title: Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence.
abstract: The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.
authors: Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA.
authors: Swati
authors: S
authors: Bhattacharya
authors: Ian M
authors: IM
authors: Derrington
authors: Mikhail
authors: M
authors: Pavlenok
authors: Michael
authors: M
authors: Niederweis
authors: Jens H
authors: JH
authors: Gundlach
authors: Aleksei
authors: A
authors: Aksimentiev
mesh_terms: D001120:Arginine / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods*; D003198:Computer Simulation; D003217:Conductometry / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004553:Electric Conductivity; D015640:Ion Channel Gating; D008956:Models, Chemical; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D018272:Porins / Q000737:chemistry* / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014178:Translocation, Genetic / Q000235:genetics
chemical_list: D018272:Porins; C121838:mspA protein, Mycobacterium smegmatis; D004247:DNA; D001120:Arginine