Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

Wen Ma, Kevin D. Whitley, Yann Robert Chemla, Zaida Ann Luthey-Schulten, Klaus Schulten

Research output: Contribution to journalArticle

Abstract

Helicases play key roles in genome maintenance, yet it remains elusive how these enzymes change conformations and how transitions between different conformational states regulate nucleic acid reshaping. Here, we developed a computational technique combining structural bioinformatics approaches and atomic-level free-energy simulations to characterize how the Escherichia coli DNA repair enzyme UvrD changes its conformation at the fork junction to switch its function from unwinding to rezipping DNA. The lowest free-energy path shows that UvrD opens the interface between two domains, allowing the bound ssDNA to escape. The simulation results predict a key metastable ’tilted’ state during ssDNA strand switching. By simulating FRET distributions with fluorophores attached to UvrD, we show that the new state is supported quantitatively by single-molecule measurements. The present study deciphers key elements for the ’hyper-helicase’ behavior of a mutant and provides an effective framework to characterize directly structure-function relationships in molecular machines.

Original languageEnglish (US)
Article numbere34186
JournaleLife
Volume7
DOIs
StatePublished - Apr 17 2018

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DNA Repair Enzymes
DNA Helicases
Computational Biology
Nucleic Acids
Free energy
Conformations
Switches
Maintenance
Genome
Escherichia coli
Fluorophores
DNA
Enzymes
Bioinformatics
Genes
Molecules

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase. / Ma, Wen; Whitley, Kevin D.; Chemla, Yann Robert; Luthey-Schulten, Zaida Ann; Schulten, Klaus.

In: eLife, Vol. 7, e34186, 17.04.2018.

Research output: Contribution to journalArticle

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