Ph.D. Research Proposal - Deciphering the Grammar of Protein-Protein Interactions: A Multidimensional Enrichment Analysis using Databases on Protein Domains and Motifs
Date: September 18, 2009
Time: 1:00 PM
Location: Bossone Research Enterprise Center, Room: 709
Speaker(s):
Liu Yichuan
Advisor: Aydin Tozeren, Ph.D.
Details:
The specific aim of my doctoral thesis is to predict transient interactions between proteins based on their domain/motif composition. Phosphorylation events direct and modulate the flow of signals and metabolites along cellular protein networks. Protein kinase/substrate binding interactions have been quantified for hundreds of kinases and their substrates using a variety of experimental procedures but the annotations of PPI in phosphorylation are far from complete. Moreover, viral proteins often out-compete host kinase substrates in phosphorylation resulting in viral proteins hijacking function. Similarly, transient interactions between transcription factors and promoters play fundamental roles in the regulation of gene expression.
In this study, I use statistical methods for domain and domain cluster enrichment and scan through large protein databases to identify patterns in domain composition of interacting proteins. My preliminary studies point to PPI prediction in terms of domain composition with high specificity in the case of phosphorylation events. Future work will extend these studies into transcription factor binding interactions with promoters.
Biosketch:
Directions:
The Bossone Research Enterprise Center is located at the corner of 32nd and Market Streets.
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