Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model

Biophysical Journal
Rajendra Kumar, Helmut Grubmüller

Abstract

During replication of the ϕ29 bacteriophage inside a bacterial host cell, a DNA packaging motor transports the viral DNA into the procapsid against a pressure difference of up to 40 ± 20 atm. Several models have been proposed for the underlying molecular mechanism. Here we have used molecular dynamics simulations to examine the role of the connector part of the motor, and specifically the one-way revolution and the push-roll model. We have focused at the structure and intermolecular interactions between the DNA and the connector, for which a near-complete structure is available. The connector is found to induce considerable DNA deformations with respect to its canonical B-form. We further assessed by force-probe simulations to which extent the connector is able to prevent DNA leakage and found that the connector can act as a partial one-way valve by a check-valve mechanism via its mobile loops. Analysis of the geometry, flexibility, and energetics of channel lysine residues suggested that this arrangement of residues is incompatible with the observed DNA packaging step-size of ∼2.5 bp, such that the step-size is probably determined by the other components of the motor. Previously proposed DNA revolution and rolling motions insi...Continue Reading

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Citations

May 24, 2016·The Journal of Physical Chemistry. B·James T WatersStephen C Harvey
Jan 21, 2016·Biophysical Journal·Paul J Jardine

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Methods Mentioned

BETA
optical tweezers
AFM
PCAs
PCA
x-ray crystallographic
fluorescence spectroscopy
fluorescence

Software Mentioned

Nucleic Acid Builder
GROMACS
SAMD
ArchPred
SimA
AMBER

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