Insights into the conformational, secondary structural, dynamical and hydration pattern changes of glucose mediated glycated HSA: a molecular dynamics approach

References

• Abou-Zied, O. K., & Al-Lawatia, N. (2011). Exploring the drug-binding site Sudlow I of human serum albumin: The role of water and Trp214 in molecular recognition and ligand binding. Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 12(2), 270–274. https://doi.org/10.1002/cphc.201000742
   PubMed Web of Science ®Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2(2), 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Awasthi, S., Murugan, N. A., & Saraswathi, N. T. (2015). Advanced glycation end products modulate structure and drug binding properties of albumin. Molecular Pharmaceutics, 12(9), 3312–3322. https://doi.org/10.1021/acs.molpharmaceut.5b00318
   PubMed Web of Science ®Google Scholar
• Awasthi, S., Ravi, A., & Saraswathi, N. T. (2017). Troxerutin imparts preservative effects on albumin by preventing Maillard reaction-mediated early and advanced glycation modification. Journal of Biomolecular Structure & Dynamics, 35(12), 2681–2687. https://doi.org/10.1080/07391102.2016.1229218
   PubMed Web of Science ®Google Scholar
• Awasthi, S., Sankaranarayanan, K., & Saraswathi, N. T. (2016). Advanced glycation end products induce differential structural modifications and fibrillation of albumin. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 163, 60–67. https://doi.org/10.1016/j.saa.2016.03.023
   PubMed Web of Science ®Google Scholar
• Awasthi, S., & Saraswathi, N. T. (2016a). Elucidating the molecular interaction of sinigrin, a potent anticancer glucosinolate from cruciferous vegetables with bovine serum albumin: Effect of methylglyoxal modification. Journal of Biomolecular Structure & Dynamics, 34(10), 2224–2232. https://doi.org/10.1080/07391102.2015.1110835
   PubMed Web of Science ®Google Scholar
• Awasthi, S., & Saraswathi, N. T. (2016b). Vanillin restrains non-enzymatic glycation and aggregation of albumin by chemical chaperone like function. International Journal of Biological Macromolecules, 87, 1–6. https://doi.org/10.1016/j.ijbiomac.2016.02.041
   PubMed Web of Science ®Google Scholar
• Balsera, M. A., Wriggers, W., Oono, Y., & Schulten, K. (1996). Principal component analysis and long time protein dynamics. The Journal of Physical Chemistry, 100(7), 2567–2572. https://doi.org/10.1021/jp9536920
   Web of Science ®Google Scholar
• Baraka-Vidot, J., Guerin-Dubourg, A., Bourdon, E., & Rondeau, P. (2012). Impaired drug-binding capacities of in vitro and in vivo glycated albumin. Biochimie, 94(9), 1960–1967. https://doi.org/10.1016/j.biochi.2012.05.017
   PubMed Web of Science ®Google Scholar
• Barnaby, O. S., Cerny, R. L., Clarke, W., & Hage, D. S. (2011). Quantitative analysis of glycation patterns in human serum albumin using 16O/18O-labeling and MALDI-TOF MS. Clinica Chimica Acta; International Journal of Clinical Chemistry, 412(17–18), 1606–1615. https://doi.org/10.1016/j.cca.2011.05.012
   PubMed Web of Science ®Google Scholar
• Barzegar, A., Moosavi-Movahedi, A. A., Sattarahmady, N., Hosseinpour-Faizi, M. A., Aminbakhsh, M., Ahmad, F., Saboury, A. A., Ganjali, M. R., & Norouzi, P. (2007). Spectroscopic studies of the effects of glycation of human serum albumin on L-Trp binding. Protein and Peptide Letters, 14(1), 13–18. https://doi.org/10.2174/092986607779117191
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., & Hayward, S. (2000). Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10(2), 165–169. https://doi.org/10.1016/s0959-440x(00)00061-0
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bhattacharya, A. A., Grüne, T., & Curry, S. (2000). Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. Journal of Molecular Biology, 303(5), 721–732. https://doi.org/10.1006/jmbi.2000.4158
   PubMed Web of Science ®Google Scholar
