Mechanisms and Research Methods of Protein Modification in Virus Entry.

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Titel: Mechanisms and Research Methods of Protein Modification in Virus Entry.
Autoren: Xiao Y; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Gao M; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Mo X; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China.; Xiangya School of Public Health, Central South University, Changsha, 410013, Hunan Province, China., Lang J; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Wang Z; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Ma Z; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Yang M; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China., Tang B; Changde Research Center for Agricultural Biomacromolecule, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, Hunan Province, China., Liu D; Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, 530021, Guangxi Province, China. liudan.forever@163.com., He H; Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, China. helenhe@csu.edu.cn.; School of Life Sciences, Central South University, Changsha, 410013, Hunan Province, China. helenhe@csu.edu.cn.
Quelle: Applied biochemistry and biotechnology [Appl Biochem Biotechnol] 2025 Oct; Vol. 197 (10), pp. 6283-6313. Date of Electronic Publication: 2025 Jul 19.
Publikationsart: Journal Article; Review
Sprache: English
Info zur Zeitschrift: Publisher: Humana Press Country of Publication: United States NLM ID: 8208561 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1559-0291 (Electronic) Linking ISSN: 02732289 NLM ISO Abbreviation: Appl Biochem Biotechnol Subsets: MEDLINE
Imprint Name(s): Original Publication: Clifton, N.J. : Humana Press, c1981-
MeSH-Schlagworte: Protein Processing, Post-Translational* , Virus Internalization*, Humans ; Glycosylation ; Phosphorylation ; Ubiquitination ; Animals ; Protein Array Analysis
Abstract: Protein interactions are of paramount importance for the performance of biological functions within organisms. Post-translational modifications, including glycosylation and phosphorylation, regulate protein-protein interactions through non-covalent mechanisms. Glycosylation typically facilitates binding by altering surface properties, whereas phosphorylation can either enhance or disrupt interactions depending on context, collectively amplifying the biological impact of proteins. The entry of viruses and certain intracellular parasites into host cells is facilitated by these modifications, which permit the binding of ligands to receptors and the traversal of the cell membrane barrier. As research in this domain progresses, innovative methodologies are being developed, including protein microarrays and proximity-labeling techniques. These developments are being increasingly employed in disease prevention, therapeutics, and fundamental medical research. In light of the recent surge in emerging infectious diseases, the study of protein interactions has assumed heightened relevance. This review explores protein modifications, including glycosylation, phosphorylation, and ubiquitination, and focuses on their roles in viral entry. It highlights advanced methods for analyzing protein-protein interactions (PPIs), notably proximity labeling and protein microarrays, and concludes with novel insights into therapeutic development, aiming to inspire innovation in this evolving field.
(© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
Competing Interests: Declarations. Ethics Approval and Consent to Participate: Not applicable. Consent for Publication: All authors agree to publish the paper in your esteemed journal. Competing interests: The authors declare no competing interests.
References: Slater, O., Miller, B., & Kontoyianni, M. (2020). Decoding protein-protein interactions: An overview. Current Topics in Medicinal Chemistry, 20(10), 855–882. https://doi.org/10.2174/1568026620666200226105312. (PMID: 10.2174/156802662066620022610531232101126)
Benešová, I., Paulin Urminský, A., Halámková, J., & Hernychová, L. (2022). Changes of serum protein N-glycosylation in cancer. Klinická Onkologie, 35(3), 174–180. https://doi.org/10.48095/ccko2022174. (PMID: 10.48095/ccko202217435760569)
Pondugula, S. R., Dong, H., & Chen, T. (2009). Phosphorylation and protein-protein interactions in PXR-mediated CYP3A repression. Expert Opinion on Drug Metabolism & Toxicology, 5(8), 861–873. https://doi.org/10.1517/17425250903012360. (PMID: 10.1517/17425250903012360)
Stewart, V., & Ronald, P. C. (2022). Sulfotyrosine residues: Interaction specificity determinants for extracellular protein-protein interactions. The Journal of Biological Chemistry, 298(8), 102232. https://doi.org/10.1016/j.jbc.2022.102232. (PMID: 10.1016/j.jbc.2022.102232357981409372746)
Xu, J., & Richard, S. (2021). Cellular pathways influenced by protein arginine methylation: Implications for cancer. Molecular Cell, 81(21), 4357–4368. https://doi.org/10.1016/j.molcel.2021.09.011. (PMID: 10.1016/j.molcel.2021.09.011346190918571027)
Chapman, D. E., Steck, J. K., & Nerenberg, P. S. (2014). Optimizing protein-protein van der Waals interactions for the AMBER ff9x/ff12 force field. Journal of Chemical Theory and Computation, 10(1), 273–281. https://doi.org/10.1021/ct400610x. (PMID: 10.1021/ct400610x26579910)
Tam, J. Z., Palumbo, T., Miwa, J. M., & Chen, B. Y. (2022). Analysis of protein-protein interactions for intermolecular bond prediction. Molecules. https://doi.org/10.3390/molecules27196178.
Walch, P., Selkrig, J., Knodler, L. A., Rettel, M., Stein, F., Fernandez, K., et al. (2021). Global mapping of Salmonella enterica-host protein-protein interactions during infection. Cell Host & Microbe, 29(8), 1316–32.e12. https://doi.org/10.1016/j.chom.2021.06.004. (PMID: 10.1016/j.chom.2021.06.004)
Zheng, N., Wang, K., Zhan, W., & Deng, L. (2019). Targeting virus-host protein interactions: Feature extraction and machine learning approaches. Current Drug Metabolism, 20(3), 177–184. https://doi.org/10.2174/1389200219666180829121038. (PMID: 10.2174/138920021966618082912103830156155)
Chothia, C., & Janin, J. (1975). Principles of protein-protein recognition. Nature, 256(5520), 705–708. https://doi.org/10.1038/256705a0. (PMID: 10.1038/256705a01153006)
Garg, S., Alam, M. S., Bajpai, R., Kishan, K. R., & Agrawal, P. (2009). Redox biology of Mycobacterium tuberculosis H37Rv: Protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide. BMC Biochemistry, 10, 1. https://doi.org/10.1186/1471-2091-10-1. (PMID: 10.1186/1471-2091-10-1191212282631452)
Kusova, A. M., Sitnitsky, A. E., Faizullin, D. A., & Zuev, Y. F. (2019). Protein translational diffusion and intermolecular interactions of globular and intrinsically unstructured proteins. The Journal of Physical Chemistry. A, 123(46), 10190–10196. https://doi.org/10.1021/acs.jpca.9b08601. (PMID: 10.1021/acs.jpca.9b0860131657566)
Acuner Ozbabacan, S. E., Engin, H. B., Gursoy, A., & Keskin, O. (2011). Transient protein-protein interactions. Protein Engineering, Design & Selection, 24(9), 635–648. https://doi.org/10.1093/protein/gzr025. (PMID: 10.1093/protein/gzr025)
Nooren, I. M., & Thornton, J. M. (2003). Diversity of protein-protein interactions. The EMBO Journal, 22(14), 3486–3492. https://doi.org/10.1093/emboj/cdg359. (PMID: 10.1093/emboj/cdg35912853464165629)
Gerold, G., Bruening, J., & Pietschmann, T. (2016). Decoding protein networks during virus entry by quantitative proteomics. Virus Research, 218, 25–39. https://doi.org/10.1016/j.virusres.2015.09.006. (PMID: 10.1016/j.virusres.2015.09.00626365680)
