ArticleScientific reports2015
DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Biological Nanopores: Engineering on Demand.Life (Basel, Switzerland) · 2021Review
- Atomistic level characterisation of ssDNA translocation through theComputational and structural biotechnology journal · 2021Article
- Rapid Nanopore Assay for Carbapenem-ResistantFrontiers in microbiology · 2019Article
- Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates.PLoS computational biology · 2016Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MspA has been identified as a promising candidate protein as a component of a nanopore-based DNA-sequencing device. However the wildtype protein must be engineered to incorporate all of the features desirable for an accurate and efficient device. In the present study we have utilized atomistic molecular dynamics to perform umbrella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation of the four DNA nucleotides through MspA. We show there is an energetic barrier to translocation of individual nucleotides through a mutant that closely resembles the wildtype protein, but not through a mutant engineered for the purpose of sequencing. Crucially we are able to quantify the change in free energy for mutating key residues. Thus providing a quantitative characterisation of the energetic impact of individual amino acid sidechains on nucleotide translocation through the pore of MspA.
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