4hop - Revision history

OCA at 15:09, 20 September 2023

OCA — Wed, 20 Sep 2023 15:09:17 GMT

←Older revision		Revision as of 15:09, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HOP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HOP 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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [https://pdbe.org/4hop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [https://www.ebi.ac.uk/pdbsum/4hop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop 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]] 2.29Å</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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [https://pdbe.org/4hop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [https://www.ebi.ac.uk/pdbsum/4hop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:30, 3 November 2022

OCA — Thu, 03 Nov 2022 08:30:03 GMT

←Older revision		Revision as of 08:30, 3 November 2022
Line 1:		Line 1:

	==Crystal structure of the computationally designed NNOS-Syntrophin complex==		==Crystal structure of the computationally designed NNOS-Syntrophin complex==
-	<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>	+	<StructureSection load='4hop' size='340' side='right'caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4HOP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HOP FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [https://pdbe.org/4hop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [https://www.ebi.ac.uk/pdbsum/4hop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [~~http~~://pdbe.org/4hop PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4hop PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE]] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate. [[http://www.uniprot.org/uniprot/NOS1_RAT NOS1_RAT]] Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum. Probably has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such SRR. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum.	+	[https://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 19:

	==See Also==		==See Also==
-	*[[Nitric Oxide Synthase\|Nitric Oxide Synthase]]	+	*[[Nitric Oxide Synthase 3D structures\|Nitric Oxide Synthase 3D structures]]
		+	*[[Syntrophin\|Syntrophin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Harwood~~, I M~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Kortemme, T]]	+	[[Category: Harwood IM]]
-	[[Category: Melero, C]]	+	[[Category: Kortemme T]]
-	[[Category: Ollikainen, N]]	+	[[Category: Melero C]]
-	~~[[Category: Dimerization]]~~	+	[[Category: Ollikainen N]]
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Membrane protein-oxidoreductase complex]]~~	+
-	~~[[Category: Mutation]]~~	+
-	~~[[Category: Pdz]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 22:55, 4 August 2016

OCA — Thu, 04 Aug 2016 22:55:09 GMT

←Older revision		Revision as of 22:55, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the computationally designed NNOS-Syntrophin complex==		==Crystal structure of the computationally designed NNOS-Syntrophin complex==
	<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://pdbe.org/4hop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hop ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4hop" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 13:47, 25 December 2014

OCA — Thu, 25 Dec 2014 13:47:19 GMT

←Older revision		Revision as of 13:47, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE]] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate. [[http://www.uniprot.org/uniprot/NOS1_RAT NOS1_RAT]] Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum. Probably has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such SRR. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Harwood, I M]]		[[Category: Harwood, I M]]
	[[Category: Kortemme, T]]		[[Category: Kortemme, T]]

OCA at 07:35, 12 November 2014

OCA — Wed, 12 Nov 2014 07:35:37 GMT

←Older revision		Revision as of 07:35, 12 November 2014
Line 15:		Line 15:
	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>
		+
		+	==See Also==
		+	*[[Nitric Oxide Synthase\|Nitric Oxide Synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Harwood, I M.]]	+	[[Category: Harwood, I M]]
-	[[Category: Kortemme, T.]]	+	[[Category: Kortemme, T]]
-	[[Category: Melero, C.]]	+	[[Category: Melero, C]]
-	[[Category: Ollikainen, N.]]	+	[[Category: Ollikainen, N]]
	[[Category: Dimerization]]		[[Category: Dimerization]]
	[[Category: Membrane]]		[[Category: Membrane]]

OCA at 09:32, 29 October 2014

OCA — Wed, 29 Oct 2014 09:32:46 GMT

←Older revision		Revision as of 09:32, 29 October 2014
Line 2:		Line 2:
	<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.
		+
		+	Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.,Melero C, Ollikainen N, Harwood I, Karpiak J, Kortemme T Proc Natl Acad Sci U S A. 2014 Oct 13. pii: 201410624. PMID:25313039<ref>PMID:25313039</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
-	[[Category: Lk3 transgenic mice]]
	[[Category: Harwood, I M.]]		[[Category: Harwood, I M.]]
	[[Category: Kortemme, T.]]		[[Category: Kortemme, T.]]

