2e4e - Revision history

OCA at 16:34, 13 December 2023

2023-12-13T16:34:46Z

← Older revision		Revision as of 16:34, 13 December 2023
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	==NMR structure of D4P/K7G mutant of GPM12==		==NMR structure of D4P/K7G mutant of GPM12==
	<StructureSection load='2e4e' size='340' side='right'caption='[[2e4e~~]], [[NMR_Ensembles_of_Models \| 23 NMR models~~]]' scene=''>		<StructureSection load='2e4e' size='340' side='right'caption='[[2e4e]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E4E 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [https://pdbe.org/2e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [https://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4e ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [https://pdbe.org/2e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [https://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4e ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Chignolin is a 10-residue peptide (GYDPETGTWG) that forms a stable beta-hairpin structure in water. However, its design template, GPM12 (GYDDATKTFG), does not have a specific structure. To clarify which amino acids give it the ability to form the beta-hairpin structure, we calculated the folding free-energy landscapes of chignolin, GPM12, and their chimeric peptides using multicanonical molecular dynamics (MD) simulation. Cluster analysis of the conformational ensembles revealed that the native structure of chignolin was the lowest in terms of free energy while shallow local minima were widely distributed in the free energy landscape of GPM12, in agreement with experimental observations. Among the chimeric peptides, GPM12(D4P/K7G) stably formed the same beta-hairpin structure as that of chignolin in the MD simulation. This was confirmed by nuclear magnetic resonance (NMR) spectroscopy. A comparison of the free-energy landscapes showed that the conformational distribution of the Asp3-Pro4 sequence was inherently biased in a way that is advantageous both to forming hydrogen bonds with another beta-strand and to initiating loop structure. In addition, Gly7 helps stabilize the loop structure by having a left-handed alpha-helical conformation. Such a conformation is necessary to complete the loop structure, although it is not preferred by other amino acids. Our results suggest that the consistency between the short-range interactions that determine the local geometries and the long-range interactions that determine the global structure is important for stable tertiary structure formation.

			Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation.,Terada T, Satoh D, Mikawa T, Ito Y, Shimizu K Proteins. 2008 Nov 15;73(3):621-31. doi: 10.1002/prot.22100. PMID:18473359<ref>PMID:18473359</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2e4e" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ito, Y]]		[[Category: Ito Y]]
	[[Category: Mikawa, T]]		[[Category: Mikawa T]]
	[[Category: Satoh, D]]		[[Category: Satoh D]]
	[[Category: Shimizu, K]]		[[Category: Shimizu K]]
	[[Category: Terada, T]]		[[Category: Terada T]]
	~~[[Category: B1 domain of protein g]]~~
	~~[[Category: Beta-hairpin]]~~
	~~[[Category: Chignolin]]~~
	~~[[Category: De novo protein]]~~
	~~[[Category: Mini-protein~~]]

OCA at 17:20, 15 December 2021

2021-12-15T17:20:33Z

← Older revision		Revision as of 17:20, 15 December 2021
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	<StructureSection load='2e4e' size='340' side='right'caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>		<StructureSection load='2e4e' size='340' side='right'caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E4E 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [~~http~~://pdbe.org/2e4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4e 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [https://pdbe.org/2e4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [https://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4e ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 08:27, 11 March 2020

2020-03-11T08:27:13Z

← Older revision		Revision as of 08:27, 11 March 2020
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	==NMR structure of D4P/K7G mutant of GPM12==		==NMR structure of D4P/K7G mutant of GPM12==
	<StructureSection load='2e4e' size='340' side='right' caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>		<StructureSection load='2e4e' size='340' side='right'caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Ito, Y]]		[[Category: Ito, Y]]
	[[Category: Mikawa, T]]		[[Category: Mikawa, T]]

OCA at 06:41, 6 June 2018

2018-06-06T06:41:55Z

← Older revision		Revision as of 06:41, 6 June 2018
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	==NMR structure of D4P/K7G mutant of GPM12==		==NMR structure of D4P/K7G mutant of GPM12==
	<StructureSection load='2e4e' size='340' side='right' caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>		<StructureSection load='2e4e' size='340' side='right' caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://pdbe.org/2e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://pdbe.org/2e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4e ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 23:41, 9 September 2015

2015-09-09T23:41:31Z

← Older revision		Revision as of 23:41, 9 September 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://pdbe.org/2e4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e PDBsum]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 17:42, 15 January 2015

2015-01-15T17:42:06Z

← Older revision		Revision as of 17:42, 15 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e 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=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e PDBsum]</span></td></tr>
	<table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Ito, Y.]]		[[Category: Ito, Y]]
	[[Category: Mikawa, T.]]		[[Category: Mikawa, T]]
	[[Category: Satoh, D.]]		[[Category: Satoh, D]]
	[[Category: Shimizu, K.]]		[[Category: Shimizu, K]]
	[[Category: Terada, T.]]		[[Category: Terada, T]]
	[[Category: B1 domain of protein g]]		[[Category: B1 domain of protein g]]
	[[Category: Beta-hairpin]]		[[Category: Beta-hairpin]]

