Abstract:
A grand challenge in atomistic simulations is achieving large-scale conformation changes and observing multiple binding and unbinding events in a large molecular machine, such as the ribosome. These dynamics typically unfold at timescales ranging from milliseconds to seconds, which are impractical to achieve with current simulation methods and supercomputing capabilities. Here, we introduce a coarse-grained technique, termed MUON, a novel multi-rigid body simulation approach which employs a constrained dynamics algorithm. This innovative approach allows for the modelling of molecular machines as numerous independent rigid bodies or as interconnected chains of rigid bodies linked by flexible connections. We harness the capabilities of constrained algorithms to temperate accelerate the simulation, thereby facilitating the exploration of slow transitions, such as association or dissociation of macromolecules within molecular complexes, over a reduced timescale. We successfully simulated the dissociation of deacylated tRNA from the E site of the Escherichia coli ribosome—a process that typically occurs on the timescale of seconds—while utilizing minimal computational resources and achieving results in a reduced timeframe. Our study captured 100 tRNA dissociation events from each of the last three recognized stages of the translocation cycle (INT2, INT3, and POST) in a manner that is biologically relevant. The derivation of kinetic and thermodynamic parameters, along with the elucidation of transition pathways, has provided profound insights into the unbinding mechanism of deacylated tRNA.