Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited
| Autor: | Takahisa Yamato, Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Stereochemistry
Ab initio Pyrimidine dimer Molecular Dynamics Simulation Cyanobacteria 010402 general chemistry 01 natural sciences Photoinduced electron transfer Electron Transport Molecular dynamics Electron transfer 0103 physical sciences Materials Chemistry Molecular orbital Physical and Theoretical Chemistry Photolyase 010304 chemical physics Chemistry Adenine Electron transport chain Hydroquinones 0104 chemical sciences Surfaces Coatings and Films Pyrimidine Dimers Flavin-Adenine Dinucleotide Quantum Theory Asparagine Deoxyribodipyrimidine Photo-Lyase |
| Zdroj: | The Journal of Physical Chemistry B. 122:6912-6921 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | The photoinduced electron transfer (ET) reaction of cyclobutane pyrimidine dimer (CPD) photolyase plays an essential role in its DNA repair reaction, and the molecular mechanism of the ET reaction has attracted a large number of experimental and theoretical studies. We investigated the quantum mechanical nature of their ET reactions, characterized by multiple ET pathways of the CPD photolyase derived from Anacystis nidulans. Using the generalized Mulliken-Hush (GMH) method and the bridge green function (GF) methods, we estimated the electronic coupling matrix element, TDA, to be 36 ± 30 cm-1 from the donor (FADH-) to the acceptor (CPD). The estimated ET time was 386 ps, in good agreement with the experimental value (250 ps) in the literature. Furthermore, we performed the molecular dynamics (MD) simulations and ab initio molecular orbital (MO) calculations, and explored the electron tunneling pathway. We examined 20 different structures during the MD trajectory and quantitatively evaluated the electron tunneling currents for each of them. As a result, we demonstrated that the ET route via Asn349 was the dominant pathway among the five major routes via (Adenine/Asn349), (Adenine/Glu283), (Adenine/Glu283/Asn349/Met353), (Met353/Asn349), and (Asn349), indicating that Asn349 is an essential amino acid residue in the ET reaction. |
| Databáze: | OpenAIRE |
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