• Bourdon, E., Loreau, N., & Blache, D. (1999). Glucose and free radicals impair the antioxidant properties of serum albumin. FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology, 13(2), 233–244. https://doi.org/10.1096/fasebj.13.2.233
   PubMed Web of Science ®Google Scholar
• Chadborn, N., Bryant, J., Bain, A. J., & O'Shea, P. (1999). Ligand-dependent conformational equilibria of serum albumin revealed by tryptophan fluorescence quenching. Biophysical Journal, 76(4), 2198–2207. https://doi.org/10.1016/S0006-3495(99)77375-3
   PubMed Web of Science ®Google Scholar
• Chaudhuri, J., Bains, Y., Guha, S., Kahn, A., Hall, D., Bose, N., Gugliucci, A., & Kapahi, P. (2018). The role of advanced glycation end products in aging and metabolic diseases: Bridging association and causality. Cell Metabolism, 28(3), 337–352. https://doi.org/10.1016/j.cmet.2018.08.014
   PubMed Web of Science ®Google Scholar
• Colmenarejo, G. (2003). In silico prediction of drug-binding strengths to human serum albumin. Medicinal Research Reviews, 23(3), 275–301. https://doi.org/10.1002/med.10039
   PubMed Web of Science ®Google Scholar
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.), 1084, 193–226. https://doi.org/10.1007/978-1-62703-658-0_11
   PubMedGoogle Scholar
• Díaz, N., Suárez, D., Sordo, T. L., & Merz, K. M. Jr (2001). Molecular dynamics study of the IIA binding site in human serum albumin: Influence of the protonation state of Lys195 and Lys199. Journal of Medicinal Chemistry, 44(2), 250–260. https://doi.org/10.1021/jm000340v
   PubMed Web of Science ®Google Scholar
• Esackimuthu, P., & Saraswathi, N. T. (2021). Non enzymatic covalent modification by glycolysis end product converts hemoglobin into its oxidative stress potency state. Biochemical and Biophysical Research Communications, 534, 387–394. https://doi.org/10.1016/j.bbrc.2020.11.072
   PubMed Web of Science ®Google Scholar
• Fanali, G., di Masi, A., Trezza, V., Marino, M., Fasano, M., & Ascenzi, P. (2012). Human serum albumin: From bench to bedside. Molecular Aspects of Medicine, 33(3), 209–290. https://doi.org/10.1016/j.mam.2011.12.002
   PubMed Web of Science ®Google Scholar
• Fasano, M., Curry, S., Terreno, E., Galliano, M., Fanali, G., Narciso, P., Notari, S., & Ascenzi, P. (2005). The extraordinary ligand binding properties of human serum albumin. IUBMB Life, 57(12), 787–796. https://doi.org/10.1080/15216540500404093
   PubMed Web of Science ®Google Scholar
• Fossum, C. J., Johnson, B. O. V., Golde, S. T., Kielman, A. J., Finke, B., Smith, M. A., Lowater, H. R., Laatsch, B. F., Bhattacharyya, S., & Hati, S. (2023). Insights into the mechanism of tryptophan fluorescence quenching due to synthetic crowding agents: A combined experimental and computational study. ACS Omega, 8(47), 44820–44830. https://doi.org/10.1021/acsomega.3c06006
   PubMed Web of Science ®Google Scholar
• Ghuman, J., Zunszain, P. A., Petitpas, I., Bhattacharya, A. A., Otagiri, M., & Curry, S. (2005). Structural basis of the drug-binding specificity of human serum albumin. Journal of Molecular Biology, 353(1), 38–52. https://doi.org/10.1016/j.jmb.2005.07.075
   PubMed Web of Science ®Google Scholar
• Guizado, T. R. (2014). Analysis of the structure and dynamics of human serum albumin. Journal of Molecular Modeling, 20(10), 2450. https://doi.org/10.1007/s00894-014-2450-y
   PubMed Web of Science ®Google Scholar
• Havlikova, M., Zatloukalova, M., Ulrichova, J., Dobes, P., & Vacek, J. (2015). Electrocatalytic assay for monitoring methylglyoxal-mediated protein glycation. Analytical Chemistry, 87(3), 1757–1763. https://doi.org/10.1021/ac503705d
   PubMed Web of Science ®Google Scholar
• Hermans, J., Berendsen, H. J. C., van Gunsteren, W. F., & Postma, J. P. M. (1984). A consistent empirical potential for water-protein interactions. Biopolymers, 23(8), 1513–1518. https://doi.org/10.1002/bip.360230807
