Novel Regulatory Mechanisms Identified in Viral DNA Packaging Proteins using Molecular Dynamics Simulations

Abstract

Many viruses use large terminase proteins (TerL) to convert chemical energy from ATP hydrolysis into mechanical work in order to package their genome into a viral pro-capsid. TerL proteins belong to the Additional Strand, Conserved Glutamate superfamily of P-loop ATPases, which contain canonical Walker motifs and a catalytic glutamate residue downstream of the Walker B motif. Although several crystal structures of TerL proteins are now available, these structures do not provide sufficient information to form a detailed mechanism of ATP hydrolysis and signal transduction. Through molecular dynamics simulations of three representative TerLs (from T4, Sf6, and P74-26 phages) in apo and ATP-bound states we identify a novel “arginine toggle” mechanism, whereby a conserved Walker A arginine toggles its interaction between two glutamate residues - one located in the lid subdomain and one located in the ATPase active site - in order to couple ATP binding to conformational change. Not only is this one of the first steps in the mechanochemical coupling pathway, but it also promotes catalysis of hydrolysis, both of which are consistent with experimental biochemical and single-molecule data. We go on to simulate mutant TerL proteins modified in silico to provide new insights into the specific binding pocket deformations that correspond with hindered ATP hydrolysis and slowed DNA packaging observed experimentally. Lastly, we present evidence that a “glutamate switch” residue found in other AAA+ motor proteins, which holds the catalytic glutamate residue in an inactive pose to regulate the rate of ATP hydrolysis, might also be conserved in some TerL proteins.