Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities

Nucleic Acids Research
Yuma TeraiJunpei Yamamoto

Abstract

(6-4) Photolyases ((6-4)PLs) are flavoenzymes that repair the carcinogenic UV-induced DNA damage, pyrimidine(6-4)pyrimidone photoproducts ((6-4)PPs), in a light-dependent manner. Although the reaction mechanism of DNA photorepair by (6-4)PLs has been intensively investigated, the molecular mechanism of the lesion recognition remains obscure. We show that a well-conserved arginine residue in Xenopus laevis (6-4)PL (Xl64) participates in DNA binding, through Coulomb and CH-π interactions. Fragment molecular orbital calculations estimated attractive interaction energies of -80-100 kcal mol-1 for the Coulomb interaction and -6 kcal mol-1 for the CH-π interaction, and the loss of either of them significantly reduced the affinity for (6-4)PP-containing oligonucleotides, as well as the quantum yield of DNA photorepair. From experimental and theoretical observations, we formulated a DNA binding model of (6-4)PLs. Based on the binding model, we mutated this Arg in Xl64 to His, which is well conserved among the animal cryptochromes (CRYs), and found that the CRY-type mutant exhibited reduced affinity for the (6-4)PP-containing oligonucleotides, implying the possible molecular origin of the functional diversity of the photolyase/cryptochr...Continue Reading

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Citations

Jul 23, 2018·Nucleic Acids Research·Sophie FranzLars-Oliver Essen
Sep 3, 2019·Physical Chemistry Chemical Physics : PCCP·Antonio Frontera, Antonio Bauzá
Nov 17, 2020·Biophysics and Physicobiology·Ryuma SatoMakoto Taiji
May 24, 2019·The Journal of Physical Chemistry. B·Yuhei HosokawaJunpei Yamamoto

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Methods Mentioned

BETA
PCR
electrophoresis
Fluorescence

Software Mentioned

tLeap
GAMESS
PIEDA
AMBER - EE
AMBER
ONIOM
Gaussian09
MultiGauge
Winmostar
PL

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