title: Continuum and atomistic modeling of ion partitioning into a peptide nanotube.
abstract: Continuum and atomistic descriptions of the partitioning of ions into a self-assembled (D,L)-octapeptide nanotube, cyclo[-(L-Ala-D-Ala)(4)-], are presented. Perturbation free energy calculations, including Ewald electrostatics, are used to estimate the electrostatic component of the excess free energy of charging Li(+), Na(+), Rb(+), and Cl(minus sign) ions inside the nanotube. The radial density and orientational distribution of water around the ion is calculated for the ion at two different positions inside the tube; it is seen that the calculated distributions are sensitive to the location of the ions. Two different continuum electrostatic models are formulated to describe the ion solvation inside the nanotube. When enhanced orientational structuring of water dipoles is evidenced, explicitly including the first solvation shell as part of the low dielectric nanotube environment provides good agreement with molecular dynamics simulations. When water orientational structuring is as in the reference bulk solvent, we find that treating the first shell water explicitly or as a high dielectric continuum leads to similar results. These results are discussed, and their importance for continuum electrostatic modeling of ion channels are highlighted.
authors.affiliation: Department of Molecular Biology, TPC-15, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: D
authors.initials: D
authors.lastname: Asthagiri
authors.forename: D
authors.initials: D
authors.lastname: Bashford
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D002713:Chlorine / Q000737:chemistry; D003198:Computer Simulation; D007473:Ion Channels / Q000502:physiology*; D007477:Ions; D008094:Lithium / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D012413:Rubidium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D007473:Ion Channels; D007477:Ions; D010455:Peptides; D014867:Water; D002713:Chlorine; D008094:Lithium; D012964:Sodium; D012413:Rubidium