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SUMMARY:Computational insights into the mechanism of a ubiquitin conjugatin
 g enzyme
LOCATION:Chemistry A101
TZID:America/Denver
DTSTART:20186001T000000
UID:2026-04-06-03-52-11@natsci.colostate.edu
DTSTAMP:20260406T035211
Description: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 act
 ivity. Ubiquitination also plays a role in DNA repair and inflammatory res
 ponse. 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 th
 rough an oxyanion intermediate. This intermediate is hypothesized to be st
 abilized by the sidechain of a nearby asparagine residue\, which is known 
 as the “oxyanion hole.” However\, recent experimental results on mutat
 ed Ubc13 have suggested an alternate role for the asparagine. In our study
 \, we use a combination of simulation techniques – Born-Oppenheimer Mole
 cular 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 ind
 icate that instead of just stabilizing the negative charge on the oxyanion
 \, the asparagine may also reduce the fluctuations of the substrate\, allo
 wing it to more easily form a reactive geometry. Furthermore\, our simulat
 ions pinpoint the base responsible for deprotonating the substrate lysine.
  4:00 pm
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