Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

Controlling molecular transport through nanopores.

Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse t...

SDS-assisted protein transport through solid-state nanopores.

Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodi...

Simulations of DNA translocation through nanopores

Long-time scale fluctuations of human prion protein determined by restrained MD simulations.

Cellular prion protein (PrP(C)) has the ability to trigger transmissible lethal diseases after in vivo maturation into a toxic amyloidogenic misfolded form (PrP(Sc)). Here, we use hydrogen exchange protection factors in restrained molecular dynamics simulations to characterize long-time scale fluctuations in human PrP(C). We find that the regions of residues 138-141 and 183-192 form new β-stran...

Analysis of electrolyte transport through charged nanopores.

We revisit the classical problem of flow of electrolyte solutions through charged capillary nanopores or nanotubes as described by the capillary pore model (also called "space charge" theory). This theory assumes very long and thin pores and uses a one-dimensional flux-force formalism which relates fluxes (electrical current, salt flux, and fluid velocity) and driving forces (difference in elec...