Characterization and nanoparticle synthesis of peroxidase by computational and experimental methods

Nano protein structures can be formed by the intrinsic ability of molecular self-assembly or via intermediates which improve their assembly. Hydrophobicity is the most important factor among the other intrinsic self-assembly factors and the other intermediates such as glutaraldehyde may lead to protein-assembly and nanoparticles formation. In this study, Aggrescan 3D software was employed to investigate protein self-assembly properties. Peroxidase enzyme was selected to form protein nanoparticle, and glutaraldehyde changed it to a nano enzyme.FESEM and DLS analysis represented that the average size of nano enzyme is about 500 nanometers. Comparing biochemical properties of peroxidase enzyme before and after changing into nano, showed that the activity of nano enzyme at 20°C, pH7 has decreased as compared to the monomeric enzyme. Based on homology, the PDB structure of two peroxidase enzyme was identified. Then, the connection between glutaraldehyde and two peroxidase enzymes was detected. Enzyme residues with hydrogen binding connections to glutaraldehyde were also detected by using LigPlot software and the residues in active side of enzyme were determined by COACH server. Glutaraldehyde is connected to residues in active siteof the enzyme. Molecular dynamic Simulation was performed in the time duration of 5 nanoseconds and 30°C and it showed that monomer enzyme and nano enzyme are both stable in this time duration and temperature.