2jua - Revision history

OCA at 12:48, 20 December 2023

OCA — Wed, 20 Dec 2023 12:48:44 GMT

←Older revision		Revision as of 12:48, 20 December 2023
Line 1:		Line 1:

	==Assignment, structure, and dynamics of de novo designed protein S836==		==Assignment, structure, and dynamics of de novo designed protein S836==
-	<StructureSection load='2jua' size='340' side='right'caption='[[2jua~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2jua' size='340' side='right'caption='[[2jua]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JUA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[1p68\|1p68]]</div~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [https://pdbe.org/2jua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [https://www.ebi.ac.uk/pdbsum/2jua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua 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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [https://pdbe.org/2jua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [https://www.ebi.ac.uk/pdbsum/2jua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Unidentified]]		[[Category: Unidentified]]
-	[[Category: Baum~~, J S~~]]	+	[[Category: Baum JS]]
-	[[Category: Go, A]]	+	[[Category: Go A]]
-	[[Category: Hecht~~, M H~~]]	+	[[Category: Hecht MH]]
-	[[Category: Kim, S]]	+	[[Category: Kim S]]
-	~~[[Category: De novo protein~~]]	+

OCA at 07:29, 27 January 2022

OCA — Thu, 27 Jan 2022 07:29:21 GMT

←Older revision		Revision as of 07:29, 27 January 2022
Line 3:		Line 3:
	<StructureSection load='2jua' size='340' side='right'caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2jua' size='340' side='right'caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2JUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1p68\|1p68]]</div></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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [~~http~~://pdbe.org/2jua PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jua PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua 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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [https://pdbe.org/2jua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [https://www.ebi.ac.uk/pdbsum/2jua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:28, 22 April 2020

OCA — Wed, 22 Apr 2020 06:28:34 GMT

←Older revision		Revision as of 06:28, 22 April 2020
Line 1:		Line 1:

	==Assignment, structure, and dynamics of de novo designed protein S836==		==Assignment, structure, and dynamics of de novo designed protein S836==
-	<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2jua' size='340' side='right'caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://pdbe.org/2jua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua ProSAT]</span></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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://pdbe.org/2jua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Unidentified]]		[[Category: Unidentified]]
	[[Category: Baum, J S]]		[[Category: Baum, J S]]

OCA at 11:13, 18 July 2018

OCA — Wed, 18 Jul 2018 11:13:50 GMT

←Older revision		Revision as of 11:13, 18 July 2018
Line 1:		Line 1:
		+
	==Assignment, structure, and dynamics of de novo designed protein S836==		==Assignment, structure, and dynamics of de novo designed protein S836==
	<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JUA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://pdbe.org/2jua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://pdbe.org/2jua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jua ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:09, 10 September 2015

OCA — Thu, 10 Sep 2015 22:09:00 GMT

←Older revision		Revision as of 22:09, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JUA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://pdbe.org/2jua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2jua" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:46, 22 December 2014

OCA — Mon, 22 Dec 2014 06:46:44 GMT

←Older revision		Revision as of 06:46, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>	+	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JUA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 12:
	Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.,Go A, Kim S, Baum J, Hecht MH Protein Sci. 2008 May;17(5):821-32. PMID:18436954<ref>PMID:18436954</ref>		Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.,Go A, Kim S, Baum J, Hecht MH Protein Sci. 2008 May;17(5):821-32. PMID:18436954<ref>PMID:18436954</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 20:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Unidentified]]		[[Category: Unidentified]]
-	[[Category: Baum, J S.]]	+	[[Category: Baum, J S]]
-	[[Category: Go, A.]]	+	[[Category: Go, A]]
-	[[Category: Hecht, M H.]]	+	[[Category: Hecht, M H]]
-	[[Category: Kim, S.]]	+	[[Category: Kim, S]]
	[[Category: De novo protein]]		[[Category: De novo protein]]

OCA at 09:56, 1 May 2014

OCA — Thu, 01 May 2014 09:56:02 GMT

←Older revision		Revision as of 09:56, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>	+	<table><tr><td colspan='2'>[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>
-	<b>[[Related_structure\|Related:]]</b> [[1p68\|1p68]]<br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1p68\|1p68]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span><br>	+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.		Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.
Line 12:		Line 14:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:22, 30 April 2014

OCA — Wed, 30 Apr 2014 10:22:11 GMT

←Older revision		Revision as of 10:22, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>		[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>
-	<b>Related:</b> [[1p68\|1p68]]<br>	+	<b>[[Related_structure\|Related:]]</b> [[1p68\|1p68]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jua OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jua RCSB], [http://www.ebi.ac.uk/pdbsum/2jua PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.		Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.

OCA at 08:39, 30 April 2014

OCA — Wed, 30 Apr 2014 08:39:08 GMT

←Older revision		Revision as of 08:39, 30 April 2014
Line 1:		Line 1:
-	[[~~Image:~~2jua.~~png~~\|~~left\|200px~~]]	+	==Assignment, structure, and dynamics of de novo designed protein S836==
		+	<StructureSection load='2jua' size='340' side='right' caption='[[2jua]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	[[2jua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA]. <br>
		+	<b>Related:</b> [[1p68\|1p68]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	Libraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4-helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S-836. Protein S-836 proved to be a 4-helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4-helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well-packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue-by-residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.

-	<!--	+	Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.,Go A, Kim S, Baum J, Hecht MH Protein Sci. 2008 May;17(5):821-32. PMID:18436954<ref>PMID:18436954</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2jua"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_2jua\| PDB=2jua \| SCENE= }}~~	+

-	~~===Assignment~~, ~~structure, and dynamics~~ of ~~de novo designed protein S836===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-		+	<references/>
-	~~<!--~~	+	__TOC__
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_18436954}}, adds~~ the ~~Publication Abstract to the page~~	+	</StructureSection>
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 18436954 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_18436954}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~[[2jua]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Unidentified Unidentified]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUA OCA].~~	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra">PMID:018436954</ref><references group="xtra"~~/>	+
	[[Category: Unidentified]]		[[Category: Unidentified]]
	[[Category: Baum, J S.]]		[[Category: Baum, J S.]]

OCA: Protected "2jua" [edit=sysop:move=sysop]

OCA — Sat, 02 Jun 2012 15:29:16 GMT

Protected "2jua" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:29, 2 June 2012