Calculation of the Redox Potential of the Protein Azurin and Some Mutants

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Abstract
Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy calculations based on classical molecular-dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials. The precision of the free-energy calculations with the λ coupling-parameter approach is evaluated as function of the number and sequence of λ values, the sampling time and initial conditions. It is found that the precision is critically dependent on the relaxation of hydrogen-bonding networks when changing the atomic-charge distribution due to a change of redox state or pH value. The errors in the free energies range from 1 to 10 kBT, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.