BIOPHYSICAL, BIOCHEMICAL AND MICROSCOPIC STUDIES ON WHOLE HISTONE GLYCATED BY DEOXYRIBOSE
DOI:
https://doi.org/10.48165/Keywords:
2-Deoxy-D-ribose, histones, mass spectrometry, Nε carboxymethyl-L-lysine, pentosidine, transmission electron microscopyAbstract
Histones, upon reaction with reducing sugars, are known to generate highly reactive advanced glycation end products (AGEs). In this study, we investigated the structural changes associated with the glycation of whole histone by 2-deoxyD-ribose. The deoxy pentose was incubated with whole histone for 12 days and the resultant biophysical and structural changes in the deoxyribose modified-whole histone were investigated thoroughly using biochemical assays, various spectroscopic techniques like UV-visible, fluorescence, FT-IR, and CD, UPLC-MS, and transmission electron microscopy. We found that deoxyribosylation of whole histone formed ptosidine and Nε-carboxymethyl-L-lysine AGEs and was accompanied by an increase in oxidative stress. The histone-AGEs caused gross structural changes in the protein and formed large amorphous aggregates. The presence of such AGE aggregates is likely to interfere with the proper functioning of histones and chromatin, besides exhibiting immunogenicity and generation oautoantibodies against nuclear antigens.
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Ahmed, M.U., Frye, E.B., Degenhardt, T.P., Thorpe, S.R. and Baynes, J.W. 1997. N-epsilon- (carboxyethyl) lysine, a product of the chemical modification of proteins by methylglyoxal, increases with age in human lens proteins. The Biochemical Journal, 324: 565-570.
Allgen, L.G. 1950. A dielectric study of nucleohistone from calf thymus. Acta Physiologica Scandinavica. Supplementum, 22: 1-140.
Arena, S., Salzano, A.M., Renzone, G., D’Ambrosio, C. and Scaloni, A. 2014. Non-enzymatic glycation and glycoxidation protein products in foods and diseases: An interconnected, complex scenario fully open to innovative proteomic studies. Mass Spectrometry Reviews, 33: 49-77.
Arfat, M.Y., Ashraf, J.M., Arif, Z., Moinuddin and Alam, K. 2014. Fine characterization of glucosylated human IgG by biochemical and biophysical methods. International Journal of Biological Macromolecules, 69: 408-415.
Ashraf, J.M., Ahmad, S., Rabbani, G., Jan, A.T., Lee, E.J., Khan, R.H. and Choi, I. 2014. Physicochemical analysis of structural alteration and advanced glycation end products generation during glycation of H2A histone by 3-deoxyglucosone. IUBMB Life, 66: 686-693. Ashraf, J.M., Rabbani, G., Ahmad, S., Hasan, Q., Khan, R.H., Alam, K. and Choi, I.C. 2015.
Shireen Naaz Islam et al.
Glycation of H1 histone by 3-deoxyglucosone: Effects on protein structure and generation of different advanced glycation end products. PLoS ONE, 10: [DOI:10.1371/journal.pone.0130630].
Bunn, H.F., Shapiro, R., McManus, M., Garrick, L., McDonald, M.J., Gallop, P.M. and Gabbay, K.H. 1979. Structural heterogeneity of human hemoglobin A due to nonenzymatic glycosylation. The Journal of Biological Chemistry, 254: 3892-3898.
Corbin, J., Méthot, N., Wang, H.H., Baenziger, J.E. and Blanton, M.P. 1998. Secondary structure analysis of individual transmembrane segments of the nicotinic acetylcholine receptor by circular dichroism and Fourier transform infrared spectroscopy. The Journal of Biological Chemistry, 273: 771-777.
Cruft, H.J., Mauritzen, C.M. and Stedman, E. 1958. The isolation of beta-histone from calf thymocytes and the factors affecting its aggregation. Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character. Royal Society (Great Britain), 149: 21-35.
Dyer, D.G., Blackledge, J.A., Thorpe, S.R. and Baynes, J.W. 1991. Formation of pentosidine during nonenzymatic browning of proteins by glucose: Identification of glucose and other carbohydrates as possible precursors of pentosidine in vivo. The Journal of Biological Chemistry, 266: 11654-11660.
Ellman, G.L. 1959. Tissue sulfhydryl groups. Archives of Biochemistry and Biophysics, 82: 70-77. Guedes, S., Vitorino, R., Domingues, M.R.M., Amado, F. and Domingues, P. 2011. Glycation and oxidation of histones H2B and H1: In vitro study and characterization by mass spectrometry. Analytical and Bioanalytical Chemistry, 399: 3529-3539.
