1grm: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1grm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GRM FirstGlance]. <br> | <table><tr><td colspan='2'>[[1grm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GRM FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</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=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tk2|1tk2]], [[2xdc|2xdc]], [[1av2|1av2]], [[1bdw|1bdw]], [[1c4d|1c4d]], [[1gmk|1gmk]], [[1jno|1jno]], [[1kqe|1kqe]], [[1mag|1mag]], [[1mic|1mic]], [[1ng8|1ng8]], [[1nrm|1nrm]], [[1nru|1nru]], [[1nt5|1nt5]], [[1jo3|1jo3]], [[1jo4|1jo4]], [[1nt6|1nt6]], [[1tkq|1tkq]], [[1w5u|1w5u]], [[2izq|2izq]], [[3l8l|3l8l]], [[1al4|1al4]], [[1alx|1alx]], [[1alz|1alz]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tk2|1tk2]], [[2xdc|2xdc]], [[1av2|1av2]], [[1bdw|1bdw]], [[1c4d|1c4d]], [[1gmk|1gmk]], [[1jno|1jno]], [[1kqe|1kqe]], [[1mag|1mag]], [[1mic|1mic]], [[1ng8|1ng8]], [[1nrm|1nrm]], [[1nru|1nru]], [[1nt5|1nt5]], [[1jo3|1jo3]], [[1jo4|1jo4]], [[1nt6|1nt6]], [[1tkq|1tkq]], [[1w5u|1w5u]], [[2izq|2izq]], [[3l8l|3l8l]], [[1al4|1al4]], [[1alx|1alx]], [[1alz|1alz]]</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=1grm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB], [http://www.ebi.ac.uk/pdbsum/1grm 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=1grm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB], [http://www.ebi.ac.uk/pdbsum/1grm PDBsum]</span></td></tr> | ||
<table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Brevibacillus brevis]] | [[Category: Brevibacillus brevis]] | ||
[[Category: Arseniev, A S | [[Category: Arseniev, A S]] | ||
[[Category: Barsukov, I L | [[Category: Barsukov, I L]] | ||
[[Category: Bystrov, V F | [[Category: Bystrov, V F]] | ||
[[Category: Lomize, A L | [[Category: Lomize, A L]] | ||
[[Category: Orekhov, V Y | [[Category: Orekhov, V Y]] | ||
[[Category: Antibacterial]] | [[Category: Antibacterial]] | ||
[[Category: Antibiotic]] | [[Category: Antibiotic]] | ||
Revision as of 23:07, 22 December 2014
REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)
Structural highlights
Publication Abstract from PubMedThe spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A. [Refinement of the spatial structure of the gramicidin A ion channel],Lomize AL, Orekhov VIu, Arsen'ev AS Bioorg Khim. 1992 Feb;18(2):182-200. PMID:1376600[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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