6dkm - Revision history

OCA at 14:35, 13 March 2024

2024-03-13T14:35:15Z

←Older revision		Revision as of 14:35, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dkm' size='340' side='right'caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='6dkm' size='340' side='right'caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dkm]] is a 8 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=6DKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DKM 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=6dkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dkm OCA], [~~http~~://pdbe.org/6dkm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dkm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dkm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dkm 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]] 2.38Å</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=6dkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dkm OCA], [https://pdbe.org/6dkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dkm RCSB], [https://www.ebi.ac.uk/pdbsum/6dkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dkm ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity(1), which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions(2)) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions(3,4). Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations(5) to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
-
-	Programmable design of orthogonal protein heterodimers.,Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, Sgourakis NG, Wysocki VH, Baker D Nature. 2018 Dec 19. pii: 10.1038/s41586-018-0802-y. doi:, 10.1038/s41586-018-0802-y. PMID:30568301<ref>PMID:30568301</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6dkm" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Bick~~, M J~~]]	+	[[Category: Bick MJ]]
-	[[Category: Chen, Z]]	+	[[Category: Chen Z]]
-	~~[[Category: Coiled-coil]]~~	+
-	~~[[Category: Computational design]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Heterodimer~~]]	+

OCA at 17:19, 20 November 2019

2019-11-20T17:19:07Z

←Older revision		Revision as of 17:19, 20 November 2019
Line 1:		Line 1:

	==DHD131==		==DHD131==
-	<StructureSection load='6dkm' size='340' side='right' caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>	+	<StructureSection load='6dkm' size='340' side='right'caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKM FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKM FirstGlance]. <br>
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 06:19, 2 January 2019

2019-01-02T06:19:47Z

←Older revision		Revision as of 06:19, 2 January 2019
Line 3:		Line 3:
	<StructureSection load='6dkm' size='340' side='right' caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='6dkm' size='340' side='right' caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKM 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=6dkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dkm OCA], [http://pdbe.org/6dkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dkm RCSB], [http://www.ebi.ac.uk/pdbsum/6dkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dkm ProSAT]</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=6dkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dkm OCA], [http://pdbe.org/6dkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dkm RCSB], [http://www.ebi.ac.uk/pdbsum/6dkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dkm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity(1), which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions(2)) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions(3,4). Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations(5) to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
		+
		+	Programmable design of orthogonal protein heterodimers.,Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, Sgourakis NG, Wysocki VH, Baker D Nature. 2018 Dec 19. pii: 10.1038/s41586-018-0802-y. doi:, 10.1038/s41586-018-0802-y. PMID:30568301<ref>PMID:30568301</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dkm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Bick, M J]]		[[Category: Bick, M J]]

OCA at 08:19, 19 December 2018

2018-12-19T08:19:28Z

←Older revision		Revision as of 08:19, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dkm ~~is ON HOLD until Paper Publication~~	+	==DHD131==
-		+	<StructureSection load='6dkm' size='340' side='right' caption='[[6dkm]], [[Resolution\|resolution]] 2.38Å' scene=''>
-	~~Authors~~: ~~Bick~~, M.J., ~~Chen~~, Z., ~~Baker~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dkm]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DKM FirstGlance]. <br>
-	~~Description: DHD131~~	+	</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=6dkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dkm OCA], [http://pdbe.org/6dkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dkm RCSB], [http://www.ebi.ac.uk/pdbsum/6dkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dkm ProSAT]</span></td></tr>
-	~~[[Category: Unreleased Structures]]~~	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Baker, D]]		[[Category: Baker, D]]
		+	[[Category: Bick, M J]]
	[[Category: Chen, Z]]		[[Category: Chen, Z]]
-	[[Category: ~~Bick, M.J~~]]	+	[[Category: Coiled-coil]]
		+	[[Category: Computational design]]
		+	[[Category: De novo protein]]
		+	[[Category: Heterodimer]]

OCA at 04:00, 20 June 2018

2018-06-20T04:00:36Z

←Older revision		Revision as of 04:00, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dkm is ON HOLD	+	The entry 6dkm is ON HOLD until Paper Publication

	Authors: Bick, M.J., Chen, Z., Baker, D.		Authors: Bick, M.J., Chen, Z., Baker, D.

OCA at 05:39, 14 June 2018

2018-06-14T05:39:06Z

←Older revision		Revision as of 05:39, 14 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dkm is ON HOLD ~~until sometime in the future~~	+	The entry 6dkm is ON HOLD

	Authors: Bick, M.J., Chen, Z., Baker, D.		Authors: Bick, M.J., Chen, Z., Baker, D.

OCA: Protected "6dkm" [edit=sysop:move=sysop]

2018-06-06T04:22:54Z

Protected "6dkm" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:22, 6 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dkm is ON HOLD until sometime in the future Authors: Bick, M.J., Chen, Z., Baker, D. Description: DHD131 Category: Unreleased Structures [[Cat...

2018-06-06T04:22:53Z

New page: '''Unreleased structure''' The entry 6dkm is ON HOLD until sometime in the future Authors: Bick, M.J., Chen, Z., Baker, D. Description: DHD131 Category: Unreleased Structures [[Cat...

New page

'''Unreleased structure'''

The entry 6dkm is ON HOLD until sometime in the future

Authors: Bick, M.J., Chen, Z., Baker, D.

Description: DHD131
[[Category: Unreleased Structures]]
[[Category: Baker, D]]
[[Category: Chen, Z]]
[[Category: Bick, M.J]]