This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1grm

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:55, 3 May 2023

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.
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 [https://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 [https://proteopedia.org/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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[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]]</div></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>
@@ Line 24: / Line 23: @@
 __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

From Proteopedia

Revision as of 07:55, 3 May 2023

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

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox