ABSTRACT

This study was carried out to investigate the higher Hb affinity for CO over O2, on the basis of the perpendicularity of the bond angle the Fe-CO axis makes with the heme plane by the method of molecular dynamics and simulation using Avogadro software. HbCO and HbO2 3D molecule with PDB code of 6BWU and 1HHO were used respectively. The molecular dynamic simulation was carried out using Avogadro software 1.2.0 on HP DESKTOP-5AQ9GFH. The molecules were imported into the Avogadro workspace, visualized and simulated. The simulation was carried out by the geometric optimization of the molecules using UFF(Universal Force Field), a step per update of two(2) and algorithm levels of steepest descent and conjugate gradients. In HbCO, the binding with the heme iron, Fe is in the Fe2+-CO orientation, as a result, the C-Fe-N angles were taken to ascertain the perpendicularity with the heme plane. The bond angles of the Fe-O2 axis in HbO2 were also taken. In HbO2, the bond angles of the Fe-O2 axis showed a bent end-on geometry about the O1 atom, which resulted in the bending away of the O2 atom from linearity with the other constituent atoms making up the Fe-O2 axis. The result from the bond angles of C-Fe-N showed the perpendicularity of the Fe-CO axis on the heme plane with small deviations of .