Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. A QM/MM Investigation of Thymine Dimer Repair by DNA Photolyase
 
research article

A QM/MM Investigation of Thymine Dimer Repair by DNA Photolyase

Masson, F.
•
Laino, T.
•
Rothlisberger, U.  
Show more
2009
ChemPhysChem

DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. Herein, we investigate the repair reaction of the thymine dimer by means of hybrid quantum mechanical/molecular mechanical QM/MM) dynamics simulations based on the X-ray structure of on enzyme-DNA complex. In analogy to the self-repair reaction, we find that the splitting mechanism of the cyclobutane ring is asynchronously concerted and is complete within a few picoseconds upon electron uptake. A few distinct processes characterize the dynamics of splitting of the thymine dimer radical anion within the DNA photolyase active site: continuous solvation reordering of the catalytic region, proton transfer from Glu283 to the dimer, as well as tight interactions of the cationic side chains of Arg232 and Arg350 with the thymine dimer. This points to the important role of the active-site hydrogen bond and salt-bridge patterns in stabilizing the thymine dimer anion and slowing down the electron back-transfer process. Comparison of the repair efficiency with respect to the self-repair reaction is also discussed.

  • Details
  • Metrics
Type
research article
DOI
10.1002/cphc.200800624
Web of Science ID

WOS:000263372400015

Author(s)
Masson, F.
Laino, T.
Rothlisberger, U.  
Hutter, J.
Date Issued

2009

Published in
ChemPhysChem
Volume

10

Start page

400

End page

410

Subjects

density functional calculations

•

DNA damage

•

molecular dynamics

•

photolyase

•

thymine dimer

•

Space Gaussian Pseudopotentials

•

Pyrimidine Model Dimers

•

Electron-Transfer

•

Molecular-Dynamics

•

Photoenzymic Repair

•

Photodamaged Dna

•

Cofactor Fadh(-)

•

Self-Repair

•

Duplex Dna

•

Ab-Initio

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBC  
Available on Infoscience
April 11, 2009
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/37077
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés