Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study

Abstract

Abstract:Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise).

Accurate modeling of a biological nanopore with an extended continuum framework

“…Because these properties can only emerge from the collective behavior or interactions between small groups of atoms (i.e., the mean-field approximation), great care must be taken when using them to compute fluxes and fields at the nanoscale, where computational elements may only contain a few molecules. 65,66 Nevertheless, the PNP equations have been used extensively for the simulation of ion channels, 53,67,68 biological nanopores 58,63,69,70 and their solid-state counterparts 39,[71][72][73] -often with excellent qualitative, if not quantitative results. 3,4,6 To remedy the shortcomings of PNP and NS theory, a number of modifications have been proposed over the years.…”

Scaling Behavior of Ionic Transport in Membrane Nanochannels

“…To understand the origin of the dominant contributions to conductance scaling we use a three-dimensional Poisson–Nernst–Planck (PNP-3D) model implemented as described in detail elsewhere. , We use the 3D atomic structure of gA and OmpF available at the Protein Data Bank (codes 1JNO and 2OMF, respectively). Note that no structure is available for Ala or CoV-E proteolipidic pores.…”

Kulturimmobilien – Erfolgsfaktor Projektmanagement

“…For the case of electrostatics, the review by Collins provides an exhaustive set of reasons why continuum methods are unrealistic at the nanoscale, with the lack of explicit ion-water interactions being the main culprit [183]. Nevertheless, the mean-field approximation has been used extensively, and successfully, for the (qualitative) simulation of ion channels [287,288,289], BNPs [290,249,291,292] and SSNPs [293,294,295,194], providing meaningful physical insights at a fraction of the computational cost of a MD simulation.…”

“…Because these properties can only emerge from the collective behavior or interactions between small groups of atoms (i.e., the mean-field approximation), great care must be taken when using them to compute fluxes and fields at the nanoscale, where computational elements may only contain a few molecules [308,183]. Nevertheless, even though the PNP equations have been used extensively for the qualitative simulation of ion channels [287,288,289], biological nanopores [290,249,291,292] and their solid-state counterparts [293,294,295,194], the extent to which they are quantitatively accurate is often challenged [308,183,315,406,408]. To remedy the shortcomings of PNP and NS theory, a number of modifications have been proposed over the years.…”