4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation

Yapici, I.; Dao, E. H.; Yokoi, S.; Destan, E.; Ayan, E.; Shafiei Kamel, A.; Ertem, F. B.; Kulakman, C.; Yilmaz, M.; Tosun, B.; Ciftci, H.; Kepceoglu, A.; Johnson, J. A.; Guven, O.; Ergul, A.; Hayes, B.; Rao, Y.; Kupitz, C. J.; Poitevin, F.; Liang, M.; Hunter, M. S.; Milon, P.; Mitsutake, A.; Sierra, R. G.; Wakatsuki, S.; DeMirci, H.

doi:10.1101/2023.10.27.564398

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bioRxiv · 10.1101/2023.10.27.564398

4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation

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Abstract

Initiation factor 1 (IF1) is one of multiple key ligands involved in the initiation of mRNA translation, a highly dynamic and carefully-orchestrated process. However, details surrounding IF1 transient interactions with the small 30S ribosomal subunit remain incompletely understood despite characterization of unbound and fully-bound 30S states. Improvements in X-ray light sources and crystallographic techniques are now enabling time-resolved structural studies at near-physiological temperature and near-atomic resolution and thus the structural investigation of such dynamic processes. Here, we employed time-resolved serial femtosecond X-ray crystallography (TR-SFX) to probe the binding of IF1 to the small 30S ribosomal subunit in real time. Our time-resolved structural data demonstrates transient cryptic short-, mid-, and long-range allostery among different regions of the small 30 ribosomal subunit during IF1 binding, revealing small- and large-scale protein-target interactions and dynamics within intermediate macromolecular states at unprecedented temporal and spatial resolution. These data represent one of the first such 4D crystallographic studies assessing protein-protein and protein-RNA interactions and could serve as the basis for subsequent studies of the ribosome and of the multitudinous dynamic processes which underpin biology, and therefore, of life.

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Yapici, I., Dao, E. H., Yokoi, S., Destan, E., Ayan, E., Shafiei Kamel, A., Ertem, F. B., Kulakman, C., Yilmaz, M., Tosun, B., Ciftci, H., Kepceoglu, A., Johnson, J. A., Guven, O., Ergul, A., Hayes, B., Rao, Y., Kupitz, C. J., Poitevin, F., Liang, M., Hunter, M. S., Milon, P., Mitsutake, A., Sierra, R. G., Wakatsuki, S., DeMirci, H.. 2023-10-29. 4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation. https://doi.org/10.1101/2023.10.27.564398

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