1grm: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|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...
 
No edit summary
 
(18 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1grm.gif|left|200px]]<br /><applet load="1grm" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1grm" />
'''REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)'''<br />


==Overview==
==REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)==
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.
<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/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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 5 models</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></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>
<div style="background-color:#fffaf0;">
== 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.


==About this Structure==
[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<ref>PMID:1376600</ref>
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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GRM OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[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]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1grm" style="background-color:#fffaf0;"></div>
[[Category: Arseniev, A.S.]]
[[Category: Barsukov, I.L.]]
[[Category: Bystrov, V.F.]]
[[Category: Lomize, A.L.]]
[[Category: Orekhov, V.Y.]]
[[Category: FOR]]
[[Category: peptide antibiotic]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:44:01 2007''
==See Also==
*[[Gramicidin|Gramicidin]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Brevibacillus brevis]]
[[Category: Large Structures]]
[[Category: Arseniev AS]]
[[Category: Barsukov IL]]
[[Category: Bystrov VF]]
[[Category: Lomize AL]]
[[Category: Orekhov VY]]

Latest revision as of 03:01, 21 November 2024

REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN)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.
Method:Solution NMR, 5 models
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.

See Also

References

  1. ↑ 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
Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1grm&oldid=4202961"