Kinetic Master Equation Modeling of an Artificial Protein Pump

Abstract

Biological ion channels and pumps have inspired many efforts to generate artificial counterparts due to their fundamental importance and practical applications. Recent work by Hinds et al. (Adv. Funct. Mater. 2014, 24, 4317–4323) demonstrated a selective protein pump based on an artificial nanopore in which the pump cycles are based on selective binding and release of His-tagged GFP protein ions to a NTA–Ni2+ transition metal complex. In this work, a kinetic master equation method is presented to model this pump and to establish the origin of the variation of selectivity with concentration of imidazole that is involved in the release mechanism. A two-site model with multiple species of proteins is used to mimic the pump mechanism under nonequilibrium conditions. Numerical simulation qualitatively reproduces the experimental selectivity, and uncovers essential ingredients of the pump mechanism. In addition, the binding mechanism between His-tags and NTA–Ni2+ is investigated using molecular dynamics simulat...