Gugliucci, A. 1994. Advanced glycation of rat liver histone octamers: An in vitro study. Biochemical and Biophysical Research Communications, 203: 588-593.
Gugliucci, A. and Bendayan, M. 1995. Histones from diabetic rats contain increased levels of advanced glycation end products. Biochemical and Biophysical Research Communications, 212: 56-62.
Haynes, R., Osuga, D.T. and Feeney, R.E. 1967. Modification of amino groups in inhibitors of proteolytic enzymes. Biochemistry, 6: 541-547.
Hodge, J.E. 1953. Chemistry of browning reaction in model systems. Agricultural and Food Chemistry, 1: 928-943.
Ikeda, K., Higashi, T., Sano, H., Jinnouchi, Y., Yoshida, M., Araki, Ueda, S. and Horiuchi, S. 1996. Nε-(carboxymethyl) lysine protein adduct is a major immunological epitope in proteins modified with advanced glycation end products of the maillard reaction. Biochemistry, 35: 8075-8083.
Jobst, K. and Lakatos, A. 1996. The liver cell histones of diabetic patients contain glycation endproducts (AGEs) which may be lipofuscin components. Clinica Chimica Acta, 256: 203- 204.
Johnson, R.N., Metcalf, P.A. and Baker, J.R. 1983. Fructosamine: A new approach to the estimation of serum glycosylprotein. An index of diabetic control. Clinica Chimica Acta, 127: 87-95.
Kelly, S.M. and Price, N.C. 1997. The application of circular dichroism to studies of protein folding and unfolding. Biochimica et Biophysica Acta, 1338: 161-185.
Khan, M.A., Dixit, K., Jabeen, S., Moinuddin and Alam, K. 2009. Impact of peroxynitrite modification on structure and immunogenicity of H2A histone. Scandinavian Journal of Immunology, 69: 99-109.
Khan, M.A, Arif, Z., Moinuddin and Alam, K. 2017. Characterization of methylglyoxal-modified human IgG by physicochemical methods. Journal of Biomolecular Structure and Dynamics, 1102: 1-12.
Koh, G., Lee, D.H. and Woo, J.T. 2010. 2-Deoxy-D-ribose induces cellular damage by increasing oxidative stress and protein glycation in a pancreatic beta-cell line. Metabolism: Clinical and
Glycation of whole histone by deoxyribose 207
Experimental, 59: 325-332.
Koh, G., Suh, K.S., Chon, S., Oh, S., Woo, J.T., Kim, S.W., Kim, J.W and Kim, Y.S. 2005. Elevated cAMP level attenuates 2-deoxy-d-ribose-induced oxidative damage in pancreatic β cells. Archives of Biochemistry and Biophysics, 438: 70-79.
Levine, R.L., Garland, D., Oliver, C.N., Amici, A., Climent, I., Lenz, A.G., Ahn, B.W., Shaltiel, S. and Stdtman, E.R. 1990. Determination of carbonyl content in oxidatively modified proteins. Methods in Enzymology, 186: 464-478.
Levine, R.L., Williams, J.A., Stadtman, E.P. and Shacter, E. 1994. Carbonyl assays for determination of oxidatively modified proteins. Methods in Enzymology, 233: 346-357. Liebich, H.M., Gesele, E., Wirth, C., Wöl, J., Jobst, K. and Lakatos, A. 1993. Non-enzymatic glycation of histones. Biological Mass Spectrometry, 22: 121-123.
Liu, Y., Xie, M., Kang, J. and Zheng, D. 2003. Studies on the interaction of total saponins of Panax notoginseng and human albumin by Fourier transform infrared spectroscopy. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 59: 2747-2758.
McGeown, M.G. and Malpress, F.H. 1952. Synthesis of deoxyribose in animal tissues. Nature (London), 170: 575-576.
Mir, A.R., Habib, S. and Moinuddin. 2021. Recent advances in histone glycation: Emerging role in diabetes and cancer. Glycobiology, [DOI: 10.1093/glycob/cwab011].
Mir, A.R., Moinuddin, Habib, S., Khan, F., Alam, K. and Ali, A. 2015a. Structural changes in histone H2A by methylglyoxal generate highly immunogenic amorphous aggregates with implications in auto-immune response in cancer. Glycobiology, 26: 129-141.
Mir, A.R., Uddin, M., Khan, F., Alam, K. and Ali, A. 2015b. Dicarbonyl induced structural perturbations make histone H1 highly immunogenic and generate an auto-immune response in cancer. PLoS ONE, 10(8): e0136197 [DOI: 10.1371/journal.pone.0136197].
