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Research Articles

In silico analysis of the predicted protein-protein interaction of syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein

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Pages 3956-3963 | Received 05 Oct 2021, Accepted 24 Mar 2022, Published online: 04 Apr 2022

References

  • Albertini, A. A. V., Baquero, E., Ferlin, A., & Gaudin, Y. (2012). Molecular and cellular aspects of rhabdovirus entry. Viruses, 4(1), 117–139. https://doi.org/10.3390/v4010117
  • Alviar, K. B., Rotenberg, D., Martin, K. M., & Whitfield, A. E. (2022). Identification of interacting proteins of maize mosaic virus glycoprotein in its vector, Peregrinus maidis. BioRxiv, 1–26 20220201478665. https://doi.org/10.1101/2022.02.01.478665
  • Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E., Grosdidier, A., Hernandez, C., Ioannidis, V., Kuznetsov, D., Liechti, R., Moretti, S., Mostaguir, K., Redaschi, N., Rossier, G., Xenarios, I., & Stockinger, H. (2012). ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(Web Server issue), W597–W603.
  • Balch, W. E., Elliott, M. M., & Keller, D. S. (1986). ATP-coupled transport of vesicular stomatitis virus G protein between the endoplasmic reticulum and the Golgi. Journal of Biological Chemistry, 261(31), 14681–14689. https://doi.org/10.1016/S0021-9258(18)66925-X
  • Barandoc-Alviar, K., Ramirez, G. M., Rotenberg, D., & Whitfield, A. E. (2016). Analysis of acquisition and titer of maize mosaic Rhabdovirus in its vector, peregrinus maidis (Hemiptera: Delphacidae). Journal of Insect Science (Online), 16(1). https://doi.org/10.1093/jisesa/iev154 28076276
  • Belot, L., Albertini, A., & Gaudin, Y. (2019). Structural and cellular biology of rhabdovirus entry. Advances in Virus Research, 104, 147–183. https://doi.org/10.1016/bs.aivir.2019.05.003 31439148
  • Bossis, I., Roden, R. B. S., Gambhira, R., Yang, R., Tagaya, M., Howley, P. M., & Meneses, P. I. (2005). Interaction of tSNARE syntaxin 18 with the papillomavirus minor capsid protein mediates infection. Journal of Virology, 79(11), 6723–6731. https://doi.org/10.1128/JVI.79.11.6723-6731.2005 15890910
  • Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/10.1107/S0907444909042073 20057044
  • Christoffer, C., Chen, S., Bharadwaj, V., Aderinwale, T., Kumar, V., Hormati, M., & Kihara, D. (2021). LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acids Research, 49(W1), W359–W365. https://doi.org/10.1093/nar/gkab336 33963854
  • Coll, J. M. (1995). The glycoprotein G of rhabdoviruses. Archives of Virology, 140(5), 827–851. https://doi.org/10.1007/BF01314961 7605197
  • De Vries, S. J., Van Dijk, M., & Bonvin, A. M. J. J. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5(5), 883–897. https://doi.org/10.1038/nprot.2010.32 20431534
  • Dietzgen, R., Mann, K., & Johnson, K. (2016). Plant Virus–Insect Vector Interactions: Current and Potential Future Research Directions. Viruses, 8(11), 303. https://doi.org/10.3390/v8110303
  • Du, Z., Su, H., Wang, W., Ye, L., Wei, H., Peng, Z., Anishchenko, I., Baker, D., & Yang, J. (2021). The trRosetta server for fast and accurate protein structure prediction. Nature Protocols, 16(12), 5634–5651.
  • Fasshauer, D., Sutton, R. B., Brunger, A. T., & Jahn, R. (1998). Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q-and R-SNAREs. Proceedings of the National Academy of Sciences, 95(26), 15781–15786. https://doi.org/10.1073/pnas.95.26.15781
  • Gaudin, Y., Ruigrok, R. W. H., Tuffereau, C., Knossow, M., & Flamand, A. (1992). Rabies virus glycoprotein is a trimer. Virology, 187(2), 627–632.
  • Guo, Y., Duan, M., Wang, X., Gao, J., Guan, Z., & Zhang, M. (2019). Early events in rabies virus infection-Attachment, entry, and intracellular trafficking. In Virus Research, 263, 217–225. https://doi.org/10.1016/j.virusres.2019.02.006
  • Hatsuzawa, K., Hirose, H., Tani, K., Yamamoto, A., Scheller, R. H., & Tagaya, M. (2000). Syntaxin 18, a SNAP receptor that functions in the endoplasmic reticulum, intermediate compartment, and cis-Golgi vesicle trafficking. Journal of Biological Chemistry, 275(18), 13713–13720. https://doi.org/10.1074/jbc.275.18.13713
  • Heo, L., Lee, H., & Seok, C. (2016). GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking. Scientific Reports, 6(1), 1–10. https://doi.org/10.1038/srep32153
  • Jackson, A. O., Dietzgen, R. G., Goodin, M. M., Bragg, J. N., & Deng, M. (2005). Biology of plant rhabdoviruses. Annual Review of Phytopathology, 43, 623–660.
  • Janin, J., Bahadur, R. P., & Chakrabarti, P. (2008). Protein–protein interaction and quaternary structure. Quarterly Reviews of Biophysics, 41(2), 133–180.
  • Jiménez-García, B., Pons, C., & Fernández-Recio, J. (2013). pyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics (Oxford, England), 29(13), 1698–1699. https://doi.org/10.1093/bioinformatics/btt262
  • Jourdan-Ruf, C., Marchand, J.-L., Pham, H., Markham, P., & Buduca, C. (1995). Maize streak, maize stripe and maize mosaic virus diseases in the tropics (Africa and islands in the Indian Ocean) (pp. 55–69). Agriculture et Développement.
  • Kannan, M., Ismail, I., & Bunawan, H. (2018). Maize dwarf mosaic virus: From genome to disease management. Viruses, 10(9), 492. https://doi.org/10.3390/v10090492
