Molecular Dynamics Study of Triosephosphate Isomerase from Trypanosoma cruzi in Water/Decane Mixtures
mediaposted on 20.03.2008, 00:00 by Norma Díaz-Vergara, Ángel Piñeiro
A comprehensive study of the triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) in water, in decane, and in three water/decane mixtures was performed using molecular dynamics (MD) simulations in a time scale of 40 ns. The structure and dynamics of the enzyme, as well as the solvent molecules' distribution and mobility, were analyzed in detail. In the presence of decane, the amplitudes of the most important internal motions of the enzyme backbone were observed to depend on the solvent concentration: the higher the water concentration, the greater the amplitudes. Contrary to this trend, the amplitudes of the TcTIM motions in pure water were similar to those of the simulation with the lowest water concentration. The enzyme was observed to be almost motionless in pure decane due to a sharp increase of the number of intramolecular hydrogen bonds. This caused a contraction of the enzyme structure accompanied by a loss of secondary structure and of a decrease of the hydrophilic solvent accessible surface. A similar behavior, although to a lesser extent, was observed in the simulation at the lowest water concentration. Our results suggest that the presence of decane molecules located at specific sites of the enzyme might accelerate its internal movements, although a minimum number of water molecules is needed for the protein to keep its structure and dynamics. Altogether, this work provides new insight into protein and water behavior in organic solvents as well as into the dynamics of TcTIM itself.