[Computer modeling of the three-dimensional structure of full-length cytochrome B5]

Abstract

The computer-aided reconstruction of 3D structure of full-length cytochrome b5 was done. Software Sybyl 6.4 from Tripos running on workstation Silicon Graphics Indigo2 (R4400, XZ) was used. The reconstruction was carried out by computer modelling of membrane part of cytochrom b5 with subsequent linking with known structure of water-soluble b5 part (fragment 5-91 of amino acid residues-file 3B5C in the protein data bank, PDB). The obtained structure of full-length cytochrome b5 was refined in the mixture of polar and nonpolar solvents by molecular dynamics simulation and deterministic minimization. Molecular dynamics simulation was performed in periodic box of binary system of solvents with a step of 1 fs during 550 ps at constant number of particles, pressure and temperature. The balance of system was achieved after 400 ps. With period in 5 ps the potential energy was minimized without molecular dynamics interruption. As a result 100 conformations of full-length cytochrome b5 were obtained. Distribution of potential energy was from -2.7 x 10(4) to -4.2 x 10(4) kcal/mol. Conformation of cytochrome b5 with minimal value of potential energy was accepted as the final. Analysis of lipophilic surface of obtained model have shown that membrane bounded part is more hydrophobic and forms a loop structure. This model corresponds to some known experimental data about cytochrome b5 structure.