A Computational Study of the Effect of Protonation States on the N79D Mutation in UBC13

Abstract

Post translational modification is the process of changing the function of a protein after it has already been synthesized without changing the entire protein. Ubiquitination is one of these processes and is the covalent attachment of the small protein ubiquitin to a lysine on a target protein through a series of reactions catalyzed by three types of enzymes the E1 (ubiquitin activating enzymes), the E2 (ubiquitin conjugating enzymes), and the E3 (ubiquitin ligases). If this process does not occur properly, it can cause many diseases such as Alzheimer's, Parkinson's and certain anemias. A popular hypothesis is that a conserved asparagine in the E2 enzyme (N79 in UBC13) stabilizes a reaction intermediate in the ubiquitination pathway because of its proximity to the active site, it is highly conserved and mutation studies show it is important for catalysis. MD simulations were run on several structures with the asparagine 79 mutated to a protonated aspartate (N79D), a deprotonated aspartate (N79D-) and an alanine (N79A), from those simulations hydrogen bonding and root-mean-square fluctuation (RMSF) data were obtained. The N79D mutation prefers to hydrogen bond to the substrate, the wild type shows lower fluctuations compared to all of the mutations and without more data no other definitive conclusions can be made.