PubMed1992
The crystal structure of the membrane-active antibiotic-cyclopeptide gramicidin S complex with urea was determined by the X-ray structure analysis. The gramicidin S molecule possesses an antiparallel beta-structure, its slightly twisted 30-membered cycle has a roughly rectangular form about 4.8 x 13.6 A in size, with the lesser side being formed by the main chain atoms of Phe and Pro residues. The maximum size of the molecule is 22.9 A. A characteristic feature of the molecule is the position of the extended side chains of the Orn residues on one side of the molecular cycle in the form of peculiar "legs--tentacles". One of these legs is "fastened" by the intramolecular H-bond to O atom of the nearer Phe4 residue, the other being free. The distance between the terminal NE atoms of the Orn residues is 5.7 A. The side chains of the Phe and Orn2 residues have trans-orientation, those of the Val, Orn7, Leu residues gauche-orientation. For Val1 and Leu3 side chains statistical disorder of the terminal C atoms is realized. The pyrrolidine rings of the Pro residues adopt Cs-C beta-exo conformation. There are one urea and 20 water molecules per one antibiotic molecule in the structure. The positions of three water molecules are fully occupied, the others with the probability of 0.56-0.20. One of the "water" positions is occupied on 2/3 by water, and on 1/3 by the O atom of the alcohol. There is a complicated system of intra- and intermolecular H-bonds in the structure, with and without the participation of water, alcohol and urea molecules. The gramicidin S molecules, collecting around 3(1) axis according to the left-handed double helix, form the channels whose outside hydrophobic surface is built of the side uncharged radicals, the inside surface being built of the main chain atoms, mainly of the O and N atoms and of the ornithine "tails" with uncharged NE atoms at the termini. The outer diameter of the channel is 29-43 A, inner (without ornithine "tails") is about 12.7 A. At the expense of the change of these "tails" conformation, the inner diameter of the channel filled with water molecules may change from 3.4 up to 6.3 A. Thus, the ions and particles of a rather large size may pass through the channel. The gramicidin channels are discovered and described for the first time. The channels in the crystal structure are close-packed under the hexagonal law.(ABSTRACT TRUNCATED AT 400 WORDS)