Forces from the Portal Govern the Late-Stage DNA Transport in a Viral DNA Packaging Nanomotor

Abstract

In the Phi29 bacteriophage, the DNA packaging nanomotor packs its double-stranded DNA genome into the virus capsid. At the late stage of DNA packaging, the negatively charged genome is increasingly compacted at a higher density in the capsid with a higher internal pressure. During the process, two Donnan effects, osmotic pressure and Donnan equilibrium potentials, are significantly amplified, which, in turn, affect the channel activity of the portal protein, GP10, embedded in the semipermeable capsid shell. In the research, planar lipid bilayer experiments were used to study the channel activities of the viral protein. The Donnan effect on the conformational changes of the viral protein was discovered, indicating GP10 may not be a static channel at the late stage of DNA packaging. Due to the conformational changes, GP10 may generate electrostatic forces that govern the DNA transport. For the section of the genome DNA that remains outside of the connector channel, a strong repulsive force from the viral protein would be generated against the DNA entry; however, for the section of the genome DNA within the channel, the portal protein would become a Brownian motor, which adopts the flash Brownian ratchet mechanism to pump the DNA against the increasingly built-up internal pressure (up to 20 atm) in the capsid. Therefore, the DNA transport in the nanoscale viral channel at the late stage of DNA packaging could be a consequence of Brownian movement of the genomic DNA, which would be rectified and harnessed by the forces from the interior wall of the viral channel under the influence of the Donnan effect.

Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism

“…The importance of subtle conformational changes in the context of DNA translocation has also been claimed in modeling studies. In this regard, the distribution of regions differing in the degree of stiffness, thus allowing specific compressions and DNA-dependent distortions, as well as the existence of quasi-equivalent contacts, have been proposed to play important roles in DNA packaging 43–45 . Recently, it was also described for bacteriophage P23–45 that the portal may adopt different conformations depending on the stage of virus assembly, with synchronized movements of different domains communicating the inner part of the capsid to the exterior 46 .…”

Rhinovirus Inhibitors: Including a New Target, the Viral RNA

“…The RNA inside the viral shell is compact but not pressurised like dsDNA in some bacteriophages [ 182 ]. Nevertheless, it was suggested that viral RNAs are ‘unusually compact’ in order to fit into the limited space of the shell [ 183 ], but calculations show that they are definitely not under pressure [ 184 ].…”

ATP/ADP modulates gp16–pRNA conformational change in the Phi29 DNA packaging motor

“…This RNP complex actively transports DNA inside the prohead capsid using energy derived from ATP binding and hydrolysis (6–8). Understanding the mechanism for this molecular motor can provide insights to molecular transport (9), anti-viral therapeutics (10,11) and nanomedicine (12,13).…”