A Molecular Dynamics Simulation Study of putative ions in CrPV capsid

AYELEN DIGILIO; RODOLFO D. PORASSO; DIEGO GUERIN; MARIA MARTA BRANDA

Bilbao

Congreso; 8th International Iberian Biophysics Congress; 2022

Icosahedral viruses, such as those of the genus Picornavirales, are sphertical of about 300Å in diameter, non-enveloped, and are pathogenic of plants and animals, including humans. These viruses show a cavity at the 5-fold symmetry axis and, in some of them, the crystallographic structure shows density attributable to ions. The role/s these putative ions could play is still speculative. In our recent theoretical study run on Triatoma virus (TrV; Dicistroviridae:Triatovirus) we proposed that the cavity and the ion could function as ion channel. Using molecular dynamics (MD) and quantum mechanics we have shown that a cation located at the 5-fold axis allows the waters to fill a hydrophobic neck and make a hydrogen-bond network of about 2nm long, and that through this water wire protons can exit but not to enter the capsid.2,3 In this MD work we analyze Cricket paralysis Virus (CrPV; Dicistroviridae: Cripaviridae), a virus with very similar structure to TrV 4, and we conclude that these ions could play only a structural role, as it was initially proposed for CrPV 6 and for other icosahedral viruses.