Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study

References

• Abdullah, S. M., Fatma, S., Rabbani, G., & Ashraf, J. M. (2017). A spectroscopic and molecular docking approach on the binding of tinzaparin sodium with human serum albumin. Journal of Molecular Structure, 1127, 283–288. https://doi.org/10.1016/j.molstruc.2016.07.108
   Web of Science ®Google Scholar
• Adam, N., Adam, C., Keskitalo, M., Pfeuffer-Rooschüz, J., & Panak, P. J. (2019). Interaction of Cm(III) with human serum albumin studied by time-resolved laser fluorescence spectroscopy and NMR. Journal of Inorganic Biochemistry, 192, 45–51. https://doi.org/10.1016/j.jinorgbio.2018.12.007
   PubMed Web of Science ®Google Scholar
• Adam, N., Reitz, C. Y., Ditter, A., & Panak, P. J. (2021). Complexation of Cm(III) with blood serum proteins: recombinant human serum albumin (rHSA). Radiochimica Acta, 109(7), 547–550. https://doi.org/10.1515/ract-2021-1029
   Web of Science ®Google Scholar
• Ahmad, E., Rabbani, G., Zaidi, N., Khan, M. A., Qadeer, A., Ishtikhar, M., Singh, S., & Khan, R. H. (2013). Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. Journal of Biomolecular Structure & Dynamics, 31(6), 630–648. https://doi.org/10.1080/07391102.2012.706081
   PubMed Web of Science ®Google Scholar
• Ali, M., Kumar, A., Kumar, M., & Pandey, B. N. (2016). The interaction of human serum albumin with selected lanthanide and actinide ions: Binding affinities, protein unfolding and conformational changes. Biochimie, 123, 117–129. https://doi.org/10.1016/j.biochi.2016.01.012
   PubMed Web of Science ®Google Scholar
• Bal, W., Sokołowska, M., Kurowska, E., & Faller, P. (2013). Binding of transition metal ions to albumin: sites, affinities and rates. Biochimica et Biophysica Acta, 1830(12), 5444–5455.
   PubMed Web of Science ®Google Scholar
• Barducci, A., Bonomi, M., & Parrinello, M. (2011). Metadynamics. WIREs Computational Molecular Science, 1(5), 826–843. https://doi.org/10.1002/wcms.31
   Google Scholar
• Barducci, A., Bussi, G., & Parrinello, M. (2008). Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Physical Review Letters, 100(2), 020603–020606.
   PubMed Web of Science ®Google Scholar
• Barreca, D., Laganà, G., Bruno, G., Magazù, S., & Bellocco, E. (2013). Diosmin binding to human serum albumin and its preventive action against degradation due to oxidative injuries. Biochimie, 95(11), 2042–2049.
   PubMed Web of Science ®Google Scholar
• Bauer, N., & Panak, P. J. (2015). Influence of carbonate on the complexation of Cm(III) with human serum transferrin studied by time-resolved laser fluorescence spectroscopy (TRLFS). New Journal of Chemistry, 39(2), 1375–1381. https://doi.org/10.1039/C4NJ01877J
   Web of Science ®Google Scholar
• Bauer, N., Frohlich, D. R., & Panak, P. J. (2014). Interaction of Cm(III) and Am(III) with human serum transferrin studied by time-resolved laser fluorescence and EXAFS spectroscopy. Dalton Transactions (Cambridge, England : 2003), 43(18), 6689–6700.
   PubMed Web of Science ®Google Scholar
• Bauer, N., Smith, V. C., MacGillivray, R. T. A., & Panak, P. J. (2015). Complexation of Cm(III) with the recombinant N-lobe of human serum transferrin studied by time-resolved laser fluorescence spectroscopy (TRLFS). Dalton Transactions (Cambridge, England: 2003), 44(4), 1850–1857.
   PubMed Web of Science ®Google Scholar
• Benavides-Garcia, M. G., & Balasubramanian, K. (2009). Structural insights into the binding of uranyl with human serum protein apotransferrin structure and spectra of protein − uranyl interactions. Chemical Research in Toxicology, 22(9), 1613–1621.
   PubMed Web of Science ®Google Scholar
• Bonomi, M., Barducci, A., & Parrinello, M. (2009). Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. Journal of Computational Chemistry, 30(11), 1615–1621.
   PubMed Web of Science ®Google Scholar
• Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., & Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications. 180(10), 1961–1972. https://doi.org/10.1016/j.cpc.2009.05.011
   Web of Science ®Google Scholar
• Bourassa, P., Dubeau, S., Maharvi, G. M., Fauq, A. H., Thomas, T. J., & Tajmir-Riahi, H. A. (2011). Binding of antitumor tamoxifen and its metabolites 4-hydroxytamoxifen and endoxifen to human serum albumin. Biochimie, 93(7), 1089–1101. https://doi.org/10.1016/j.biochi.2011.03.006
   PubMed Web of Science ®Google Scholar
• Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., & Baker, N. A. (2004). PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research, 32(Web Server issue), W665–W667. https://doi.org/10.1093/nar/gkh381
   PubMedGoogle Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics. 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Gao, J., Bosco, D. A., Powers, E. T., & Kelly, J. W. (2009). Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nature Structural & Molecular Biology, 16(7), 684–690.
   PubMed Web of Science ®Google Scholar
• Handing, K. B., Shabalin, I. G., Kassaar, O., Khazaipoul, S., Blindauer, C. A., Stewart, A. J., Chruszcz, M., & Minor, W. (2016). Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins. Chemical Science, 7(11), 6635–6648.
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E., & GROMACS, 4. (2008). Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447.
   PubMed Web of Science ®Google Scholar
• Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31(3), 1695–1697. https://doi.org/10.1103/PhysRevA.31.1695
   PubMed Web of Science ®Google Scholar
• International Commission on Radiological Protection. (2002). Guide for the practical application of the ICRP human respiratory tract model. ICRP Supporting Guidance, 3, 32.
   Google Scholar
• International Commission on Radiological Protection. (1994). Dose coefficients for intake of radionuclides by workers. ICRP Publication, 24, 68.
   Google Scholar
• International commission on radiological protection. (1997). Individual monitoring for internal exposure of workers. ICRP Publication, 78, 27. vol
   Google Scholar
• Ishtikhar, M., Rabbani, G., & Khan, R. H. (2014). Interaction of 5-fluoro-5'-deoxyuridine with human serum albumin under physiological and non-physiological condition: A biophysical investigation. Colloids and Surfaces B Biointerfaces, 123, 469–477.
   PubMed Web of Science ®Google Scholar
• Ishtikhar, M., Rabbani, G., Khan, S., & Khan, R. H. (2015). Biophysical investigation of thymoquinone binding to 'N' and 'B' isoforms of human serum albumin: Exploring the interaction mechanism and radical scavenging activity. RSC Advances, 5(24), 18218–18232. https://doi.org/10.1039/C4RA09892G
   Web of Science ®Google Scholar
• Jeanson, A., Ferrand, M., Funke, H., Hennig, C., Moisy, P., Solari, P., Vidaud, C., & Den Auwer, C. (2010). The role of transferrin in actinide (IV) uptake: Comparison with iron(III). Chemistry A European Journal, 16(4), 1378–1387. https://doi.org/10.1002/chem.200901209
   PubMed Web of Science ®Google Scholar
• Justino, G. C., Garribba, E., & Pessoa, J. C. (2013). Binding of VIVO2+ to the Fe binding sites of human serum transferrin. A theoretical study. Journal of Biological Inorganic Chemistry, 18(7), 803–813. https://doi.org/10.1007/s00775-013-1029-x
   PubMed Web of Science ®Google Scholar
• Kragh-Hansen, U., Minchiotti, L., Galliano, M., & Peters, T. (2013). Human serum albumin isoforms: genetic and molecular aspects and functional consequences. Biochimica Biophysica Acta, 1830(12), 5405–5417. https://doi.org/10.1016/j.bbagen.2013.03.026
   PubMed Web of Science ®Google Scholar
• Leines, G. D., & Ensing, B. (2012). Path finding on high-dimensional free energy landscapes. Physical Review Letters, 109(2), 020601.
