Bridging molecular studies of model and real biological systems with biophysics experiments on complex samples

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The theme of the NSERC-based research in our lab is bridging model and real biological systems. The rationale for this approach is that detailed, molecular level, structural and dynamics research on biological molecules is generally done with systems of very simple composition, e.g. with one type of lipid and one type of protein. However, it's not always clear how the results from these simple systems compare to what goes on in the real, much more complex biological systems. Thus, our approach is to build bridges between the biophysical methods that have been developed for simple systems and extend them to much more complex biological systems in order to gain important insights into real life molecular structure and dynamics. ******With this Discovery Grant renewal, I am planning two main foci. Objective 1 will build on our already successful NSERC research into how antimicrobial peptides (AMPs) interact with intact bacteria. AMPs are a crucial component of the innate immune system of many organisms and can protect against a variety of invading pathogens including bacteria, viruses, and microbial eukaryotes. However, our understanding of how AMPs work does not extend much past how they interact with one component of pathogens: the lipids. With Objective 2, we will apply our expertise in performing biophysics with complex biological samples into a new area to us, soft interactions in molecular crowding, initially as applied to Intrinsically Disordered Proteins (IDPs). Molecular crowding, i.e. the effect of the very high concentration of biomolecules inside cells, is important because it can modify the structure and function of biological molecules compared to what is observed in dilute conditions via traditional biochemistry experiments.******The potential impact of Objective 1 relates to the enormous disparity between conditions used for studies of AMP molecular mechanisms, versus experiments where biological functional is actually observed; it takes an AMP to lipid ratio of ~10,000 greater to see inhibition of cell growth as compared to the ratio needed to see lipid bilayer disruption with a model lipid system. Thus, it is of high interest to find out with which components, besides the lipids, the AMP is interacting and how the non-lipid interactions modify the AMP-induced membrane disruption. There has been a high level of interest in the earlier phase of our work in this area, as evidenced by three invited reviews on the topic, and we expect this high interest to continue.******Our results from Objective 2 will impact the field via building a much needed and novel bridge to better understand how the large body of work performed on simple crowding systems can be applied to real cells. Conversely, our results should also help explain observations gleaned from in-cell experiments. Additionally, our work will provide valuable insights into parameters of interest in getting quality data with any kind of protein via in-cell NMR.**