MOLECULAR DYNAMICS STUDIES OF THE NOROVIRUS-HOST CELL INTERACTION MEDIATED BY H-TYPE 1 ANTIGEN

Yıl 2019, Cilt: 20 Sayı: 1, 19 - 26, 15.04.2019

Abdulkadir Kocak Müslüm Yıldız

https://doi.org/10.23902/trkjnat.508120

Cited By: 3

Öz

Noroviruses are the main cause for acute gastroenteritis disease. They
infect the host cell via interaction with HGBA receptors on the cell surface. Virus makes complex
with cell surface receptors through its capsid protein VP1 to enter the cell.
Although the protein has been successfully crystallized in the presence of some
common glycans, the dynamic change in the protein structure when interacting
with sugar moieties has yet to be fully elucidated. This is critically
important since it leads to understanding the protein’s recognition mechanism of
HBGAs and develop therapeutic strategies against the gastroenteritis disease.
Here, we computationally assessed the dynamic features of wild type VP1
envelope protein to get insights into the interactions that can be important
for virus infectivity. We have found that the binding of sugar moiety does not
cause noticeable dynamic changes in the binding region. However, interestingly,
a drastic change occurs in a distant loop lying at the residue numbers of
395-400, which might be indication of an allosteric effect.

Anahtar Kelimeler

Norovirus, therapeutic antibody, HBGA blockage, molecular dynamics

Kaynakça

• 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
• Aliabadi, N., Lopman, B.A., Parashar, U.D. & Hall, A.J. 2015. Progress toward norovirus vaccines: considerations for further development and implementation in potential target populations. Expert Review of Vaccines, 14(9): 1241-1253. https://doi.org/10.1586/14760584.2015.1073110
• Belliot, G., Lopman, B.A., Ambert-Balay, K. & Pothier, P. 2014. The burden of norovirus gastroenteritis: an important foodborne and healthcare-related infection. Clinical Microbiology and Infection, 20(8): 724-730. https://doi.org/10.1111/1469-0691.12722
• Caddy, S., Breiman, A., le Pendu, J. & Goodfellow, I. 2014. Genogroup IV and VI canine noroviruses interact with histo-blood group antigens. Journal of Virology, 88(18): 10377-10391. https://doi.org/10.1128/JVI.01008-14
• Choi, J.-M., Hutson, A.M., Estes, M.K. & Prasad, B.V.V. 2008. Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus. Proceedings of the National Academy of Sciences, 105(27): 9175-9180. https://doi.org/10.1073/pnas.0803275105
• de Graaf, M., van Beek, J., & Koopmans, M.P. 2016. Human norovirus transmission and evolution in a changing world. Nature Reviews: Microbiology, 14(7): 421-433. https://doi.org/10.1038/nrmicro.2016.48
• Garaicoechea, L., Aguilar, A., Parra, G.I., Bok, M., Sosnovtsev, S.V., Canziani, G., Green, K.Y., Bok, K. & Parreno, V. 2015. Llama nanoantibodies with therapeutic potential against human norovirus diarrhea. PLoS One, 10(8): e0133665. https://doi.org/10.1371/journal.pone.0133665
• Hoa Tran, T.N., Trainor, E., Nakagomi, T., Cunliffe, N.A. & Nakagomi, O. 2013. Molecular epidemiology of noroviruses associated with acute sporadic gastroenteritis in children: global distribution of genogroups, genotypes and GII.4 variants. Journal of Clinical Virology, 56(3): 185-193. https://doi.org/10.1016/j.jcv.2012.11.011
• Ishida, T. 2018. Computational analysis of carbohydrate recognition based on hybrid QM/MM modeling: a case study of norovirus capsid protein in complex with Lewis antigen. Physical Chemistry Chemical Physics, 20(7): 4652-4665. https://doi.org/10.1039/C7CP07701G
• Kambhampati, A., Koopmans, M. & Lopman, B.A. 2015. Burden of norovirus in healthcare facilities and strategies for outbreak control. Journal of Hospital Infection, 89(4): 296-301. https://doi.org/10.1016/j.jhin.2015.01.011
• Karst, S.M., Wobus, C.E., Goodfellow, I.G., Green, K.Y. & Virgin, H.W. 2014. Advances in norovirus biology. Cell Host Microbe, 15(6): 668-680. https://doi.org/ 10.1016/j.chom.2014.05.015
• Kocak, A., Erol, I., Yildiz, M. & Can, H. 2016. Computational insights into the protonation states of catalytic dyad in BACE1-acyl guanidine based inhibitor complex. Journal of Molecular Graphics and Modeling, 70: 226-235. https://doi.org/10.1016/j.jmgm.2016.10.013
• Kocak, A. & Yildiz, M. 2017. Docking, molecular dynamics and free energy studies on aspartoacylase mutations involved in Canavan disease. Journal of Molecular Graphics and Modeling, 74: 44-53. https://doi.org/ 10.1016/j.jmgm.2017.03.011
• Kotloff, K.L., Nataro, J.P., Blackwelder, W.C., Nasrin, D., Farag, T.H., Panchalingam, S., Wu, Y., Sow, S.O., Sur, D., Breiman, R.F., Faruque, A.S., Zaidi, A.K., Saha, D., Alonso, P.L., Tamboura, B., Sanogo, D., Onwuchekwa, U., Manna, B., Ramamurthy, T., Kanungo, S., Ochieng, J.B., Omore, R., Oundo, J.O., Hossain, A., Das, S.K., Ahmed, S., Qureshi, S., Quadri, F., Adegbola, R.A., Antonio, M., Hossain, M.J., Akinsola, A., Mandomando, I., Nhampossa, T., Acacio, S., Biswas, K., O'Reilly, C.E., Mintz, E.D., Berkeley, L.Y., Muhsen, K., Sommerfelt, H., Robins-Browne, R.M. & Levine, M.M. 2013. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet, 382(9888): 209-222. https://doi.org/10.1016/S0140-6736(13)60844-2
• Kubota, T., Kumagai, A., Ito, H., Furukawa, S., Someya, Y., Takeda, N., Ishii, K., Wakita, T., Narimatsu, H. & Shirato, H. 2012. Structural basis for the recognition of Lewis antigens by genogroup I norovirus. Journal of Virology, 86(20): 11138-11150. https://doi.org/10.1128/JVI.00278-12
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J.L., Dror, R.O. & Shaw, D.E. 2010. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8): 1950-1958. https://doi.org/10.1002/prot.22711
• Lochridge, V.P., Jutila, K.L., Graff, J.W. & Hardy, M.E. 2005. Epitopes in the P2 domain of norovirus VP1 recognized by monoclonal antibodies that block cell interactions. Journal of General Virology, 86(Pt 10): 2799-2806. https://doi.org/10.1099/vir.0.81134-0
• Olsson, M.H., Sondergaard, C.R., Rostkowski, M. & Jensen, J.H. 2011. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. Journal of Chemical Theory and Computation, 7(2): 525-537. https://doi.org/10.1021/ct100578z
• Patel, M.M., Hall, A.J., Vinje, J. & Parashar, U.D. 2009. Noroviruses: a comprehensive review. Journal of Clinical Virology, 44(1): 1-8. https://doi.org/10.1016/j.jcv.2008.10.009
• Rocha-Pereira, J., Neyts, J. & Jochmans, D. 2014. Norovirus: targets and tools in antiviral drug discovery. Biochemical Pharmacology, 91(1): 1-11. https://doi.org/10.1016/j.bcp.2014.05.021
• Sapparapu, G., Czako, R., Alvarado, G., Shanker, S., Prasad, B.V., Atmar, R.L., Estes, M.K. & Crowe, J.E., Jr. 2016. Frequent Use of the IgA Isotype in Human B Cells Encoding Potent Norovirus-Specific Monoclonal Antibodies That Block HBGA Binding. PLoS Pathog, 12(6): e1005719. https://doi.org/10.1371/journal.ppat.1005719
• Schrödinger, L. 2015. Maestro. New York, NY: Schrödinger, LLC.
• Shanker, S., Czako, R., Sankaran, B., Atmar, R.L., Estes, M.K. & Prasad, B.V. 2014. Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses. Journal of Virology, 88(11): 6168-6180. https://doi.org/10.1128/JVI.00201-14
• Tamminen, K., Malm, M., Vesikari, T. & Blazevic, V. 2016. Mucosal Antibodies Induced by Intranasal but Not Intramuscular Immunization Block Norovirus GII.4 Virus-Like Particle Receptor Binding. Viral Immunology, 29(5): 315-319. https://doi.org/10.1089/vim.2015.0141
• Tan, M. & Jiang, X. 2014. Vaccine against norovirus. Hum Vaccin Immunother, 10(6): 1449-1456. https://doi.org/ 10.4161/hv.28626
• Toukan, K. & Rahman, A. 1985. Molecular-dynamics study of atomic motions in water. Physical Review B: Condensed Matter and Materials Physics, 31(5): 2643-2648.
• Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A. & Case, D.A. 2004. Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9): 1157-1174. https://doi.org/10.1002/jcc.20035
• Wang, J., Wang, W., Kollman, P.A. & Case, D.A. 2006. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25(2): 247-260. doi: https://doi.org/10.1016/j.jmgm.2005.12.005
• White, P.A. 2014. Evolution of norovirus. Clinical Microbiology and Infection, 20(8): 741-745. https://doi.org/10.1111/1469-0691.12746