DNA sequencing with MspA: molecular dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants
DNA sequencing with MspA: molecular dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants
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.
1-7
Manara, Richard M.A.
c66437d0-5c4b-4f42-802a-1fd105f8f889
Wallace, E. Jayne
d1261a27-c118-40b6-b425-f761fdd3cb32
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
10 August 2015
Manara, Richard M.A.
c66437d0-5c4b-4f42-802a-1fd105f8f889
Wallace, E. Jayne
d1261a27-c118-40b6-b425-f761fdd3cb32
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Manara, Richard M.A., Wallace, E. Jayne and Khalid, Syma
(2015)
DNA sequencing with MspA: molecular dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants.
Scientific Reports, 5 (12783), .
(doi:10.1038/srep12783).
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.
Text
srep12783.pdf
- Version of Record
More information
Accepted/In Press date: 30 June 2015
Published date: 10 August 2015
Organisations:
Computational Systems Chemistry
Identifiers
Local EPrints ID: 402193
URI: http://eprints.soton.ac.uk/id/eprint/402193
PURE UUID: ed9010e1-e69d-40cf-b3f9-4274ec18f961
Catalogue record
Date deposited: 03 Nov 2016 14:10
Last modified: 15 Mar 2024 03:29
Export record
Altmetrics
Contributors
Author:
Richard M.A. Manara
Author:
E. Jayne Wallace
Author:
Syma Khalid
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics