Exposing the Injection Machinery Dynamics of Bacteriophage T4 through Multi-Scale Modeling

Abstract

Bacteriophage T4 is one of the most well studied contractile-tailed viruses from the family Myoviridae which infects the bacterium Escherichia coli using an intriguing contractile tail assembly. The phage T4 is composed of three major structures: 1) a large capsid containing the viral genome (DNA), 2) a contractile tail structure that generates the driving force to pierce the host membrane and transfer DNA from the capsid into the host, and 3) a baseplate equipped with fibers that recognize and bind to the host. The contractile tail consists of a needle-like tail tube surrounded by an elastic sheath. During injection, the sheath undergoes a large conformational transition from a high-energy (extended) state to a low-energy (contracted) state, thereby releasing the energy needed for the tail tube to penetrate the host. Bacteriophages are employed as an alternative to antibiotics to treat infectious diseases and, importantly, those now growing resistant to antibiotics. In addition, because phages T4 are highly efficient genome delivery machines, understanding their function has major implications for future bio-nanotechnology devices. Thus, there is ample motivation for extending engineering methods to reveal the basic science underlying phage function. Despite extensive progress in resolving the structure of T4, the dynamics of the injection machinery remains largely unknown. This dissertation contributes the first system-level model describing the nonlinear dynamics of the phage T4 injection machinery interacting with a host cell. We employ a three-dimensional continuum dynamic model (based on Kirchhoff rod theory) to simulate the nonlinear dynamics of the six protein strands that constitute the sheath coupled to a model for the remainder of the virus interacting with host cell. The resulting continuum model for the contractile sheath employs elastic constants determined a priori from molecular dynamics simulations. The resulting system-level model captures virus-cell interactions as well as competing energetic mechanisms that release and dissipate energy during the injection process. The sources of energy dissipation include the hydrodynamic dissipation on the capsid and sheath from the surrounding environment, the internal dissipation of the sheath strands, the dissipation from the host cell membrane interacting with the tip of the tail tube, and the hydrodynamic interaction between the sheath and the tail tube. The new findings and major conclusions drawn from this system model are as follows. The model estimates that the injection process is driven by approximately 14500 kT of elastic energy stored in the extended sheath which is consistent with the reported enthalpic change reported in the experimental literature. The model also reveals that the dynamical pathway of the injection progresses as a “contraction wave” that propagates along the sheath, a finding consistent with published micrographs observed in experiments. The model further estimates that cell rupture arises when the tip of the tail tube exerts a force of ~330 pN and at a membrane indentation of ~60 Å. Finally, the model enables broad exploration of the four energy dissipation mechanisms and reveals the mechanisms and parameters that control the time scale of the injection process.