(5as) Simulations of Biopolymer Translocation through Nanopores: Insight into Structure and Macromolecular Complexation

The bacterial toxin alpha-hemolysin (AHL) forms a mushroom shaped nanopore (2 nm internal diameter at its stem) across a phospholipid membrane, and has been used as a model system for investigating translocation of charged polymers, such as single stranded DNA and RNA, through nanometer sized pores. In translocation experiments a polymer is driven through the AHL pore by applying a potential difference across the phospholipid membrane. As the polymer passes through the nanopore, it blocks the flow of ions inside the nanopore, which is registered as a drop in the ionic current across the pore. The extent of blocked current and its duration are unique signatures of the size and the chemical identity of the chain. These parameters can also provide information regarding chain conformation outside the pore and its complexation with other species which may be present in the system. We use a combination of molecular simulation and numerical techniques, namely Langevin dynamics to study polymer translocation and numerical solution of Poisson-Nernst-Planck equations for calculating ionic current, to understand the process of polymer translocation through a nanopore. We use a coarse-grained united atom description for the polymer, which allows us to explore large length scales and capture experimentally relevant time scales. The structure of the AHL pore used in the simulation is coarse-grained from its atomistic three-dimensional structure. We apply this set of simulation tools to investigate the role of secondary structure in polymer translocation through nanopores. Specifically, we study how secondary structures, such as helices and hairpin loops, influence distributions of translocation times and blocked currents. The ability to discriminate between secondary structures is important in achieving single base recognition in genomics. Understanding the role of secondary structures is also relevant to several fundamental processes in biology which involve macromolecular transport through nanopores.