Masashi Iwayama

A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules

A simple calculation method to evaluate the redox potential of molecules by using a hybrid-type calculation with molecular dynamics (MD) and density functional theory calculations is presented with discussions of the difference of the redox potential. In our hybrid method, the standard Gibbs free energy of the molecules, acetone and 3-pentanone, in the redox reaction, is estimated from the average of ionisation free energy and the excess chemical potentials of the reduced and oxidised molecules according to the Born–Haber cycle by sampled configurations from the MD simulation. The difference of the redox potentials between the two molecules is in agreement with the experimental data within the standard deviation.

Theoretical model for assessing properties of local structures in metalloprotein

For model structures containing two aromatic rings such as the indole of Trp5 and the imidazole of His64 in human carbonic anhydrase (hCAII), the location and orientation of the rings with regard to each other contribute to the magnitude of the entire interaction energy. Here the energetic contribution of the indole ring of Trp5 on the imidazole ring of the “out” conformation of His64 were calculated to compare with that of the alternative “in” conformation of His64 by using the MP2/6-311++G(d,p)//B3LYP/6-31G(d,p) method. We suggest that 1) Trp5 and the “out” conformation of His64 are predicted to form a stack of planar parallel rings via π-stacking interaction and 2) the energy is 1.73-1.83 kcal/mol to stabilize the “out” conformation, compared with the “in” conformation.

Molecular Dynamics Study of Glutathione S-Transferase: Structure and Binding Character of Glutathione

Molecular dynamics simulations of the glutathione S-transferase (GST) dimer in the absence or the presence of glutathione were carried out in order to investigate the binding effects of glutathione on the dynamical structure and thermal stability of the GST dimer in water. Enhanced local fluctuations in the GST dimer backbone were observed in the absence of glutathione. The hydrogen bonds formed between glutathione and the GST dimer were changed in the absence of glutathione, and these hydrogen bonds mediate the binding between the subunits of the GST dimer. The free energy analysis showed that the hydrogen bonds between glutathione and the GST dimer largely contribute to the binding energy of glutathione and the thermal stability of the glutathione-GST dimer.