STRUCTURE OF VALINOMYCIN AND ITS COMPLEXES
Jindřich Hašek 1*, Emanuel Makrlík2, Michal Dušek3, Ivana Císařová 4,
Jan Dohnálek1, Jarmila Dušková1, Tereza Skálová1
1 Institute of Macromolecular
Chemistry, AS CR, Heyrovského nám.2, 162 06 Praha 6,
2 Faculty of Applied Sciences, University of West Bohemia, Husova 11, 30614 Plzeň,,
3 Physical Institute, Academy of Sciences of CR, Cukrovarnická 2, 16000 Praha 6,
4 Institute of inorganic chemistry, Charles University, Hlavova 2030, 128 40 Praha 2.
Valinomycin is a cyclic dodecadepsipeptide composed of twelve a-aminoacid-like residues, all with hydrophobic side chains. More accurately, it can be described as a trimer Ì® [Val – ODVal –DVal - OAla]3 ¬É, where Val is for L-valine, ODVal for deamino-oxy-D-valine, DVal for D-valine and OAla for deamino-oxy-L-alanine. The chemical composition of valinomycin gives it a principle importance in any living organisms because of its role in selective transport of ions across the cell membranes. The Cambridge structure database of organic and organometalic compounds  contains 20 records, 16 of them representing independent observations. All structures deposited in the CCDC except a single one have very low accuracy of structure determination (R-factors are in the interval 9 % – 19 %). The only exception is a complex of valinomycin with a single water molecule and 1,5-dioxan determined by Lang in 1992 ( R=3.8 %). Surprisingly, none of the structures solved by now was with higher water content. Therefore, we determined two structures with different numbers of water molecules per single molecule of valinomycin.
Newly determined structures
In the new structures, a single valinomycin molecule is complexed with two waters (R = 4.2 %) or with 12 water molecules (R = 8.5 %). The results show that the macrocycle of a single valinomycin folds into a shape similar to the seam on a tennis ball. In this way, it forms a large barrel with hydrophobic external surface (formed by side chains of all monomers) and a large hydrophilic cavity inside the barrel with 12 carbonyls and 6 ether oxygens. In case that hydrophilic cavity has small volume, the cavity is more spherical. In the case of higher content of water, the cavity swells and takes an elongated ellipsoidal shape.
The solved structures show clearly that water molecules concentrate inside the valinomycin cavity. In excess of water, two valinomycins form a dimer of the elongated barrel shape filled by at least 24 water molecules. The external surface of the barrel formed by all side chains of both valinomycin molecules is highly hydrophobic and therefore the complexes stack side by side to form layers similar to a membrane. In other words, the whole system tends to form bilayers of valinomycin dimers. It is in agreement with the fact that the measured single crystal with higher water content is formed by parallel stacking of these bilayers. Figure 1 shows a perpendicular view on a single layer of the above mentioned bilayer.
Figure 1. A single layer of valinomycin molecules in the valinomycin-HCl-water complex with stoichiometry 1:1:12. In the central valinomycin ring, all water molecules in the tunnel are shown. In the side rings, only the water molecules directly bound to the valinomycin molecule are present. Stability of the structure is strengthened by chloride ions (small balls) fixed in all cases to three amine groups of three neighbor valinomycin molecules.
Valinomycin in the lipid membrane
The pattern formed in the high-water-content structure is an excellent model for valinomycin action in the cell membrane. Some of single valinomycin molecules sit on the surface of cell membrane forming thus small cavities and decreasing locally the thickness of membrane. Other valinomycin molecules form dimers inserted inside the membrane similarly to those described in the crystal structure. The valinomycin dimers (barrels with hydrophobic external surface and filled by solution) form water-filled tunnels across the membrane allowing the passive transport of ions or small molecules with good affinity for the cavity interior offering 24 carbonyls and 12 ether oxygens for hydrogen bonding on its surface.
These observations explain the mechanism of the valinomycin activity in the selective transport of ions and small hydrophilic molecules across the cell membrane. The study brings better understanding of the processes taking place in living organisms.
The work was supported by projects GA ČR 305/07/1073 and GA AV ČR IAA500500701.
1. F.H. Allen, Acta Crystallogr., B58, (2002), 380-388.