Simulations and Modelling of Biomimetic Nanopores

Abstract

Nanopores are fast becoming a major scientific tool in molecular analysis and detection due to their ability to detect polynucleotides, proteins, and small molecules. Previous work has included the manipulation of α-hemolysin into a DNA sequencing pore however further development is needed for the use of a simple, monomeric pore for this purpose.Biomimetic modelling of nanopores allows for a specific function to be built into the model based on the replication and analysis of existing selectivity present in proteins.An initial analysis of known porin structures using computational techniques (pore radius profiles and electrostatic calculations) has identified potential structures for manipulation. Steered Molecular Dynamics simulations on a select number of membrane proteins have given insight into possible residue motifs of interest. With this, “simple protein” pores have been made with varying number of beta strands based on models of existing barrel proteins. Motifs have been modelled for exploration via MD simulations.