4yxx - Revision history

OCA at 13:04, 1 March 2024

OCA — Fri, 01 Mar 2024 13:04:40 GMT

←Older revision		Revision as of 13:04, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yxx]] 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=4YXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YXX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yxx]] 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=4YXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YXX 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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [https://pdbe.org/4yxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [https://www.ebi.ac.uk/pdbsum/4yxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yxx 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]] 2.18Å</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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [https://pdbe.org/4yxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [https://www.ebi.ac.uk/pdbsum/4yxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yxx ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.
-
-	Rational design of alpha-helical tandem repeat proteins with closed architectures.,Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P Nature. 2015 Dec 24;528(7583):585-8. doi: 10.1038/nature16191. Epub 2015 Dec 16. PMID:26675735<ref>PMID:26675735</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4yxx" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:30, 10 May 2023

OCA — Wed, 10 May 2023 07:30:38 GMT

←Older revision		Revision as of 07:30, 10 May 2023
Line 3:		Line 3:
	<StructureSection load='4yxx' size='340' side='right'caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='4yxx' size='340' side='right'caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YXX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yxx]] 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=4YXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YXX 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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [~~http~~://pdbe.org/4yxx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yxx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yxx 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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [https://pdbe.org/4yxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [https://www.ebi.ac.uk/pdbsum/4yxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yxx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bolduc, J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Bradley, P~~]]	+	[[Category: Bolduc J]]
-	[[Category: ~~Doyle, L~~]]	+	[[Category: Bradley P]]
-	[[Category: ~~Stoddard, B~~ L]]	+	[[Category: Doyle L]]
-	[[Category: ~~Alpha helix]]~~	+	[[Category: Stoddard BL]]
-	~~[[Category: Computationally designed]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Left-handed]]~~	+
-	~~[[Category: Rosetta]]~~	+
-	~~[[Category: Toroid~~]]	+

OCA at 10:52, 25 December 2019

OCA — Wed, 25 Dec 2019 10:52:37 GMT

←Older revision		Revision as of 10:52, 25 December 2019
Line 1:		Line 1:

	==Computationally designed left-handed alpha/alpha toroid with 6 repeats==		==Computationally designed left-handed alpha/alpha toroid with 6 repeats==
-	<StructureSection load='4yxx' size='340' side='right' caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='4yxx' size='340' side='right'caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YXX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YXX FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bolduc, J]]		[[Category: Bolduc, J]]
	[[Category: Bradley, P]]		[[Category: Bradley, P]]

OCA at 09:41, 22 November 2017

OCA — Wed, 22 Nov 2017 09:41:59 GMT

←Older revision		Revision as of 09:41, 22 November 2017
Line 1:		Line 1:
		+
	==Computationally designed left-handed alpha/alpha toroid with 6 repeats==		==Computationally designed left-handed alpha/alpha toroid with 6 repeats==
	<StructureSection load='4yxx' size='340' side='right' caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='4yxx' size='340' side='right' caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YXX FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YXX 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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [http://pdbe.org/4yxx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [http://www.ebi.ac.uk/pdbsum/4yxx PDBsum]</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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [http://pdbe.org/4yxx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [http://www.ebi.ac.uk/pdbsum/4yxx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yxx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:37, 30 December 2015

OCA — Wed, 30 Dec 2015 11:37:28 GMT

←Older revision		Revision as of 11:37, 30 December 2015
Line 5:		Line 5:
	</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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [http://pdbe.org/4yxx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [http://www.ebi.ac.uk/pdbsum/4yxx PDBsum]</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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [http://pdbe.org/4yxx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [http://www.ebi.ac.uk/pdbsum/4yxx PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.
		+
		+	Rational design of alpha-helical tandem repeat proteins with closed architectures.,Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P Nature. 2015 Dec 24;528(7583):585-8. doi: 10.1038/nature16191. Epub 2015 Dec 16. PMID:26675735<ref>PMID:26675735</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yxx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:55, 16 December 2015

OCA — Wed, 16 Dec 2015 13:55:10 GMT

←Older revision		Revision as of 13:55, 16 December 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Computationally designed left-handed alpha/alpha toroid with 6 repeats==
-		+	<StructureSection load='4yxx' size='340' side='right' caption='[[4yxx]], [[Resolution\|resolution]] 2.18Å' scene=''>
-	~~The entry~~ 4yxx is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yxx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YXX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YXX FirstGlance]. <br>
-	~~Authors~~: ~~Doyle~~, L., ~~Bolduc, J~~., ~~Stoddard, B~~.L., ~~Bradley, P~~.	+	</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=4yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yxx OCA], [http://pdbe.org/4yxx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yxx RCSB], [http://www.ebi.ac.uk/pdbsum/4yxx PDBsum]</span></td></tr>
-		+	</table>
-	~~Description: Computationally designed left-handed alpha~~/~~alpha toroid with 6 repeats~~	+	__TOC__
-	[[Category: ~~Unreleased Structures~~]]	+	</StructureSection>
		+	[[Category: Bolduc, J]]
	[[Category: Bradley, P]]		[[Category: Bradley, P]]
	[[Category: Doyle, L]]		[[Category: Doyle, L]]
-	[[Category: ~~Bolduc~~, J]]	+	[[Category: Stoddard, B L]]
-	[[Category: ~~Stoddard, B.L~~]]	+	[[Category: Alpha helix]]
		+	[[Category: Computationally designed]]
		+	[[Category: De novo protein]]
		+	[[Category: Left-handed]]
		+	[[Category: Rosetta]]
		+	[[Category: Toroid]]

OCA at 23:46, 30 November 2015

OCA — Mon, 30 Nov 2015 23:46:29 GMT

←Older revision		Revision as of 23:46, 30 November 2015
Line 7:		Line 7:
	Description: Computationally designed left-handed alpha/alpha toroid with 6 repeats		Description: Computationally designed left-handed alpha/alpha toroid with 6 repeats
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Doyle, L]]
-	[[Category: Stoddard, B.L]]
	[[Category: Bradley, P]]		[[Category: Bradley, P]]
		+	[[Category: Doyle, L]]
	[[Category: Bolduc, J]]		[[Category: Bolduc, J]]
		+	[[Category: Stoddard, B.L]]

OCA at 09:55, 8 April 2015

OCA — Wed, 08 Apr 2015 09:55:08 GMT

←Older revision		Revision as of 09:55, 8 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yxx is ON HOLD	+	The entry 4yxx is ON HOLD until Paper Publication

	Authors: Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P.		Authors: Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P.

OCA: Protected "4yxx" [edit=sysop:move=sysop]

OCA — Wed, 01 Apr 2015 12:01:59 GMT

Protected "4yxx" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:01, 1 April 2015

OCA: New page: '''Unreleased structure''' The entry 4yxx is ON HOLD Authors: Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P. Description: Computationally designed left-handed alpha/alpha toroid wi...

OCA — Wed, 01 Apr 2015 12:01:57 GMT

New page: '''Unreleased structure''' The entry 4yxx is ON HOLD Authors: Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P. Description: Computationally designed left-handed alpha/alpha toroid wi...

New page

'''Unreleased structure'''

The entry 4yxx is ON HOLD

Authors: Doyle, L., Bolduc, J., Stoddard, B.L., Bradley, P.

Description: Computationally designed left-handed alpha/alpha toroid with 6 repeats
[[Category: Unreleased Structures]]
[[Category: Doyle, L]]
[[Category: Stoddard, B.L]]
[[Category: Bradley, P]]
[[Category: Bolduc, J]]