Tyl, M. D., Betsinger, C. N., & Cristea, I. M. (2022). Virus-host protein interactions as footprints of human cytomegalovirus replication. Current Opinion in Virology, 52, 135–147. https://doi.org/10.1016/j.coviro.2021.11.016. (PMID: 10.1016/j.coviro.2021.11.01634923282)
Wang, S., Osgood, A. O., & Chatterjee, A. (2022). Uncovering post-translational modification-associated protein-protein interactions. Current Opinion in Structural Biology, 74, 102352. https://doi.org/10.1016/j.sbi.2022.102352. (PMID: 10.1016/j.sbi.2022.102352353342549464464)
Hsu, J. M., Li, C. W., Lai, Y. J., & Hung, M. C. (2018). Posttranslational modifications of PD-L1 and their applications in cancer therapy. Cancer Research, 78(22), 6349–6353. https://doi.org/10.1158/0008-5472.Can-18-1892. (PMID: 10.1158/0008-5472.Can-18-1892304428146242346)
Pei, J., Zhang, J., Wang, X. D., Kim, C., Yu, Y., & Cong, Q. (2023). Impact of Asp/Glu-ADP-ribosylation on protein-protein interaction and protein function. Proteomics, 23(17), e2200083. https://doi.org/10.1002/pmic.202200083. (PMID: 10.1002/pmic.20220008336453556)
Betts, M. J., Wichmann, O., Utz, M., Andre, T., Petsalaki, E., Minguez, P., et al. (2017). Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Computational Biology, 13(3), Article e1005462. https://doi.org/10.1371/journal.pcbi.1005462. (PMID: 10.1371/journal.pcbi.1005462283465095386296)
Buetow, L., & Huang, D. T. (2016). Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nature Reviews Molecular Cell Biology, 17(10), 626–642. https://doi.org/10.1038/nrm.2016.91. (PMID: 10.1038/nrm.2016.91274858996211636)
Wang, Y., & Bedford, M. T. (2023). Effectors and effects of arginine methylation. Biochemical Society Transactions, 51(2), 725–734. https://doi.org/10.1042/bst20221147. (PMID: 10.1042/bst202211473701396910212539)
Narita, T., Weinert, B. T., & Choudhary, C. (2019). Functions and mechanisms of non-histone protein acetylation. Nature Reviews Molecular Cell Biology, 20(3), 156–174. https://doi.org/10.1038/s41580-018-0081-3. (PMID: 10.1038/s41580-018-0081-330467427)
Shajahan, A., Pepi, L. E., Rouhani, D. S., Heiss, C., & Azadi, P. (2021). Glycosylation of SARS-CoV-2: Structural and functional insights. Analytical and Bioanalytical Chemistry, 413(29), 7179–7193. https://doi.org/10.1007/s00216-021-03499-x. (PMID: 10.1007/s00216-021-03499-x342355688262766)
Sheng, Y., Vinjamuri, A., Alvarez, M. R. S., Xie, Y., McGrath, M., Chen, S., et al. (2022). Host cell glycocalyx remodeling reveals SARS-CoV-2 spike protein glycomic binding sites. Frontiers in Molecular Biosciences, 9, 799703. https://doi.org/10.3389/fmolb.2022.799703. (PMID: 10.3389/fmolb.2022.799703353725208964299)
Eisenreichova, A., & Boura, E. (2022). Structural basis for SARS-CoV-2 nucleocapsid (N) protein recognition by 14–3-3 proteins. Journal of Structural Biology, 214(3), 107879. https://doi.org/10.1016/j.jsb.2022.107879. (PMID: 10.1016/j.jsb.2022.107879357810259245327)
Huang, C., Jiang, T., Pan, W., Feng, T., Zhou, X., Wu, Q., et al. (2024). Ubiquitination of NS1 confers differential adaptation of Zika virus in mammalian hosts and mosquito vectors. Advanced Science, 11(39), e2408024. https://doi.org/10.1002/advs.202408024. (PMID: 10.1002/advs.20240802439159062)
Doores, K. J. (2015). The HIV glycan shield as a target for broadly neutralizing antibodies. The FEBS Journal, 282(24), 4679–4691. https://doi.org/10.1111/febs.13530. (PMID: 10.1111/febs.13530264115454950053)
Blumenthal, R., Durell, S., & Viard, M. (2012). HIV entry and envelope glycoprotein-mediated fusion. The Journal of Biological Chemistry, 287(49), 40841–40849. https://doi.org/10.1074/jbc.R112.406272. (PMID: 10.1074/jbc.R112.406272230431043510787)
Llorente García, I., & Marsh, M. (2020). A biophysical perspective on receptor-mediated virus entry with a focus on HIV. Biochimica Et Biophysica Acta, 1862(6), Article 183158. https://doi.org/10.1016/j.bbamem.2019.183158. (PMID: 10.1016/j.bbamem.2019.18315831863725)
Herrscher, C., Roingeard, P., & Blanchard, E. (2020). Hepatitis B virus entry into cells. Cells. https://doi.org/10.3390/cells9061486. (PMID: 10.3390/cells9061486325708937349259)
Wu, N. C., & Wilson, I. A. (2020). Influenza hemagglutinin structures and antibody recognition. Cold Spring Harbor Perspectives in Medicine. https://doi.org/10.1101/cshperspect.a038778. (PMID: 10.1101/cshperspect.a038778318712367528863)
Hutchinson, E. C. (2018). Influenza virus. Trends in Microbiology, 26(9), 809–810. https://doi.org/10.1016/j.tim.2018.05.013. (PMID: 10.1016/j.tim.2018.05.01329909041)
Luo, M. (2012). Influenza virus entry. Advances in Experimental Medicine and Biology, 726, 201–221. https://doi.org/10.1007/978-1-4614-0980-9_9. (PMID: 10.1007/978-1-4614-0980-9_922297515)
Schoeman, D., & Fielding, B. C. (2019). Coronavirus envelope protein: Current knowledge. Virology Journal, 16(1), 69. https://doi.org/10.1186/s12985-019-1182-0. (PMID: 10.1186/s12985-019-1182-0311330316537279)
Millet, J. K., Jaimes, J. A., & Whittaker, G. R. (2021). Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiology Reviews. https://doi.org/10.1093/femsre/fuaa057. (PMID: 10.1093/femsre/fuaa05733118022)
Reily, C., Stewart, T. J., Renfrow, M. B., & Novak, J. (2019). Glycosylation in health and disease. Nature Reviews Nephrology, 15(6), 346–366. https://doi.org/10.1038/s41581-019-0129-4. (PMID: 10.1038/s41581-019-0129-4308585826590709)
Schjoldager, K. T., Narimatsu, Y., Joshi, H. J., & Clausen, H. (2020). Global view of human protein glycosylation pathways and functions. Nature Reviews Molecular Cell Biology, 21(12), 729–749. https://doi.org/10.1038/s41580-020-00294-x. (PMID: 10.1038/s41580-020-00294-x33087899)
Hirata, T., & Kizuka, Y. (2021). N-glycosylation. Advances in Experimental Medicine and Biology, 1325, 3–24. https://doi.org/10.1007/978-3-030-70115-4_1. (PMID: 10.1007/978-3-030-70115-4_134495528)
Bagdonaite, I., & Wandall, H. H. (2018). Global aspects of viral glycosylation. Glycobiology, 28(7), 443–467. https://doi.org/10.1093/glycob/cwy021. (PMID: 10.1093/glycob/cwy02129579213)
Magalhães, A., Duarte, H. O., & Reis, C. A. (2021). The role of O-glycosylation in human disease. Molecular Aspects of Medicine, 79, 100964. https://doi.org/10.1016/j.mam.2021.100964. (PMID: 10.1016/j.mam.2021.10096433775405)
Sun, X., Zhan, M., Sun, X., Liu, W., & Meng, X. (2021). C1GALT1 in health and disease. Oncology Letters, 22(2), 589. https://doi.org/10.3892/ol.2021.12850. (PMID: 10.3892/ol.2021.12850341499008200938)
Zhang, X. L., & Qu, H. (2021). The role of glycosylation in infectious diseases. Advances in Experimental Medicine and Biology, 1325, 219–237. https://doi.org/10.1007/978-3-030-70115-4_11. (PMID: 10.1007/978-3-030-70115-4_1134495538)
Watanabe, Y., Bowden, T. A., Wilson, I. A., & Crispin, M. (2019). Exploitation of glycosylation in enveloped virus pathobiology. Biochimica Et Biophysica Acta, 1863(10), 1480–1497. https://doi.org/10.1016/j.bbagen.2019.05.012. (PMID: 10.1016/j.bbagen.2019.05.01231121217)
Huang, Y., Harris, B. S., Minami, S. A., Jung, S., Shah, P. S., Nandi, S., et al. (2022). SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction. Biophysical Journal, 121(1), 79–90. https://doi.org/10.1016/j.bpj.2021.12.002. (PMID: 10.1016/j.bpj.2021.12.00234883069)
Kurebayashi, Y., & Takeuchi, H. (2023). Special issue: New insights into protein glycosylation. Molecules. https://doi.org/10.3390/molecules28073263.
Kremsreiter SM, Kroell AH, Weinberger K, Boehm H. (2021). Glycan-lectin interactions in cancer and viral infections and how to disrupt them. International Journal of Molecular Sciences, 22(19). https://doi.org/10.3390/ijms221910577.
Casalino, L., Gaieb, Z., Goldsmith, J. A., Hjorth, C. K., Dommer, A. C., Harbison, A. M., et al. (2020). Beyond shielding: The roles of glycans in the SARS-CoV-2 spike protein. ACS Central Science, 6(10), 1722–1734. https://doi.org/10.1021/acscentsci.0c01056. (PMID: 10.1021/acscentsci.0c01056331400347523240)
Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–92.e6. https://doi.org/10.1016/j.cell.2020.02.058. (PMID: 10.1016/j.cell.2020.02.058321554447102599)
Encinas-Garcia, T., Mendoza-Cano, F., Muhlia-Almazan, A., Porchas-Cornejo, M., & Sanchez-Paz, A. (2024). A review of shrimp cellular receptors for WSSV: Potential targets for antiviral strategies in shrimp aquaculture. Reviews in Fisheries Science & Aquaculture, 32(1), 99–126. https://doi.org/10.1080/23308249.2023.2254401. (PMID: 10.1080/23308249.2023.2254401)
Yang, Z. S., Huang, S. W., Wang, W. H., Lin, C. Y., Wang, C. F., Urbina, A. N., et al. (2021). Identification of important N-linked glycosylation sites in the hemagglutinin protein and their functional impact on DC-SIGN mediated avian influenza H5N1 infection. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms22020743. (PMID: 10.3390/ijms22020743350088718745139)
Carbaugh, D. L., & Lazear, H. M. (2020). Flavivirus envelope protein glycosylation: Impacts on viral infection and pathogenesis. Journal of Virology. https://doi.org/10.1128/jvi.00104-20.
Bindeman, W. E., & Fingleton, B. (2022). Glycosylation as a regulator of site-specific metastasis. Cancer Metastasis Reviews, 41(1), 107–129. https://doi.org/10.1007/s10555-021-10015-1. (PMID: 10.1007/s10555-021-10015-134967926)
Gandy, L. A., Canning, A. J., Lou, H., Xia, K., He, P., Su, G., et al. (2022). Molecular determinants of the interaction between HSV-1 glycoprotein D and heparan sulfate. Frontiers in Molecular Biosciences, 9, 1043713. https://doi.org/10.3389/fmolb.2022.1043713. (PMID: 10.3389/fmolb.2022.1043713364199329678342)
Qing, E., Hantak, M., Perlman, S., & Gallagher, T. (2020). Distinct roles for sialoside and protein receptors in coronavirus infection. MBio. https://doi.org/10.1128/mBio.02764-19.
Gruszewska, E., Grytczuk, A., & Chrostek, L. (2021). Glycosylation in viral hepatitis. Biochimica Et Biophysica Acta, 1865(11), 129997. https://doi.org/10.1016/j.bbagen.2021.129997. (PMID: 10.1016/j.bbagen.2021.12999734474116)
Li, Q., Wu, J., Nie, J., Zhang, L., Hao, H., Liu, S., et al. (2020). The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell, 182(5), 1284–94.e9. https://doi.org/10.1016/j.cell.2020.07.012. (PMID: 10.1016/j.cell.2020.07.012327308077366990)
Shajahan, A., Supekar, N. T., Gleinich, A. S., & Azadi, P. (2020). Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2. Glycobiology, 30(12), 981–988. https://doi.org/10.1093/glycob/cwaa042. (PMID: 10.1093/glycob/cwaa042323633917239183)
Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science, 367(6485), 1444–1448. https://doi.org/10.1126/science.abb2762. (PMID: 10.1126/science.abb2762321321847164635)
Gahmberg, C. G., & Grönholm, M. (2022). How integrin phosphorylations regulate cell adhesion and signaling. Trends in Biochemical Sciences, 47(3), 265–278. https://doi.org/10.1016/j.tibs.2021.11.003. (PMID: 10.1016/j.tibs.2021.11.00334872819)
Wang, C. W., Chuang, H. C., & Tan, T. H. (2023). ACE2 in chronic disease and COVID-19: Gene regulation and post-translational modification. Journal of Biomedical Science, 30(1), 71. https://doi.org/10.1186/s12929-023-00965-9. (PMID: 10.1186/s12929-023-00965-93760827910464117)
Cai, Z., Bai, H., Ren, D., Xue, B., Liu, Y., Gong, T., et al. (2024). Integrin αvβ1 facilitates ACE2-mediated entry of SARS-CoV-2. Virus Research, 339, 199251. https://doi.org/10.1016/j.virusres.2023.199251. (PMID: 10.1016/j.virusres.2023.19925137884208)
Palakkott, A. R., Alneyadi, A., Muhammad, K., Eid, A. H., Amiri, K. M. A., Akli Ayoub, M., et al. (2023). The SARS-CoV-2 spike protein activates the epidermal growth factor receptor-mediated signaling. Vaccines. https://doi.org/10.3390/vaccines11040768.
Engler, M., Albers, D., Von Maltitz, P., Groß, R., Münch, J., & Cirstea, I. C. (2023). ACE2-EGFR-MAPK signaling contributes to SARS-CoV-2 infection. Life Science Alliance. https://doi.org/10.26508/lsa.202201880.
Han, Y., Kim, S., Park, T., Hwang, H., Park, S., Kim, J., et al. (2024). Reduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection by blocking the epidermal growth factor receptor (EGFR) pathway. Microbiology Spectrum, 12(11), e0158324. https://doi.org/10.1128/spectrum.01583-24. (PMID: 10.1128/spectrum.01583-2439291996)
Haneef, K., Ghaffar Memon, A., Saleem, R., Batool, F., & Sadeeq, M. (2021). B cell receptor (BCR) guided mechanotransduction: Critical hypothesis to instruct SARS-CoV-2 specific B cells to trigger proximal signalling and antibody reshaping. Medical Hypotheses, 153, 110640. https://doi.org/10.1016/j.mehy.2021.110640. (PMID: 10.1016/j.mehy.2021.110640342715118259033)
Byrd-Leotis, L., Jia, N., Dutta, S., Trost, J. F., Gao, C., Cummings, S. F., et al. (2019). Influenza binds phosphorylated glycans from human lung. Science Advances, 5(2), eaav2554. https://doi.org/10.1126/sciadv.aav2554. (PMID: 10.1126/sciadv.aav2554307884376374103)
Zhu, R., Wu, J., Chen, R., Zhou, M., Cao, S., Wu, Z., et al. (2024). HA198 mutations in H9N2 avian influenza: Molecular dynamics insights into receptor binding. Frontiers in Veterinary Science, 11, 1526600. https://doi.org/10.3389/fvets.2024.1526600. (PMID: 10.3389/fvets.2024.152660039846021)
Suchanti, S., Stephen, B. J., Chaurasia, T. P., Raghuwanshi, A. P., Singh, G., Singh, A., et al. (2023). In-silico CLEC5A mRNA expression analysis to predict dengue susceptibility in cancer patients. Biochemistry and Biophysics Reports, 35, 101501. https://doi.org/10.1016/j.bbrep.2023.101501. (PMID: 10.1016/j.bbrep.2023.1015013741585010320400)
Sung, P. S., & Hsieh, S. L. (2019). CLEC2 and CLEC5A: Pathogenic host factors in acute viral infections. Frontiers in Immunology, 10, 2867. https://doi.org/10.3389/fimmu.2019.02867.
Watson, A. A., Lebedev, A. A., Hall, B. A., Fenton-May, A. E., Vagin, A. A., Dejnirattisai, W., et al. (2011). Structural flexibility of the macrophage dengue virus receptor CLEC5A: Implications for ligand binding and signaling. Journal of Biological Chemistry, 286(27), 24208–24218. https://doi.org/10.1074/jbc.M111.226142. (PMID: 10.1074/jbc.M111.226142215661233129202)
Morton, P. E., Hicks, A., Nastos, T., Santis, G., & Parsons, M. (2013). CAR regulates epithelial cell junction stability through control of E-cadherin trafficking. Scientific Reports, 3, 2889. https://doi.org/10.1038/srep02889. (PMID: 10.1038/srep02889240963223791454)
Herrador, A., Fedeli, C., Radulovic, E., Campbell, K. P., Moreno, H., Gerold, G., et al. (2019). Dynamic dystroglycan complexes mediate cell entry of Lassa virus. MBio. https://doi.org/10.1128/mBio.02869-18. (PMID: 10.1128/mBio.02869-18309145166437060)
Moraz, M. L., Pythoud, C., Turk, R., Rothenberger, S., Pasquato, A., Campbell, K. P., et al. (2013). Cell entry of Lassa virus induces tyrosine phosphorylation of dystroglycan. Cellular Microbiology, 15(5), 689–700. https://doi.org/10.1111/cmi.12078. (PMID: 10.1111/cmi.1207823279385)
Wang, C. C., Sivashanmugan, K., Chen, C. K., Hong, J. R., Sung, W. I., Liao, J. D., et al. (2017). Specific unbinding forces between mutated human P-selectin glycoprotein ligand-1 and viral protein-1 measured using force spectroscopy. The Journal of Physical Chemistry Letters, 8(21), 5290–5295. https://doi.org/10.1021/acs.jpclett.7b02373. (PMID: 10.1021/acs.jpclett.7b0237329016136)
Farzan, M., Mirzabekov, T., Kolchinsky, P., Wyatt, R., Cayabyab, M., Gerard, N. P., et al. (1999). Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell, 96(5), 667–676. https://doi.org/10.1016/s0092-8674(00)80577-2. (PMID: 10.1016/s0092-8674(00)80577-210089882)
Maginnis, M. S. (2018). Virus-receptor interactions: The key to cellular invasion. Journal of Molecular Biology, 430(17), 2590–2611. https://doi.org/10.1016/j.jmb.2018.06.024. (PMID: 10.1016/j.jmb.2018.06.024299249656083867)
Cheng, N., Liu, M., Li, W., Sun, B., Liu, D., Wang, G., et al. (2022). Protein post-translational modification in SARS-CoV-2 and host interaction. Frontiers in Immunology, 13, 1068449. https://doi.org/10.3389/fimmu.2022.1068449. (PMID: 10.3389/fimmu.2022.106844936713387)
Liu, Q., Wang, H., Zhang, H., Sui, L., Li, L., Xu, W., et al. (2022). The global succinylation of SARS-CoV-2-infected host cells reveals drug targets. Proceedings of the National Academy of Sciences of the United States of America, 119(30), e2123065119. https://doi.org/10.1073/pnas.2123065119. (PMID: 10.1073/pnas.2123065119358584079335334)
Ramadan, A. A., Mayilsamy, K., McGill, A. R., Ghosh, A., Giulianotti, M. A., Donow, H. M., et al. (2022). Identification of SARS-CoV-2 spike palmitoylation inhibitors that results in release of attenuated virus with reduced infectivity. Viruses. https://doi.org/10.3390/v14030531. (PMID: 10.3390/v14030531353369388950683)
Jakhmola, S., Indari, O., Kashyap, D., Varshney, N., Das, A., Manivannan, E., et al. (2021). Mutational analysis of structural proteins of SARS-CoV-2. Heliyon, 7(3), e06572. https://doi.org/10.1016/j.heliyon.2021.e06572. (PMID: 10.1016/j.heliyon.2021.e06572337781797980187)
Urban, S., Neumann-Haefelin, C., & Lampertico, P. (2021). Hepatitis D virus in 2021: Virology, immunology and new treatment approaches for a difficult-to-treat disease. Gut, 70(9), 1782–1794. https://doi.org/10.1136/gutjnl-2020-323888. (PMID: 10.1136/gutjnl-2020-32388834103404)
Malhi, M., Norris, M. J., Duan, W., Moraes, T. J., & Maynes, J. T. (2021). Statin-mediated disruption of rho GTPase prenylation and activity inhibits respiratory syncytial virus infection. Communications Biology, 4(1), 1239. https://doi.org/10.1038/s42003-021-02754-2. (PMID: 10.1038/s42003-021-02754-2347164038556396)
Kumar, R., Mehta, D., Mishra, N., Nayak, D., & Sunil, S. (2020). Role of host-mediated post-translational modifications (PTMs) in RNA virus pathogenesis. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms22010323.
Lüscher, B., Verheirstraeten, M., Krieg, S., & Korn, P. (2022). Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cellular and Molecular Life Sciences, 79(6), 288. https://doi.org/10.1007/s00018-022-04290-6. (PMID: 10.1007/s00018-022-04290-6355364849087173)
Fields, S., & Song, O. (1989). A novel genetic system to detect protein-protein interactions. Nature, 340(6230), 245–246. https://doi.org/10.1038/340245a0. (PMID: 10.1038/340245a02547163)
Cao, Y. Q., Yuan, L., Zhao, Q., Yuan, J. L., Miao, C., Chang, Y. F., et al. (2019). Hsp40 protein DNAJB6 interacts with viral NS3 and inhibits the replication of the Japanese encephalitis virus. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms20225719.
Tanaka, S. (2019). An efficient method for the isolation of interaction-null/impaired mutants using the yeast two-hybrid technique. Genes and Cells, 24(12), 781–788. https://doi.org/10.1111/gtc.12724. (PMID: 10.1111/gtc.12724)
Leanna, C. A., & Hannink, M. (1996). The reverse two-hybrid system: A genetic scheme for selection against specific protein/protein interactions. Nucleic Acids Research, 24(17), 3341–3347. https://doi.org/10.1093/nar/24.17.3341. (PMID: 10.1093/nar/24.17.33418811088146093)
Vidal, M., & Legrain, P. (1999). Yeast forward and reverse ‘n’-hybrid systems. Nucleic Acids Research, 27(4), 919–929. https://doi.org/10.1093/nar/27.4.919. (PMID: 10.1093/nar/27.4.9199927722148269)
Cauchy, P., Kahn-Perlès, B., Ferrier, P., Imbert, J., & Lécine, P. (2019). 2hybridtools, a handy software to facilitate clone identification and mutation mapping from yeast two-hybrid screening. PeerJ, 7, e7245. https://doi.org/10.7717/peerj.7245. (PMID: 10.7717/peerj.7245313090036612259)
Vidal, M., Brachmann, R. K., Fattaey, A., Harlow, E., & Boeke, J. D. (1996). Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proceedings of the National Academy of Sciences of the United States of America, 93(19), 10315–10320. https://doi.org/10.1073/pnas.93.19.10315. (PMID: 10.1073/pnas.93.19.10315881679738381)
Vincent, O., Gutierrez-Nogués, A., Trejo-Herrero, A., & Navas, M. A. (2020). A novel reverse two-hybrid method for the identification of missense mutations that disrupt protein-protein binding. Scientific Reports, 10(1), 21043. https://doi.org/10.1038/s41598-020-77992-1. (PMID: 10.1038/s41598-020-77992-1332735867713115)
Nordgren, I. K., & Tavassoli, A. (2014). A bidirectional fluorescent two-hybrid system for monitoring protein-protein interactions. Molecular BioSystems, 10(3), 485–490. https://doi.org/10.1039/c3mb70438f. (PMID: 10.1039/c3mb70438f24382456)
Syed, A. J., & Anderson, J. C. (2021). Applications of bioluminescence in biotechnology and beyond. Chemical Society Reviews, 50(9), 5668–5705. https://doi.org/10.1039/d0cs01492c. (PMID: 10.1039/d0cs01492c33735357)
Yee-Lin, V., Pooi-Fong, W., & Soo-Beng, A. K. (2018). Nutlin-3, a p53-Mdm2 antagonist for nasopharyngeal carcinoma treatment. Mini-Reviews in Medicinal Chemistry, 18(2), 173–183. https://doi.org/10.2174/1389557517666170717125821. (PMID: 10.2174/1389557517666170717125821287143985769085)
Zeng, X., Zeng, W. H., Zhou, J., Liu, X. M., Huang, G., Zhu, H., et al. (2022). Removal of nonspecific binding proteins is required in co-immunoprecipitation with nuclear proteins. BioTechniques, 73(6), 289–296. https://doi.org/10.2144/btn-2022-0048. (PMID: 10.2144/btn-2022-004836401550)
Heuschkel, M. J., Bach, C., Meiss-Heydmann, L., Gerges, E., Felli, E., Giannone, F., et al. (2024). JAK1 promotes HDV replication and is a potential target for antiviral therapy. Journal of Hepatology, 80(2), 220–231. https://doi.org/10.1016/j.jhep.2023.10.030. (PMID: 10.1016/j.jhep.2023.10.03037925078)
Burckhardt, C. J., Minna, J. D., & Danuser, G. (2021). Co-immunoprecipitation and semi-quantitative immunoblotting for the analysis of protein-protein interactions. STAR Protocols, 2(3), 100644. https://doi.org/10.1016/j.xpro.2021.100644. (PMID: 10.1016/j.xpro.2021.100644342783318264609)
Pollard, D. A., Pollard, T. D., & Pollard, K. S. (2019). Empowering statistical methods for cellular and molecular biologists. Molecular Biology of the Cell, 30(12), 1359–1368. https://doi.org/10.1091/mbc.E15-02-0076. (PMID: 10.1091/mbc.E15-02-0076311456706724699)
Lasswitz, L., Chandra, N., Arnberg, N., & Gerold, G. (2018). Glycomics and proteomics approaches to investigate early adenovirus-host cell interactions. Journal of Molecular Biology, 430(13), 1863–1882. https://doi.org/10.1016/j.jmb.2018.04.039. (PMID: 10.1016/j.jmb.2018.04.039297468517094377)
Gnanasekaran, P., & Pappu, H. R. (2023). Detection of protein-protein interactions using glutathione-S-transferase (GST) pull-down assay technique. Methods in Molecular Biology, 2690, 111–115. https://doi.org/10.1007/978-1-0716-3327-4_10. (PMID: 10.1007/978-1-0716-3327-4_1037450141)
Kim, S. Y., & Hakoshima, T. (2019). GST pull-down assay to measure complex formations. Methods in Molecular Biology, 1893, 273–280. https://doi.org/10.1007/978-1-4939-8910-2_20. (PMID: 10.1007/978-1-4939-8910-2_2030565140)
Schäfer, F., Seip, N., Maertens, B., Block, H., & Kubicek, J. (2015). Purification of GST-tagged proteins. Methods in Enzymology, 559, 127–139. https://doi.org/10.1016/bs.mie.2014.11.005. (PMID: 10.1016/bs.mie.2014.11.00526096507)
Lyu, S., Zhang, C., Hou, X., & Wang, A. (2022). Tag-based pull-down assay. Methods in Molecular Biology, 2400, 105–114. https://doi.org/10.1007/978-1-0716-1835-6_11. (PMID: 10.1007/978-1-0716-1835-6_1134905195)
Han, B., Lv, Y., Moser, D., Zhou, X., Woehrle, T., Han, L., et al. (2023). ACE2-independent SARS-CoV-2 virus entry through cell surface GRP78 on monocytes - Evidence from a translational clinical and experimental approach. EBioMedicine, 98, 104869. https://doi.org/10.1016/j.ebiom.2023.104869. (PMID: 10.1016/j.ebiom.2023.1048693796750910679867)
Louche, A., Salcedo, S. P., & Bigot, S. (2017). Protein-protein interactions: Pull-down assays. Methods in Molecular Biology, 1615, 247–255. https://doi.org/10.1007/978-1-4939-7033-9_20. (PMID: 10.1007/978-1-4939-7033-9_2028667618)
Arakawa, M., & Morita, E. (2023). Protein pull-down assay using HiBiT-tag-dependent luciferase activity measurement. Bio-protocol, 13(6), e4640. https://doi.org/10.21769/BioProtoc.4640. (PMID: 10.21769/BioProtoc.46403696843810031519)
Pompey, S. N., Michaely, P., & Luby-Phelps, K. (2013). Quantitative fluorescence co-localization to study protein-receptor complexes. Methods in Molecular Biology, 1008, 439–453. https://doi.org/10.1007/978-1-62703-398-5_16. (PMID: 10.1007/978-1-62703-398-5_1623729262)
Kok, T. W., Costabile, M., Tannock, G. A., & Li, P. (2018). Colocalization of intracellular specific IgA (icIgA) with influenza virus in patients’ nasopharyngeal aspirate cells. Journal of Virological Methods, 252, 8–14. https://doi.org/10.1016/j.jviromet.2017.10.022. (PMID: 10.1016/j.jviromet.2017.10.02229102516)
Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., et al. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science, 313(5793), 1642–1645. https://doi.org/10.1126/science.1127344. (PMID: 10.1126/science.112734416902090)
Rust, M. J., Bates, M., & Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods, 3(10), 793–795. https://doi.org/10.1038/nmeth929. (PMID: 10.1038/nmeth929168963392700296)
Truong, K., & Ikura, M. (2001). The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Current Opinion in Structural Biology, 11(5), 573–578. https://doi.org/10.1016/s0959-440x(00)00249-9. (PMID: 10.1016/s0959-440x(00)00249-911785758)
Wysocki, L. M., & Lavis, L. D. (2011). Advances in the chemistry of small molecule fluorescent probes. Current Opinion in Chemical Biology, 15(6), 752–759. https://doi.org/10.1016/j.cbpa.2011.10.013. (PMID: 10.1016/j.cbpa.2011.10.01322078994)
Leong, F. J., Brady, M., & McGee, J. O. (2003). Correction of uneven illumination (vignetting) in digital microscopy images. Journal of Clinical Pathology, 56(8), 619–621. https://doi.org/10.1136/jcp.56.8.619. (PMID: 10.1136/jcp.56.8.619128908151770032)
Hu, C. D., Chinenov, Y., & Kerppola, T. K. (2002). Visualization of interactions among bZIP and rel family proteins in living cells using bimolecular fluorescence complementation. Molecular Cell, 9(4), 789–798. https://doi.org/10.1016/s1097-2765(02)00496-3. (PMID: 10.1016/s1097-2765(02)00496-311983170)
Fan, J., Cui, Z., & Zhang, X. (2008). Optical spectra diversity and in vitro molecular evolution of red fluorescent proteins. Progress in Biochemistry and Biophysics, 35, 1112–1120.
