4ndl - Revision history

OCA at 12:32, 1 March 2024

OCA — Fri, 01 Mar 2024 12:32:49 GMT

←Older revision		Revision as of 12:32, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NDL 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [https://pdbe.org/4ndl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [https://www.ebi.ac.uk/pdbsum/4ndl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ndl 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]] 3.5Å</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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [https://pdbe.org/4ndl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [https://www.ebi.ac.uk/pdbsum/4ndl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ndl ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein-protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by beta-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a alpha-helix-mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.
-
-	Computational design and experimental verification of a symmetric protein homodimer.,Mou Y, Huang PS, Hsu FC, Huang SJ, Mayo SL Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10714-9. doi:, 10.1073/pnas.1505072112. Epub 2015 Aug 12. PMID:26269568<ref>PMID:26269568</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ndl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:23, 11 January 2023

OCA — Wed, 11 Jan 2023 08:23:31 GMT

←Older revision		Revision as of 08:23, 11 January 2023
Line 3:		Line 3:
	<StructureSection load='4ndl' size='340' side='right'caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4ndl' size='340' side='right'caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NDL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NDL 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [~~http~~://pdbe.org/4ndl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ndl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ndl 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [https://pdbe.org/4ndl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [https://www.ebi.ac.uk/pdbsum/4ndl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ndl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hsu~~, F C~~]]	+	[[Category: Hsu FC]]
-	[[Category: Huang~~, P S~~]]	+	[[Category: Huang PS]]
-	[[Category: Huang~~, S J~~]]	+	[[Category: Huang SJ]]
-	[[Category: Mayo~~, S L~~]]	+	[[Category: Mayo SL]]
-	[[Category: Mou, Y]]	+	[[Category: Mou Y]]
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Helix-turn-helix~~]]	+

OCA at 05:07, 13 February 2020

OCA — Thu, 13 Feb 2020 05:07:56 GMT

←Older revision		Revision as of 05:07, 13 February 2020
Line 1:		Line 1:

	==Computational design and experimental verification of a symmetric homodimer==		==Computational design and experimental verification of a symmetric homodimer==
-	<StructureSection load='4ndl' size='340' side='right' caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='4ndl' size='340' side='right'caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL FirstGlance]. <br>
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Drome]]		[[Category: Drome]]
		+	[[Category: Large Structures]]
	[[Category: Hsu, F C]]		[[Category: Hsu, F C]]
	[[Category: Huang, P S]]		[[Category: Huang, P S]]

OCA at 17:36, 16 November 2017

OCA — Thu, 16 Nov 2017 17:36:31 GMT

←Older revision		Revision as of 17:36, 16 November 2017
Line 1:		Line 1:
		+
	==Computational design and experimental verification of a symmetric homodimer==		==Computational design and experimental verification of a symmetric homodimer==
	<StructureSection load='4ndl' size='340' side='right' caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4ndl' size='340' side='right' caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://pdbe.org/4ndl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://pdbe.org/4ndl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ndl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Hsu, F C]]		[[Category: Hsu, F C]]
	[[Category: Huang, P S]]		[[Category: Huang, P S]]

OCA at 06:48, 30 September 2015

OCA — Wed, 30 Sep 2015 06:48:59 GMT

←Older revision		Revision as of 06:48, 30 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://pdbe.org/4ndl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 13:		Line 13:
	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 4ndl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:33, 2 September 2015

OCA — Wed, 02 Sep 2015 06:33:06 GMT

←Older revision		Revision as of 06:33, 2 September 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl 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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein-protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by beta-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a alpha-helix-mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.
		+
		+	Computational design and experimental verification of a symmetric protein homodimer.,Mou Y, Huang PS, Hsu FC, Huang SJ, Mayo SL Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10714-9. doi:, 10.1073/pnas.1505072112. Epub 2015 Aug 12. PMID:26269568<ref>PMID:26269568</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:59, 25 January 2015

OCA — Sun, 25 Jan 2015 10:59:54 GMT

←Older revision		Revision as of 10:59, 25 January 2015
Line 7:		Line 7:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Hsu, F C.]]	+	[[Category: Hsu, F C]]
-	[[Category: Huang, P S.]]	+	[[Category: Huang, P S]]
-	[[Category: Huang, S J.]]	+	[[Category: Huang, S J]]
-	[[Category: Mayo, S L.]]	+	[[Category: Mayo, S L]]
-	[[Category: Mou, Y.]]	+	[[Category: Mou, Y]]
	[[Category: De novo protein]]		[[Category: De novo protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

OCA at 08:55, 5 November 2014

OCA — Wed, 05 Nov 2014 08:55:02 GMT

←Older revision		Revision as of 08:55, 5 November 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Computational design and experimental verification of a symmetric homodimer==
-		+	<StructureSection load='4ndl' size='340' side='right' caption='[[4ndl]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~The entry~~ 4ndl is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ndl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NDL FirstGlance]. <br>
-	~~Authors~~: ~~Mou~~, Y., ~~Huang, P~~.S., Hsu, F.C., Huang, S.J., Mayo, S.L.	+	</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=4ndl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ndl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ndl RCSB], [http://www.ebi.ac.uk/pdbsum/4ndl PDBsum]</span></td></tr>
-		+	</table>
-	~~Description~~: ~~Computational design and experimental verification of a symmetric homodimer~~	+	__TOC__
		+	</StructureSection>
		+	[[Category: Hsu, F C.]]
		+	[[Category: Huang, P S.]]
		+	[[Category: Huang, S J.]]
		+	[[Category: Mayo, S L.]]
		+	[[Category: Mou, Y.]]
		+	[[Category: De novo protein]]
		+	[[Category: Helix-turn-helix]]

OCA at 09:12, 8 January 2014

OCA — Wed, 08 Jan 2014 09:12:09 GMT

←Older revision		Revision as of 09:12, 8 January 2014
Line 3:		Line 3:
	The entry 4ndl is ON HOLD until Paper Publication		The entry 4ndl is ON HOLD until Paper Publication

-	Authors: Mou, Y., Mayo, S.L.	+	Authors: Mou, Y., Huang, P.S., Hsu, F.C., Huang, S.J., Mayo, S.L.

	Description: Computational design and experimental verification of a symmetric homodimer		Description: Computational design and experimental verification of a symmetric homodimer

OCA at 13:03, 11 December 2013

OCA — Wed, 11 Dec 2013 13:03:14 GMT

←Older revision		Revision as of 13:03, 11 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Mou, Y, Mayo, SL	+	Authors: Mou, Y., Mayo, S.L.

-	Description: ~~Crystal structure~~ of a ~~computational designed~~ homodimer ~~based on the engrailed homeodomain structure~~	+	Description: Computational design and experimental verification of a symmetric homodimer