Ions at the 5-fold axis of icosahedral virus capsids: Cricket Paralysis virus

DIGILIO AYELEN; GUÉRIN DIEGO M.A.; BRANDA MARÍA MARTA; PORASSO RODOLFO

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Congreso; CMD2020GEFES; 2020

Many crystallographic structures of non-enveloped, small viruses (of about 30nm in dia), of animals, plants and insects, show the presence of ions at the non-crystallographic axis. The role these ions play supporting the multiple capsid functions remains unclear. Theoretical studies based on molecular dynamics (DM) and quantum mechanics (MC) on Triatoma virus (TrV) [1,2], have shown that a cation located into the 5-fold axis allows waters fill a hydrophobic neck. Moreover, ion and water molecules build a proton diode, a net through which protons can exit the capsid but not enter to it. Inspired on these results, in this works we studied the cricket paralysis virus (CrPV) structure [3], a close related virus to TrV and with a very similar capsid structure. Our finding indicates that along the 5-fold axis are two binding sites for calcium. The position of one of these sites agrees with an observed bulge at the crystallographic electron density map. The second ion position, energetically less favorable than the first, is located deep the 5-fold axis, right at the internal capsid surface. Similar to what was observed in TrV and called hydrophobic gate, in CrPV capsid exists a narrow region of about of 7Å long along the 5-fold axis (Fig. 1a). But unlike what happens in TrV in which the gate gets hydrated when the cation is present, the hydrophobic region in CrPV remains devoid of waters even when both cations are in place.