Gramicidin A in a Slice of Membrane with Surrounding
Layers of Water.
Gramicidin A is shown Spacefill, colored Amino. This theoretical model
also contains several molecules of phospholipid (POP), shown as thick wireframe
and arranged as they would occur in a bilayer membrane. About 400 H2O
molecules form a 6 Å layer around the phospholipid head groups.
The numbered "Highlight" buttons display features of the gramicidin-membrane
structure, the valinomycin-K+ complex, and two other naturally
occuring gramicidin structures.
1. Gramicidin-Membrane.
The phospholipid and H2O can be toggled, i.e. removed
and added back to the display with successive clicks.
The gramicidin side chain residues are labeled; the backbone
carbons are colored green in chain A and cyan in chain B.
The backbone display emphasizes the channel at the center of
the "b-helix" by showing the H2O
molecules that occupy the volume.
2. Valinomycin
Loading the valinomycin structure shows this carrier initially
as Sticks with a Spacefill K+ ion. The first of the repeating
four-residue units are labeled.
The "Backbone" display shows the ring of main chain groups that
surround the K+. Each of the four side chain groups are colored
differently.
The octahedral geometry display shows as Spacefill, the carbonyl
oxygens of the L-Val and D-Val residues that contact the K+.
All eight distances between the oxygens and the K+
are within the range shown.
3. Gramicidin A, B, & C
The natural product, gramicidin, is a mixture of several forms. The
three principal species (A, B, & C) differ only in the amino acid at
position 11. Structures of each were determined using NMR spectroscopy.
Loading the superposed structures shows all three models as
Backbone, colored Group (N-terminus, blue to C-Terminus, red). The tail-to-tail
arrangement of the dimer is apparent as are the nearly identical backbone
structures
The separate gramicidin A, B, and C buttons allow pairwise comparisons
between all three models. Residue 11 (Phe or Tyr) is labeled when gramicidin
B or C is viewed separately.
References and Links
The gramicidin-membrane structure and its calculated dynamic properties
are described in Crouzy S, Woolf TB, Roux B (1994) "A molecular dynamics
study of gating in dioxolane-linked gramicidin A channels." Biophys
J 67: 1370-1386. PubMed.
The valinomycin structure is described in Neupert-Laves K, & Dobler
M (1975) "The crystal structure of a K+ complex of valinomycin." Helv
Chim Acta 58: 432-442. PubMed.
The valinomycin.mol coordinates were prepared for Minerals & Molecules
Project, a part of The
Virtual Museum of Minerals and Molecules by P. Barak.
The gramicidin A, B, and C structures are described in Townsley, LE,
Tucker, WA, ShamS, HintonJF. (2001) "Structures of Gramicidins A, B, and
C Incorporated Into Sodium Dodecyl Sulfate Micelles." Biochemistry
40: 11676 PubMed.
[1JNO.pdb, 1JO3.pdb, 1JO4.pdb] |
Membrane Channel & Pump Structures Introduction
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