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Research Article

Binding site prediction between lysozyme and glucose-regulated protein 78, a hope to fight amyloidosis

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Received 28 Aug 2023, Accepted 14 Feb 2024, Published online: 23 Feb 2024

References

  • Aarsland, D., Perry, R., Brown, A., Larsen, J. P., & Ballard, C. (2005). Neuropathology of dementia in Parkinson’s disease: A prospective, community‐based study. Annals of Neurology, 58(5), 773–776. https://doi.org/10.1002/ana.20635
  • 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, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Adasme, M. F., Linnemann, K. L., Bolz, S. N., Kaiser, F., Salentin, S., Haupt, V. J., & Schroeder, M. (2021). PLIP 2021: Expanding the scope of the protein–ligand interaction profiler to DNA and RNA. Nucleic Acids Research, 49(W1), W530–W534. https://doi.org/10.1093/nar/gkab294
  • Booth, D. R., Sunde, M., Bellotti, V., Robinson, C. V., Hutchinson, W. L., Fraser, P. E., Hawkins, P. N., Dobson, C. M., Radford, S. E., Blake, C. C., & Pepys, M. B. (1997). Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature, 385(6619), 787–793. https://doi.org/10.1038/385787a0
  • Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614. https://doi.org/10.1002/jcc.21287
  • Chen, Y., & Brandizzi, F. (2013). IRE1: ER stress sensor and cell fate executor. Trends in Cell Biology, 23(11), 547–555. https://doi.org/10.1016/j.tcb.2013.06.005
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr, 40(1), 82–92. https://docplayer.net/14026575-Pymol-an-open-source-molecular-graphics-tool.html
  • Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., Wiewiora, R. P., Brooks, B. R., & Pande, V. S. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659
  • Elfiky, A. A. (2020). Human papillomavirus E6: Host cell receptor, GRP78, binding site prediction. Journal of Medical Virology, 92(12), 3759–3765. https://doi.org/10.1002/jmv.25737
  • Elfiky, A. A., & Ibrahim, I. M. (2021). Zika virus envelope–heat shock protein A5 (GRP78) binding site prediction. Journal of Biomolecular Structure & Dynamics, 39(14), 5248–5260. https://doi.org/10.1080/07391102.2020.1784794
  • Elfiky, A. A., Ibrahim, I. M., Ibrahim, M. N., & Elshemey, W. M. (2022). Host-cell recognition of SARS-CoV-2 spike receptor binding domain from different variants. The Journal of Infection, 85(6), 702–769. https://doi.org/10.1016/j.jinf.2022.10.009
  • Fu, X. L., & Gao, D. S. (2014). Endoplasmic reticulum proteins quality control and the unfolded protein response: The regulative mechanism of organisms against stress injuries. BioFactors (Oxford, England), 40(6), 569–585. https://doi.org/10.1002/biof.1194
  • Funahashi, J., Takano, K., Yamagata, Y., & Yutani, K. (2000). Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions. Biochemistry, 39(47), 14448–14456. https://doi.org/10.1021/bi0015717
  • Garg, V. K., Avashthi, H., Tiwari, A., Jain, P. A., Ramkete, P. W., Kayastha, A. M., & Singh, V. K. (2016). MFPPI–multi FASTA ProtParam interface. Bioinformation, 12(2), 74–77. https://doi.org/10.6026/97320630012074
  • Ghosh, S., Patel, N., & Chakrabarti, R. (2016). Probing the salt concentration dependent nucleobase distribution in a single-stranded DNA–single-walled carbon nanotube hybrid with molecular dynamics. The Journal of Physical Chemistry B, 120(3), 455–466. https://doi.org/10.1021/acs.jpcb.5b12044
