Brett Thurlow, Ph.D. (front left) describes his and his colleagues experience at McMaster University characterizing the key factors involved in ribosome assembly when he was a Ph.D. student there. Brett is currently an Application Specialist at NanoTemper.
Analyzing protein-RNA interactions can be a daunting task
Establishing if two molecules interact with each other and characterizing how “tight” that interaction is can be a very challenging task. Often researchers can spend months or years preparing their samples and running rather crude binding assays to assess the various binding interactions of interest. An example of this binding affinity characterization assay is when two potential binding partners are incubated together to allow them bind to each other, and then run through a gel by electrophoresis to assess the interaction. There are several problems with this type of experimental set up, including non-equilibrium conditions, limitations in the concentrations of sample that can be used and difficulty quantifying the binding interaction. For these reasons, analyzing protein-RNA interactions involved in ribosome assembly can be a daunting task. To circumvent these problems, we turned to a technique known as MicroScale Thermophoresis (MST), which enabled rapid characterization of challenging binding interactions involved in the biogenesis of the ribosome.
Ribosome biogenesis could provide a new source for novel therapeutics
Although the ribosome serves as a platform for targeting antimicrobials, the biogenesis pathway remains to be utilized and there have been no therapeutics developed that specifically target ribosome assembly. Therefore, ribosome biogenesis could provide a new source for novel therapeutics. Accordingly, the purpose of this research project was to better understand how protein assembly factors build the ribosome and obtain a more comprehensive understanding of macromolecular assembly.
Binding analysis on the Monolith was fast and easy to use
Initially, a series of binding assays were performed by incubating ribosome samples and potential binding partners, separating the bound from the unbound species, and then utilizing gel electrophoresis to analyze the various protein-ribosome interactions. These assays consumed large amounts of sample, were tedious, time consuming and ultimately led to results that were difficult to interpret. At the end of the day (or years!), we had a lot of interesting data, but did not quite know what to make of it. Fortunately, a top bioanalytics professor at the University of Toronto had recently acquired the Monolith NT.115, which enabled researchers to use MST for assessing binding interactions. Binding analysis on the Monolith required extremely low amounts of sample, was performed completely in solution, was fast and easy to use. These were all prominent features that were important for driving our research forward and therefore we were excited to jump into binding affinity experiments on the Monolith.
Quantitative nature of results allowed easy interpretation of data and understanding of interactions
After performing assay optimization, we were able to obtain unambiguous binding affinity constants (KD) between our assembly factors of interest and the ribosome. The quantitative nature of these results allowed us to easily interpret the data and substantially improved our understanding of these interactions. Therefore, MST provided us with a biophysical tool that enabled rapid characterization of challenging molecular interactions, without consuming large amounts of precious sample and ultimately aided our understanding of how protein assembly factors interact with the ribosome.
Learn more in this on-demand webinar
In this on-demand webinar, learn more about my experience utilizing methodologies such as MST to monitor and characterize the key factors involved in ribosome assembly. I share examples detailing the fate, binding interactions and structure of immature particles that accumulate in assembly factor knockout or depletion strains.