Viruses

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Last Updated: Friday, 14 July 2023 09:32

virion-martini.jpgThe need for detailed models and dynamics of virus particles is clear, as part of our fight against pandemics such as COVID. Given the size and composition of typical viruses, the use of Martini to simulate their behavior is apparent. Indeed, viruses have already been targeted with Martini, including the capsid of the Cowpea Mosaic virus [1], and enveloped ones such as Influenza A virion [2],  Dengue [3], and flavivirus [4]. More examples are reviewed in [5,6].

Also the COVID virus envelope itself is now available at the Martini level [7] !

[1] X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition. J. Chem. Th. Comp., 5:2531-2543, 2009. abstract

[2] T. Reddy, D. Shorthouse, D.L. Parton, E. Jefferys, P.W. Fowler, M. Chavent, M. Baaden, M.S.P. Sansom. Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure, 23:584-597, 2015. Article
 
[3] T. Reddy, M.S.P. Sansom. The role of the membrane in the structure and biophysical robustness of the dengue virion envelope. Structure 24:375-382, 2016. https://doi.org/10.1016/j.str.2015.12.011
 
[4] R.G. Huber, J.K. Marzinek, P.L.S. Boon, W. Yue, P.J. Bond. Computational modelling of flavivirus dynamics: The ins and outs. Methods 185:28-38, 2021. https://doi.org/10.1016/j.ymeth.2020.06.004
 
[5] E.E. Jefferys, M.S.P. Sansom. Computational virology: molecular simulations of virus dynamics and interactions. Physical Virology, 201-233, 2019. https://doi.org/10.1007/978-3-030-14741-9_10
 
[6] J.K. Marzinek, R.G. Huber, P.J. Bond. Multiscale modelling and simulation of viruses. Current Opinion in Structural Biology 61, 146-152, 2020. https://doi.org/10.1016/j.sbi.2019.12.019
 
[7] W. Pezeshkian, F. Grünewald, O. Narykov, S. Lu, T.A. Wassenaar, S.J. Marrink, D. Korkin. Molecular architecture of SARS-CoV-2 envelope by integrative modeling. Structure 31 (4), 492-503, 2023. doi:10.1016/j.str.2023.02.006