Chen, M., Wang, M. H., Shen, X. G., Liu, H., Zhang, Y. Y., Peng, J. M., et al. (2022). Neuropilin-1 facilitates pseudorabies virus replication and viral glycoprotein B promotes its degradation in a furin-dependent manner. Journal of Virology, 96(20), e0131822. https://doi.org/10.1128/jvi.01318-22. (PMID: 10.1128/jvi.01318-2236173190)
Lee, B. S., Huang, J. S., Jayathilaka, L. P., Lee, J., & Gupta, S. (2016). Antibody production with synthetic peptides. Methods in Molecular Biology, 1474, 25–47. https://doi.org/10.1007/978-1-4939-6352-2_2. (PMID: 10.1007/978-1-4939-6352-2_227515072)
Hu, C. D., & Kerppola, T. K. (2003). Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis. Nature Biotechnology, 21(5), 539–545. https://doi.org/10.1038/nbt816. (PMID: 10.1038/nbt816126925601820765)
Kerppola, T. K. (2006). Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells. Nature Protocols, 1(3), 1278–1286. https://doi.org/10.1038/nprot.2006.201. (PMID: 10.1038/nprot.2006.201174064122518326)
Pratt, E. P., Owens, J. L., Hockerman, G. H., & Hu, C. D. (2016). Bimolecular fluorescence complementation (BiFC) analysis of protein-protein interactions and assessment of subcellular localization in live cells. Methods in Molecular Biology, 1474, 153–170. https://doi.org/10.1007/978-1-4939-6352-2_9. (PMID: 10.1007/978-1-4939-6352-2_927515079)
Lum, K. K., & Cristea, I. M. (2016). Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. Expert Review of Proteomics, 13(3), 325–340. https://doi.org/10.1586/14789450.2016.1147353. (PMID: 10.1586/14789450.2016.1147353268176134919574)
Reitsma, J. M., Savaryn, J. P., Faust, K., Sato, H., Halligan, B. D., & Terhune, S. S. (2011). Antiviral inhibition targeting the HCMV kinase pUL97 requires pUL27-dependent degradation of Tip60 acetyltransferase and cell-cycle arrest. Cell Host & Microbe, 9(2), 103–114. https://doi.org/10.1016/j.chom.2011.01.006. (PMID: 10.1016/j.chom.2011.01.006)
Furlan, C., Dirks, R. A. M., Thomas, P. C., Jones, R. C., Wang, J., Lynch, M., et al. (2019). Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements. Nature Communications, 10(1), 1525. https://doi.org/10.1038/s41467-019-09533-y. (PMID: 10.1038/s41467-019-09533-y309487246449397)
Liu, X., Salokas, K., Weldatsadik, R. G., Gawriyski, L., & Varjosalo, M. (2020). Combined proximity labeling and affinity purification-mass spectrometry workflow for mapping and visualizing protein interaction networks. Nature Protocols, 15(10), 3182–3211. https://doi.org/10.1038/s41596-020-0365-x. (PMID: 10.1038/s41596-020-0365-x32778839)
Vera-Peralta, H., Najburg, V., Combredet, C., Douché, T., Gianetto, Q. G., Matondo, M., et al. (2024). Applying reverse genetics to study measles virus interactions with the host. Methods in Molecular Biology, 2808, 89–103. https://doi.org/10.1007/978-1-0716-3870-5_7. (PMID: 10.1007/978-1-0716-3870-5_738743364)
Mukherjee, S., Sengupta, N., Chaudhuri, A., Akbar, I., Singh, N., Chakraborty, S., et al. (2018). PLVAP and GKN3 are two critical host cell receptors which facilitate Japanese encephalitis virus entry into neurons. Scientific Reports, 8(1), 11784. https://doi.org/10.1038/s41598-018-30054-z. (PMID: 10.1038/s41598-018-30054-z300827096079088)
Barrass, S. V., & Butcher, S. J. (2020). Advances in high-throughput methods for the identification of virus receptors. Medical Microbiology and Immunology, 209(3), 309–323. https://doi.org/10.1007/s00430-019-00653-2. (PMID: 10.1007/s00430-019-00653-231865406)
Liu, Q., Zheng, J., Sun, W., Huo, Y., Zhang, L., Hao, P., et al. (2018). A proximity-tagging system to identify membrane protein-protein interactions. Nature Methods, 15, 715. https://doi.org/10.1038/s41592-018-0100-5. (PMID: 10.1038/s41592-018-0100-530104635)
Qin, W., Cho, K. F., Cavanagh, P. E., & Ting, A. Y. (2021). Deciphering molecular interactions by proximity labeling. Nature Methods, 18(2), 133–143. https://doi.org/10.1038/s41592-020-01010-5. (PMID: 10.1038/s41592-020-01010-53343224210548357)
Bley, H., Krisp, C., Schöbel, A., Hehner, J., Schneider, L., Becker, M., et al. (2024). Proximity labeling of host factor ANXA3 in HCV infection reveals a novel LARP1 function in viral entry. Journal of Biological Chemistry, 300(5), 107286. https://doi.org/10.1016/j.jbc.2024.107286. (PMID: 10.1016/j.jbc.2024.1072863863665711101947)
Chou, C. C., Zhang, Y., Umoh, M. E., Vaughan, S. W., Lorenzini, I., Liu, F., et al. (2018). TDP-43 pathology disrupts nuclear pore complexes and nucleocytoplasmic transport in ALS/FTD. Nature Neuroscience, 21(2), 228–239. https://doi.org/10.1038/s41593-017-0047-3. (PMID: 10.1038/s41593-017-0047-3293117435800968)
Couzens, A. L., Knight, J. D., Kean, M. J., Teo, G., Weiss, A., Dunham, W. H., et al. (2013). Protein interaction network of the mammalian hippo pathway reveals mechanisms of kinase-phosphatase interactions. Science Signaling, 6(302), rs15. https://doi.org/10.1126/scisignal.2004712. (PMID: 10.1126/scisignal.200471224255178)
Grainger, S., Nguyen, N., Richter, J., Setayesh, J., Lonquich, B., Oon, C. H., et al. (2019). EGFR is required for Wnt9a-Fzd9b signalling specificity in haematopoietic stem cells.Nature Cell Biology, 21(6), 721–730. https://doi.org/10.1038/s41556-019-0330-5. (PMID: 10.1038/s41556-019-0330-5311102876559346)
Minde, D. P., Ramakrishna, M., & Lilley, K. S. (2020). Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. Communications Biology, 3(1), 38. https://doi.org/10.1038/s42003-020-0758-y. (PMID: 10.1038/s42003-020-0758-y319696496976632)
Syu, G. D., Dunn, J., & Zhu, H. (2020). Developments and applications of functional protein microarrays. Molecular and Cellular Proteomics, 19(6), 916–927. https://doi.org/10.1074/mcp.R120.001936. (PMID: 10.1074/mcp.R120.001936323035877261817)
