Quantum Simulation of Proton Channeling in Icosahedral Viral Capsids

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

Baltimore

Encuentro; 63rd Annual Meeting of the Biophysical Society; 2019

Viral capsids of many human, animal, and plant viruses consist of proteins arranged as an icosahedral envelope. Capsids arecompact and lack cavities large enough through which solvent molecules could be freely interchanged with the external milieu.However, upon genome encapsidation and assembly, narrow cavities that traverse the capsid, just at the frontier of the capsidproteins, can lodge both water molecules and coordinated ions. In addition to the known capacity of the ions to stabilize thecapsid, a recent study on Triatoma virus (Viso et al. 2018. PLOS Comp. Biol. DOI: 10.1371/journal.pcbi.1006082) shows thatthey can also allow hydrate hydrophobic cavities by forming water chains known as water wires. In this study we show how thecombination of few structural factors, a cation located in a narrow cavity accessible from the bulk solvent, can permit protonsto traverse the viral capsid through a Grotthuss-like mechanism. Moreover, due to proton transit occurs along a thin and long(ca. 20 nm) water chain, this conduction can be interrupted if a hydronium ion gets close to the bonded ion. Most likely thiscan be a mechanism for the virus to sense the environmental pH (Branda & Guérin (2019) Chapter 8. Springer book series:Advances in Experimental Medicine and Biology - Issue on Physical Virology. In press).Through this analysis, we support the hypothesis of the existence of ion channels in icosahedral viral capsids (Kalko et al.1992. Biophys J. 63(4): 1133-1145).