Biomimetic design of a brush-like nanopore: simulation studies.
Pongprayoon P., Beckstein O., Sansom MS.
Combining a high degree of selectivity and nanoscale dimensions, biological pores are attractive potential components for nanotechnology devices and applications. Biomimetic design will facilitate production of stable synthetic nanopores with defined functionality. Bacterial porins offer a good source of possible templates for such nanopores as they form stable, selective pores in lipid bilayers. Molecular dynamics simulations have been used to design simple model nanopores with permeation free energy profiles that can be made to mimic a template protein, the OprP porin, which forms pores selective for anions. In particular, we explored the effects of varying the nature of pore-lining groups on free energy profiles for phosphate and chloride ions along the pore axis and the total charge of the permeation pathway of the pore. Cationic side chains lining the model nanopore are required to model the local detail of the OprP permeation landscape, whereas the total charge contributes to its magnitude. These studies indicate that a locally accurate biomimetic design has captured the essentials of the structure/function relationship of the parent protein.