Soft wall ion channel in continuum representation with application to modeling ion currents in α-hemolysin.

ABSTRACT: A soft repulsion (SR) model of short-range interactions between mobile ions and protein atoms is introduced in the framework of continuum representation of the protein and solvent. The Poisson-Nernst-Plank (PNP) theory of ion transport through biological channels is modified to incorporate this soft wall protein model. Two sets of SR parameters are introduced. The first is parametrized for all essential amino acid residues using all atom molecular dynamic simulations; the second is a truncated Lennard-Jones potential. We have further designed an energy-based algorithm for the determination of the ion accessible volume, which is appropriate for a particular system discretization. The effects of these models of short-range interactions were tested by computing current-voltage characteristics

SUBMITTER: Simakov NA 

PROVIDER: S-EPMC3059120 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature