Cadaverine modulates bovine alkaline phosphatase kinetics and structure: spectroscopic and bioinformatics study

Posted on
cadaverine-modulates-bovine-alkaline-phosphatase-kinetics-and-structure:-spectroscopic-and-bioinformatics-study
Cadaverine modulates bovine alkaline phosphatase kinetics and structure: spectroscopic and bioinformatics study

References

  1. B, A. et al. A, J., J, L. & in Molecular Biology of the Cell (New York: Garland Science, (2002).

  2. Zhou, H. X. & Pang, X. Electrostatic interactions in protein Structure, Folding, Binding, and condensation. Chem. Rev. 118, 1691–1741. https://doi.org/10.1021/acs.chemrev.7b00305 (2018).

    Google Scholar 

  3. Robinson, P. K. Enzymes: principles and biotechnological applications. Essays Biochem. 59, 1–41. https://doi.org/10.1042/bse0590001 (2015).

    Google Scholar 

  4. Singh, R. K., Tiwari, M. K., Singh, R. & Lee, J. K. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int. J. Mol. Sci. 14, 1232–1277. https://doi.org/10.3390/ijms14011232 (2013).

    Google Scholar 

  5. Imamura, K. et al. Characteristics of sugar surfactants in stabilizing proteins during Freeze–Thawing and Freeze-Drying. J. Pharm. Sci. 103 https://doi.org/10.1002/jps.23988 (2014).

  6. Pisano, R. et al. Freeze-drying of enzymes in case of water-binding and non-water-binding substrates. Eur. J. Pharm. Biopharmaceutics: Official J. Arbeitsgemeinschaft Fur Pharmazeutische Verfahrenstechnik eV. 85, 974–983. https://doi.org/10.1016/j.ejpb.2013.02.008 (2013).

    Google Scholar 

  7. Strambini, G. B., Balestreri, E., Galli, A. & Gonnelli, M. Effects of sugars and polyols on the stability of Azurin in ice. J. Phys. Chem. B. 112, 4372–4380. https://doi.org/10.1021/jp711185r (2008).

    Google Scholar 

  8. Zaroog, M. S., Kadir, A. & Tayyab, S. H. Stabilizing Effect of Various Polyols on the Native and the Denatured States of Glucoamylase. The Scientific World Journal 570859, (2013). https://doi.org/10.1155/2013/570859 (2013).

  9. Rajan, R. et al. Review of the current state of protein aggregation Inhibition from a materials chemistry perspective: special focus on polymeric materials. Mater. Adv. 2 https://doi.org/10.1039/D0MA00760A (2021).

  10. Sharma, N., Rajan, R., Makhaik, S. & Matsumura, K. Comparative study of protein aggregation arrest by zwitterionic polysulfobetaines: using contrasting raft agents. ACS Omega. 4, 12186–12193. https://doi.org/10.1021/acsomega.9b01409 (2019).

    Google Scholar 

  11. Berthoud, H., Wechsler, D. & Irmler, S. Production of Putrescine and cadaverine by Paucilactobacillus wasatchensis. Front. Microbiol. 13 https://doi.org/10.3389/fmicb.2022.842403 (2022).

  12. Sagar, N. A. et al. Functions, Metabolism, and role in human disease management. Med. Sci. (Basel Switzerland). 9 https://doi.org/10.3390/medsci9020044 (2021).

  13. Stasiulewicz, M., Panuszko, A., Bruździak, P. & Stangret, J. Mechanism of osmolyte Stabilization–Destabilization of proteins: experimental evidence. J. Phys. Chem. B. 126, 2990–2999. https://doi.org/10.1021/acs.jpcb.2c00281 (2022).

    Google Scholar 

  14. Gomez-Gomez, H. A., Borges, C. V., Minatel, I. O., Luvizon, A. C. & Lima, G. P. P. in Bioactive Molecules in Food (eds (eds Mérillon, J. M. & Ramawat, K. G.) 1–25 (Springer International Publishing, (2018).

  15. Ouameur, A. A. & Tajmir-Riahi, H. A. Structural analysis of DNA interactions with biogenic polyamines and cobalt(III)hexamine studied by fourier transform infrared and capillary electrophoresis. J. Biol. Chem. 279, 42041–42054. https://doi.org/10.1074/jbc.M406053200 (2004).

    Google Scholar 

  16. Babaknejad, N., Shareghi, B. & Saboury, A. A. Study of alkaline phosphatase interaction with Putrescine using multi-spectroscopic and Docking methods. Colloids Surf., B. 185, 110509. https://doi.org/10.1016/j.colsurfb.2019.110509 (2020).

