Krishtalik L I, Kuznetsov A M, Mertz E L
A.N. Frumkin Institute of Electrochemistry, Russian Academy of Sciences, Moscow.
Proteins. 1997 Jun;28(2):174-82.
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.
在蛋白质内部电荷形成（或转移）能量的半连续处理中，能量不可避免地存在两个组成部分：离子与蛋白质内部预先存在的电场的相互作用能，以及新形成的电荷对介质极化产生的能量。预先存在的电场是由固定在特定结构中的蛋白质原子的电荷（部分或全部）建立的。该电场的计算仅涉及蛋白质的电子极化（光学介电常数ε(o)），因为重原子位移引起的极化已由其平衡坐标考虑在内。同时，由于水分子位置不固定，水相环境应以静态常数ε(sw)来描述。在平衡X射线结构中不存在的新电荷的形成会导致电子和极性原子的位移，即它涉及由蛋白质静态介电常数ε(s)描述的各种介质极化。因此，在总能量的计算中，蛋白质的两个不同介电常数同时起作用。这与广泛使用的算法不同，后者对离子能量的两个组成部分都采用一个有效介电常数。