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jeevanandam, J., Burra, V. L. S. P., & Saraswathi, N. T. (2023a). Conformational variation of site specific glycated albumin: A molecular dynamics approach. Computers in Biology and Medicine, 164, 107276. https://doi.org/10.1016/j.compbiomed.2023.107276
   PubMed Web of Science ®Google Scholar
• Jeevanandam, J., Paramasivam, E., & Saraswathi, N. T. (2023b). Glycation restrains open-closed conformation of Insulin. Computational Biology and Chemistry, 102, 107803. https://doi.org/10.1016/j.compbiolchem.2022.107803
   PubMed Web of Science ®Google Scholar
• Kamal, J. K., Zhao, L., & Zewail, A. H. (2004). Ultrafast hydration dynamics in protein unfolding: Human serum albumin. Proceedings of the National Academy of Sciences of the United States of America, 101(37), 13411–13416. https://doi.org/10.1073/pnas.0405724101
   PubMed Web of Science ®Google Scholar
• Ketrat, S., Japrung, D., & Pongprayoon, P. (2020). Exploring how structural and dynamic properties of bovine and canine serum albumins differ from human serum albumin. Journal of Molecular Graphics & Modelling, 98, 107601. https://doi.org/10.1016/j.jmgm.2020.107601
   PubMed Web of Science ®Google Scholar
• Kim, K. J., & Lee, B. W. (2012). The roles of glycated albumin as intermediate glycation index and pathogenic protein. Diabetes & Metabolism Journal, 36(2), 98–107. https://doi.org/10.4093/dmj.2012.36.2.98
   PubMedGoogle Scholar
• Kisugi, R., Kouzuma, T., Yamamoto, T., Akizuki, S., Miyamoto, H., Someya, Y., Yokoyama, J., Abe, I., Hirai, N., & Ohnishi, A. (2007). Structural and glycation site changes of albumin in diabetic patient with very high glycated albumin. Clinica Chimica Acta; International Journal of Clinical Chemistry, 382(1-2), 59–64. https://doi.org/10.1016/j.cca.2007.04.001
   PubMed Web of Science ®Google Scholar
• Krämer, A. C., & Davies, M. J. (2019). Effect of methylglyoxal-induced glycation on the composition and structure of β-lactoglobulin and α-lactalbumin. Journal of Agricultural and Food Chemistry, 67(2), 699–710. https://doi.org/10.1021/acs.jafc.8b05809
   PubMed Web of Science ®Google Scholar
• Laurent, B., Chavent, M., Cragnolini, T., Dahl, A. C., Pasquali, S., Derreumaux, P., Sansom, M. S., & Baaden, M. (2015). Epock: Rapid analysis of protein pocket dynamics. Bioinformatics (Oxford, England), 31(9), 1478–1480. https://doi.org/10.1093/bioinformatics/btu822
   PubMed Web of Science ®Google Scholar
• Lee, P., & Wu, X. (2015). Review: Modifications of human serum albumin and their binding effect. Current Pharmaceutical Design, 21(14), 1862–1865. https://doi.org/10.2174/1381612821666150302115025
   PubMed Web of Science ®Google Scholar
• Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. https://doi.org/10.1021/ct200196m
   PubMed Web of Science ®Google Scholar
• Moriyama, Y., Ohta, D., Hachiya, K., Mitsui, Y., & Takeda, K. (1996). Fluorescence behavior of tryptophan residues of bovine and human serum albumins in ionic surfactant solutions: A comparative study of the two and one tryptophan(s) of bovine and human albumins. Journal of Protein Chemistry, 15(3), 265–272. https://doi.org/10.1007/BF01887115
   PubMedGoogle Scholar
• Neviere, R., Yu, Y., Wang, L., Tessier, F., & Boulanger, E. (2016). Implication of advanced glycation end products (Ages) and their receptor (Rage) on myocardial contractile and mitochondrial functions. Glycoconjugate Journal, 33(4), 607–617. https://doi.org/10.1007/s10719-016-9679-x
   PubMed Web of Science ®Google Scholar
• Ni, M., Song, X., Pan, J., Gong, D., & Zhang, G. (2021). Vitexin inhibits protein glycation through structural protection, methylglyoxal trapping, and alteration of glycation site. Journal of Agricultural and Food Chemistry, 69(8), 2462–2476. https://doi.org/10.1021/acs.jafc.0c08052
   PubMed Web of Science ®Google Scholar
