[gmx-users] ZNO-HSA (Human Serum albumin) Interaction

[Hassan Aaryapour]

Dear Gromacs Users;

I am studying the toxicity effect of ZnO nanoparticle (with a partial
charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on
the Albumin structure by Gromacs. For MD simulation the nanoparticle was
placed at a distance of 1nm of protein, after running pdb2gmx, the
simulation box was solvated by TIP3P waters. The net charge of protein in
physiological condition is -14 that was neutralized by adding sodium and
chloride ions to box. Then, energy minimization, NVT and NPT were done.
>From the beginning of md simulation, the protein structure began to be
unfolded slowly before binding nanoparticle to it and after binding, the
protein structure changed dramatically. I cannot consider the charge of ZnO
as zero like silver or gold nanoparticles. So, I am confused that whether
the study method is correct or wrong for this interaction? Do the results
seem logical?

Thanks
Hassan Aryapour