2l56 - Revision history

OCA at 12:09, 15 November 2023

OCA — Wed, 15 Nov 2023 12:09:49 GMT

←Older revision		Revision as of 12:09, 15 November 2023
Line 1:		Line 1:

	==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==		==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==
-	<StructureSection load='2l56' size='340' side='right'caption='[[2l56~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='2l56' size='340' side='right'caption='[[2l56]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L56 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L56 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene~~></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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height~~: ~~3em;~~'>~~[[2ovn\|2ovn]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [https://pdbe.org/2l56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [https://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [https://pdbe.org/2l56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [https://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful~~ coiled-coil ~~design strategies therefore require a detailed understanding~~ of ~~coiled~~-~~coil folding~~. ~~One common feature shared by coiled coils is~~ the ~~presence of a short autonomous helical folding unit~~, ~~termed "trigger sequence~~," that is ~~indispensable for folding~~. ~~Detailed knowledge~~ of trigger ~~sequences at~~ the ~~molecular level is thus key to a general understanding~~ of ~~coiled-coil formation~~. ~~Using a multidisciplinary approach~~, we ~~identify and characterize here~~ the ~~molecular determinants~~ that ~~specify~~ the ~~helical conformation~~ of the ~~monomeric early folding intermediate~~ of the ~~GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding~~ and ~~electrostatic interactions stabilize~~ the ~~trigger-sequence helix. This network is rearranged in~~ the ~~final dimeric coiled~~-~~coil structure~~, ~~and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for~~ the ~~molecular mechanism~~ of ~~coiled-coil formation~~.	+	Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and (3) J(H(N,) H(Calpha) )-coupling constants, and a set of 20 model structures was proposed. Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured (3) J(H(N) -H(Calpha) )-coupling constant values, indicating that the alpha-helical propensity is not uniform along the GCN4 trigger sequence. A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation (3) J-coupling restraints could satisfy the entire set of the experimental data. In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures. Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures.

-	~~Molecular basis~~ of coiled-coil ~~formation~~.~~,Steinmetz MO, Jelesarov I, Matousek WM, Honnappa S, Jahnke W~~, Missimer JH, ~~Frank S~~, ~~Alexandrescu AT~~, ~~Kammerer RA Proc Natl Acad~~ Sci ~~U S A~~. ~~2007 Apr 24~~;~~104~~(17):~~7062~~-7. ~~Epub 2007 Apr 16~~. PMID:~~17438295~~<ref>PMID:~~17438295~~</ref>	+	Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements.,Missimer JH, Dolenc J, Steinmetz MO, van Gunsteren WF Protein Sci. 2010 Dec;19(12):2462-74. doi: 10.1002/pro.528. PMID:20954244<ref>PMID:20954244</ref>

	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>
Line 19:		Line 19:

	==See Also==		==See Also==
		+	*[[Gcn4 3D Structures\|Gcn4 3D Structures]]
	*[[Gnc4 3D Structures\|Gnc4 3D Structures]]		*[[Gnc4 3D Structures\|Gnc4 3D Structures]]
	== References ==		== References ==
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dolenc, J]]	+	[[Category: Dolenc J]]
-	~~[[Category: Gunsteren, W F.van~~]]	+	[[Category: Missimer JH]]
-	[[Category: Missimer~~, J H~~]]	+	[[Category: Steinmetz MO]]
-	[[Category: Steinmetz~~, M O~~]]	+	[[Category: Van Gunsteren WF]]
-	[[Category: ~~Coiled-coil]]~~	+
-	~~[[Category: Gcn4]]~~	+
-	~~[[Category: Molecular dynamics simulation]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Trigger peptide~~]]	+

OCA at 07:48, 9 February 2022

OCA — Wed, 09 Feb 2022 07:48:32 GMT

←Older revision		Revision as of 07:48, 9 February 2022
Line 3:		Line 3:
	<StructureSection load='2l56' size='340' side='right'caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2l56' size='340' side='right'caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2L56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L56 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ovn\|2ovn]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [~~http~~://pdbe.org/2l56 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [https://pdbe.org/2l56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [https://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:59, 6 May 2020

OCA — Wed, 06 May 2020 06:59:13 GMT

←Older revision		Revision as of 06:59, 6 May 2020
Line 1:		Line 1:

	==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==		==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==
-	<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='2l56' size='340' side='right'caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2L56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2L56 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://pdbe.org/2l56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://pdbe.org/2l56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[~~Gcn4~~\|~~Gcn4~~]]	+	*[[Gnc4 3D Structures\|Gnc4 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dolenc, J]]		[[Category: Dolenc, J]]
	[[Category: Gunsteren, W F.van]]		[[Category: Gunsteren, W F.van]]

OCA at 20:04, 1 August 2018

OCA — Wed, 01 Aug 2018 20:04:55 GMT

←Older revision		Revision as of 20:04, 1 August 2018
Line 1:		Line 1:
		+
	==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==		==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==
	<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://pdbe.org/2l56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://pdbe.org/2l56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l56 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:13, 10 September 2015

OCA — Thu, 10 Sep 2015 00:13:30 GMT

←Older revision		Revision as of 00:13, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://pdbe.org/2l56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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>
		+	<div class="pdbe-citations 2l56" style="background-color:#fffaf0;"></div>

