Impact of Cd(II) on the stability of human uracil DNA glycosylase enzyme; an implication of molecular dynamics trajectories on stability analysis

References

• Abraham, M. J., Van Der Spoel, D., Lindahl, E., & Hess, B. (2018). GROMACS User Manual version 2018. www.gromacs.org
   Google Scholar
• Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). The structure and function of DNA. In Molecular biology of the cell (4th ed.). Garland Science. https://www.ncbi.nlm.nih.gov/books/NBK26821/
   Google Scholar
• Arnittali, M., Rissanou, A. N., & Harmandaris, V. (2019). Structure of biomolecules through molecular dynamics simulations. Procedia Computer Science, 156, 69–78. https://www.sciencedirect.com/science/article/pii/S1877050919311007 https://doi.org/10.1016/j.procs.2019.08.181
   Google Scholar
• Base excision repair | biochemistry | Britannica. (n.d.). Retrieved January 21, 2021, from https://www.britannica.com/science/base-excision-repair
   Google Scholar
• Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Mutations involve changes in the base sequence of DNA. In W. H. Freeman (Ed.), Biochemistry (5th ed.). New York. https://www.ncbi.nlm.nih.gov/books/NBK22525/
   Google Scholar
• Borjian Boroujeni, M., Shahbazi Dastjerdeh, M., Shokrgozar, M. A., Rahimi, H., & Omidinia, E. (2021). Computational driven molecular dynamics simulation of keratinocyte growth factor behavior at different pH conditions. Informatics in Medicine Unlocked, 23, 100514. https://doi.org/10.1016/j.imu.2021.100514
   Google Scholar
• Cohen, F. E., & Sternberg, M. J. (1980). On the prediction of protein structure: The significance of the root-mean-square deviation. Journal of Molecular Biology, 138(2), 321–333.
   PubMed Web of Science ®Google Scholar
• Dushanan, R., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2021). An In-Silico Approach to Evaluate the Inhibitory Potency of Selected Hydroxamic Acid Derivatives on Zinc-Dependent Histone Deacetylase Enzyme. Journal of Computational Biophysics and Chemistry, 20(6), 603–618. https://doi.org/10.1142/S2737416521500356
   Web of Science ®Google Scholar
• Gokey, T., Hang, B., & Guliaev, A. B. (2016). Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation. Scientific Reports, 6(1), 39137–39111. https://doi.org/10.1038/srep39137
   PubMedGoogle Scholar
• Kawai, A., Higuchi, S., Tsunoda, M., Nakamura, K. T., Yamagata, Y., & Miyamoto, S. (2015). Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding. FEBS Letters, 589(19), 2675–2682. https://doi.org/10.1016/j.febslet.2015.08.019
   PubMed Web of Science ®Google Scholar
• Kommu, A., Namsani, S., & Singh, J. K. (2016). Removal of heavy metal ions using functionalized graphene membranes: A molecular dynamics study. RSC Advances, 6(68), 63190–63199. https://doi.org/10.1039/C6RA06817K
   Web of Science ®Google Scholar
• Krokan, H. E., Drabløs, F., & Slupphaug, G. (2002). Uracil in DNA - occurrence, consequences and repair. Oncogene, 21(58), 8935–8948. https://doi.org/10.1038/sj.onc.1205996
   Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m 24850022
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One, 10(3), e0119264. https://doi.org/10.1371/journal.pone.0119264
   PubMed Web of Science ®Google Scholar
• Nick Pace, C., Martin Scholtz, J., & Grimsley, G. R. (2014). Forces stabilizing proteins. FEBS Letters, 588(14), 2177–2184. https://doi.org/10.1016/j.febslet.2014.05.006
   PubMed Web of Science ®Google Scholar
• Paligaspe, P., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2021). Identify the effect of As(III) on the structural stability of monomeric PKM2 and its carcinogenicity: A molecular dynamics and QM/MM based approach. Journal of Molecular Structure, 1235, 130257. https://doi.org/10.1016/j.molstruc.2021.130257
   Web of Science ®Google Scholar
• Ploetz, E. A., & Smith, P. E. (2011). A Kirkwood-Buff force field for the aromatic amino acids. Physical Chemistry Chemical Physics : PCCP, 13(40), 18154–18167. https://doi.org/10.1039/c1cp21883b
   PubMed Web of Science ®Google Scholar
• Raha, K., & Merz, K. M. (2005). Calculating binding free energy in protein–ligand interaction. Annual Reports in Computational Chemistry, 1(C), 113–130. https://doi.org/10.1016/S1574-1400(05)01009-1
   Google Scholar
• Schneider, R., Sharma, A. R., & Rai, A. (2008). Introduction to molecular dynamics. In Fehske H., Schneider R., and Weiße A. (Eds.), Lecture notes in physics (Vol. 739, pp. 3–40). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-540-74686-7_1
   Google Scholar
• Schormann, N., Ricciardi, R., & Chattopadhyay, D. (2014). Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein Science : A Publication of the Protein Society, 23(12), 1667–1685. https://doi.org/10.1002/pro.2554
   PubMed Web of Science ®Google Scholar
• Slupphaug, G., Eftedal, I., Kavli, B., Bharati, S., Helle, N. M., Haug, T., Levine, D. W., & Krokan, H. E. (1995). Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase. Biochemistry, 34(1), 128–138. https://doi.org/10.1021/bi00001a016
   PubMed Web of Science ®Google Scholar
• Wang, P., Guliaev, A. B., & Hang, B. (2006). Metal inhibition of human N-methylpurine-DNA glycosylase activity in base excision repair. Toxicology Letters, 166(3), 237–247. https://doi.org/10.1016/j.toxlet.2006.06.647
   PubMed Web of Science ®Google Scholar
• Xu, Y., Wang, S., Hu, Q., Gao, S., Ma, X., Zhang, W., Shen, Y., Chen, F., Lai, L., & Pei, J. (2018). CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction. Nucleic Acids Research, 46(W1), W374–W379. https://doi.org/10.1093/nar/gky380 29750256
   PubMed Web of Science ®Google Scholar