Understanding How Distal Residues Play a Role in Parkin Activity

Abstract

Partial Order Optimum Likelihood (POOL) is a machine learning method that predicts catalytically important residues based on the tertiary structure of the protein, with computed chemical and electrostatic properties of the residues as input features. POOL has predicted spatially extended active sites, where residues that are not in direct contact with the substrate still contribute to catalysis for many enzymes, including for parkin. Parkin is an E3 ubiquitin ligase protein involved in the ubiquitin‐proteosome system that mediates the targeting of proteins for degradation. Mutations in parkin lead to the accumulation of toxic substrates that damage dopaminergic neurons, causing the autosomal recessive form of Parkinson's disease (PD). POOL has predicted a dozen residues in parkin that are important for catalytic activity. Interestingly, half of these residues are positions that when mutated lead to the onset of PD. Enzyme variants were created through single‐site directed mutagenesis to further look into how these residues may play a role in catalysis through biochemical and biophysical techniques.Support or Funding InformationSupported by NSF MCB‐1517290This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.