Electrostatics of proteins: description in terms of two dielectric constants simultaneously.

In the semi-continuum treatment of the energetics of charge formation (or transfer) inside a protein, two components of the energy are inevitably present: the energy of interaction of the ion with the pre-existing intraprotein electric field, and the energy due to polarization of the medium by the newly formed charge. The pre-existing field is set up by charges (partial or full) of the protein atoms fixed in a definite structure. The calculation of this field involves only the electronic polarization (the optical dielectric constant epsilon(o)) of the protein because the polarization due to shifts of heavy atoms has already been accounted for by their equilibrium coordinates. At the same time, the aqueous surroundings should be described by the static constant epsilon(sw), as the positions of water molecules are not fixed. The formation of a new charge, absent in the equilibrium X-ray structure, results in shifts of electrons and polar atoms, i.e., it involves all kinds of medium polarization described by the static dielectric constant of protein epsilon(s). Thus, in calculations of the total energy, two different dielectric constants of the protein are operative simultaneously. This differs from a widely used algorithm employing one effective dielectric constant for both components of the ion's energy.