Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b5

AbstractIn this article, a description of the statistics and dynamics of cytochrome b5 in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R1 and R1ρ nuclear magnetic relaxation parameters of 15N in the protein backbone have been calculated and compared with experiments. Slight changes in charge density in the heme upon oxidation produces a cascade of changes in charge distributions from heme propionates up to charged residues ∼1.5nm from Fe. These changes in charge distributions modify the molecular surface and the water shell surrounding the protein. The statistical changes upon oxidation can be included in diffusive models that physically explain the upper and lower limits of R1ρ relaxation parameters at high off-resonance fields