title: Effective pore radius of the gramicidin channel. Electrostatic energies of ions calculated by a three-dielectric model.
abstract: Electrostatic calculation of the gramicidin channel is performed on the basis of a three-dielectric model in which the peptide backbone of the channel is added as a third dielectric region to the conventional two-dielectric channel model (whose pore radius is often referred to as the effective pore radius reff). A basic principle for calculating electrostatic fields in three-dielectric models is introduced. It is shown that the gramicidin channel has no unique value of reff. The reff with respect to the "self-image energy" (i.e., the image energy in the presence of a single ion) is 2.6-2.7 A, slightly depending upon the position of the ion (the least-square value over the whole length of the pore is 2.6 A). In contrast, the reff with respect to the electric potential due to an ion (and hence the reff with respect to the interaction energy between two ions) is dependent upon the distance s of separation; it ranges from 2.6 to greater than 5 A, increasing with an increase in s. However, for the purpose of rough estimation, the reff with respect to the self-image energy can also be used in calculating the electric potential and the interaction energy, because the error introduced by this approximation is an overestimation of the order of 30% at most. It is also shown that the apparent dielectric constant for the interaction between two charges depends markedly upon the positions of the charges. In the course of this study, the dielectric constant and polarizability of the peptide backbone in the beta-sheet structure is estimated to be 10 and 8.22 A3.
authors.affiliation: Department of Physiology, Tohoku University School of Medicine, Sendai, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Monoi
mesh_terms: D004563:Electrochemistry / Q000379:methods; D006096:Gramicidin; D007473:Ion Channels; D008433:Mathematics; D008962:Models, Theoretical; D011487:Protein Conformation
chemical_list: D007473:Ion Channels; D006096:Gramicidin