8ek4 - Revision history

OCA at 07:26, 3 April 2024

OCA — Wed, 03 Apr 2024 07:26:37 GMT

←Older revision		Revision as of 07:26, 3 April 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8ek4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ek4 OCA], [https://pdbe.org/8ek4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ek4 RCSB], [https://www.ebi.ac.uk/pdbsum/8ek4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ek4 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=8ek4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ek4 OCA], [https://pdbe.org/8ek4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ek4 RCSB], [https://www.ebi.ac.uk/pdbsum/8ek4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ek4 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
-
-	De novo designed ice-binding proteins from twist-constrained helices.,de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2220380120. doi: , 10.1073/pnas.2220380120. Epub 2023 Jun 26. PMID:37364125<ref>PMID:37364125</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8ek4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:19, 12 July 2023

OCA — Wed, 12 Jul 2023 07:19:33 GMT

←Older revision		Revision as of 07:19, 12 July 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8ek4 is ~~ON HOLD until Paper~~ Publication	+	==De novo designed ice-binding proteins from twist-constrained helices==
		+	<StructureSection load='8ek4' size='340' side='right'caption='[[8ek4]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ek4]] is a 2 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=8EK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8EK4 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.35Å</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=8ek4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ek4 OCA], [https://pdbe.org/8ek4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ek4 RCSB], [https://www.ebi.ac.uk/pdbsum/8ek4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ek4 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

-	~~Authors~~:	+	De novo designed ice-binding proteins from twist-constrained helices.,de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R Proc Natl Acad Sci U S A. 2023 Jul 4;120(27):e2220380120. doi: , 10.1073/pnas.2220380120. Epub 2023 Jun 26. PMID:37364125<ref>PMID:37364125</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8ek4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Bera AK]]
		+	[[Category: De Haas RJ]]

OCA: Protected "8ek4" [edit=sysop:move=sysop]

OCA — Wed, 28 Sep 2022 04:46:33 GMT

Protected "8ek4" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:46, 28 September 2022

OCA: New page: '''Unreleased structure''' The entry 8ek4 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 28 Sep 2022 04:46:31 GMT

New page: '''Unreleased structure''' The entry 8ek4 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8ek4 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]