2l56
From Proteopedia
(Difference between revisions)
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==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 | + | <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=' | + | </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=' | + | <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 == | ||
| - | + | 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. | |
| - | + | 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> | ||
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==See Also== | ==See Also== | ||
| + | *[[Gcn4 3D Structures|Gcn4 3D Structures]] | ||
*[[Gnc4 3D Structures|Gnc4 3D Structures]] | *[[Gnc4 3D Structures|Gnc4 3D Structures]] | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Dolenc | + | [[Category: Dolenc J]] |
| - | + | [[Category: Missimer JH]] | |
| - | [[Category: Missimer | + | [[Category: Steinmetz MO]] |
| - | [[Category: Steinmetz | + | [[Category: Van Gunsteren WF]] |
| - | [[Category: | + | |
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Revision as of 12:09, 15 November 2023
NMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations
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