1grm
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(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)
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 FOR 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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