Research Mentor(s): Peter Freddolino, Assistant Professor
Research Mentor School/College/Department: Biological Chemistry, Michigan Medicine
Presentation Date: Thursday, April 22, 2021
Session: Session 2 (11am – 11:50am)
Breakout Room: Room 7
Gene regulation in E. coli bacteria is determined primarily by transcriptional regulatory proteins and their interactions with DNA. These proteins, such as LER and H-NS, are vital to determining virulence in E. coli, and while much research has been done on the proteins themselves and the genes they express, work still needs to be done to determine which DNA structures and/or sequences are preferred by these proteins. We hypothesize that proteins like H-NS and LER prefer to bind to structures, rather than sequence, with an affinity for bent or elongated DNA. Using the molecular simulation software NAMD, and its analysis counterpart VMD, it is possible to simulate interactions between the proteins and DNA. Laboratory testing using Spect-seq and gel shift assays will work in conjunction with the simulations to test the findings of the computational side of this research, and provide additional insights into the reality of protein-DNA interaction in a laboratory setting. If we can better understand how these proteins regulate the bacterial genome, we will expand our knowledge of regulating virulence, and thus find better ways of treating bacterial infections without the harmful effects and risks of traditional antibiotics, as well as providing valuable insight on protein-DNA interaction of any form.