Determinants of Photolyase’s DNA Repair Mechanism in Mesophiles and Extremophiles

Abstract

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.

Ultrafast flavin/tryptophan radical pair kinetics in a magnetically sensitive artificial protein

“…Considerable protein motions that reorganize redox active amino acids or cofactors are known to affect electron-transfer rates in flavoprotein BLUF domains 38 and may also be in play in FAD-dependent DNA photolyase. 39,40 Molecular dynamics simulations predict similar motion in Arabidopsis cryptochrome and photolyase. 39,41 With redox center dimensions of 8 and 5 Å for the riboflavin and tryptophan respectively, rotations about the beta carbons could in principle sample donor-acceptor edge-to-edge distances from van der Waals contact to ~17 Å (Fig.…”

“…39,40 Molecular dynamics simulations predict similar motion in Arabidopsis cryptochrome and photolyase. 39,41 With redox center dimensions of 8 and 5 Å for the riboflavin and tryptophan respectively, rotations about the beta carbons could in principle sample donor-acceptor edge-to-edge distances from van der Waals contact to ~17 Å (Fig. 7).…”

Theoretical insights into the DNA repair function of <i>Arabidopsis thaliana</i> cryptochrome-DASH

“…This result indicates that the T DA value might decrease when the adenine moiety is located away from CPD. Rousseau et al also reported that the contribution of the superexchange mechanism decreased when the adenine moiety was separated from CPD [39]. Therefore, the adenine moiety is very important for the ET reaction.…”

“…Although the outline of the DNA repair mechanism for CPD-PLs has been revealed during the last two decades by theoretical [29][30][31][32][33][34][35][36][37][38][39] and experimental studies [23][24][25][26][40][41][42][43][44][45], there is room for further research on the DNA repair mechanism because the primary process in the DNA repair reaction, i.e., the recognition of UV-induced DNA lesions by PLs, is not clearly…”

DNA Photodamage and Repair: Computational Photobiology in Action

“…The authors conclude to the coexistence of the two mechanisms, in agreement with experiments. The comparison of a set of four CPD photolyases from mesophiles and (hyper)-thermophiles species, based on classical MDs and electron tunneling analysis, shows that the adenine significantly contributes to the electronic coupling of the electron transfer to the damage in the most rigid proteins [127]. At higher temperature, water molecules can compete with adenine to form the best tunneling pathway.…”