1grm
From Proteopedia
(New page: 200px<br /><applet load="1grm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1grm" /> '''REFINEMENT OF THE SPATIAL STRUCTURE OF THE G...) |
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'''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)'''<br /> | '''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The spatial structure of the gramicidin A (GA) transmembrane ion-channel | + | 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 Structure== | ==About this Structure== | ||
| - | 1GRM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with FOR as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1GRM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=FOR:'>FOR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=1376600 1376600] | [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://ispc.weizmann.ac.il//pmbin/getpm?pmid=1376600 1376600] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Arseniev, A | + | [[Category: Arseniev, A S.]] |
| - | [[Category: Barsukov, I | + | [[Category: Barsukov, I L.]] |
| - | [[Category: Bystrov, V | + | [[Category: Bystrov, V F.]] |
| - | [[Category: Lomize, A | + | [[Category: Lomize, A L.]] |
| - | [[Category: Orekhov, V | + | [[Category: Orekhov, V Y.]] |
[[Category: FOR]] | [[Category: FOR]] | ||
[[Category: peptide antibiotic]] | [[Category: peptide antibiotic]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:53:12 2008'' |
Revision as of 10:53, 21 February 2008
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REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)
Overview
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 Structure
1GRM is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from 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:1376600
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