Analysis of the 5-fold symmetry axis of Triatoma Virus using Hybrid Molecular Dynamics.

JUAN FRANCISCO VISO; FERNANDO ZAMARREÑO; MARÍA JULIA AMUNDARAIN; SERGIO PANTANO; DIEGO MARCELO GUÉRIN AGUILAR; MARCELO DANIEL COSTABEL

Trieste

Workshop; School in Computational Condensed Matter Physics: Atomistic Simulations to Universal Model Hamiltonians; 2015

Abdus Salam: Internatial Center of Theoretical Physics

In this work we study the capsid of the Triatoma Virus (TrV, Dicistroviridae: Cripavirus), an insect virus whose capsid has icosahedral symmetry. We focused our attention to the 5-fold symmetry axis in which exists a cavity or 'pore' that radially traverses the capsid. Although this cavity has a narrowing at its middle part, fluctuations in the protein could allow the passage of solvent molecules and/or ions. The TrV crystallographic structure shows that the cavity is partially filled with solvent molecules, but it also displays some unexplained density bulges along the 5-fold axis.Using molecular dynamics simulations with the help of the Sirah Force-Field we were able to simulate the whole capsid by means of a hybrid method of Coarse Grain ? Molecular Mechanics (CG/MM). As result we observed the presence of a dehydrated region along thepore near a ring of Valines, which creates a supposed hydrophobic gate. Others simulation showed that the presence of a magnesium ion near this region could lead to the pore full hydration. This results correspond with the electronic density map.