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Discovery Of Novel Ubiquitin- And Methylation-Dependent Interactions Using Protein Domain Microarrays, Jianji Chen
Discovery Of Novel Ubiquitin- And Methylation-Dependent Interactions Using Protein Domain Microarrays, Jianji Chen
Dissertations & Theses (Open Access)
Post-translational modifications (PTMs) drive signal transduction by interacting with "reader" proteins. Protein domain microarray is a high throughput platform to identify novel readers for PTMs. In this dissertation, I applied two protein domain microarrays identifying novel readers for histone H2Aub1 and H2Bub1, and H3TM K4me3. Ubiquitinations of histone H2A at K119 (H2Aub1) and histone H2B at K120 (H2Bub1) function in distinct transcription regulation and DNA damage repair pathways, likely mediated by specific "reader" proteins. There are only two H2Aub1-specific readers identified and no known H2Bub1-specific readers. Using a ubiquitin-binding domain microarray, I discovered the phospholipase A2-activating protein (PLAA) PFU domain …
Hub Proteins, Paralogs, And Unknown Proteins In Bacterial Interaction Networks, Neha Sakhawalkar
Hub Proteins, Paralogs, And Unknown Proteins In Bacterial Interaction Networks, Neha Sakhawalkar
Theses and Dissertations
Proteins are the functional units of cells. However, a major portion of the proteome does not have a known functional annotation. This dissertation explores protein -protein interactions, involving these uncharacterized or unknown function proteins. Initially, protein – protein interactions were tested and analyzed for paralogous proteins in Escherichia coli. To expand this concept further and to get an overview, protein – protein interactions were analyzed using ‘comparative interactomics’ for four pathogenic bacterial species including Escherichia coli, Yersinia pestis, Vibrio cholerae and Staphylococcus aureus. This approach was used to study unknown function protein pairs as well as to …
The Drosophila Interactions Database: Integrating The Interactome And Transcriptome, Thilakam Murali
The Drosophila Interactions Database: Integrating The Interactome And Transcriptome, Thilakam Murali
Wayne State University Dissertations
In this thesis I describe the integration of heterogeneous interaction data for Drosophila into DroID, the Drosophilainteractions database, making it a one-stop public resource for interaction data. I have also made it possible to filter the interaction data using gene expression data to generate context-relevant networks making DroID a one-of-a kind resource for biologists. In the two years since the upgraded DroID has been available, several studies have used the heterogeneous interaction data in DroID to advance our understanding of Drosophila biology thus validating the need for such a resource for biologists. In addition to this, I have identified …
Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan
Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan
Computer Science Theses & Dissertations
Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. …