1GRM

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

Summary for 1GRM

• Entry DOI: 10.2210/pdb1grm/pdb
• Related: 1AL4 1ALX 1ALZ 1AV2 1BDW 1C4D 1GMK 1JNO 1JO3 1JO4 1KQE 1MAG 1MIC 1NG8 1NRM 1NRU 1NT5 1NT6 1TK2 1TKQ 1W5U 2IZQ 2XDC 3L8L
• Related PRD ID: PRD_000150
• Descriptor: GRAMICIDIN A (1 entity in total)
• Functional Keywords: antibiotic, gramicidin, antifungal, antibacterial, membrane ion channel, linear gramicidin
• Biological source: BREVIBACILLUS BREVIS
• Total number of polymer chains: 2
• Total formula weight: 3764.59

Authors

Arseniev, A.S.,Barsukov, I.L.,Lomize, A.L.,Orekhov, V.Y.,Bystrov, V.F. (deposition date: 1993-10-18, release date: 1994-01-31, Last modification date: 2024-11-20)

Primary citation

Lomize, A.L.,Orekhov, V.I.U.,Arsen'Ev, A.S.
Refinement of the Spatial Structure of the Gramicidin a Ion Channel
Biol.Membr.(Ussr), 18:182-, 1992

PubMed Abstract: 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.

PubMed: 1376600

Experimental method

SOLUTION NMR