7n1k - Revision history

OCA at 07:19, 3 April 2024

OCA — Wed, 03 Apr 2024 07:19:29 GMT

←Older revision		Revision as of 07:19, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='7n1k' size='340' side='right'caption='[[7n1k]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='7n1k' size='340' side='right'caption='[[7n1k]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7n1k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n1k]] 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=7N1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N1K FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max~~-~~height: 3em;'>~~[[~~7n1j~~\|~~7n1j~~]]~~</div>~~</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]] 3.01Å</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=7n1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n1k OCA], [https://pdbe.org/7n1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n1k RCSB], [https://www.ebi.ac.uk/pdbsum/7n1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n1k 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=7n1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n1k OCA], [https://pdbe.org/7n1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n1k RCSB], [https://www.ebi.ac.uk/pdbsum/7n1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n1k ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains an outstanding challenge(1-5). We describe a general solution to this problem which starts with a broad exploration of the very large space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate its very broad applicability by de novo design of binding proteins to 12 diverse protein targets with very different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and following experimental optimization bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five are very close to the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvement of both. Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
-
-	Design of protein binding proteins from target structure alone.,Cao L, Coventry B, Goreshnik I, Huang B, Park JS, Jude KM, Markovic I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D Nature. 2022 Mar 24. pii: 10.1038/s41586-022-04654-9. doi:, 10.1038/s41586-022-04654-9. PMID:35332283<ref>PMID:35332283</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7n1k" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lee, S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Park, J~~ S]]	+	[[Category: Lee S]]
-	[[Category: ~~Binder]]~~	+	[[Category: Park JS]]
-	~~[[Category: De novo protein~~]]	+

OCA at 10:22, 18 May 2022

OCA — Wed, 18 May 2022 10:22:44 GMT

←Older revision		Revision as of 10:22, 18 May 2022
Line 1:		Line 1:

	==Crystal structure of a de novo-designed mini-protein targeting FGFR==		==Crystal structure of a de novo-designed mini-protein targeting FGFR==
-	<StructureSection load='7n1k' size='340' side='right'caption='[[7n1k]]' scene=''>	+	<StructureSection load='7n1k' size='340' side='right'caption='[[7n1k]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n1k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N1K 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=7n1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n1k OCA], [https://pdbe.org/7n1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n1k RCSB], [https://www.ebi.ac.uk/pdbsum/7n1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n1k ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7n1j\|7n1j]]</div></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=7n1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n1k OCA], [https://pdbe.org/7n1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n1k RCSB], [https://www.ebi.ac.uk/pdbsum/7n1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n1k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains an outstanding challenge(1-5). We describe a general solution to this problem which starts with a broad exploration of the very large space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate its very broad applicability by de novo design of binding proteins to 12 diverse protein targets with very different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and following experimental optimization bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five are very close to the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvement of both. Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
		+
		+	Design of protein binding proteins from target structure alone.,Cao L, Coventry B, Goreshnik I, Huang B, Park JS, Jude KM, Markovic I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D Nature. 2022 Mar 24. pii: 10.1038/s41586-022-04654-9. doi:, 10.1038/s41586-022-04654-9. PMID:35332283<ref>PMID:35332283</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7n1k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lee S]]	+	[[Category: Lee, S]]
-	[[Category: Park JS]]	+	[[Category: Park, J S]]
		+	[[Category: Binder]]
		+	[[Category: De novo protein]]

OCA at 10:23, 6 April 2022

OCA — Wed, 06 Apr 2022 10:23:35 GMT

←Older revision		Revision as of 10:23, 6 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7n1k is ON HOLD until Paper Publication~~	+	==Crystal structure of a de novo-designed mini-protein targeting FGFR==
-		+	<StructureSection load='7n1k' size='340' side='right'caption='[[7n1k]]' scene=''>
-	~~Authors: Park, J.S., Lee, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N1K FirstGlance]. <br>
-	~~Description:~~ Crystal structure of a de novo-designed mini-protein targeting FGFR	+	</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=7n1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n1k OCA], [https://pdbe.org/7n1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n1k RCSB], [https://www.ebi.ac.uk/pdbsum/7n1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n1k ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Park~~, J.S]]	+	__TOC__
-	[[Category: Lee, S]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lee S]]
		+	[[Category: Park JS]]

OCA at 11:58, 17 November 2021

OCA — Wed, 17 Nov 2021 11:58:28 GMT

←Older revision		Revision as of 11:58, 17 November 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7n1k is ON HOLD	+	The entry 7n1k is ON HOLD until Paper Publication

	Authors: Park, J.S., Lee, S.		Authors: Park, J.S., Lee, S.

OCA at 14:51, 20 October 2021

OCA — Wed, 20 Oct 2021 14:51:20 GMT

←Older revision		Revision as of 14:51, 20 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7n1k is ON HOLD ~~until Paper Publication~~	+	The entry 7n1k is ON HOLD

	Authors: Park, J.S., Lee, S.		Authors: Park, J.S., Lee, S.

OCA at 07:51, 21 July 2021

OCA — Wed, 21 Jul 2021 07:51:17 GMT

←Older revision		Revision as of 07:51, 21 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7n1k is ON HOLD	+	The entry 7n1k is ON HOLD until Paper Publication

	Authors: Park, J.S., Lee, S.		Authors: Park, J.S., Lee, S.

OCA at 06:13, 25 June 2021

OCA — Fri, 25 Jun 2021 06:13:19 GMT

←Older revision		Revision as of 06:13, 25 June 2021
Line 5:		Line 5:
	Authors: Park, J.S., Lee, S.		Authors: Park, J.S., Lee, S.

-	Description: ~~Structure~~ of a designed ~~binder~~ targeting ~~FGFR2 domain 3~~	+	Description: Crystal structure of a de novo-designed mini-protein targeting FGFR
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Park, J.S]]		[[Category: Park, J.S]]
	[[Category: Lee, S]]		[[Category: Lee, S]]

OCA: Protected "7n1k" [edit=sysop:move=sysop]

OCA — Wed, 02 Jun 2021 13:34:07 GMT

Protected "7n1k" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:34, 2 June 2021

OCA: New page: '''Unreleased structure''' The entry 7n1k is ON HOLD Authors: Park, J.S., Lee, S. Description: Structure of a designed binder targeting FGFR2 domain 3 [[Category: Unreleased Structures...

OCA — Wed, 02 Jun 2021 13:34:06 GMT

New page: '''Unreleased structure''' The entry 7n1k is ON HOLD Authors: Park, J.S., Lee, S. Description: Structure of a designed binder targeting FGFR2 domain 3 [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 7n1k is ON HOLD

Authors: Park, J.S., Lee, S.

Description: Structure of a designed binder targeting FGFR2 domain 3
[[Category: Unreleased Structures]]
[[Category: Park, J.S]]
[[Category: Lee, S]]