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

E B Dushanov; Kh T Kholmurodov

doi:10.2174/1874091X01408010035

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

Open Biochem J. 2014 Mar 7:8:35-43. doi: 10.2174/1874091X01408010035. eCollection 2014.

Authors

E B Dushanov¹, Kh T Kholmurodov²

Affiliations

¹ Laboratory of Radiation Biology, JINR, 141980, Dubna, Moscow Region, Russia ; Institute of Nuclear Physics, 100214, Ulugbek, Tashkent, Uzbekistan.
² Laboratory of Radiation Biology, JINR, 141980, Dubna, Moscow Region, Russia ; Dubna International University, 141980, Dubna, Moscow Region, Russia.

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; DNA repair; chromophore cofactors; cyclobutane pyrimidine dimer; flavin adenine dinucleotide; molecular dynamics modeling; photolyase enzyme..