Dr. John Hunt === Columbia University === May 2026 - August 2026
Determining whether order to disorder transitions in the PTC of the ribosome are universal throughout life:
Within the ribosome, the peptidal transverse center (PTC) is responsible for the catalysis of peptide bond formation. Thus, in the process of translation, the PTC is crucial to the elongation of the polypeptide chain. Being in the center of the 50S subunit of the ribosome, the PTC is thought to be in a stable regime with little conformational changes. However, in an E. coli cryoelectron microscopy (cryoEM) ribosome dataset, an order to disorder transition has been noticed in the PTC, signaling a need for further analysis. This naturally leads to the question of if this order to disorder transition in the PTC is universal throughout all of life. Since this phenomena has gone unnoticed in the E. coli ribosome, there is high possibility that it has also been overlooked in ribosomes of other organisms as well. By closer inspection of various cryoEM datasets of different organisms using advanced cryoSPARC classification techniques, it can be concluded if the order to disorder transition is universal or not. Ribosomes catalyze peptide-bond formation by rigidly holding the substrates in the optimal reaction geometry. While rigidity is essential for that mode of catalysis, it will tend to prevent movement of the nascent polypeptide, which is needed to elongate it using the same active site. The physical basis of that movement is unclear, but the observation of the disordered state of the PTC could explain it. Therefore, generalizing the order to disorder transition could generalize the physical basis of movement.I analyzed large Cryogenic Electron Microscopy (CryoEM) datasets while remaining well organized throughout the process, applying CryoSPARC, PyMOL, and ChimeraX to follow a single-particle reconstruction pipeline using advanced classification techniques. Using this pipeline, I interpreted ribosome structures to determine whether an order-to-disorder transition in the peptidyl transferase center — originally identified in an E. coli dataset — could also be observed in other organisms. I presented my findings at a conference, a poster session, and group meetings.