   PubMed Web of Science ®Google Scholar
• Li, P., Song, L. F., & Merz, K. M., Jr. (2015). Parameterization of highly charged metal ions using the 12-6-4 LJ type nonbonded model in explicit water. The Journal of Physical Chemistry. B, 119(3), 883–895.
   PubMed Web of Science ®Google Scholar
• Limongelli, V., Marinelli, L., Cosconati, S., Motta, C. L., Sartini, S., Mugnaini, L., Settimo, F. D., Novellino, E., & Parrinello, M. (2012). Sampling protein motion and solvent effect during ligand binding. Proceedings of the National Academy of Sciences of the United States of America, 109(5), 1467–1472. https://doi.org/10.1073/pnas.1112181108
   PubMed Web of Science ®Google Scholar
• Mishra, L., Sawant, P. D., Sundararajan, M., & Bandyopadhyay, T. (2019). Binding of Cm(III) and Th(IV) with human transferrin at serum pH: Combined QM and MD investigations. The Journal of Physical Chemistry. B, 123(13), 2729–2744. https://doi.org/10.1021/acs.jpcb.8b09473
   PubMed Web of Science ®Google Scholar
• Mishra, L., Singh, I. S., Patni, H. K., & Rao, D. D. (2018). Comparing lungs, liver and knee measurement geometries at various times post inhalation of 239Pu and 241Am. Radiation Protection Dosimetry, 181(2), 168–177. https://doi.org/10.1093/rpd/ncy004
   PubMed Web of Science ®Google Scholar
• Mishra, L., Sundararajan, M., & Bandyopadhyay, T. (2020). MD simulations of plutonium binding and its decorporation from the binding-cleft of human serum transferrin. Journal of Biological Inorganic Chemistry, 25(2), 213–231. https://doi.org/10.1007/s00775-020-01753-8
   PubMed Web of Science ®Google Scholar
• Mishra, L., Sundararajan, M., & Bandyopadhyay, T. (2021). MD simulation reveals dierential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH. Proteins, 89(2), 193–206. https://doi.org/10.1002/prot.26006
   PubMedGoogle Scholar
• Mongan, J., Case, D. A., & McCammon, J. A. (2004). Constant pH molecular dynamics in generalized Born implicit solvent. Journal of Computational Chemistry, 25(16), 2038–2048. https://doi.org/10.1002/jcc.20139
   PubMed Web of Science ®Google Scholar
• Montavon, G., Apostolidis, C., Bruchertseifer, F., Repinc, U., & Morgenstern, A. (2009). Spectroscopic study of the interaction of U(VI) with transferrin and albumin for speciation of U(VI) under blood serum conditions. Journal of Inorganic Biochemistry, 103(12), 1609–1616.
   PubMed Web of Science ®Google Scholar
• Mujika, J. I., Escribano, B., Akhmatskaya, E., Ugalde, J. M., & Lopez, X. (2012). Molecular dynamics simulations of Iron- and aluminum loaded serum transferrin: Protonation of Tyr188 is necessary to prompt metal release. Biochemistry, 51(35), 7017–7027. https://doi.org/10.1021/bi300584p
   PubMed Web of Science ®Google Scholar
• Mujika, J. I., Lopez, X., Rezabal, E., Castillo, R., Marti, S., Moliner, V., & Ugalde, J. M. (2011). A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH. Journal of Inorganic Biochemistry. 1456, 105–1446.
   Google Scholar
• Nose, S. (1984). A molecular dynamics method for simulations in the canonical ensemble. Journal of Chemical Physics, 81, 511.
