7ur8 - Revision history

OCA at 07:22, 3 April 2024

2024-04-03T07:22:52Z

←Older revision		Revision as of 07:22, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ur8]] 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=7UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UR8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ur8]] 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=7UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UR8 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=7ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ur8 OCA], [https://pdbe.org/7ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/7ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ur8 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]] 1.5Å</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=7ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ur8 OCA], [https://pdbe.org/7ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/7ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ur8 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 A rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.
-
-	De novo design of small beta barrel proteins.,Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2207974120. doi: , 10.1073/pnas.2207974120. Epub 2023 Mar 10. PMID:36897987<ref>PMID:36897987</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7ur8" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:15, 22 March 2023

2023-03-22T07:15:13Z

←Older revision		Revision as of 07:15, 22 March 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ur8 is ~~ON HOLD until Paper~~ Publication	+	==170_h_ob, a small beta-barrel de novo designed protein==
		+	<StructureSection load='7ur8' size='340' side='right'caption='[[7ur8]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7ur8]] 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=7UR8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UR8 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=7ur8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ur8 OCA], [https://pdbe.org/7ur8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ur8 RCSB], [https://www.ebi.ac.uk/pdbsum/7ur8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ur8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 A rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

-	~~Authors~~:	+	De novo design of small beta barrel proteins.,Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2207974120. doi: , 10.1073/pnas.2207974120. Epub 2023 Mar 10. PMID:36897987<ref>PMID:36897987</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7ur8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Baker D]]
		+	[[Category: Bera AK]]
		+	[[Category: Kim D]]

OCA at 11:31, 4 May 2022

2022-05-04T11:31:12Z

←Older revision		Revision as of 11:31, 4 May 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ur8 is ON HOLD	+	The entry 7ur8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ur8" [edit=sysop:move=sysop]

2022-04-27T10:28:25Z

Protected "7ur8" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:28, 27 April 2022

OCA: New page: '''Unreleased structure''' The entry 7ur8 is ON HOLD Authors: Description: Category: Unreleased Structures

2022-04-27T10:28:24Z

New page: '''Unreleased structure''' The entry 7ur8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ur8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]