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

OCA at 06:47, 22 December 2014

OCA — Mon, 22 Dec 2014 06:47:00 GMT

←Older revision		Revision as of 06:47, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>	+	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L56 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span></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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 13:
	Molecular basis of coiled-coil formation.,Steinmetz MO, Jelesarov I, Matousek WM, Honnappa S, Jahnke W, Missimer JH, Frank S, Alexandrescu AT, Kammerer RA Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7062-7. Epub 2007 Apr 16. PMID:17438295<ref>PMID:17438295</ref>		Molecular basis of coiled-coil formation.,Steinmetz MO, Jelesarov I, Matousek WM, Honnappa S, Jahnke W, Missimer JH, Frank S, Alexandrescu AT, Kammerer RA Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7062-7. Epub 2007 Apr 16. PMID:17438295<ref>PMID:17438295</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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==
		+	*[[Gcn4\|Gcn4]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dolenc, J.]]	+	[[Category: Dolenc, J]]
-	[[Category: Gunsteren, W F.van.]]	+	[[Category: Gunsteren, W F.van]]
-	[[Category: Missimer, J H.]]	+	[[Category: Missimer, J H]]
-	[[Category: Steinmetz, M O.]]	+	[[Category: Steinmetz, M O]]
	[[Category: Coiled-coil]]		[[Category: Coiled-coil]]
	[[Category: Gcn4]]		[[Category: Gcn4]]

OCA at 09:56, 1 May 2014

OCA — Thu, 01 May 2014 09:56:59 GMT

←Older revision		Revision as of 09:56, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>	+	<table><tr><td colspan='2'>[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>
-	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene><br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	<b>[[Related_structure\|Related:]]</b> [[2ovn\|2ovn]]<br>	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ovn\|2ovn]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span><br>	+	<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=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.		Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.
Line 13:		Line 15:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:22, 30 April 2014

OCA — Wed, 30 Apr 2014 10:22:43 GMT

←Older revision		Revision as of 10:22, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>		[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>
-	<b>Related:</b> [[2ovn\|2ovn]]<br>	+	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene><br>
		+	<b>[[Related_structure\|Related:]]</b> [[2ovn\|2ovn]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l56 RCSB], [http://www.ebi.ac.uk/pdbsum/2l56 PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.		Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.

OCA at 08:39, 30 April 2014

OCA — Wed, 30 Apr 2014 08:39:47 GMT

←Older revision		Revision as of 08:39, 30 April 2014
Line 1:		Line 1:
-	[[~~Image:~~2l56.~~png~~\|~~left\|200px~~]]	+	==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==
		+	<StructureSection load='2l56' size='340' side='right' caption='[[2l56]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA]. <br>
		+	<b>Related:</b> [[2ovn\|2ovn]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.

-	<!--	+	Molecular basis of coiled-coil formation.,Steinmetz MO, Jelesarov I, Matousek WM, Honnappa S, Jahnke W, Missimer JH, Frank S, Alexandrescu AT, Kammerer RA Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7062-7. Epub 2007 Apr 16. PMID:17438295<ref>PMID:17438295</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2l56"~~, ~~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_2l56\| PDB=2l56 \| SCENE= }}~~	+

-	~~===NMR structure~~ of the ~~GCN4 trigger peptide refined using biased molecular dynamics simulations===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-		+	<references/>
-	~~<!--~~	+	__TOC__
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_17438295}}, adds the Publication Abstract to the page~~	+	</StructureSection>
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 17438295 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_17438295}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~[[2l56]] is a 1 chain structure. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA].~~	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra">PMID:017438295</ref><ref group="xtra">PMID:020954244</ref><references group="xtra"~~/>	+
	[[Category: Dolenc, J.]]		[[Category: Dolenc, J.]]
	[[Category: Gunsteren, W F.van.]]		[[Category: Gunsteren, W F.van.]]

OCA at 08:05, 30 October 2011

OCA — Sun, 30 Oct 2011 08:05:53 GMT

←Older revision		Revision as of 08:05, 30 October 2011
Line 13:		Line 13:

	<!--		<!--
-	The line below this paragraph, {{~~ABSTRACT_PUBMED_20954244~~}}, adds the Publication Abstract to the page	+	The line below this paragraph, {{ABSTRACT_PUBMED_17438295}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where ~~20954244~~ is the PubMed ID number.	+	(as it appears on PubMed at http://www.pubmed.gov), where 17438295 is the PubMed ID number.
	-->		-->
-	{{~~ABSTRACT_PUBMED_20954244~~}}	+	{{ABSTRACT_PUBMED_17438295}}

	==About this Structure==		==About this Structure==
Line 22:		Line 22:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20954244~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017438295</ref><ref group="xtra">PMID:020954244</ref><references group="xtra"/>
	[[Category: Dolenc, J.]]		[[Category: Dolenc, J.]]
	[[Category: Gunsteren, W F.van.]]		[[Category: Gunsteren, W F.van.]]
	[[Category: Missimer, J H.]]		[[Category: Missimer, J H.]]
	[[Category: Steinmetz, M O.]]		[[Category: Steinmetz, M O.]]
		+	[[Category: Coiled-coil]]
		+	[[Category: Gcn4]]
		+	[[Category: Molecular dynamics simulation]]
		+	[[Category: Transcription]]
		+	[[Category: Trigger peptide]]