Probing the Conformational Change of Contractile Tails using Coarse-Grained Normal Mode Analysis

Abstract

Significant development in nanotechnology is expected to come from understanding the mechanisms of biomolecular machines. Contractile tails are unique organelles present in certain biomolecular machines which aid in piercing a host membrane and injecting macromolecules inside the host. These tails consist of an inner tail tube with a spring-like sheath wrapped around it. The inner tail tube ends at a spike tip surrounded by a baseplate. During the injection mechanism the sheath undergoes a large conformational from an extended state to a contracted state,thereby pushing the tail tube like a needle through the membrane. This conformational change involves ∼1.3 million atoms and is estimated to be on the millisecond-to-second timescale. Recent efforts have yielded information regarding the structure of the sheath. Conventional methods such as molecular dynamics simulations are not possible for a system of this size. Instead, the collective motions can be observed using the anisotropic network model (ANM), a coarse-grained normal mode analysis method. The ANM model shows that the slowest, global modes are encoded within the sheath's structure. Using these modes we show how it is possible to observe a coarse grained representation of the contraction pathway. Furthermore the work presented could be applied to other large biological structures which undergo conformational changes.