Cantor Chemical Biology & Biophysics Seminar Series
Friday, April 14th in Havemeyer 209 at 1pm
Talks
Nina Michael, Gonzalez Lab
Title: Elucidating the mechanism of bacterial release factor II during polypeptide hydrolysis on the ribosome
Abstract: Peptide release factor II (RF2) is a bacterial multi-purpose translation factor that releases the newly formed polypeptide from the ribosomal complex either at the end of translation or during alternative rescue factor A (ArfA)-mediated non-stop ribosome rescue, when the ribosomal complex is stalled due to the lack of a stop codon. In spite of the important role that the kinetics of RF2 stable association and conformational dynamics play in the timing of polypeptide release and recycling of the translational machinery, the full dynamic pathway followed by RF2 in these contexts remains elusive. Here, using single-molecule fluorescence energy transfer (smFRET), we characterize the conformational landscape that RF2 explores on the ribosomal complex during both canonical translation termination and ArfA-mediated non-stop ribosome rescue. We show that, in both pathways, RF2 stably associates with and dissociates from the ribosomal complex in a cascading ensemble of conformations. Additionally, we find that while the structural rearrangements that RF2 undergoes while in complex with the ribosome are partly an inherent behavior of RF2 within the ribosomal environment, interactions with the ribosomal complex are necessary to position RF2 for peptide release.
Korak Ray, Gonzalez Lab
Title: Atomic resolution in cryoEM
Abstract: Recent advances in cryoEM methodology, both technological and computational, have significantly furthered our ability to determine the atomic structures of biomolecules, driven by an increase in the quality of experimental cryoEM maps, and a consequent increase in the precision and accuracy with which atomic co-ordinates may be determined from them. This improvement in the quality of cryoEM maps has been hailed as a cryoEM ‘resolution revolution’. Yet these advances have been coupled with debate about the ‘resolution’ of cryoEM maps, and how these reported resolutions relate to the spatial information on specific structural features, particularly individual atoms, identified in these maps. A corollary concern is the quality of the structural model that is inferred from cryoEM experiments, and how much of the assignment of atomic coordinates in these models is grounded in experimental evidence. In this work, we show how these two questions are intimately related using a hierarchy of models that may describe a cryoEM map using structural features at different length scales. Comparison between these models allowed us to determine the model which explains the experimental data best, leading to a resolution criterion-based framework which reports on the resolution of specific features across different lengths scales. Using this approach, we investigated the local atomic resolution for a range of cryoEM maps and accurately captured the specific range of atomic level information present in a particular cryoEM map.
