1grm: Difference between revisions
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[[Image:1grm.gif|left|200px]] | [[Image:1grm.gif|left|200px]] | ||
'''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)''' | {{Structure | ||
|PDB= 1grm |SIZE=350|CAPTION= <scene name='initialview01'>1grm</scene> | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=FOR:FORMYL GROUP'>FOR</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1GRM is a [ | 1GRM 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]. | ||
==Reference== | ==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:// | [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: Protein complex]] | ||
[[Category: Arseniev, A S.]] | [[Category: Arseniev, A S.]] | ||
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[[Category: peptide antibiotic]] | [[Category: peptide antibiotic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:26:59 2008'' | ||
Revision as of 12:27, 20 March 2008
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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
1GRM is a Protein complex structure of sequences from [1]. 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
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