5w9f - Revision history

OCA at 10:29, 14 June 2023

2023-06-14T10:29:11Z

←Older revision		Revision as of 10:29, 14 June 2023
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	==Solution structure of the de novo mini protein gHEEE_02==		==Solution structure of the de novo mini protein gHEEE_02==
-	<StructureSection load='5w9f' size='340' side='right'caption='[[5w9f~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5w9f' size='340' side='right'caption='[[5w9f]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W9F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W9F FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [~~http~~://pdbe.org/5w9f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f 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=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [https://pdbe.org/5w9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [https://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f 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: Bahl~~, C D~~]]	+	[[Category: Bahl CD]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Garry~~, B W~~]]	+	[[Category: Garry BW]]
-	[[Category: Pulavarti~~, S V.S R.K~~]]	+	[[Category: Pulavarti SVSRK]]
-	[[Category: Shaw~~, E A~~]]	+	[[Category: Shaw EA]]
-	[[Category: Szyperski, T]]	+	[[Category: Szyperski T]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: De-novo design~~]]	+

OCA at 08:49, 30 September 2020

2020-09-30T08:49:33Z

←Older revision		Revision as of 08:49, 30 September 2020
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	==Solution structure of the de novo mini protein gHEEE_02==		==Solution structure of the de novo mini protein gHEEE_02==
-	<StructureSection load='5w9f' size='340' side='right' caption='[[5w9f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5w9f' size='340' side='right'caption='[[5w9f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W9F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W9F 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=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [http://pdbe.org/5w9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [http://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [http://pdbe.org/5w9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [http://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Bahl, C D]]		[[Category: Bahl, C D]]

OCA at 07:46, 12 September 2018

2018-09-12T07:46:47Z

←Older revision		Revision as of 07:46, 12 September 2018
Line 3:		Line 3:
	<StructureSection load='5w9f' size='340' side='right' caption='[[5w9f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='5w9f' size='340' side='right' caption='[[5w9f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W9F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W9F 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=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [http://pdbe.org/5w9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [http://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f ProSAT]</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=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [http://pdbe.org/5w9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [http://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Disulfide-rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide-rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly (13) C- and (15) N-labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long-time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro, but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design. This article is protected by copyright. All rights reserved.
		+
		+	Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides.,Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD Protein Sci. 2018 Aug 26. doi: 10.1002/pro.3453. PMID:30152054<ref>PMID:30152054</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5w9f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Bahl, C D]]		[[Category: Bahl, C D]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 05:35, 11 July 2018

2018-07-11T05:35:19Z

←Older revision		Revision as of 05:35, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w9f ~~is ON HOLD until Paper Publication~~	+	==Solution structure of the de novo mini protein gHEEE_02==
-		+	<StructureSection load='5w9f' size='340' side='right' caption='[[5w9f]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~: ~~Pulavarti, S~~.V.S.R.K.~~, Shaw, E~~.A., ~~Bahl, C~~.D., ~~Garry~~, B.W., ~~Baker, D~~., ~~Szyperski, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5w9f]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W9F FirstGlance]. <br>
-	~~Description: Solution structure of the de novo mini protein gHEEE_02~~	+	</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=5w9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w9f OCA], [http://pdbe.org/5w9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w9f RCSB], [http://www.ebi.ac.uk/pdbsum/5w9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w9f ProSAT]</span></td></tr>
-	~~[[Category: Unreleased Structures]]~~	+	</table>
-	[[Category: ~~Pulavarti~~, ~~S.V.S.R.K~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bahl, C D]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
-	[[Category: ~~Bahl~~, ~~C.D~~]]	+	[[Category: Garry, B W]]
-	[[Category: ~~Garry~~, B.W]]	+	[[Category: Pulavarti, S V.S R.K]]
-	[[Category: Shaw, E.A]]	+	[[Category: Shaw, E A]]
	[[Category: Szyperski, T]]		[[Category: Szyperski, T]]
		+	[[Category: De novo protein]]
		+	[[Category: De-novo design]]

OCA at 05:06, 28 March 2018

2018-03-28T05:06:25Z

←Older revision		Revision as of 05:06, 28 March 2018
Line 3:		Line 3:
	The entry 5w9f is ON HOLD until Paper Publication		The entry 5w9f is ON HOLD until Paper Publication

-	Authors: ~~Szyperski, T.,~~ Pulavarti, S.V.S.R.K., Shaw, E.A., Bahl, C.D., Garry, B.W., Baker, D.	+	Authors: Pulavarti, S.V.S.R.K., Shaw, E.A., Bahl, C.D., Garry, B.W., Baker, D., Szyperski, T.

	Description: Solution structure of the de novo mini protein gHEEE_02		Description: Solution structure of the de novo mini protein gHEEE_02
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Pulavarti, S.V.S.R.K]]
		+	[[Category: Baker, D]]
	[[Category: Bahl, C.D]]		[[Category: Bahl, C.D]]
	[[Category: Garry, B.W]]		[[Category: Garry, B.W]]
	[[Category: Shaw, E.A]]		[[Category: Shaw, E.A]]
-	[[Category: Baker, D]]
	[[Category: Szyperski, T]]		[[Category: Szyperski, T]]
-	[[Category: Pulavarti, S.V.S.R.K]]

OCA: Protected "5w9f" [edit=sysop:move=sysop]

2017-09-27T14:35:45Z

Protected "5w9f" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w9f is ON HOLD until Paper Publication Authors: Szyperski, T., Pulavarti, S.V.S.R.K., Shaw, E.A., Bahl, C.D., Garry, B.W., Baker, D. Description: ...

2017-09-27T14:35:43Z

New page: '''Unreleased structure''' The entry 5w9f is ON HOLD until Paper Publication Authors: Szyperski, T., Pulavarti, S.V.S.R.K., Shaw, E.A., Bahl, C.D., Garry, B.W., Baker, D. Description: ...

New page

'''Unreleased structure'''

The entry 5w9f is ON HOLD until Paper Publication

Authors: Szyperski, T., Pulavarti, S.V.S.R.K., Shaw, E.A., Bahl, C.D., Garry, B.W., Baker, D.

Description: Solution structure of the de novo mini protein gHEEE_02
[[Category: Unreleased Structures]]
[[Category: Bahl, C.D]]
[[Category: Garry, B.W]]
[[Category: Shaw, E.A]]
[[Category: Baker, D]]
[[Category: Szyperski, T]]
[[Category: Pulavarti, S.V.S.R.K]]