  • Gonzalez–Gronow, M., Angelica Selim, M., Papalas, J., Pizzo, S. V. (2009). GRP78: A multifunctional receptor on the cell surface. Antioxidants & Redox Signaling, 11(9), 2299–2306. https://doi.org/10.1089/ARS.2009.2568
  • Gregersen, N., Bolund, L., & Bross, P. (2005). Protein misfolding, aggregation, and degradation in disease. Molecular Biotechnology, 31(2), 141–150. https://doi.org/10.1385/MB:31:2:141
  • Hetz, C. (2012). The unfolded protein response: Controlling cell fate decisions under ER stress and beyond. Nature Reviews Molecular Cell Biology, 13(2), 89–102. https://doi.org/10.1038/nrm3270
  • 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
  • Ibrahim, I. M., Abdelmalek, D. H., & Elfiky, A. A. (2019). GRP78: A cell’s response to stress. Life Sciences, 226, 156–163. https://doi.org/10.1016/j.lfs.2019.04.022
  • Ibrahim, I. M., Abdelmalek, D. H., Elshahat, M. E., & Elfiky, A. A. (2020). COVID-19 spike-host cell receptor GRP78 binding site prediction. The Journal of Infection, 80(5), 554–562. https://doi.org/10.1016/j.jinf.2020.02.026
  • Inaka, K., Kanaya, E., Kikuchi, M., & Miki, K. (2001). Crystal structure of a mutant human lysozyme with a substituted disulfide bond. Proteins, 43(4), 413–419. https://doi.org/10.1002/prot.1054
  • Jurrus, E., Engel, D., Star, K., Monson, K., Brandi, J., Felberg, L. E., Brookes, D. H., Wilson, L., Chen, J., Liles, K., Chun, M., Li, P., Gohara, D. W., Dolinsky, T., Konecny, R., Koes, D. R., Nielsen, J. E., Head-Gordon, T., Geng, W., … Baker, N. A. (2018). Improvements to the APBS biomolecular solvation software suite. Protein Science: A Publication of the Protein Society, 27(1), 112–128. https://doi.org/10.1002/pro.3280
  • Kamada, Y., Kusakabe, T., & Sugimoto, Y. (2015). Amyloidogenic lysozymes accumulate in the endoplasmic reticulum accompanied by the augmentation of ER stress signals. Biochimica et Biophysica Acta, 1850(6), 1107–1119. https://doi.org/10.1016/j.bbagen.2015.01.018
  • Kamada, Y., Nawata, Y., & Sugimoto, Y. (2016). Lysozyme mutants accumulate in cells while associated at their N-terminal alpha-domain with the endoplasmic reticulum chaperone GRP78/BiP. International Journal of Biological Sciences, 12(2), 184–197. https://doi.org/10.7150/ijbs.13710
  • Kim, Y., Lillo, A. M., Steiniger, S. C. J., Liu, Y., Ballatore, C., Anichini, A., Mortarini, R., Kaufmann, G. F., Zhou, B., Felding-Habermann, B., & Janda, K. D. (2006). Targeting heat shock proteins on cancer cells: Selection, characterization, and cell-penetrating properties of a peptidic GRP78 ligand. Biochemistry, 45(31), 9434–9444. https://doi.org/10.1021/bi060264j
  • Kumita, J. R., Helmfors, L., Williams, J., Luheshi, L. M., Menzer, L., Dumoulin, M., Lomas, D. A., Crowther, D. C., Dobson, C. M., & Brorsson, A. C. (2012). Disease-related amyloidogenic variants of human lysozyme trigger the unfolded protein response and disturb eye development in Drosophila melanogaster. FASEB Journal, 26(1), 192–202. https://doi.org/10.1096/fj.11-185983
  • Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935
  • Lindgren, M., & Hammarström, P. (2010). Amyloid oligomers: Spectroscopic characterization of amyloidogenic protein states. The FEBS Journal, 277(6), 1380–1388. https://doi.org/10.1111/j.1742-4658.2010.07571.x
  • Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2022). ColabFold: Making protein folding accessible to all. Nature Methods, 19(6), 679–682. https://doi.org/10.1038/s41592-022-01488-1
