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1grm

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REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)

Structural highlights

1grm is a 2 chain structure with sequence from Brevibacillus brevis. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The 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.

References

↑ Lomize AL, Orekhov VIu, Arsen'ev AS. [Refinement of the spatial structure of the gramicidin A ion channel] Bioorg Khim. 1992 Feb;18(2):182-200. PMID:1376600

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1grm"

@@ Line 1: / Line 1: @@
 ==REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)==
-<StructureSection load='1grm' size='340' side='right'caption='[[1grm]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
+<StructureSection load='1grm' size='340' side='right'caption='[[1grm]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1grm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_8246 Atcc 8246]. 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 [https://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 [https://proteopedia.org/fgij/fg.htm?mol=1GRM FirstGlance]. <br>
-</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>
+</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">[[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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=PRD_000150:GRAMICIDIN+A'>PRD_000150</scene></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://pdbe.org/1grm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB], [http://www.ebi.ac.uk/pdbsum/1grm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1grm 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=1grm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grm OCA], [https://pdbe.org/1grm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB], [https://www.ebi.ac.uk/pdbsum/1grm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1grm ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 8246]]
+[[Category: Brevibacillus brevis]]
 [[Category: Large Structures]]
-[[Category: Arseniev, A S]]
+[[Category: Arseniev AS]]
-[[Category: Barsukov, I L]]
+[[Category: Barsukov IL]]
-[[Category: Bystrov, V F]]
+[[Category: Bystrov VF]]
-[[Category: Lomize, A L]]
+[[Category: Lomize AL]]
-[[Category: Orekhov, V Y]]
+[[Category: Orekhov VY]]
-[[Category: Antibacterial]]
-[[Category: Antibiotic]]
-[[Category: Antifungal]]
-[[Category: Gramicidin]]
-[[Category: Linear gramicidin]]
-[[Category: Membrane ion channel]]

1grm

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Current revision

REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

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