Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly

In this work, we assess a previously advanced hypothesis that predicts the existence of ion channels in the capsid of small and non-enveloped icosahedral viruses. With this purpose we examine Triatoma Virus (TrV) as a case study. This virus has a stable capsid under highly acidic conditions but disassembles and releases the genome in alkaline environments. Our calculations range from a subtle sub-atomic proton interchange to the dismantling of a large-scale system representing several million of atoms. Our results provide structure-based explanations for the three roles played by the capsid to enable genome release. First, we observe, for the first time, the formation of a hydrophobic gate in the cavity along the five-fold axis of the wild-type virus capsid, which can be disrupted by an ion located in the pore. Second, the channel enables protons to permeate the capsid through a unidirectional Grotthuss-like mechanism, which is the most likely process through which the capsid senses pH. Finally, assuming that the proton leak promotes a charge imbalance in the interior of the capsid, we model an internal pressure that forces shell cracking using coarse-grained simulations. Although qualitatively, this last step could represent the mechanism of capsid opening that allows RNA release. All of our calculations are in agreement with current experimental data obtained using TrV and describe a cascade of events that could explain the destabilization and disassembly of similar icosahedral viruses.This work was partially supported by a grant to DMAG from the Ministerio de Ciencia e Innovacion (MICINN) (BFU2012-36241), and from the Basque Government (Grupos Consolidados IT849-13; Elkartek KK-2017/00008), Spain. DMAG thanks a 2016 Mobility fellowship from Universidad del Pais Vasco (UPV/EHU), and the 2016-17 networking grant from the CYTED (216RT0506). MMB and PB thank the financial support of CONICET (PIP 112-2010100949), ANPCYT (PICT 2010-No 0830) and Universidad Nacional del Sur (PGI-UNS No 24/F051). SP and MM are partially funded by FOCEM (MERCOSUR Structural Convergence Fund), COF 03/11 and the SNI program of ANII. MDC has support from PGI - UNS No 24/F064. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript