Journal of Molecular Modeling

, Volume 14, Issue 3, pp 201–213

Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase

Authors

  • Magne Olufsen
    • The Norwegian Structural Biology Centre, Department of ChemistryUniversity of Tromsø
  • Arne O. Smalås
    • The Norwegian Structural Biology Centre, Department of ChemistryUniversity of Tromsø
    • The Norwegian Structural Biology Centre, Department of ChemistryUniversity of Tromsø
Original Paper

DOI: 10.1007/s00894-007-0261-0

Cite this article as:
Olufsen, M., Smalås, A.O. & Brandsdal, B.O. J Mol Model (2008) 14: 201. doi:10.1007/s00894-007-0261-0

Abstract

Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased kcat and reduced Km relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (Km) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation.

https://static-content.springer.com/image/art%3A10.1007%2Fs00894-007-0261-0/MediaObjects/894_2007_261_Figa_HTML.jpg
Figure

Electrostatic isosurfaces of cod uracil DNA glycosylase in complex with double stranded DNA

Keywords

Continuum electrostaticsFree energy calculationsMolecular simulationsProtein-DNA bindingUracil DNA glycosylase

Copyright information

© Springer-Verlag 2007