Vb. Luzhkov et Nf. Surkov, PENTAGONAL MODEL OF MEMBRANE CHANNEL OF NA,K-ATPASE - COMPUTER-SIMULATIONS OF STRUCTURE AND ELECTROSTATIC PROPERTIES, JOURNAL OF MOLECULAR MODELING, 4(2), 1998, pp. 61-72
Computational modeling of the membrane channel of a sodium pump (Na,K-
ATPase) is performed and the role of selected amino acids in binding o
f sodium ions is discussed. The channel is build as a pentameric 10-he
lix bundle. The transmembrane a-helices are determined from hydropathy
calculations. The spatial arrangement of transmembrane a-helices is c
hosen according to the size of a pore, intersegment loops geometry, an
d orientation hydrophobicities of transmembrane segments. The latter p
roperty provides the numerical estimate of the distribution of the hyd
rophobic properties at the helical wheels. The model system involves t
he peptide part and 150 water molecules that soak the pore. The channe
l structure is submitted to geometry minimization and molecular dynami
cs relaxation. The relative stability of the channel states with the n
egatively charged acidic residues belonging to the pore interior decre
ase in the order Glu-334 > Asp-810 > Glu-785 > Asp-814. The estimated
binding energies of 1-3 Na+ ions with the channel with the ionized Glu
-334 and Glu-785 amino acids are in the range allowing the exothermic
complexation.