Kashiwagi, H., Morishima, N., Obuse, S., Isoshima, T., Akimoto, J., & Ito, Y. (2021). SARS-CoV-2 proteins microarray by photoimmobilization for serodiagnosis of the antibodies. Bulletin of the Chemical Society of Japan, 94, 2435–2443. https://doi.org/10.1246/bcsj.20210215. (PMID: 10.1246/bcsj.20210215)
Du, P. X., Chou, Y. Y., Santos, H. M., Keskin, B. B., Hsieh, M. H., Ho, T. S., et al. (2021). Development and application of human coronavirus protein microarray for specificity analysis. Analytical Chemistry, 93(21), 7690–7698. https://doi.org/10.1021/acs.analchem.1c00614. (PMID: 10.1021/acs.analchem.1c0061434011150)
Jun, B. H., Kang, H., Lee, Y. S., & Jeong, D. H. (2012). Fluorescence-based multiplex protein detection using optically encoded microbeads. Molecules, 17(3), 2474–2490. https://doi.org/10.3390/molecules17032474. (PMID: 10.3390/molecules17032474223825266268487)
Parsa, S. F., Vafajoo, A., Rostami, A., Salarian, R., Rabiee, M., Rabiee, N., et al. (2018). Early diagnosis of disease using microbead array technology: A review. Analytica Chimica Acta, 1032, 1–17. https://doi.org/10.1016/j.aca.2018.05.011. (PMID: 10.1016/j.aca.2018.05.011301432066152944)
Zhang, H., Xu, T., Li, C. W., & Yang, M. (2010). A microfluidic device with microbead array for sensitive virus detection and genotyping using quantum dots as fluorescence labels. Biosensors & Bioelectronics, 25(11), 2402–2407. https://doi.org/10.1016/j.bios.2010.02.032. (PMID: 10.1016/j.bios.2010.02.032)
Haynes, B. F., Wiehe, K., Borrow, P., Saunders, K. O., Korber, B., Wagh, K., et al. (2023). Author correction: Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nature Reviews Immunology, 23(4), 265. https://doi.org/10.1038/s41577-023-00854-0. (PMID: 10.1038/s41577-023-00854-03685959710300647)
Dai, L., & Gao, G. F. (2021). Viral targets for vaccines against COVID-19. Nature Reviews Immunology, 21(2), 73–82. https://doi.org/10.1038/s41577-020-00480-0. (PMID: 10.1038/s41577-020-00480-033340022)
Stewart, A., Fisher, R. A. (2012). Co-immunoprecipitation: Isolation of protein signaling complexes from native tissues. Laboratory Methods in Cell Biology 112, 33-54. https://doi.org/10.1016/B978-0-12-405914-6.00002-0.
Wang, S., Wu, R., Lu, J., Jiang, Y., Huang, T., & Cai, Y. D. (2022). Protein-protein interaction networks as miners of biological discovery. Proteomics, 22(15–16), e2100190. https://doi.org/10.1002/pmic.202100190. (PMID: 10.1002/pmic.20210019035567424)
Markham, K., Bai, Y., & Schmitt-Ulms, G. (2007). Co-immunoprecipitations revisited: An update on experimental concepts and their implementation for sensitive interactome investigations of endogenous proteins. Analytical and Bioanalytical Chemistry, 389(2), 461–473. https://doi.org/10.1007/s00216-007-1385-x. (PMID: 10.1007/s00216-007-1385-x17583802)
Bajar, B. T., Wang, E. S., Zhang, S., Lin, M. Z., & Chu, J. (2016). A guide to fluorescent protein FRET pairs. Sensors (Basel). https://doi.org/10.3390/s16091488.
Sun, S., Yang, X., Wang, Y., & Shen, X. (2016). In vivo analysis of protein-protein interactions with bioluminescence resonance energy transfer (BRET): Progress and prospects. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms17101704. (PMID: 10.3390/ijms17101704280360455297689)
Cretich, M., Damin, F., & Chiari, M. (2014). Protein microarray technology: How far off is routine diagnostics? The Analyst, 139(3), 528–542. https://doi.org/10.1039/c3an01619f. (PMID: 10.1039/c3an01619f24326290)
Dunham, W. H., Mullin, M., & Gingras, A. C. (2012). Affinity-purification coupled to mass spectrometry: Basic principles and strategies. Proteomics, 12(10), 1576–1590. https://doi.org/10.1002/pmic.201100523. (PMID: 10.1002/pmic.20110052322611051)
Morris, J. H., Knudsen, G. M., Verschueren, E., Johnson, J. R., Cimermancic, P., Greninger, A. L., et al. (2014). Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nature Protocols, 9(11), 2539–2554. https://doi.org/10.1038/nprot.2014.164. (PMID: 10.1038/nprot.2014.164252757904332878)
Ergin, E., Dogan, A., Parmaksiz, M., Elçin, A. E., & Elçin, Y. M. (2016). Time-resolved fluorescence resonance energy transfer [TR-FRET] assays for biochemical processes. Current Pharmaceutical Biotechnology, 17(14), 1222–1230. https://doi.org/10.2174/1389201017666160809164527. (PMID: 10.2174/138920101766616080916452727604358)
Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., et al. (2006). The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology, 24(9), 1151–1161. https://doi.org/10.1038/nbt1239. (PMID: 10.1038/nbt123916964229)
Chai, L., Zhang, J., Zhang, L., & Chen, T. (2015). Miniature fiber optic spectrometer-based quantitative fluorescence resonance energy transfer measurement in single living cells. Journal of Biomedical Optics, 20(3), 037008. https://doi.org/10.1117/1.Jbo.20.3.037008. (PMID: 10.1117/1.Jbo.20.3.03700825793494)
Chi, X., Yan, R., Zhang, J., Zhang, G., Zhang, Y., Hao, M., et al. (2020). A neutralizing human antibody binds to the N-terminal domain of the spike protein of SARS-CoV-2. Science, 369(6504), 650–655. https://doi.org/10.1126/science.abc6952. (PMID: 10.1126/science.abc6952325718387319273)
Cai, Y., Zhang, J., Xiao, T., Peng, H., Sterling, S. M., Walsh, R. M., Jr., et al. (2020). Distinct conformational states of SARS-CoV-2 spike protein. Science, 369(6511), 1586–1592. https://doi.org/10.1126/science.abd4251. (PMID: 10.1126/science.abd425132694201)
Premkumar, L., Segovia-Chumbez, B., Jadi, R., Martinez, D. R., Raut, R., Markmann, A., et al. (2020). The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients. Science Immunology. https://doi.org/10.1126/sciimmunol.abc8413.
