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Updated: May 20, 2026
CD Spectroscopy to Study DNA-Protein Interactions
Published on: February 10, 2022
Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades
Swati Bhattacharya1, Ian M Derrington, Mikhail Pavlenok
1Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, USA.
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.
Insights
Modifying the Mycobacteria smegmatis porin A (MspA) protein nanopore with arginine mutations significantly slows DNA translocation. This allows for clearer nucleotide sensing, crucial for advancing nanopore sequencing technology.
Area of Science:
- Biophysics
- Nanotechnology
- Genomics
Background:
- The Mycobacteria smegmatis porin A (MspA) protein nanopore shows potential for DNA sequencing by sensing individual nucleotides.
- High DNA translocation velocity through nanopores currently hinders accurate nucleotide signal detection against noise.
Purpose of the Study:
- To investigate the impact of positively charged residues on DNA translocation rate and ionic current blockades in the MspA nanopore.
- To assess the feasibility of slowing DNA translocation for improved nucleotide discrimination.
Main Methods:
- Extensive all-atom molecular dynamics simulations (~100 μs total).
- Analysis of MspA nanopore behavior with several arginine mutations.
- Comparison with engineering efforts on the α-hemolysin nanopore.
Main Results:
- Arginine mutations reduced DNA translocation speed by approximately 10-30 fold.
- Nucleotide-induced current blockages were preserved despite reduced translocation speed.
- Nanopore geometry significantly influences ionic current blockades in mutant nanopores, differing from other nanopore studies.
Conclusions:
- Positively charged residue mutations in MspA can effectively reduce DNA translocation velocity.
- This modification holds promise for enhancing the signal-to-noise ratio in nanopore DNA sequencing.
- Nanopore structure plays a critical role in the efficacy of mutations for signal detection.
