Protein-ligand Interaction Exploration Based on Proteome-wide Tertiary Structure Prediction and Further in vitro Validation
Shaowei Dong · TSpace (University of Toronto) · 2017
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 hasnâ 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.