  • Karavina, C. (2014). Maize streak virus: A review of pathogen occurrence, biology and management options for smallholder farmers. African Journal of Agricultural Research, 9(36), 2736–2742.
  • Klobasa, W., Chu, F.-C., Huot, O., Grubbs, N., Rotenberg, D., Whitfield, A. E., & Lorenzen, M. D. (2021). ). Microinjection of corn planthopper, Peregrinus maidis, Embryos for CRISPR/Cas9 genome editing. Journal of Visualized Experiments: Jove, 169. e62417
  • Ko, J., Park, H., Heo, L., & Seok, C. (2012). GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research, 40(Web Server issue), W294–W297.
  • Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein–protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/10.1038/nprot.2016.169
  • Krissinel, E., & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, 372(3), 774–797.
  • Laniosz, V., Nguyen, K. C., & Meneses, P. I. (2007). Bovine Papillomavirus Type 1 infection is mediated by SNARE Syntaxin 18. Journal of Virology, 81(14), 7435–7448. https://doi.org/10.1128/JVI.00571-07
  • Liu, H., Liu, Y., Liu, S., Pang, D.-W., & Xiao, G. (2011). Clathrin-mediated endocytosis in living host cells visualized through quantum dot labeling of infectious hematopoietic necrosis virus. Journal of Virology, 85(13), 6252–6262. https://doi.org/10.1128/JVI.00109-11
  • Lu, H., Zhou, Q., He, J., Jiang, Z., Peng, C., Tong, R., & Shi, J. (2020). Recent advances in the development of protein–protein interactions modulators: Mechanisms and clinical trials. Signal Transduction and Targeted Therapy, 5(1), 1–23. https://doi.org/10.1038/s41392-020-00315-3
  • Lyles, D. S., Varela, V. A., & Parce, J. W. (1990). Dynamic nature of the quaternary structure of the vesicular stomatitis virus envelope glycoprotein. Biochemistry, 29(10), 2442–2449.
  • Nyfeler, B., Michnick, S. W., & Hauri, H.-P. (2005). Capturing protein interactions in the secretory pathway of living cells. Proceedings of the National Academy of Sciences, 102(18), 6350–6355. https://doi.org/10.1073/pnas.0501976102
  • Pelham, H. R. B. (1999). SNAREs and the secretory pathway-lessons from yeast. Experimental Cell Research, 247(1), 1–8. https://doi.org/10.1006/excr.1998.4356
  • Perkins, J. R., Diboun, I., Dessailly, B. H., Lees, J. G., & Orengo, C. (2010). Transient protein-protein interactions: Structural, functional, and network properties. Structure (London, England: 1993), 18(10), 1233–1243.
  • Pierce, B. G., Wiehe, K., Hwang, H., Kim, B.-H., Vreven, T., & Weng, Z. (2014). ZDOCK server: Interactive docking prediction of protein–protein complexes and symmetric multimers. Bioinformatics (Oxford, England), 30(12), 1771–1773.
  • Quignot, C., Rey, J., Yu, J., Tufféry, P., Guerois, R., & Andreani, J. (2018). InterEvDock2: An expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. Nucleic Acids Research, 46(W1), W408–W416.
  • Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. (2014). Protein-protein interaction detection: methods and analysis. International Journal of Proteomics, 2014, 147648. https://doi.org/10.1155/2014/147648
  • Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738.
  • Schneidman‐Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). Geometry‐based flexible and symmetric protein docking. Proteins: Structure, Function, and Bioinformatics, 60(2), 224–231. https://doi.org/10.1002/prot.20562
  • Sun, X., Yau, V. K., Briggs, B. J., & Whittaker, G. R. (2005). Role of clathrin-mediated endocytosis during vesicular stomatitis virus entry into host cells. Virology, 338(1), 53–60. https://doi.org/10.1016/j.virol.2005.05.006
  • Szklarczyk, D., Gable, A., Nastou, K., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N., Legeay, M., Fang, T., Bork, P., Jensen, L., & von Mering, C. (2021). The STRING database in 2021: Customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research, 49(D1), D605–D612. https://doi.org/10.1093/nar/gkab835
  • Tovchigrechko, A., & Vakser, I. A. (2006). GRAMM-X public web server for protein–protein docking. Nucleic Acids Research, 34(Web Server issue), W310–W314.
  • Weir, D. L., Laing, E. D., Smith, I. L., Wang, L. F., & Broder, C. C. (2014). Host cell virus entry mediated by Australian bat lyssavirus G envelope glycoprotein occurs through a clathrin-mediated endocytic pathway that requires actin and Rab5. Virology Journal, 11(1), 40. https://doi.org/10.1186/1743-422X-11-40
  • Yan, Y., Tao, H., He, J., & Huang, S.-Y. (2020). The HDOCK server for integrated protein-protein docking. Nature Protocols, 15(5), 1829–1852. https://doi.org/10.1038/s41596-020-0312-x
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8.
  • Yao, J., Rotenberg, D., Afsharifar, A., Barandoc-Alviar, K., & Whitfield, A. E. (2013). Development of RNAi methods for Peregrinus maidis, the corn planthopper. PLoS One, 8(8), e70243.
  • Yoon, T.-Y., & Munson, M. (2018). SNARE complex assembly and disassembly. Current Biology: CB, 28(8), R397–R401.
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9(1), 40–48. https://doi.org/10.1186/1471-2105-9-40
  • Zhang, Y., & Skolnick, J. (2005). TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research, 33(7), 2302–2309. https://doi.org/10.1093/nar/gki524

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