1grm: Difference between revisions

Revision as of 17:55, 2 May 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

[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 Page seeded by OCA on Fri May 2 17:55:41 2008

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OCA

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 [[Image:1grm.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1grm |SIZE=350|CAPTION= <scene name='initialview01'>1grm</scene>
+The line below this paragraph, containing "STRUCTURE_1grm", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FOR:FORMYL+GROUP'>FOR</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-|GENE=
+-->
-|DOMAIN=
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-|RELATEDENTRY=
-|RESOURCES=<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.ebi.ac.uk/pdbsum/1grm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1grm RCSB]</span>
-}}
 '''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)'''
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 ==About this Structure==
-GRM is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRM OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRM OCA].
 ==Reference==
 [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:[http://www.ncbi.nlm.nih.gov/pubmed/1376600 1376600]
-[[Category: Protein complex]]
 [[Category: Arseniev, A S.]]
 [[Category: Barsukov, I L.]]
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 [[Category: Lomize, A L.]]
 [[Category: Orekhov, V Y.]]
-[[Category: peptide antibiotic]]
+[[Category: Peptide antibiotic]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 17:55:41 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:49:53 2008''