OCA at 07:15, 22 March 2023

OCA — Wed, 22 Mar 2023 07:15:14 GMT

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

-	~~The entry~~ 7uwy is ~~ON HOLD until Paper~~ Publication	+	==NMR solution structure of the De novo designed small beta-barrel protein 29_bp_sh3==
		+	<StructureSection load='7uwy' size='340' side='right'caption='[[7uwy]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7uwy]] 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=7UWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UWY 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=7uwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uwy OCA], [https://pdbe.org/7uwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uwy RCSB], [https://www.ebi.ac.uk/pdbsum/7uwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uwy 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: Peterson, F.C~~., Kim~~, D.E.~~, Jensen, D~~.R.~~, ~~Saleem~~, A., Chow, ~~C.M.~~, Volkman, ~~B.F.~~, Baker, D.	+	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: NMR solution structure~~ of the ~~De novo designed small beta~~-~~barrel protein 29_bp_sh3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Chow, C.M~~]]	+	<div class="pdbe-citations 7uwy" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Saleem, A~~]]	+	== References ==
-	[[Category: ~~Baker, D~~]]	+	<references/>
-	[[Category: ~~Peterson, F.C~~]]	+	__TOC__
-	[[Category: ~~Volkman, B.F~~]]	+	</StructureSection>
-	[[Category: ~~Jensen, D.R~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kim, D.E~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Baker D]]
		+	[[Category: Chow CM]]
		+	[[Category: Jensen DR]]
		+	[[Category: Kim DE]]
		+	[[Category: Peterson FC]]
		+	[[Category: Saleem A]]
		+	[[Category: Volkman BF]]

OCA at 03:53, 8 June 2022

OCA — Wed, 08 Jun 2022 03:53:43 GMT

←Older revision		Revision as of 03:53, 8 June 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D.		Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D.

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

OCA — Thu, 12 May 2022 04:51:03 GMT

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

←Older revision

Revision as of 04:51, 12 May 2022

OCA: New page: '''Unreleased structure''' The entry 7uwy is ON HOLD Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D. Description: NMR solution struct...

OCA — Thu, 12 May 2022 04:51:01 GMT

New page: '''Unreleased structure''' The entry 7uwy is ON HOLD Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D. Description: NMR solution struct...

New page

'''Unreleased structure'''

The entry 7uwy is ON HOLD

Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D.

Description: NMR solution structure of the De novo designed small beta-barrel protein 29_bp_sh3
[[Category: Unreleased Structures]]
[[Category: Chow, C.M]]
[[Category: Saleem, A]]
[[Category: Baker, D]]
[[Category: Peterson, F.C]]
[[Category: Volkman, B.F]]
[[Category: Jensen, D.R]]
[[Category: Kim, D.E]]

7uwy - Revision history

OCA at 07:15, 22 March 2023

OCA at 03:53, 8 June 2022

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

OCA: New page: '''Unreleased structure''' The entry 7uwy is ON HOLD Authors: Peterson, F.C., Kim, D.E., Jensen, D.R., Saleem, A., Chow, C.M., Volkman, B.F., Baker, D. Description: NMR solution struct...