• Paris, G., Ramseyer, C., & Enescu, M. (2014). A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin. Biopolymers, 101(5), 561–572. https://doi.org/10.1002/bip.22418
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Prasanna, G., & Saraswathi, N. T. (2017). Linolenic acid prevents early and advanced glycation end-products (AGEs) modification of albumin. International Journal of Biological Macromolecules, 95, 121–125. https://doi.org/10.1016/j.ijbiomac.2016.11.035
   PubMed Web of Science ®Google Scholar
• Qiu, W., Zhang, L., Okobiah, O., Yang, Y., Wang, L., Zhong, D., & Zewail, A. H. (2006). Ultrafast solvation dynamics of human serum albumin: Correlations with conformational transitions and site-selected recognition. The Journal of Physical Chemistry. B, 110(21), 10540–10549. https://doi.org/10.1021/jp055989w
   PubMed Web of Science ®Google Scholar
• Rondeau, P., & Bourdon, E. (2011). The glycation of albumin: Structural and functional impacts. Biochimie, 93(4), 645–658. https://doi.org/10.1016/j.biochi.2010.12.003
   PubMed Web of Science ®Google Scholar
• Sattarahmady, N., Moosavi-Movahedi, A. A., Habibi-Rezaei, M., Ahmadian, S., Saboury, A. A., Heli, H., & Sheibani, N. (2008). Detergency effects of nanofibrillar amyloid formation on glycation of human serum albumin. Carbohydrate Research, 343(13), 2229–2234. https://doi.org/10.1016/j.carres.2008.04.036
   PubMed Web of Science ®Google Scholar
• Schrödinger, L., & DeLano, W. (2020). PyMOL. Retrieved from http://www.pymol.org/pymol
   Google Scholar
• Shaklai, N., Garlick, R. L., & Bunn, H. F. (1984). Nonenzymatic glycosylation of human serum albumin alters its conformation and function. The Journal of Biological Chemistry, 259(6), 3812–3817. https://doi.org/10.1016/S0021-9258(17)43168-1
   PubMed Web of Science ®Google Scholar
• Silva, T. F. D., Vila-Viçosa, D., Reis, P. B. P. S., Victor, B. L., Diem, M., Oostenbrink, C., & Machuqueiro, M. (2018). The impact of using single atomistic long-range cutoff schemes with the GROMOS 54A7 force field. Journal of Chemical Theory and Computation, 14(11), 5823–5833. https://doi.org/10.1021/acs.jctc.8b00758
   PubMed Web of Science ®Google Scholar
• Singh, V. P., Bali, A., Singh, N., & Jaggi, A. S. (2014). Advanced glycation end products and diabetic complications. The Korean Journal of Physiology & Pharmacology: Official Journal of the Korean Physiological Society and the Korean Society of Pharmacology, 18(1), 1–14. https://doi.org/10.4196/kjpp.2014.18.1.1
   PubMed Web of Science ®Google Scholar
• Stank, A., Kokh, D. B., Fuller, J. C., & Wade, R. C. (2016). Protein binding pocket dynamics. Accounts of Chemical Research, 49(5), 809–815. https://doi.org/10.1021/acs.accounts.5b00516
   PubMed Web of Science ®Google Scholar
• Sugio, S., Kashima, A., Mochizuki, S., Noda, M., & Kobayashi, K. (1999). Crystal structure of human serum albumin at 2.5 A resolution. Protein Engineering, 12(6), 439–446. https://doi.org/10.1093/protein/12.6.439
   PubMedGoogle Scholar
• Tayeh, N., Rungassamy, T., & Albani, J. R. (2009). Fluorescence spectral resolution of tryptophan residues in bovine and human serum albumins. Journal of Pharmaceutical and Biomedical Analysis, 50(2), 107–116. https://doi.org/10.1016/j.jpba.2009.03.015
   PubMed Web of Science ®Google Scholar
• Yao, F., Coquery, J., & Lê Cao, K. A. (2012). Independent principal component analysis for biologically meaningful dimension reduction of large biological data sets. BMC Bioinformatics, 13(1), 24. https://doi.org/10.1186/1471-2105-13-24
   PubMedGoogle Scholar
• Żurawska-Płaksej, E., Rorbach-Dolata, A., Wiglusz, K., & Piwowar, A. (2018). The effect of glycation on bovine serum albumin conformation and ligand binding properties with regard to gliclazide. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 189, 625–633. https://doi.org/10.1016/j.saa.2017.08.071
   PubMed Web of Science ®Google Scholar