2l56

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[[Image:2l56.png|left|200px]]
 
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==NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations==
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The line below this paragraph, containing "STRUCTURE_2l56", creates the "Structure Box" on the page.
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<StructureSection load='2l56' size='340' side='right'caption='[[2l56]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 10 models</td></tr>
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<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>
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{{STRUCTURE_2l56| PDB=2l56 | SCENE= }}
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2l56" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20954244}}, adds the Publication Abstract to the page
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*[[Gcn4 3D Structures|Gcn4 3D Structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20954244 is the PubMed ID number.
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*[[Gnc4 3D Structures|Gnc4 3D Structures]]
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== References ==
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{{ABSTRACT_PUBMED_20954244}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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[[2l56]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L56 OCA].
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[[Category: Large Structures]]
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[[Category: Dolenc J]]
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==Reference==
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[[Category: Missimer JH]]
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<ref group="xtra">PMID:20954244</ref><references group="xtra"/>
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[[Category: Steinmetz MO]]
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[[Category: Dolenc, J.]]
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[[Category: Van Gunsteren WF]]
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[[Category: Gunsteren, W F.van.]]
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[[Category: Missimer, J H.]]
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[[Category: Steinmetz, M O.]]
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Current revision

NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations

PDB ID 2l56

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