5 Protein Degradation

• Ubiquitin is a tag/ recognition for the proteasome/ degradation

• Covalent isopeptide bonds

• The carbonyl group of ubiquitin is attached to the (additional) epsilon Amino group of Lysin in the target Protein

• It’s a dehydration: H2O is cleaved off

• A Ubiquitin contains multiple Lysin AA

• Therefore several Ubiquitin proteins can be attached to the first one -> chain of Ubiquitin

• contains 4 layers of protein rings

• Hydrolyses proteins

• Trypsin, chymotrypsin and caspase like activity

  • the trypsin and chemotrypsin like activity means an endoprotease which cuts the protein (endo= in the middle) after Lysin and Arginine)

  • The caspase like activity means a Cystein enzyme, cutting after Aspartate

Ubiquitin is very compactly folded. Therefore it is recycled to target other proteins

Immuno recognition

• MHC1 (major histo compatibility complex): presents the AA on the surface of the cell

• T-cells can monitor if something went wrong

• Cell shows what proteins it has made

Ubiquitin ligases are enzymes that can form a thioesther bond (via cystein) with Ubiquitin

There are 3 classes of Ligases for specification

• E1 Ligase

  • less than 5 different because not really specific

  • Transfer Ubiquitin to their own cystein group (via ATP)

• E2 Ligase

  • dozens because semi-specific

  • Transfer Ubiquitin from E1 to their own cystein (without ATP)

• E3 Ligase

  • hundreds because very specific, different half lifes-> different E3

  • Binds to E2 and the target Protein-> transfers Ubiquitin to the Lysin of the target protein

P53

• most suppressive Tumor protein

• Most frequent mutation (in Tumor)

• Can induce apoptosis

• Has a short half life to keep it checked and prevent cell death

• It’s a TF which recruits TF2D, RNA Polymerase 2 (-> synthesis of mRNA)

• To keep p53 in check: whenever p53 is active, it will induce MDM2 which is an E3 Ligase : makes sure that Ubiquitin is transferred from the E2 Ligase on p53.

  -> p53 induces it’s own Degradation = negative feedback loop

• (First recruits TF2D/ Mediater -> RNA Pol 2)

Hypoxia

• = low supply of oxygen

• Happens if angiogenesis is insufficient =blood vessels are no longer formed sufficiently

  Two options: die by necrosis or Tumor can make sure to get blood supply

• Tumors use HIF 1 alpha (=hypoxia inducable factor) TF: induces genes like Epo (Erythropoetin), and VEGF (vascular endothelial growth factor)

• Enough oxygen: HIF1alpha undergoes Prolin hydroxylation

  -> protein hydroxylases (PHD) uses Oxygen to hydroxylate prolin residues within HIF1alpha

  • VHL (von Hippel Lindau) protein =E3 Ligase: can recognises hydroxylated HIF1alpha and transfer Ubiquitin to HIF1alpha

  • -> HIF1alpha gets degraded

• Oxygen is running low: No hydroxylation of HIF1alpha -> can’t be recognised by VHL -> no ubiquitination -> accumulation of HIF1alpha -> works as a TF for EPO and VEGF -> formation of blood vessels