The molecular origin of high DNA-repair efficiency by photolyase

Abstract

The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel Lecture)

“…We have determined the rates of energy transfer, electron transfer, bond breakage,bond forming and electron return, in real time and at picosecond resolution ( Figure 6). [29][30][31][32][33][34][35] The entire catalytic cycle is complete in 1.2 ns,a nd the enzyme repairs T <>Twith aquantum yield of 0.9. [29,31,34] Photolyase is currently one of the best understood enzymes.…”

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

“…With femtosecond temporal resolution and single-residue spatial resolution, the entire evolution of the CPD repair process has been mapped out by probing the dynamics from all initial reactants, to various intermediates, and to the final products. In the past decade, the dynamics and mechanism of CPD repair by class I EcPL have been extensively characterized and a critical cyclic electron-tunneling mechanism was revealed [60–64]. The complete CPD repair photocycles of PLs from different classes have also been dissected recently; a unified repair photocycle with bifurcating electron-transfer pathways through the folded flavin in the conserved active-site structure is unraveled (Fig.…”

“…Mutations at the active site that modulates the active-site reduction potentials and ET reorganization energies always break the dedicated synergy of the optimization for the four elementary reactions in the two competing pairs, and thus leads to lower repair efficiency than the wild-type enzyme. [64]…”

“…For all the PLs studied, we use 2.48 eV for the S 1 ←S 0 transition of LfH − for 500-nm excitation, and assume that the reduction potential of LfH • /LfH − remains at +0.08 V vs. NHE [80] since no significant conformation variation in the active site for Lf is observed from the crystal structures. For the ET between the LfH − and substrate, a similar electron coupling J = 3.0 meV in all the PLs for the forward tunneling, and J = 2.6 meV for all the returning tunneling are used [63, 64, 70]. Due to the ultrafast C5–C5′ bond breakage and the localized electron near the 5′ site [87], we also assume the futile back ET (BET2) has the same J and λ values as FET2.…”

The quantum chemistry of attosecond molecular science

“…The acidic or basic character of a given compound, or its redox properties, is the consequence of how the electronic charge is distributed on different molecular sites over large periods of time. In charge transfer reactions initiated by light, as in photosynthesis, DNA damage and repair, sensory proteins activation or magnetoreception, electrons jump from a molecule to another, or from a particular molecular site to another. All these facts suggest that observing these electronic processes in real time is the most direct way to understand chemistry and, more importantly, to design strategies to control chemical reactivity .…”