   Web of Science ®Google Scholar
• Onufriev, A., Case, D. A., & Ullman, G. M. (2001). A novel view of pH titration in biomolecules. Biochemistry, 40(12), 3413–3419. https://doi.org/10.1021/bi002740q
   PubMed Web of Science ®Google Scholar
• Pathak, A. K. (2015a). Constant pH molecular dynamics study on the doubly mutated staphylococcal nuclease: capturing the microenvironment. RSC Advances, 5(115), 94926–94932. https://doi.org/10.1039/C5RA17983A
   Web of Science ®Google Scholar
• Pathak, A. K. (2015b). Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study. Biopolymers, 103(3), 148–157. https://doi.org/10.1002/bip.22577
   PubMed Web of Science ®Google Scholar
• Pathak, A. K., & Bandyopadhyay, T. (2015). Protein − drug interactions with effective polarization in polarizable water: oxime unbinding from AChE gorge. The Journal of Physical Chemistry B, 119(45), 14460–14471. 10.1021/acs.jpcb.5b08930[26468911]
   PubMed Web of Science ®Google Scholar
• Pathak, A. K., & Bandyopadhyay, T. (2017a). Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study. Physical Chemistry Chemical Physics, 19(7), 5560–5569. https://doi.org/10.1039/C6CP08518K
   PubMed Web of Science ®Google Scholar
• Pathak, A. K., & Bandyopadhyay, T. (2017b). Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. The Journal of Chemical Physics, 146(16), 165104.
   PubMed Web of Science ®Google Scholar
• Peter, E., & Lehmann, M. (1981). Interaction of thorium with blood serum proteins in vivo. International Journal of Radiation Biology. 40, 445–450.
   Web of Science ®Google Scholar
• Rabbani, G., & Ahn, S. N. (2019). Structure, enzymatic activities, glycation and therapeutic potential of human serum albumin: A natural cargo. International Journal of Biological Macromolecules, 123, 979–990. https://doi.org/10.1016/j.ijbiomac.2018.11.053
   PubMed Web of Science ®Google Scholar
• Rabbani, G., & Ahn, S. N. (2021). Review: Roles of human serum albumin in prediction, diagnoses and treatment of COVID-19. International Journal of Biological Macromolecules, 193(Pt A), 948–955.
   PubMedGoogle Scholar
• Rabbani, G., Ahmad, E., Khan, M. V., Ashraf, M. T., Bhat, R., & Khan, R. H. (2015). Impact of structural stability of cold adapted Candida antarctica lipase B (CaLB): in relation to pH, chemical and thermal denaturation. RSC Advances, 5(26), 20115–20131. https://doi.org/10.1039/C4RA17093H
   Web of Science ®Google Scholar
• Rabbani, G., Ahmad, E., Zaidi, N., & Khan, R. H. (2011). pH-dependent conformational transitions in conalbumin (ovotransferrin), a metalloproteinase from hen egg white. Cell Biochemistry and Biophysics, 61(3), 551–560.
   PubMed Web of Science ®Google Scholar
• Rabbani, G., Ahmad, E., Zaidi, N., Fatima, S., & Khan, R. H. (2012). pH-Induced molten globule state of Rhizopus niveus lipase is more resistant against thermal and chemical denaturation than its native state. Cell Biochemistry and Biophysics, 62(3), 487–499. https://doi.org/10.1007/s12013-011-9335-9
   PubMed Web of Science ®Google Scholar
• Rabbani, G., Baig, M. H., Jan, A. T., Ju Lee, E., Khan, M. V., Zaman, M., Farouk, A. E., Khan, R. H., & Choi, I. (2017a). Binding of erucic acid with human serum albumin using a spectroscopic and molecular docking study. International Journal of Biological Macromolecules, 105(Pt 3), 1572–1580.