    Google Scholar 

  17. Kong, J. & Yu, S. Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochim. Biophys. Sin. 39, 549–559. https://doi.org/10.1111/j.1745-7270.2007.00320.x (2007).

    Google Scholar 

  18. Yadollahi, E., Shareghi, B. & Farhadian, S. Noncovalent interactions between Quinoline yellow and trypsin: in vitro and in Silico methods. J. Mol. Liq. 353, 118826. https://doi.org/10.1016/j.molliq.2022.118826 (2022).

    Google Scholar 

  19. Böhm, G., Muhr, R. & Jaenicke, R. Quantitative analysis of protein Far UV circular dichroism spectra by neural networks. Protein Eng. 5, 191–195. https://doi.org/10.1093/protein/5.3.191 (1992).

    Google Scholar 

  20. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2 (1990).

    Google Scholar 

  21. Sali, A. & Overington, J. P. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science: Publication Protein Soc. 3, 1582–1596. https://doi.org/10.1002/pro.5560030923 (1994).

    Google Scholar 

  22. Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718. https://doi.org/10.1002/jcc.20291 (2005).

    Google Scholar 

  23. Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms for highly Efficient, Load-Balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447. https://doi.org/10.1021/ct700301q (2008).

    Google Scholar 

  24. Hoover, W. G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31, 1695–1697. https://doi.org/10.1103/PhysRevA.31.1695 (1985).

    Google Scholar 

  25. Falcón-González, J. M. et al. Assessment of the Wolf method using the Stillinger–Lovett sum rules: from strong electrolytes to weakly charged colloidal dispersions. J. Chem. Phys. 153, 234901. https://doi.org/10.1063/5.0033561 (2020).

    Google Scholar 

  26. Wang, J. et al. Interaction mechanism of Pepsin with a natural inhibitor Gastrodin studied by spectroscopic methods and molecular Docking. Med. Chem. Res. 26, 1–9. https://doi.org/10.1007/s00044-016-1760-2 (2017).

    Google Scholar 

  27. Arumugam, D. S., Srinivasan, P., Thamilarasan, V. & Sengottuvelan, N. Exploring the binding mechanism of 5-hydroxy-3′,4′,7-trimethoxyflavone with bovine serum albumin: spectroscopic and computational approach. Spectrochim. Acta Part A Mol. Biomol. Spectrosc. 157 https://doi.org/10.1016/j.saa.2015.12.028 (2015).

  28. Quemé-Peña, M. et al. Membrane association modes of natural anticancer peptides: mechanistic details on Helicity, Orientation, and surface coverage. Int. J. Mol. Sci. 22 https://doi.org/10.3390/ijms22168613 (2021).

  29. Xu, H., Liu, Q. & Wen, Y. Spectroscopic studies on the interaction between nicotinamide and bovine serum albumin. Spectrochim. Acta A. 71, 984–988. https://doi.org/10.1016/j.saa.2008.02.021 (2008).

    Google Scholar 

  30. Husain, M. A., Ishqi, H., Sarwar, T., Rehman, S. & Tabish, M. Interaction of indomethacin with calf thymus DNA: A Multi-spectroscopic, thermodynamic and molecular modelling approach. Med. Chem. Commun. 8 https://doi.org/10.1039/C7MD00094D (2017).

  31. Sadat, A. & Joye, I. Peak fitting applied to fourier transform infrared and Raman spectroscopic analysis of proteins. (2020). https://doi.org/10.3390/app10175918

  32. Suchkova, G. G. & Maklakov, L. I. Amide bands in the IR spectra of urethanes. Vib. Spectrosc. – VIB. SPECTROSC. 51, 333–339. https://doi.org/10.1016/j.vibspec.2009.09.002 (2009).

    Google Scholar 

  33. Mansouri, M., Pirouzi, M., Saberi, M. R., Ghaderabad, M. & Chamani, J. Investigation on the interaction between cyclophosphamide and lysozyme in the presence of three different kind of cyclodextrins: determination of the binding mechanism by spectroscopic and molecular modeling techniques. Molecules (Basel Switzerland). 18, 789–813. https://doi.org/10.3390/molecules18010789 (2013).

    Google Scholar 

  34. Zhang, G., Zhao, N. & Wang, L. Probing the binding of vitexin to human serum albumin by multispectroscopic techniques. J. Lumin. 131, 880–887. https://doi.org/10.1016/j.jlumin.2010.12.018 (2011).

