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Molecular dynamics of DNA translocation by FtsK.

Publication ,  Journal Article
Pajak, J; Arya, G
Published in: Nucleic acids research
August 2022

The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA translocation in FtsK by performing long timescale simulations of its hexameric assembly and individual subunits. From these simulations we predict signaling pathways that connect the ATPase active site to DNA-gripping residues, which allows the motor to coordinate its translocation activity with its ATPase activity. Additionally, we utilize well-tempered metadynamics simulations to compute free-energy landscapes that elucidate the extended-to-compact transition involved in force generation. We show that nucleotide binding promotes a compact conformation of a motor subunit, whereas the apo subunit is flexible. Together, our results support a mechanism whereby each ATP-bound subunit of the motor conforms to the helical pitch of DNA, and ATP hydrolysis/product release causes a subunit to lose grip of DNA. By ordinally engaging and disengaging with DNA, the FtsK motor unidirectionally translocates DNA.

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Published In

Nucleic acids research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

August 2022

Volume

50

Issue

15

Start / End Page

8459 / 8470

Related Subject Headings

  • Translocation, Genetic
  • Molecular Dynamics Simulation
  • Humans
  • Developmental Biology
  • DNA
  • Cell Division
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • 41 Environmental sciences
  • 34 Chemical sciences
 

Citation

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Pajak, J., & Arya, G. (2022). Molecular dynamics of DNA translocation by FtsK. Nucleic Acids Research, 50(15), 8459–8470. https://doi.org/10.1093/nar/gkac668
Pajak, Joshua, and Gaurav Arya. “Molecular dynamics of DNA translocation by FtsK.Nucleic Acids Research 50, no. 15 (August 2022): 8459–70. https://doi.org/10.1093/nar/gkac668.
Pajak J, Arya G. Molecular dynamics of DNA translocation by FtsK. Nucleic acids research. 2022 Aug;50(15):8459–70.
Pajak, Joshua, and Gaurav Arya. “Molecular dynamics of DNA translocation by FtsK.Nucleic Acids Research, vol. 50, no. 15, Aug. 2022, pp. 8459–70. Epmc, doi:10.1093/nar/gkac668.
Pajak J, Arya G. Molecular dynamics of DNA translocation by FtsK. Nucleic acids research. 2022 Aug;50(15):8459–8470.
Journal cover image

Published In

Nucleic acids research

DOI

EISSN

1362-4962

ISSN

0305-1048

Publication Date

August 2022

Volume

50

Issue

15

Start / End Page

8459 / 8470

Related Subject Headings

  • Translocation, Genetic
  • Molecular Dynamics Simulation
  • Humans
  • Developmental Biology
  • DNA
  • Cell Division
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • 41 Environmental sciences
  • 34 Chemical sciences