   PubMedGoogle Scholar
• Rabbani, G., Baig, M. H., Lee, E. J., Cho, W. K., Ma, J. Y., & Choi, I. (2017b). Biophysical study on the interaction between eperisone hydrochloride and human serum albumin using spectroscopic, calorimetric, and molecular docking analyses. Molecular Pharmaceutics, 14(5), 1656–1665. https://doi.org/10.1021/acs.molpharmaceut.6b01124
   PubMed Web of Science ®Google Scholar
• Rabbani, G., Kaur, J., Ahmad, E., Khan, R. H., & Jain, S. K. (2014a). Structural characteristics of thermostable immunogenic outer membrane protein from Salmonella enterica serovar Typhi. Applied Microbiology and Biotechnology, 98(6), 2533–2543. https://doi.org/10.1007/s00253-013-5123-3
   PubMed Web of Science ®Google Scholar
• Rabbani, G., Khan, M. J., Ahmad, A., Maskat, M. Y., & Khan, R. H. (2014b). Effect of copper oxide nanoparticles on the conformation and activity of β-galactosidase. Colloids Surface B Biointerfaces, 123, 96–105. https://doi.org/10.1016/j.colsurfb.2014.08.035
   PubMed Web of Science ®Google Scholar
• Rabbani, G., Lee, E. J., Ahmad, K., Baig, M. H., & Choi, I. (2018). Binding of tolperisone hydrochloride with human serum albumin: Effects on the conformation, thermodynamics, and activity of HSA. Molecular Pharmaceutics, 15(4), 1445–1456.
   PubMed Web of Science ®Google Scholar
• Rinaldo, D., & Field, M. J. (2003). A Computational study of the open and closed forms of the N-Lobe human serum transferrin apoprotein. Biophysical Journal, 85(6), 3485–3501.
   PubMed Web of Science ®Google Scholar
• Rinaldo, D., & Field, M. J. (2004). A density functional theory study of the iron-binding site of human serum transferrin. Australian Journal of Chemistry, 57(12), 1219–1222. https://doi.org/10.1071/CH04103
   Web of Science ®Google Scholar
• Schmidtke, P., Luque, F. J., Murray, J. B., & Barril, X. (2011). Shielded hydrogen bonds as structural determinants of binding kinetics: Application in drug design. Journal of the American Chemical Society, 133(46), 18903–18910.
   PubMed Web of Science ®Google Scholar
• Sharma, R. C., Surendran, T., Haridasan, T. K., & Sunta, C. M. (1989). In vivo measurements of low energy photon (LEP) emitters. Bulletin of Radiation Protocols, 12, 41–56.
   Google Scholar
• Sokołowska, M., Wszelaka-Rylik, M., Poznański, J., & Bal, W. (2009). Spectroscopic and thermodynamic determination of three distinct binding sites for Co(II) ions in human serum albumin. Journal of Inorganic Biochemistry, 103(7), 1005–1013.
   PubMed Web of Science ®Google Scholar
• Taylor, D. M. (1998). The bioinorganic chemistry of actinides in blood. Journal of Alloys and Compounds. 271, 6–10.
   Web of Science ®Google Scholar
• Taylor, D. M., & Farrow, L. C. (1987). Identification of transferrin as the main binding site for protactinium in rat blood serum. International Journal of Radiation Application and Instrumentation Part B, 14(1), 27–31. https://doi.org/10.1016/0883-2897(87)90157-7
   PubMedGoogle Scholar
• Taylor, D., Duffield, J., Williams, D., Yule, L., Gaskin, P., & Unalkat, P. (1991). Binding of f-elements to the iron-transport protein transferrin. European Journal of Solid State and Inorganic Chemistry. 28, 271–274.
   Google Scholar
• Tiwary, P., & Parrinello, M. (2015). A time-independent free energy estimator for metadynamics. The Journal of Physical Chemistry. B, 119(3), 736–742. https://doi.org/10.1021/jp504920s
   PubMed Web of Science ®Google Scholar
• Wang, Z., Ho, J. X., Ruble, J. R., Rose, J., Rüker, F., Ellenburg, M., Murphy, R., Click, J., Soistman, E., Wilkerson, L., & Carter, D. C. (2013). Structural studies of several clinically important oncology drugs in complex with human serum albumin. Biochimica Biophysica Acta, 1830(12), 5356–5374. https://doi.org/10.1016/j.bbagen.2013.06.032
   PubMed Web of Science ®Google Scholar
• Yang, Y., Feng, Y., Wang, Y., Wang, L., & Shi, W. (2013). Interactions between U(VI) and bovine serum albumin. Journal of Radioanalytical and Nuclear Chemistry, 298(2), 903–908. https://doi.org/10.1007/s10967-013-2487-x
   Web of Science ®Google Scholar