FIG 2.
The physical context for translation elongation can be formalized. (A) Schematic of physical and chemical processes that contribute to translation elongation latency. Multiple transport and reaction steps (dashed line) may occur before a ternary complex (green/red) encounters and reacts with an unoccupied, matching ribosome (purple). The time ternary complexes spend unbound while searching for ribosomes is defined as transport latency (τtransport), and the time ternary complexes spend bound in either mismatching (red shaded circle) or matching reactions (green shaded circle) is defined as reaction latency (τrxn). The time the entire process takes is defined as elongation latency (τelong). (B) Mathematical definitions of translation elongation latencies. Elongation latency (τelong) is the sum of transport latency (τtransport) and reaction latency (τrxn), the latter of which is the sum of both mismatching and matching reaction latencies. (C) Schematic of the kinetic mechanism of translation elongation within ribosomes (purple). Ternary complexes are either cognate (green), near-cognate (yellow), or noncognate (red) to any particular ribosome, which determines kinetic rates. Mismatching reaction latency results from reversible reactions with noncognate and near-cognate ternary complexes (red and yellow lines), while matching reaction latency results from cognate ternary complexes proceeding through the full kinetic process (green line). (D) Translation elongation is evaluated by constructing ensembles of statistically representative “translation voxels” that, in their minimal form, contain exactly 42 ternary complexes (cognate, green; noncognate, red), at least one ribosome (purple), and numerous average-sized proteins representing all other surrounding proteins (blue). The depiction of E. coli is adapted with permission from reference 44; molecular abundances are adapted from the literature (see Results and Materials and Methods).