Terra Dwayne Colvin, Jr., Masters Candidate,
Public Presentation in Olin Physical Laboratory, Room #107
Friday, November 30, 2018, at 2:30 PM
Fred Salsbury, PhD, Advisor
The defense will follow.
Molecular dynamics (MD) simulations permit the probing of biomolecular systems in both high spatial and temporal resolution. Advances in computing power and techniques combined with the proliferation of online bioinformatics resources enable highly detailed in silico experimental analysis of molecular events. Using the GPU-optimized ACEMD software package, we simulate disease-associated mutants of a zinc finger domain in IKK-gamma known to bind with ubiquitin and analyze the results using a variety of statistical and computational methods.
An overview of the essential physics for MD simulations and the biochemistry of proteins is presented followed by a discussion of the critical role that IKK-gamma plays in the regulation of inflammatory response. Finally, a series of computational experiments to assess the impact of point mutations on the conformational ensemble and dynamics of the NEMO zinc finger domain are detailed and compared to known experimental results.