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Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Jr. Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) A second generation forth field for the simulation of proteins and nucleic acids. Journal of American Chemical Society, 117, 5179-5197. doi:10.1021/ja00124a002

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• TITLE: Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

  AUTHORS: Kholmirzo Kholmurodov, Ermuhammad Dushanov, Kenji Yasuoka

  KEYWORDS: Molecular Dynamics Simulations; DNA Photolyase; Conformation Change; FAD; MTHF; DNA

  JOURNAL NAME: Advances in Bioscience and Biotechnology, Vol.3 No.3, June 19, 2012

  ABSTRACT: A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.