Computational Study on the Mechanism of the Electron-Transfer-Induced Repair of the (6–4) T–T Photoproduct of DNA by Photolyase: Possibility of a Radical Cation Pathway

Abstract

The oxetane and the non-oxetane mechanisms of the electron-transfer-driven repair of the (64) TT photolesion of DNA by photolyase are examined by density functional theory (B3LYP). We calculated the radical cation pathway in addition to the radical anion and the neutral pathways for both mechanisms in order to assess the possibility of the radical cation pathway, because relatively large energy barriers have been found for the radical anion pathway. As a result, the radical anion pathway showed a large energy barrier in both the oxetane and the non-oxetane mechanisms in agreement with previous calculations. However, it was found that the radical cation pathway of the oxetane mechanism has a realistic low energy barrier. This advantage of the radical cation pathway was ascribed to the position of the radical before the formation of the oxetane and the stability of the oxetane in energy.DNA is highly a reactive substance and is therefore readily influenced and damaged, because the inside of the cell is under chemically active conditions due to ultraviolet rays, chemical substances, and so on. In fact, DNA is routinely damaged and various types of DNA lesions are known.1 Dimerized adjacent thymines, classified as single-strand damage, is also one of such DNA lesions. Although DNA lesions can be an origin of diseases such as cancer, damaged DNA is immediately recovered through a repair process 1 in order to maintain normal genetic information.For example, formed thymine dimer is repaired by photolyase under photoirradiation in plants and bacteria.2 Many people have focused on this repair process as a model and have endeavored to understand its mechanism.3 There exist two forms of thymine dimer, cyclobutane pyrimidine dimer (CPD) and (64) photoproduct (Figure 1), and many examinations of the repair mechanism have been conducted especially for the case of CPD. Photolyase is a flavoprotein that has a chromophore cofactor flavin adenine dinucleotide (FAD) (Figure 1) playing an important role as a coenzyme. A second chromophore cofactor that functions as an antenna harvesting blue light, methenyltetrahydrofolate (MTHF) or , is also present inside the protein. The FAD, which is thought to be fully reduced to FADH ¹ inside the protein, is buried in the vicinity of the active site. On the other hand, the second cofactor is further deeply buried and a little far from FAD.The generally proposed mechanism of the repair reaction of the thymine dimer on the basis of previous findings for CPD is displayed in Figure 2A. The function of the photolyase originates in the blue-light harvest by the second chromophore cofactor. The electronic state of the second cofactor that absorbed the light is enhanced to an excited state and this excitation energy is transmitted to the other cofactor FADH

Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair

“…Furthermore, other mechanisms have been proposed on the basis of experimental and theoretical investigations . In summary, three primary repair pathways have been proposed (Figure b): (1) concerted OH transfer (oxetane-like transition state) via one-photon excitation, ,− (2) formation of a four-membered-ring oxetane intermediate either before or after one- or two-electron transfer, ,, and (3) repair mediated by water formation. , Although other mechanisms have been proposed, including conical intersection of the electronic excited state, , these repair processes are generally thought to occur in the ground state. , Most of the proposed mechanisms also assume that the first step in the reaction is proton transfer from an active site histidine (His) to the pyrimidine N3′ ,,, on the basis of observations that the (6-4)­PHR reaction rate in D 2 O (deuterated His364 in Arabidopsis thaliana, equivalence of His365 in this work) is reduced by 50% …”

Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step

“…It is important to mention that all the previous discussed mechanisms share a similar first step: namely, proton transfer from His365 to N3′ of the substrate. Recently, other oxetane-bypass mechanisms have been proposed, such as repair via a conical intersection of the electronic exited state as well as repair via the formation of a cationic radical (6-4) PP. , …”

“…Recently, other oxetane-bypass mechanisms have been proposed, such as repair via a conical intersection of the electronic exited state as well as repair via the formation of a cationic radical (6-4) PP. 15,18 The active site in (6-4) PHR from Drosophila melanogaster (D. melanogaster) contains two indispensable histidine residues, His365 and His369. 10 A previous experimental study revealed that mutation of either His deactivates the enzyme, thus demonstrating their importance for repair.…”

The crystal structure ofVibrio cholerae(6-4) photolyase reveals interactions with cofactors and a DNA binding region

“…Although reaction mechanism of the CPD photolyases is elucidated, (6-4) PLs not yet fully characterized. There are different mechanisms that are proposed for the (6–4) PL mechanism during DNA repair (7,14,24,25). In fact, mutagenesis studies with Dm (6-4) PL indicated that replacement of His365 to Asn365 result in loss of its DNA repair activity while mutagenesis of His369 into Met369 result in highly reduced activity of Dm (6-4) PL (26).…”