Abstract
Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.
Funding source: University Grants Commission- Nepal
Award Identifier / Grant number: CRG-73/74-S&T-01
Acknowledgments
We sincerely thank Professor Alexander D. MacKerell Jr. at the Computer-Aided Drug Design Center, University of Maryland, USA, for his valuable input and help with the force-field parameters. R.P.K. acknowledges the partial financial support from the Nepal Academy of Science and Technology (NAST). N.P.A. acknowledges the UGC Award No. CRG-73/74-S&T-01 and Associate membership of The Abdus Salam International Center for Theoretical Physics, Trieste, Italy.
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Author contributions: P.B.T., P.P.C., and N.P.A. guided the project. R.P.K, R.P., P.B., and P.B.T performed MD simulations. R.P.K., R.P., P.B., P.B.T., P.P.C., and N.P.A. analyzed the data. R.P.K., P.B.T., and P.P.C. wrote the manuscript. R.P., P.B., and N.P.A. contributed to the manuscript editing.
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Research funding: This work was supported by University Grants Commission- Nepal (CRG-73/74-S&T-01).
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Conflict of interest statement: The authors declare no conflict of interest.
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Supplementary Material
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