OCA at 03:57, 29 September 2014

2014-09-29T03:57:09Z

← Older revision		Revision as of 03:57, 29 September 2014
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	~~[[Image:2e4e.png\|left\|200px]]~~		==NMR structure of D4P/K7G mutant of GPM12==
			<StructureSection load='2e4e' size='340' side='right' caption='[[2e4e]], [[NMR_Ensembles_of_Models \| 23 NMR models]]' scene=''>
	~~{{STRUCTURE_2e4e\| PDB=2e4e \| SCENE= }}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E4E FirstGlance]. <br>
	===NMR structure of D4P/K7G mutant of GPM12===		</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB], [http://www.ebi.ac.uk/pdbsum/2e4e PDBsum]</span></td></tr>
			<table>
			__TOC__
	==~~About this Structure~~==		</StructureSection>
	[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA].
	[[Category: Ito, Y.]]		[[Category: Ito, Y.]]
	[[Category: Mikawa, T.]]		[[Category: Mikawa, T.]]

OCA: Protected "2e4e" [edit=sysop:move=sysop]

2012-10-24T07:54:52Z

Protected "2e4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:54, 24 October 2012
(No difference)

OCA at 07:54, 24 October 2012

2012-10-24T07:54:49Z

← Older revision		Revision as of 07:54, 24 October 2012
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	[[Image:2e4e.~~jpg~~\|left\|200px]]		[[Image:2e4e.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2e4e", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2e4e\| PDB=2e4e \| SCENE= }}		{{STRUCTURE_2e4e\| PDB=2e4e \| SCENE= }}

	~~'''~~NMR structure of D4P/K7G mutant of GPM12~~'''~~		===NMR structure of D4P/K7G mutant of GPM12===


	==About this Structure==		==About this Structure==
	~~2E4E is a~~ [[~~Single protein~~]] structure. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA].		[[2e4e]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA].
	~~[[Category: Single protein]]~~
	[[Category: Ito, Y.]]		[[Category: Ito, Y.]]
	[[Category: Mikawa, T.]]		[[Category: Mikawa, T.]]
Line 25:		Line 18:
	[[Category: De novo protein]]		[[Category: De novo protein]]
	[[Category: Mini-protein]]		[[Category: Mini-protein]]
	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 01:53:54 2008''~~

OCA at 22:53, 3 May 2008

2008-05-03T22:53:55Z

← Older revision		Revision as of 22:53, 3 May 2008
Line 1:		Line 1:
	[[Image:2e4e.jpg\|left\|200px]]		[[Image:2e4e.jpg\|left\|200px]]

	{{Structure		<!--
	\|PDB~~= 2e4e \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>2e4e</scene>~~		The line below this paragraph, containing "STRUCTURE_2e4e", creates the "Structure Box" on the page.
	~~\|SITE=~~		You may change the PDB parameter (which sets the PDB file loaded into the applet)
	~~\|LIGAND=~~		or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
	\|~~ACTIVITY~~=		or leave the SCENE parameter empty for the default display.
	\|~~GENE~~=		-->
	~~\|DOMAIN=~~		{{STRUCTURE_2e4e\| PDB=2e4e \| SCENE= }}
	~~\|RELATEDENTRY=~~
	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4e OCA], [http://www.ebi.ac.uk/pdbsum/2e4e PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e4e RCSB]</span>
	}}

	'''NMR structure of D4P/K7G mutant of GPM12'''		'''NMR structure of D4P/K7G mutant of GPM12'''
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	==About this Structure==		==About this Structure==
	2E4E is a [[Single protein]] structure ~~of sequence from [http://en.wikipedia.org/wiki/ ]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA].		2E4E is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4E OCA].
	[[Category: Single protein]]		[[Category: Single protein]]
	[[Category: Ito, Y.]]		[[Category: Ito, Y.]]
Line 23:		Line 20:
	[[Category: Shimizu, K.]]		[[Category: Shimizu, K.]]
	[[Category: Terada, T.]]		[[Category: Terada, T.]]
	[[Category: b1 domain of protein g]]		[[Category: B1 domain of protein g]]
	[[Category: ~~beta~~-hairpin]]		[[Category: Beta-hairpin]]
	[[Category: ~~chignolin~~]]		[[Category: Chignolin]]
	[[Category: de novo protein]]		[[Category: De novo protein]]
	[[Category: ~~mini~~-protein]]		[[Category: Mini-protein]]
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 01:53:54 2008''
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 02~~:43:32 2008''