    Google Scholar 

  35. Zhou, J. et al. Spectroscopic studies on the interaction of hypocrellin A and hemoglobin. Spectrochim. Acta A. 72, 151–155. https://doi.org/10.1016/j.saa.2008.09.009 (2009).

    Google Scholar 

  36. Ghisaidoobe, A. B. & Chung, S. J. Intrinsic Tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques. Int. J. Mol. Sci. 15, 22518–22538. https://doi.org/10.3390/ijms151222518 (2014).

    Google Scholar 

  37. Wang, N., Ye, L., Yan, F. & Xu, R. Spectroscopic studies on the interaction of azelnidipine with bovine serum albumin. Int. J. Pharm. 351, 55–60. https://doi.org/10.1016/j.ijpharm.2007.09.016 (2008).

    Google Scholar 

  38. Kumar, V., Sharma, V. & Kalonia, D. Second derivative Tryptophan fluorescence spectroscopy as a tool to characterize partially unfolded intermediates of proteins. Int. J. Pharm. 294, 193–199. https://doi.org/10.1016/j.ijpharm.2005.01.024 (2005).

    Google Scholar 

  39. Albani, J. R. in In Structure and Dynamics of Macromolecules: Absorption and Fluorescence Studies. 141–192 (eds Albani, J. R.) (Elsevier Science, 2004).

  40. Mátyus, L., Szöllősi, J. & Jenei, A. Steady-state fluorescence quenching applications for studying protein structure and dynamics. J. Photochem. Photobiol., B. 83, 223–236. https://doi.org/10.1016/j.jphotobiol.2005.12.017 (2006).

    Google Scholar 

  41. G, V., Kumar, Y. M., Sugumar, K. & Arunachalam, S. Spectroscopic investigation on the interaction of some polymer–cobalt(III) complexes with serum albumins. J. OfLuminescence. 157, 297–302 (2015).

    Google Scholar 

  42. Soemo, A. R. & Pemberton, J. E. Combined quenching mechanism of anthracene fluorescence by cetylpyridinium chloride in sodium Dodecyl sulfate micelles. J. Fluoresc. 24, 295–299. https://doi.org/10.1007/s10895-013-1319-2 (2014).

    Google Scholar 

  43. Liu, E. H., Qi, L. W. & Li, P. Structural relationship and binding mechanisms of five flavonoids with bovine serum albumin. Molecules (Basel Switzerland). 15, 9092–9103. https://doi.org/10.3390/molecules15129092 (2010).

    Google Scholar 

  44. Mansouri-Torshizi, H. et al. Palladium(II) complexes of biorelevant ligands. Synthesis, structures, cytotoxicity and rich DNA/HSA interaction studies. J. Biomol. Struct. Dynamics. 36, 2787–2806. https://doi.org/10.1080/07391102.2017.1372309 (2018).

    Google Scholar 

  45. Ross, P. D. & Rekharsky, M. V. Thermodynamics of hydrogen bond and hydrophobic interactions in cyclodextrin complexes. Biophys. J. 71, 2144–2154. https://doi.org/10.1016/s0006-3495(96)79415-8 (1996).

    Google Scholar 

  46. Greenfield, N. J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876–2890. https://doi.org/10.1038/nprot.2006.202 (2006).

    Google Scholar 

  47. Gorbunoff, M. J. Tyrosine environment differences in the chymotrypsins. Biochemistry 10, 250–257. https://doi.org/10.1021/bi00778a009 (1971).

    Google Scholar 

  48. Hung, H. C. & Chang, G. G. Multiple unfolding intermediates of human placental alkaline phosphatase in equilibrium Urea denaturation. Biophys. J. 81, 3456–3471. https://doi.org/10.1016/s0006-3495(01)75977-2 (2001).

    Google Scholar 

  49. Kelly, S. M. & Price, N. C. The use of circular dichroism in the investigation of protein structure and function. Curr. Protein Pept. Sci. 1, 349–384. https://doi.org/10.2174/1389203003381315 (2000).

    Google Scholar 

  50. Kelly, S. M. & Price, N. C. The application of circular dichroism to studies of protein folding and unfolding. Biochim. Et Biophys. Acta (BBA) – Protein Struct. Mol. Enzymol. 1338, 161–185. https://doi.org/10.1016/S0167-4838(96)00190-2 (1997).

    Google Scholar 

  51. Pepelnjak, M. et al. In situ analysis of osmolyte mechanisms of proteome thermal stabilization. Nat. Chem. Biol. 20, 1053–1065. https://doi.org/10.1038/s41589-024-01568-7 (2024).

    Google Scholar 

Download references