Modeling of Ion and Water Transport in the Biological Nanopore ClyA

Abstract

In recent years, the protein nanopore cytolysin A (ClyA) has become a valuable tool for the detection, characterization and quantification of biomarkers, proteins and nucleic acids at the single-molecule level. Despite this extensive experimental utilization, a comprehensive computational study of ion and water transport through ClyA is currently lacking. Such a study yields a wealth of information on the electrolytic conditions inside the pore and on the scale the electrophoretic forces that drive molecular transport. To this end we have built a computationally efficient continuum model of ClyA which, together with an extended version of Poison-Nernst-Planck-Navier-Stokes (ePNP-NS) equations, faithfully reproduces its ionic conductance over a wide range of salt concentrations. These ePNP-NS equations aim to tackle the shortcomings of the traditional PNP-NS models by self-consistently taking into account the influence of both the ionic strength and the nanoscopic scale of the pore on all relevant electrolyte properties. In this study, we give both a detailed description of our ePNP-NS 1 model and apply it to the ClyA nanopore. This enabled us to gain a deeper insight into the influence of ionic strength and applied voltage on the ionic conductance through ClyA and a plethora of quantities difficult to assess experimentally. The latter includes the cation and anion concentrations inside the pore, the shape of the electrostatic potential landscape and the magnitude of the electro-osmotic flow. Our work shows that continuum models of biological nanopores-if the appropriate corrections are applied-can make both qualitatively and quantitatively meaningful predictions that could be valuable tool to aid in both the design and interpretation of nanopore experiments.

Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores

“…The opposite ion selectivity of PlyAB-E2 and PlyAB-R suggests that the direction of their electro-osmotic flows might also be reversed. To investigate their nanofluidic behavior, we set up a computational model of both pores, in which we solved the extended Poisson−Nernst−Planck and Navier−Stokes (ePNP-NS) equations, 71 a continuum simulation framework geared toward simulating biological nanopores (eqs S2−S15), with the finite element method (COMSOL Multiphysics v5.4). These simulations enabled us to obtain detailed distribution profiles of the ion concentrations inside the pore (Figure 2a− c), the electro-osmotic flow velocity (Figure 2d and e), and the electric field (Figure 2f and g).…”

Nanopores: a versatile tool to study protein dynamics

“…The Maglia lab trapped such single protein complexes for tens of seconds to interrogate their functional dynamics [98]. A positively charged tail was attached to the DHFR to enhance (electro-osmotic with electrophoretic) trapping under negative voltage, and to orient the protein in a preferential direction [95,102]. In this way, tens to hundreds of dihydrofolate to tetrahydrofolate turnovers could be sensed at one DHFR molecule.…”