Low energy protein modes as indicators for pH dependent structural changes of iron-sulfur proteins

Using Nuclear Inelastic Scattering (NIS) we want to explore whether NIS-active protein modes can be used to investigate pH-dependent protonation effects. For that purpose we suggest to perform NIS experiments on the protein Apd1 which has an unusual 2Fe-2S cluster bound to the protein matrix via two cysteines and two histidines. Using quantum chemical density functional theory calculations coupled with molecular mechanics (QM/MM) the vibrational modes of the whole Apd1 protein will be simulated yielding pH dependent structural models.