Rabinovich A.L., Ripatti P.O., Balabaev N.K.1
Institute of Biology, Karelian Scientific Center RAS, 185610, Petrozavodsk, Pushkinskaya str. 11, Russia. Fax: (8142)779810, E-mail: rabinov@shungit.karelia.su
1Institute of Mathematical Problems of Biology RAS, 142292, Pushchino, Moscow Region, Russia. E-mail: balabaev@impb.serpukhov.su
The knowledge of polyunsaturated lipid structure and dynamics is essential for understanding of their functions on an atomic level. Molecular dynamics simulations of lipids 18:0/18:1(n-9)cis, 18:0/18:2(n-6)cis, 18:0/18:3(n-3)cis, 18:0/20:4(n-6)cis, 18:0/22:6(n-3)cis have been carried out. A polar head group was treated as an effective sphere. All the hydrogens, carbons and oxygens of saturated and unsaturated chains were treated explicitly. The intramolecular energy was calculated as the sum of the bond-stretching, the angle-bending and the torsional motion energy, the out-of-plane energy of the double bonds and the carbonyl groups, the energy of nonbonded interactions. The molecular dynamics simulations, 3 nanoseconds for each lipid were carried out at 295 K.
The distribution functions of distances between the atoms of the two hydrocarbon tails (saturated and unsaturated) of each lipid molecule was calculated. The mean atom-atom distances (between correspondent atoms C) increase with increasing of carbon numbers, decrease when unsaturation of C18 chain increases from 1 to 3, and increase when unsaturated chain increases from 18:3 up to 22:6.
This investigation was supported by Russian Foundation for Basic Researches (Grant N 97-04-48247).