Simulating activity of the bacterial ribosome.

Computational modeling studies that investigate activity of the bacterial ribosome were reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to the enormous size of the system, theoretical efforts to study the ribosome are few and challenging. For example, to extend the simulation timescales to biologically relevant ones, often, reduced models that require tedious parameterizations need to be applied. To that end, modeling of the ribosome focused on its internal dynamics, electrostatic properties, inhibition by antibiotics, polypeptide folding in the ribosome tunnel and assembly mechanisms driving the formation of the small ribosomal subunit.