BME PhD Dissertation Defense - Christine Yueh

  • Starts: 2:00 pm on Friday, December 1, 2017
Title: “Application of Computational Methods for Predicting Protein Interactions” Committee: Prof. Sandor Vajda, BME (Advisor) Prof. Maxim Frank-Kamenetskii, BME (Chair) Prof. Dima Kozakov, BME Prof. Adrian Whitty, Chemistry Prof. Karen Allen, Chemistry Abstract: Protein interactions with other proteins or small molecules are critical to most physiological processes. These interactions may be characterized experimentally, such as with yeast two-hybrid screening or affinity purification/mass spectrometry, but such experiments can be time consuming and expensive to perform. Computational methods for predicting whether two proteins interact, or which regions of a protein are most favorable for binding, are thus valuable tools for understanding how proteins of interest function, and have applications in drug discovery and identifying proteins of therapeutic interest. The ClusPro and FTMap algorithms can estimate the interaction energy of a protein-protein or protein-small molecule interaction, respectively, which can then be used to identify the most likely orientations of a protein complex or the regions on a protein surface with the greatest propensity for binding. This work describes three applications of ClusPro and FTMap: using ClusPro to determine whether a protein-protein interface is biologically relevant; predicting whether a mutation in a multimeric complex will trigger supramolecular self-assembly, and using FTMap to analyze the druggabliity of potential allosteric sites in kinases. Discrimination of proteins as dimers or monomers has been implemented as an addition to the ClusPro server, ClusPro-DC, and the results of the druggability analysis of kinases have been organized into an online resource, the Kinase Atlas.
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