  • Okada, T., Yoshida, H., Akazawa, R., Negishi, M., & Mori, K. (2002). Distinct roles of activating transcription factor 6 (ATF6) and double-stranded RNA-activated protein kinase-like endoplasmic reticulum kinase (PERK) in transcription during the mammalian unfolded protein response. The Biochemical Journal, 366(Pt 2), 585–594. https://doi.org/10.1042/BJ20020391
  • Puig, A., & Gilbert, H. F. (1994). Anti-chaperone behavior of BiP during the protein disulfide isomerase-catalyzed refolding of reduced denatured lysozyme. Journal of Biological Chemistry, 269(41), 25889–25896. https://doi.org/10.1016/S0021-9258(18)47329-2
  • Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, W320–W324. https://doi.org/10.1093/nar/gku316
  • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), 539. https://doi.org/10.1038/msb.2011.75
  • Sziegat, F., Wirmer‐Bartoschek, J., & Schwalbe, H. (2011). Characteristics of human lysozyme and its disease‐related mutants in their unfolded states. Angewandte Chemie, 123(24), 5628–5632. https://doi.org/10.1002/ange.201008040
  • Takano, K., Ota, M., Ogasahara, K., Yamagata, Y., Nishikawa, K., & Yutani, K. (1999). Experimental verification of thestability profile of mutant protein’(SPMP) data using mutant human lysozymes. Protein Engineering, 12(8), 663–672. https://doi.org/10.1093/protein/12.8.663
  • Takano, K., Yamagata, Y., & Yutani, K. (2001). Role of non‐glycine residues in left‐handed helical conformation for the conformational stability of human lysozyme. Proteins, 44(3), 233–243. https://doi.org/10.1002/prot.1088
  • Takano, K., Yamagata, Y., Kubota, M., Funahashi, J., Fujii, S., & Yutani, K. (1999). Contribution of hydrogen bonds to the conformational stability of human lysozyme: Calorimetry and x-ray analysis of six Ser→ Ala mutants. Biochemistry, 38(20), 6623–6629. https://doi.org/10.1021/bi9901228
  • Tarabara, U., et al. (2018). Molecular dynamics study of amyloidogenic mutants of human lysozyme. East European Journal of Physics, 4, 30–39. https://doi.org/10.26565/2312-4334-2018-4-04
  • Tubiana, T., Carvaillo, J. C., Boulard, Y., & Bressanelli, S. (2018). TTClust: A versatile molecular simulation trajectory clustering program with graphical summaries. Journal of Chemical Information and Modeling, 58(11), 2178–2182. https://doi.org/10.1021/acs.jcim.8b00512
  • Tyedmers, J., Mogk, A., & Bukau, B. (2010). Cellular strategies for controlling protein aggregation. Nature Reviews. Molecular Cell Biology, 11(11), 777–788. https://doi.org/10.1038/nrm2993
  • UniProt Consortium. (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100
  • van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2. 2 web server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
  • Veerhuis, R., Boshuizen, R., & Familian, A. (2005). Amyloid associated proteins in Alzheimer’s and prion disease. Current Drug Targets. CNS and Neurological Disorders, 4(3), 235–248. https://doi.org/10.2174/1568007054038184
  • Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein–protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
  • Yang, J., Nune, M., Zong, Y., Zhou, L., & Liu, Q. (2015). Close and allosteric opening of the polypeptide-binding site in a human Hsp70 chaperone BiP. Structure (London, England: 1993), 23(12), 2191–2203. https://doi.org/10.1016/j.str.2015.10.012
  • Yoshida, H., Uemura, A., & Mori, K. (2009). pXBP1 (U), a negative regulator of the unfolded protein response activator pXBP1 (S), targets ATF6 but not ATF4 in proteasome-mediated degradation. Cell Structure and Function, 34(1), 1–10. https://doi.org/10.1247/csf.06028

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