Structural Analysis In Silico

Substructures of WT1 mutants p.Pro455Ser, p.Arg467Trp, p.Cys458Arg, and p.His478Arg were prepared using MOE software12 from the 3-dimensional structure of part of wild-type WT1 (aa. 392–510, including the zinc finger region), which was obtained from PDB (PDB 6B0O chain A). The transferable intermolecular potential with 3 points (TIP3P) water model13 and the AMBER03 force field were used for structural optimization of 500-ps molecular dynamics using GROMACS software,14 as in our previous study.15 Then, these partial structures were input into APBS software for analysis of the electrostatic surface potential of the DNA-binding region, as described previously.16