Protein Degradation

• reasons to degrade proteins...

  • recycle amino acids
  • protein turnover, either to remove misfolded or degraded proteins, or for regulation
  • break down dietary proteins
• proteases = the enzymes that degrade proteins
• endopeptidases = makes cuts within the polypeptide chain

  exopeptidases = cut individual amino acids off the end of a polypeptide chain, either aminopeptidases or carboxypeptidases
• ubiquitin (UB) marks proteins for degradation, and is remarkably conserved across species!
• ubiquitination = the marking of proteins for degradation by ubiquitin
• ubiquitin is added to the carboxy end of lysine side chains of target proteins (forming isopeptide bonds) for degradation
• E1 of ubiquitination activates the ubiquitin by adenylating it (using ATP) to then attach to E1
• E2 of ubiquitination is the ubiquitin-conjugating enzyme, and Ub gets passed from E1 to E2
• E3 of ubiquitination is the ubiquitin-protein ligase, it recognizes specific E2-Ub complexes to specify what proteins get ubiquitinated, ultimately responsible for selecting the protein for degradation!
• summary of the three enzymes of ubiquitination:

  1. E1 activates Ub
  2. E2 carries Ub
  3. E3 attaches Ub
• N-end rule = one method of how E3 determines proteins for degradation; where E3 reads the N-terminus amino acid and particular amino acids are more or less likely to be targeted for degradation
• polyubiquitination (polyUb) = chains of ubiquitin attached to each other
• example of threonine protease, which uses a catalytic triad and covalent catalysis
• the protease is like a trash bin, where proteins enter the chamber that has the catalytic threonines facing inwards in order to react with substrate
• Three purposes of the proteasome 19S cap:

  1. recognize and bind polyUb selectively for target proteins
  2. isopeptidases to remove Ub from target protein and each other (in the case of polyUb)
  3. AAA+ proteins (ATPases associated with diverse cellular activities) that use ATP hydrolysis to unfold target protein
• the protease will spit out free ubiquitin and peptide fragments, which are broken down further by proteolysis to individual amino acids