7osv - Revision history

OCA at 12:55, 1 February 2024

OCA — Thu, 01 Feb 2024 12:55:40 GMT

←Older revision		Revision as of 12:55, 1 February 2024
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	<StructureSection load='7osv' size='340' side='right'caption='[[7osv]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='7osv' size='340' side='right'caption='[[7osv]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7osv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OSV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7osv]] 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=7OSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OSV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.66Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7osv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7osv OCA], [https://pdbe.org/7osv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7osv RCSB], [https://www.ebi.ac.uk/pdbsum/7osv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7osv 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=7osv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7osv OCA], [https://pdbe.org/7osv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7osv RCSB], [https://www.ebi.ac.uk/pdbsum/7osv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7osv ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hocker, B]]	+	[[Category: Synthetic construct]]
-	[[Category: Kordes, S]]	+	[[Category: Hocker B]]
-	[[Category: Romero-Romero, S]]	+	[[Category: Kordes S]]
-	~~[[Category: De novo protein]]~~	+	[[Category: Romero-Romero S]]
-	~~[[Category: Salt bridge cluster]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 11:06, 16 February 2022

OCA — Wed, 16 Feb 2022 11:06:13 GMT

←Older revision		Revision as of 11:06, 16 February 2022
Line 1:		Line 1:

	==DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)==		==DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)==
-	<StructureSection load='7osv' size='340' side='right'caption='[[7osv]]' scene=''>	+	<StructureSection load='7osv' size='340' side='right'caption='[[7osv]], [[Resolution\|resolution]] 1.66Å' 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=7OSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OSV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7osv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OSV 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=7osv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7osv OCA], [https://pdbe.org/7osv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7osv RCSB], [https://www.ebi.ac.uk/pdbsum/7osv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7osv 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7osv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7osv OCA], [https://pdbe.org/7osv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7osv RCSB], [https://www.ebi.ac.uk/pdbsum/7osv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7osv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein stability can be fine-tuned by modifying different structural features such as hydrogen-bond networks, salt bridges, hydrophobic cores, or disulfide bridges. Among these, stabilization by salt bridges is a major challenge in protein design and engineering since their stabilizing effects show a high dependence on the structural environment in the protein, and therefore are difficult to predict and model. In this work, we explore the effects on structure and stability of an introduced salt bridge cluster in the context of three different de novo TIM barrels. The salt bridge variants exhibit similar thermostability in comparison with their parental designs but important differences in the conformational stability at 25 degrees C can be observed such as a highly stabilizing effect for two of the proteins but a destabilizing effect to the third. Analysis of the formed geometries of the salt bridge cluster in the crystal structures show either highly ordered salt bridge clusters or only single salt bridges. Rosetta modeling of the salt bridge clusters results in a good prediction of the tendency on stability changes but not the geometries observed in the three-dimensional structures. The results show that despite the similarities in protein fold, the salt bridge clusters differently influence the structural and stability properties of the de novo TIM barrel variants depending on the structural background where they are introduced. This article is protected by copyright. All rights reserved.
		+
		+	A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.,Kordes S, Romero-Romero S, Lutz L, Hocker B Protein Sci. 2021 Dec 5. doi: 10.1002/pro.4249. PMID:34865275<ref>PMID:34865275</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7osv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hocker B]]	+	[[Category: Hocker, B]]
-	[[Category: Kordes S]]	+	[[Category: Kordes, S]]
-	[[Category: Romero-Romero S]]	+	[[Category: Romero-Romero, S]]
		+	[[Category: De novo protein]]
		+	[[Category: Salt bridge cluster]]
		+	[[Category: Tim barrel]]

OCA at 16:48, 15 December 2021

OCA — Wed, 15 Dec 2021 16:48:35 GMT

←Older revision		Revision as of 16:48, 15 December 2021
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-	'''Unreleased structure'''

-	~~The entry 7osv is ON HOLD until Paper Publication~~	+	==DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)==
-		+	<StructureSection load='7osv' size='340' side='right'caption='[[7osv]]' scene=''>
-	~~Authors: Kordes, S., Romero-Romero, S., Hocker, B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OSV FirstGlance]. <br>
-	~~Description:~~ DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)	+	</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=7osv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7osv OCA], [https://pdbe.org/7osv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7osv RCSB], [https://www.ebi.ac.uk/pdbsum/7osv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7osv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Hocker, B]]	+	__TOC__
-	[[Category: Kordes, S]]	+	</StructureSection>
-	[[Category: Romero-Romero, S]]	+	[[Category: Large Structures]]
		+	[[Category: Hocker B]]
		+	[[Category: Kordes S]]
		+	[[Category: Romero-Romero S]]

OCA at 06:20, 25 June 2021

OCA — Fri, 25 Jun 2021 06:20:40 GMT

←Older revision		Revision as of 06:20, 25 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7osv is ON HOLD	+	The entry 7osv is ON HOLD until Paper Publication

	Authors: Kordes, S., Romero-Romero, S., Hocker, B.		Authors: Kordes, S., Romero-Romero, S., Hocker, B.
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	Description: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)		Description: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kordes, S]]
	[[Category: Hocker, B]]		[[Category: Hocker, B]]
		+	[[Category: Kordes, S]]
	[[Category: Romero-Romero, S]]		[[Category: Romero-Romero, S]]

OCA: Protected "7osv" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:52:44 GMT

Protected "7osv" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:52, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7osv is ON HOLD Authors: Kordes, S., Romero-Romero, S., Hocker, B. Description: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge clu...

OCA — Thu, 17 Jun 2021 13:52:43 GMT

New page: '''Unreleased structure''' The entry 7osv is ON HOLD Authors: Kordes, S., Romero-Romero, S., Hocker, B. Description: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge clu...

New page

'''Unreleased structure'''

The entry 7osv is ON HOLD

Authors: Kordes, S., Romero-Romero, S., Hocker, B.

Description: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)
[[Category: Unreleased Structures]]
[[Category: Kordes, S]]
[[Category: Hocker, B]]
[[Category: Romero-Romero, S]]