Monnier, V.M. 1990. Nonenzymatic glycosylation, the Maillard reaction and the aging process. Journal of Gerontology, 45: B105-111.
Rafi, Z., Alouffi, S., Khan, M.S. and Ahmad, S. 2020. 2’-Deoxyribose mediated glycation leads to alterations in BSA structure via generation of carbonyl species. Current Protein and Peptide Science, 21: 924-935.
Sakaguchi, S. 1950. A new method for the colorimetric determination of arginine. Journal of Biochemistry, 37: 231-236.
Shacter, E. 2000. Quantification and significance of protein oxidation in biological samples. Drug Metabolism Reviews, 32: 307-326.
Singh, R., Barden, A., Mori, T. and Beilin, L. 2001. Advanced glycation end-products: A review. Diabetologia, 44: 129-146.
Suh, K.S., Oh, S., Woo, J.T., Kim, S.W., Kim, J.W., Kim, Y.S. and Chon, S. 2012. Apigenin attenuates 2-deoxy-D-ribose-iInduced oxidative cell damage in HIT-T15 pancreatic β-cells. Biological and Pharmaceutical Bulletin, 35: 121-126.
Szondy, Z., Garabuczi, E., Joós, G., Tsay, G.J. and Sarang, Z. 2014. Impaired clearance of apoptotic cells in chronic inflammatory diseases: Therapeutic implications. Frontiers in Immunology, 5: 354 [DOI: 10.3389/fimmu.2014.00354].
Talasz, H., Wasserer, S. and Puschendorf, B. 2002. Nonenzymatic glycation of histones in vitro and in vivo. Journal of Cellular Biochemistry, 85: 24-34.
Thorpe, S.R. and Baynes, J.W. 2003. Maillard reaction products in tissue proteins: New products and new perspectives. Amino Acids, 25: 275-281.
Toennies, G. and Bakay, B. 1955. Characterization and total recovery of the component proteins of a deoxyribonucleoprotein. Nature (London), 176: 696-697.
Uchiyama, A., Ohishi, O., Takahashi, M., Kushida, K., Inoue, T., Fujie, M. and Horiuchi, K. 1991. Fluorophores from aging human articular cartilage. Journal of Biochemistry, 110: 714-718. Van Holde, K.E. and Isenberg, I. 1975. Histone interactions and chromatin structure. Accounts of Chemical Research, 254: 3892-3898.
Shireen Naaz Islam et al.
Vetter, S. W. 2015. Glycated serum albumin and age receptors. Advances in Clinical Chemistry, 72: 205-275.
Von Bergen, M., Barghorn, S., Biernat, J., Mandelkow, E.M. and Mandelkow, E. 2005. Tau aggregation is driven by a transition from random coil to beta sheet structure. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1739: 158-166.
Wolffe, A.P. 1998. Packaging principle: How DNA methylation and histone acetylation control the transcriptional activity of chromatin? Journal of Experimental Zoology, 282, 239-244. Wu, D., Ingram, A., Lahti, J.H., Mazza, B., Grenet, J., Kapoor, A., Liu, L., Kidd, V.J. and Tang, D. 2002. Apoptotic release of histones from nucleosomes. The Journal of Biological Chemistry, 277: 12001-12008.
Yoshimura, Y., Lin, Y., Yagi, H., Lee, Y.H., Kitayama, H., Sakurai, K., So, M., Ogi, H., Naiki, H. and Goto, Y. 2012. Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proceedings of the National Academy of Sciences of the United States of America, 109: 14446-14451.
Zaman, A., Arif, Z. and Alam, K. 2017. Fructosylation induced structural changes in mammalian DNA examined by biophysical techniques. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 174: 171-176.
Zaman, A., Arif, Z., Moinuddin and Alam, K. 2018. Fructose-human serum albumin interaction undergoes numerous biophysical and biochemical changes before forming AGEs and aggregates. International Journal of Biological Macromolecules, 109: 896-906.
Zheng, Q., Maksimovic, I., Upad, A. and David, Y. 2020. Non-enzymatic covalent modifications: a new link between metabolism and epigenetics. Protein and Cell, 11: 401-416. Zheng, Q., Omans, N.D., Leicher, R., Osunsade, A., Agustinus, A.S., Finkin-Groner, E., D′Ambrosio, H., Liu, B., Chandarlapaty, S., Liu, S. and David, Y. 2019. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nature Communications, 10(1): 1-12 [DOI: 10.1038/s41467-019-09192-z].