Isaiah Sumner
Speaker's Institution
James Madison University
4:00 PM
Chemistry A101
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ABSTRACT  The ubiquitin conjugating enzyme, Ubc13, catalyzes lysine ubiquitination, a type of protein post-translation modification. Ubiquitinating a protein can signal for its degradation and affect its activity. Ubiquitination also plays a role in DNA repair and inflammatory response. Defects in this process are linked to different disorders including cancer, Parkinson’s and Alzheimer’s diseases. The accepted mechanism for Ubc13-catalyzed ubiquitination is a stepwise pathway that proceeds through an oxyanion intermediate. This intermediate is hypothesized to be stabilized by the sidechain of a nearby asparagine residue, which is known as the “oxyanion hole.” However, recent experimental results on mutated Ubc13 have suggested an alternate role for the asparagine. In our study, we use a combination of simulation techniques – Born-Oppenheimer Molecular Dynamics (BOMD), single point Quantum Mechanics/Molecular Mechanics energies (QM/MM), and classical Molecular Dynamics (MD) – on wild-type and mutant Ubc13 to examine its catalytic mechanism. Our calculations indicate that instead of just stabilizing the negative charge on the oxyanion, the asparagine may also reduce the fluctuations of the substrate, allowing it to more easily form a reactive geometry. Furthermore, our simulations pinpoint the base responsible for deprotonating the substrate lysine.

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