The University of Southampton
University of Southampton Institutional Repository

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with ?-hemolysin

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with ?-hemolysin
Free-energy calculations reveal the subtle differences in the interactions of DNA bases with ?-hemolysin
Next generation DNA sequencing methods that utilize protein nanopores have the potential to revolutionize this area of biotechnology. While the technique is underpinned by simple physics, the wild-type protein pores do not have all of the desired properties for efficient and accurate DNA sequencing. Much of the research efforts have focused on protein nanopores, such as ?-hemolysin from Staphylococcus aureus. However, the speed of DNA translocation has historically been an issue, hampered in part by incomplete knowledge of the energetics of translocation. Here we have utilized atomistic molecular dynamics simulations of nucleotide fragments in order to calculate the potential of mean force (PMF) through ?-hemolysin. Our results reveal specific regions within the pore that play a key role in the interaction with DNA. In particular, charged residues such as D127 and K131 provide stabilizing interactions with the anionic DNA and therefore are likely to reduce the speed of translocation. These regions provide rational targets for pore optimization. Furthermore, we show that the energetic contributions to the protein–DNA interactions are a complex combination of electrostatics and short-range interactions, often mediated by water molecules.
1549-9618
810-816
Manara, Richard M. A.
8b7f5871-b13c-4e5a-a4e8-435964a05315
Guy, Andrew T.
611827bb-86cc-4ff6-a33a-8daefe2e47c3
Wallace, E. Jayne
d1261a27-c118-40b6-b425-f761fdd3cb32
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Manara, Richard M. A.
8b7f5871-b13c-4e5a-a4e8-435964a05315
Guy, Andrew T.
611827bb-86cc-4ff6-a33a-8daefe2e47c3
Wallace, E. Jayne
d1261a27-c118-40b6-b425-f761fdd3cb32
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

Manara, Richard M. A., Guy, Andrew T., Wallace, E. Jayne and Khalid, Syma (2015) Free-energy calculations reveal the subtle differences in the interactions of DNA bases with ?-hemolysin. Journal of Chemical Theory and Computation, 11 (2), 810-816. (doi:10.1021/ct501081h).

Record type: Article

Abstract

Next generation DNA sequencing methods that utilize protein nanopores have the potential to revolutionize this area of biotechnology. While the technique is underpinned by simple physics, the wild-type protein pores do not have all of the desired properties for efficient and accurate DNA sequencing. Much of the research efforts have focused on protein nanopores, such as ?-hemolysin from Staphylococcus aureus. However, the speed of DNA translocation has historically been an issue, hampered in part by incomplete knowledge of the energetics of translocation. Here we have utilized atomistic molecular dynamics simulations of nucleotide fragments in order to calculate the potential of mean force (PMF) through ?-hemolysin. Our results reveal specific regions within the pore that play a key role in the interaction with DNA. In particular, charged residues such as D127 and K131 provide stabilizing interactions with the anionic DNA and therefore are likely to reduce the speed of translocation. These regions provide rational targets for pore optimization. Furthermore, we show that the energetic contributions to the protein–DNA interactions are a complex combination of electrostatics and short-range interactions, often mediated by water molecules.

Full text not available from this repository.

More information

Published date: 13 January 2015
Organisations: Chemistry, Faculty of Natural and Environmental Sciences, Computational Systems Chemistry

Identifiers

Local EPrints ID: 374226
URI: http://eprints.soton.ac.uk/id/eprint/374226
ISSN: 1549-9618
PURE UUID: f4edf061-9167-413d-9dcd-afbb90e0847b
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 10 Feb 2015 12:51
Last modified: 15 Sep 2021 01:53

Export record

Altmetrics

Contributors

Author: Richard M. A. Manara
Author: Andrew T. Guy
Author: E. Jayne Wallace
Author: Syma Khalid ORCID iD

University divisions

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

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×