Dai, L., Zheng, T., Xu, K., Han, Y., Xu, L., Huang, E., et al. (2020). A universal design of betacoronavirus vaccines against COVID-19, MERS, and SARS. Cell, 182(3), 722–33.e11. https://doi.org/10.1016/j.cell.2020.06.035. (PMID: 10.1016/j.cell.2020.06.035326453277321023)
Huang, Y., Yang, C., Xu, X. F., Xu, W., & Liu, S. W. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141–1149. https://doi.org/10.1038/s41401-020-0485-4. (PMID: 10.1038/s41401-020-0485-4327477217396720)
Liu, X., Huuskonen, S., Laitinen, T., Redchuk, T., Bogacheva, M., Salokas, K., et al. (2021). SARS-CoV-2-host proteome interactions for antiviral drug discovery. Molecular Systems Biology, 17(11), e10396. https://doi.org/10.15252/msb.202110396. (PMID: 10.15252/msb.202110396347097278552907)
Morse, J. S., Lalonde, T., Xu, S., & Liu, W. R. (2020). Learning from the past: Possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV. ChemBioChem, 21(5), 730–738. https://doi.org/10.1002/cbic.202000047. (PMID: 10.1002/cbic.202000047320223707162020)
Liu, H., Wei, P., Kappler, J. W., Marrack, P., & Zhang, G. (2022). SARS-CoV-2 variants of concern and variants of interest receptor binding domain mutations and virus infectivity. Frontiers in Immunology, 13, 825256. https://doi.org/10.3389/fimmu.2022.825256. (PMID: 10.3389/fimmu.2022.825256351541448828474)
Nader, D., & Kerrigan, S. W. (2022). Molecular cross-talk between integrins and cadherins leads to a loss of vascular barrier integrity during SARS-CoV-2 infection. Viruses. https://doi.org/10.3390/v14050891. (PMID: 10.3390/v14050891356326339143673)
Razzaq, A., Disoma, C., Zhou, Y., Tao, S., Chen, Z., Liu, S., et al. (2024). Targeting epidermal growth factor receptor signalling pathway: A promising therapeutic option for COVID-19. Reviews in Medical Virology, 34(1), e2500. https://doi.org/10.1002/rmv.2500. (PMID: 10.1002/rmv.250038126937)
Goethals, O., Kaptein, S. J. F., Kesteleyn, B., Bonfanti, J. F., Van Wesenbeeck, L., Bardiot, D., et al. (2023). Blocking NS3-NS4b interaction inhibits dengue virus in non-human primates. Nature, 615(7953), 678–686. https://doi.org/10.1038/s41586-023-05790-6. (PMID: 10.1038/s41586-023-05790-63692258610033419)
Kaptein, S. J. F., Goethals, O., Kiemel, D., Marchand, A., Kesteleyn, B., Bonfanti, J. F., et al. (2021). A pan-serotype dengue virus inhibitor targeting the NS3-NS4B interaction. Nature, 598(7881), 504–509. https://doi.org/10.1038/s41586-021-03990-6. (PMID: 10.1038/s41586-021-03990-634616043)
Pancera, M., Lai, Y. T., Bylund, T., Druz, A., Narpala, S., O’Dell, S., et al. (2017). Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529. Nature Chemical Biology, 13(10), 1115–1122. https://doi.org/10.1038/nchembio.2460. (PMID: 10.1038/nchembio.2460288257115676566)
Leal, L., Guardo, A. C., Bedoya, L. M., Rodríguez de Miguel, C., Climent, N., Rovira, C., Beltrán, M., Llach, J., Alcamí, J., Kashuba, A. D. M., Gatell, J. M., Plana, M., García F. (2023). Pharmacokinetics, the immunological impact, and the Effect on HIV Ex-Vivo infectivity of Maraviroc, Raltegravir, and Lopinavir in men who have sex with men using Postexposure Prophylaxis. AIDS Research and Human Retroviruses 39(5):211–221. https://doi.org/10.1089/AID.2021.0232.
Groom, C. R., & Cole, J. C. (2017). The use of small-molecule structures to complement protein-ligand crystal structures in drug discovery. Acta Crystallographica Section D, Structural Biology, 73(Pt 3), 240–245. https://doi.org/10.1107/s2059798317000675. (PMID: 10.1107/s2059798317000675282917595349436)
Feng, Y., Wang, Q., & Wang, T. (2017). Drug target protein-protein interaction networks: A systematic perspective. BioMed Research International, 2017, Article 1289259. https://doi.org/10.1155/2017/1289259. (PMID: 10.1155/2017/1289259286910145485489)
Meyer, N. L., & Chapman, M. S. (2022). Adeno-associated virus (AAV) cell entry: Structural insights. Trends in Microbiology, 30(5), 432–451. https://doi.org/10.1016/j.tim.2021.09.005. (PMID: 10.1016/j.tim.2021.09.00534711462)
Lipinski, D. M. (2019). A comparison of inducible gene expression platforms: Implications for recombinant adeno-associated virus (rAAV) vector-mediated ocular gene therapy. Advances in Experimental Medicine and Biology, 1185, 79–83. https://doi.org/10.1007/978-3-030-27378-1_13. (PMID: 10.1007/978-3-030-27378-1_1331884592)
Meng, Q., He, J., Zhong, L., & Zhao, Y. (2021). Advances in the study of antitumour immunotherapy for Newcastle disease virus. International Journal of Medical Sciences, 18(11), 2294–2302. https://doi.org/10.7150/ijms.59185. (PMID: 10.7150/ijms.59185339676058100649)
Arab, A., Behravan, N., Razazn, A., Barati, N., Mosaffa, F., Nicastro, J., et al. (2019). The viral approach to breast cancer immunotherapy. Journal of Cellular Physiology, 234(2), 1257–1267. https://doi.org/10.1002/jcp.27150. (PMID: 10.1002/jcp.2715030146692)
Bishnoi, S., Tiwari, R., Gupta, S., Byrareddy, S. N., & Nayak, D. (2018). Oncotargeting by vesicular stomatitis virus (VSV): Advances in cancer therapy. Viruses. https://doi.org/10.3390/v10020090. (PMID: 10.3390/v10020090294738685850397)
Agarwal, D. K., Nandwana, V., Henrich, S. E., Josyula, V., Thaxton, C. S., Qi, C., et al. (2022). Highly sensitive and ultra-rapid antigen-based detection of SARS-CoV-2 using nanomechanical sensor platform. Biosensors & Bioelectronics, 195, 113647. https://doi.org/10.1016/j.bios.2021.113647. (PMID: 10.1016/j.bios.2021.113647)
Dam, K. A., Mutia, P. S., & Bjorkman, P. J. (2022). Comparing methods for immobilizing HIV-1 SOSIPs in ELISAs that evaluate antibody binding. Scientific Reports, 12(1), 11172. https://doi.org/10.1038/s41598-022-15506-x. (PMID: 10.1038/s41598-022-15506-x357784739247892)
Grant Information: 2021GXNSFBA220053 Natural Science Foundation of Guangxi Province; AD23026316 Specific Research Project of Guangxi for Research Bases and Talents; 2021KY0106 Middle-aged and Young Teachers' Basic Ability Promotion Project of Guangxi; 2021JJ30029 Natural Science Foundation of Hunan Province; 42306136 National Natural Science Foundation of China; M2022-04 State Key Laboratory of Microbial Resources, Chinese Academy of Sciences
Contributed Indexing: Keywords: Glycosylation; Phosphorylation; Protein modification; Protein–protein interaction
Entry Date(s): Date Created: 20250719 Date Completed: 20251115 Latest Revision: 20251115
Update Code: 20251115
DOI: 10.1007/s12010-025-05333-x
PMID: 40682621
Datenbank: MEDLINE
Beschreibung
Abstract:Protein interactions are of paramount importance for the performance of biological functions within organisms. Post-translational modifications, including glycosylation and phosphorylation, regulate protein-protein interactions through non-covalent mechanisms. Glycosylation typically facilitates binding by altering surface properties, whereas phosphorylation can either enhance or disrupt interactions depending on context, collectively amplifying the biological impact of proteins. The entry of viruses and certain intracellular parasites into host cells is facilitated by these modifications, which permit the binding of ligands to receptors and the traversal of the cell membrane barrier. As research in this domain progresses, innovative methodologies are being developed, including protein microarrays and proximity-labeling techniques. These developments are being increasingly employed in disease prevention, therapeutics, and fundamental medical research. In light of the recent surge in emerging infectious diseases, the study of protein interactions has assumed heightened relevance. This review explores protein modifications, including glycosylation, phosphorylation, and ubiquitination, and focuses on their roles in viral entry. It highlights advanced methods for analyzing protein-protein interactions (PPIs), notably proximity labeling and protein microarrays, and concludes with novel insights into therapeutic development, aiming to inspire innovation in this evolving field.<br /> (© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
ISSN:1559-0291
DOI:10.1007/s12010-025-05333-x