The determination of pepsin dimensions at different pH values: A simulation study

The pH dependence of the size of the enzyme pepsin is investigated in aqueous medium via molecular dynamics simulations at ambient conditions. The pH value may influence both the pepsin charge and its structure at microscopic level. This investigation allows to understand the volume compatibility between pepsin and the pores size in mesoporous materials, which is a relevant issue for the production of hybrid bio-inorganic composite where a bio catalyst is encapsulated in porous inorganic matrices. The results obtained by means of simulation techniques indicate that the average pepsin dimensions along its inertia axes are consistent with the microporous silica SBA-15 pore diameter. The present study indicates that, while the total charge of the bio macromolecule varies along with the enzyme residues protonation state, there is no evidence of significant pH-induced protein size modification.