PhD Exit Seminar- Michael Dong

PhD Exit Seminar

Monday, August 14, 2017 at 1:10 pm, Earth Sciences Building, Room 3087

Michael Dong (Provart Lab)

“Protein-ligand interaction exploration based on proteome-wide tertiary structure prediction and further in vitro validation”

Abstract

Knowledge of protein structures provides us valuable information for protein function elucidation, but currently it is still unrealistic to determine proteome-wide protein structures using experimental methods. Computational modeling provides us a fast and convenient method in protein structure characterization, and but to date, there hasn’t been any systematic application of proteome-wide models in Arabidopsis due to the lack of such data sets. Our lab has determined the theoretical protein structures for the entire Arabidopsis proteome. In this work, I presented two versions of Arabidopsis predicted structure-omes (APS-V1 and APS-V2) generated by the Phyre fold recognition engine and showed that a large portion of the predicted models in our APS have enough resolution for use in protein functional studies.

In our case, the predicted models were specifically used in protein-carbohydrate and protein-protein interaction studies followed by in vitro verification using carbohydrate arrays and yeast two-hybrid assays. The enrichment of real interactions in the prediction results confirmed that our Arabidopsis predicted structure-ome is a reliable tool in protein structural and functional studies. This work also provides another perspective in large-scale protein-ligand interaction exploration and biological network reconstruction using protein structural information.