Bu Sha, Antonio: Big Data Analysis on How Protein-DNA Interactions Impact Nucleosome Folding

Title: Big Data Analysis on How Protein-DNA Interactions Impact Nucleosome Folding

Name: Antonio Bu Sha

Major: Mechanical Engineering

School affiliation: School of Engineering

Programs: Aresty Summer Science Program

Other contributors: Wilma Olson

Abstract: While it is well understood that the DNA sequence (ATCG) contains the information for how to construct the proteins and RNA that allow most life to function, the role of DNA folding in gene expression is not well understood. DNA is stored in the nucleus by being wrapped around collections of proteins called histones, to form a nucleosome. Our research group is investigating how the specific way that DNA wraps
around histones impacts the detachment and subsequent processing of the interacting DNA. Our research group used programs to produce computational models of nucleosomes from the Protein Data Bank (PDB) by analyzing the properties of individual interactions between the DNA and histones. By cataloging and analyzing these interactions, trends across multiple structures can be observed. Preliminary data suggest that DNA often binds asymmetrically to the histone core and may unravel more easily from the side with fewer interactions with histones. This research shows that analyzing histone-DNA interactions will help us better understand DNA folding in nucleosomes. Further research is planned to analyze the effects of non-histone proteins on the way that DNA wraps and unwraps around the histone core.