A Novel Approach to Simulate a Charge Transfer in DNA Repair by an Anacystis nidulans Photolyase



E.B. Dushanov1, 2, Kh.T. Kholmurodov*, 1, 3
1 Laboratory of Radiation Biology, JINR, 141980, Dubna, Moscow Region, Russia
2 Institute of Nuclear Physics, 100214, Ulugbek, Tashkent, Uzbekistan
3 Dubna International University, 141980, Dubna, Moscow Region, Russia


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© Dushanov and Kholmurodov; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Laboratory of Radiation Biology, JINR, 141980, Dubna, Moscow Region, Russia; Tel: (+7)49621-62872; Fax: (+7)49621-65948; E-mails: mirzo@jinr.ru; kholmirzo@gmail.com


Abstract

An Anacystis nidulans photolyase enzyme containing two chromophore cofactors was simulated for a photoreaction DNA repairing process via molecular dynamics (MD) method. A novel approach has been introduced for the electron transfer between the FAD (flavin adenine dinucleotide; flavin) molecule and CPD (cyclobutane pyrimidine dimer). This approach involves four simulation stages with different charges for the FAD and CPD fragments and a role of a charged state of the active cofactor was qualified during the MD modeling. Observations show that flavin has actively participated in a charge transfer process, thereby involving the conformational changes of the DNA and CPD substrate fragment. The DNA conformation behavior has shown to correlate with the electron transfer from flavin to CPD. This is manifested on the similarities of the DNA repairing process by excision repair of the UV photoproducts.

Keywords: : Charge transfer, chromophore cofactors, cyclobutane pyrimidine dimer, DNA repair, flavin adenine dinucleotide, molecular dynamics modeling, photolyase enzyme.