Biochemistry & Biophysics
I am currently a second year biochemistry/biophysics graduate student performing research for Dr. Christopher Bystroff in the area of computational protein design of green fluorescent protein (GFP)-based biosensors. The primary research focus of the Bystroff laboratory is in developing both computational and experimental processes for using GFP as a biosensor. This is accomplished by truncating the GFP beta barrel by removing one of the eleven beta strands that compose the barrel. The site of the deleted strand is then computationally designed to accommodate a peptide sequence from a pathogen whose detection is desired. In the presence of this peptide sequence, the GFP in theory will reconstitute the beta barrel, which restores green fluorescence, signaling the presence of the pathogen.
The main focus of my research is two-fold: developing a novel algorithm for designing proteins that incorporates efficient sampling of the protein backbone and developing a computational pipeline for designing biological biosensors using a GFP scaffold. Recent research has suggested that computational protein design is best performed in the context of backbone flexibility and there are numerous approaches to incorporate these movements into the design process while maintaining algorithmic efficiency. Our approach utilizes backbone and side-chain ensembles to score and predict low energy protein conformations. By using the knowledge of these ensembles we hope to improve our protein design methods to generate more reliable biosensors.
In high school, I first became interested in computer programming by taking a freshman class that taught programming in an archaic language called QBASIC. I also had the unique opportunity to take a biotechnology class, which stimulated my interest in the biological sciences. As an undergraduate, I majored in bioinformatics/molecular biology because I was interested in biology and biotechnology but was still enjoyed and was adept with computer science. Currently, there is a growing need for many scientific fields to make use of the vast computational power that is becoming readily available. However, most of these researchers are unfamiliar with computational methods and most computer scientists are not familiar with the specifics of the research problems. As I computational biologist, I wanted to help bridge this gap between biology and computer science.
In addition to academics, I am active in the RPI Knights of Columbus Council 13635 in which I enjoy participating in various Catholic fraternal, service, and spiritual activities.