Structural Origins of FRET-Observed Nascent Chain Compaction on the Ribosome

A fluorescence signal arising from a Förster resonance energy transfer process was used to monitor conformational changes of a domain within the E. coli protein HemK during its synthesis by the ribosome. An increase in fluorescence was observed to begin 10 s after translation was initiated, indicating the domain became more compact in size. Since fluorescence only reports a single value at each time point it contains very little information about the structural ensemble that gives rise to it. Here, we supplement this experimental information with coarse-grained simulations that describe protein conformations and transitions at a spatial resolution of 3.8 Å. We use these simulations to test three hypotheses that might explain the cause of domain compaction: (1) that poor solvent quality conditions drive the unfolded state to compact, (2) that a change in the dimension of the space the domain occupies upon moving outside the exit tunnel causes compaction, or (3) that domain folding causes compaction. We find that domain folding and dimensional collapse are both consistent with the experimental data, while poor-solvent collapse is inconsistent. We identify alternative dye labeling positions on HemK that upon fluorescence can differentiate between the domain folding and dimensional collapse mechanisms. Partial folding of domains has been observed in C-terminally truncated forms of proteins. Therefore, it is likely that the experimentally observed compact state is a partially folded intermediate consisting, according to our simulations, of the first three helices of the HemK N-terminal domain adopting a native, tertiary configuration. With these simulations we also identify the possible cotranslational folding pathways of HemK.