [[Resolution\|resolution]] 1.64Å' scene=''>		<StructureSection load='6yqx' size='340' side='right'caption='[[6yqx]], [[Resolution\|resolution]] 1.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yqx]] 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=6YQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqx]] 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=6YQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.638Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6yqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqx OCA], [https://pdbe.org/6yqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqx RCSB], [https://www.ebi.ac.uk/pdbsum/6yqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqx 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=6yqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqx OCA], [https://pdbe.org/6yqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqx RCSB], [https://www.ebi.ac.uk/pdbsum/6yqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqx 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 6yqx" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</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: De novo protein]]~~	+
-	~~[[Category: De novo protein design]]~~	+
-	~~[[Category: Epistasis]]~~	+
-	~~[[Category: Stability landscape]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:43, 28 July 2021

OCA — Wed, 28 Jul 2021 10:43:13 GMT

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

	==Crystal structure of DeNovoTIM13, a de novo designed TIM barrel==		==Crystal structure of DeNovoTIM13, a de novo designed TIM barrel==
-	<StructureSection load='6yqx' size='340' side='right'caption='[[6yqx]]' scene=''>	+	<StructureSection load='6yqx' size='340' side='right'caption='[[6yqx]], [[Resolution\|resolution]] 1.64Å' 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=6YQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqx]] 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=6YQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQX 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=6yqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqx OCA], [https://pdbe.org/6yqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqx RCSB], [https://www.ebi.ac.uk/pdbsum/6yqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqx 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6yqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqx OCA], [https://pdbe.org/6yqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqx RCSB], [https://www.ebi.ac.uk/pdbsum/6yqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqx 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 6yqx" 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: Shanmugaratnam, S]]
		+	[[Category: De novo protein]]
		+	[[Category: De novo protein design]]
		+	[[Category: Epistasis]]
		+	[[Category: Stability landscape]]
		+	[[Category: Tim barrel]]

OCA at 08:55, 21 July 2021

OCA — Wed, 21 Jul 2021 08:55:44 GMT

←Older revision		Revision as of 08:55, 21 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yqx ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of DeNovoTIM13, a de novo designed TIM barrel==
-		+	<StructureSection load='6yqx' size='340' side='right'caption='[[6yqx]]' scene=''>
-	~~Authors~~: ~~Romero~~-~~Romero, S~~., ~~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=6YQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQX FirstGlance]. <br>
-	~~Description: Crystal structure of DeNovoTIM13, 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=6yqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqx OCA], [https://pdbe.org/6yqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqx RCSB], [https://www.ebi.ac.uk/pdbsum/6yqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Kordes, S~~]]	+	__TOC__
-	[[Category: Hocker, B]]	+	</StructureSection>
-	[[Category: ~~Romero-Romero,~~ S]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fernandez~~-~~Velasco, D.A~~]]	+	[[Category: Fernandez-Velasco DA]]
-	[[Category: Shanmugaratnam, S]]	+	[[Category: Hocker B]]
		+	[[Category: Kordes S]]
		+	[[Category: Romero-Romero S]]
		+	[[Category: Shanmugaratnam S]]

OCA at 05:19, 24 March 2021

OCA — Wed, 24 Mar 2021 05:19:13 GMT

←Older revision		Revision as of 05:19, 24 March 2021
Line 5:		Line 5:
	Authors: Romero-Romero, S., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B.		Authors: Romero-Romero, S., Kordes, S., Shanmugaratnam, S., Fernandez-Velasco, D.A., Hocker, B.

-	Description: Crystal structure of ~~NovoTIM13~~, a de novo designed TIM barrel	+	Description: Crystal structure of DeNovoTIM13, a de novo designed TIM barrel
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Fernandez-Velasco, D.A]]
-	[[Category: Shanmugaratnam, S]]
-	[[Category: Hocker, B]]
	[[Category: Kordes, S]]		[[Category: Kordes, S]]
		+	[[Category: Hocker, B]]
	[[Category: Romero-Romero, S]]		[[Category: Romero-Romero, S]]
		+	[[Category: Fernandez-Velasco, D.A]]
		+	[[Category: Shanmugaratnam, S]]

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

OCA — Wed, 29 Apr 2020 05:25:38 GMT

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

←Older revision

Revision as of 05:25, 29 April 2020

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

OCA — Wed, 29 Apr 2020 05:25:37 GMT

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

New page

'''Unreleased structure'''

The entry 6yqx is ON HOLD until Paper Publication

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

Description: Crystal structure of NovoTIM13, 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]]