OCA at 08:53, 20 October 2014

OCA — Mon, 20 Oct 2014 08:53:05 GMT

←Older revision		Revision as of 08:53, 20 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4hop\| PDB=4hop \| SCENE= }}~~	+	==Crystal structure of the computationally designed NNOS-Syntrophin complex==
-	===Crystal structure of the computationally designed NNOS-Syntrophin complex===	+	<StructureSection load='4hop' size='340' side='right' caption='[[4hop]], [[Resolution\|resolution]] 2.29Å' scene=''>
-		+	== Structural highlights ==
-	==~~Function~~==	+	<table><tr><td colspan='2'>[[4hop]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HOP FirstGlance]. <br>
-	[[http://~~www~~.~~uniprot~~.org/~~uniprot~~/~~SNTA1_MOUSE SNTA1_MOUSE~~]~~] Adapter protein that binds to~~ and ~~probably organizes the subcellular localization of a variety of membrane proteins~~. ~~May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex~~. ~~Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse~~. ~~Binds to phosphatidylinositol 4,5-bisphosphate. [~~[http://~~www~~.~~uniprot~~.~~org~~/~~uniprot~~/~~NOS1_RAT NOS1_RAT~~]~~] Produces nitric oxide (NO) which is~~ a ~~messenger molecule with diverse functions throughout~~ the ~~body~~. ~~In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter~~. ~~Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum~~. ~~Probably has nitrosylase activity and mediates cysteine S~~-~~nitrosylation of cytoplasmic target proteins such SRR~~. ~~Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum~~.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qav\|1qav]]</td></tr>
-		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Snt1, Snta1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Bnos, Nos1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
-	==~~About this Structure=~~=	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitric-oxide_synthase_(NADPH_dependent) Nitric-oxide synthase (NADPH dependent)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.39 1.14.13.39] </span></td></tr>
-	[[~~4hop~~]] ~~is a 6 chain structure with sequence from~~ [http://en.~~wikipedia~~.~~org~~/~~wiki~~/~~Mus_musculus Mus musculus~~] ~~and~~ [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. ~~Full crystallographic information is available from~~ [http://oca.weizmann.ac.il/oca-bin/~~ocashort~~?id=~~4HOP~~ OCA].	+	<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=4hop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hop OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hop RCSB], [http://www.ebi.ac.uk/pdbsum/4hop PDBsum]</span></td></tr>
-	[[Category: ~~Mus musculus~~]]	+	</table>
-	[[Category: ~~Rattus norvegicus~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Harwood, I M.]]		[[Category: Harwood, I M.]]
	[[Category: Kortemme, T.]]		[[Category: Kortemme, T.]]

OCA at 07:40, 6 November 2013

OCA — Wed, 06 Nov 2013 07:40:20 GMT

←Older revision		Revision as of 07:40, 6 November 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4hop\| PDB=4hop \| SCENE= }}
		+	===Crystal structure of the computationally designed NNOS-Syntrophin complex===

-	~~The entry 4hop~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SNTA1_MOUSE SNTA1_MOUSE]] Adapter protein that binds to and probably organizes the subcellular localization of a variety of membrane proteins. May link various receptors to the actin cytoskeleton and the extracellular matrix via the dystrophin glycoprotein complex. Plays an important role in synapse formation and in the organization of UTRN and acetylcholine receptors at the neuromuscular synapse. Binds to phosphatidylinositol 4,5-bisphosphate. [[http://www.uniprot.org/uniprot/NOS1_RAT NOS1_RAT]] Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum. Probably has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such SRR. Inhibitory transmitter for non-adrenergic and non-cholinergic nerves in the colorectum.

-	~~Authors~~: Harwood, I.M., Melero, C., Ollikainen, N.~~, Kortemme, T.~~	+	==About this Structure==
-		+	[[4hop]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HOP OCA].
-	~~Description~~: ~~Crystal structure of the computationally designed NNOS~~-~~Syntrophin~~ complex	+	[[Category: Mus musculus]]
		+	[[Category: Rattus norvegicus]]
		+	[[Category: Harwood, I M.]]
		+	[[Category: Kortemme, T.]]
		+	[[Category: Melero, C.]]
		+	[[Category: Ollikainen, N.]]
		+	[[Category: Dimerization]]
		+	[[Category: Membrane]]
		+	[[Category: Membrane protein-oxidoreductase complex]]
		+	[[Category: Mutation]]
		+	[[Category: Pdz]]
		+	[[Category: Protein binding]]

OCA at 13:20, 20 February 2013

OCA — Wed, 20 Feb 2013 13:20:50 GMT

←Older revision		Revision as of 13:20, 20 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Harwood, I.M., Melero, C., Ollikainen, N., Kortemme, T.		Authors: Harwood, I.M., Melero, C., Ollikainen, N., Kortemme, T.

	Description: Crystal structure of the computationally designed NNOS-Syntrophin complex		Description: Crystal structure of the computationally designed NNOS-Syntrophin complex

OCA at 13:24, 8 November 2012

OCA — Thu, 08 Nov 2012 13:24:00 GMT

←Older revision		Revision as of 13:24, 8 November 2012
Line 5:		Line 5:
	Authors: Harwood, I.M., Melero, C., Ollikainen, N., Kortemme, T.		Authors: Harwood, I.M., Melero, C., Ollikainen, N., Kortemme, T.

-	Description: ~~CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED~~ NNOS-~~SYNTROPHIN COMPLEX.~~	+	Description: Crystal structure of the computationally designed NNOS-Syntrophin complex