My Thesis Work
After synthesis, a protein is still immature until it has been customized for a specific task. Post-translational modifications (PTMs) are steps in biosynthesis to perform this customization of protein for unique functionalities. PTMs are also important to protein survival because they rapidly enable protein adaptation to environmental stress factors by conformation change. The overarching contribution of this thesis is the construction of a computational profiling framework for the study of biological signals stemming from PTMs associated with stressed proteins. In particular, this work has been developed to predict and detect the biological mechanisms involved in types of stress response with PTMs in mitochondrial (Mt) and non-Mt protein.
Before any mechanism can be studied, there must first be some evidence of its existence. This evidence takes the form of signals such as biases of biological actors and types of protein interaction. Our framework has been developed to locate these signals, distilled from “Big Data” resources such as public databases and the the entire PubMed literature corpus.
We apply this framework to study the signals to learn about protein stress responses involving PTMs, modification sites (MSs). We developed of this framework, and its approach to analysis, according to three main facets: (1) by statistical evaluation to determine patterns of signal dominance throughout large volumes of data, (2) by signal location to track down the regions where the mechanisms must be found according to the types and numbers of associated actors at relevant regions in protein, and (3) by text mining to determine how these signals have been previously investigated by researchers. The results gained from our framework enable us to uncover the PTM actors, MSs and protein domains which are the major components of particular stress response mechanisms and may play roles in protein malfunction and disease.
Links to Project Documents
Links to Supporting documents
Modeling the Effects of Microgravity On Oxidation in Mitochondria: A Protein Damage Assessment Across a Diverse Set of Life. We study the content of regions which are likely causes to protein failure in protein. We find that mitochondria has some protection against protein failure which is not detected in non-mitochondrial protein.
sEncrypt: An Encryption Tool using biological data to encrypt information. We propose a conceptual encryption framework which uses the wealth of data available from bioinformatics research projects (DNA, codon bias tables for specific organisms) to render plain text unreadable. The plain text is recovered with the knowledge of which data was used. Since there is so much data available form so many different research projects, the text may never be recovered without specific information. Furthermore, since biology does not follow logical rules, brute-force approaches may prove ineffective in this system.
Post-translational modification bias between organism complexity: Trends observed across diverse lifeforms In this work, we ask how are the Post-translational modification (PTMs) distributions are different between the mitochondria (Mt) and non-Mt proteomes. We then ask, how are the PTM reactive site distributions different between the Mt and non-Mt proteomes? And, yes, there was a difference in distributions!
Flint the Beagle!
You wrote this? Wow!