Proteasome

Proteasomes are essential protein complexes responsible for the degradation of proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases. Proteasomes are found inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, proteasomes are located both in the nucleus and in the cytoplasm.^[1] The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress. The importance of proteolytic degradation inside cells and the role of ubiquitin in proteolytic pathways was acknowledged in the award of the 2004 Nobel Prize in Chemistry to Aaron Ciechanover, Avram Hershko and Irwin Rose.^[2]

The core 20S proteasome (blue in the adjacent figure) is a cylindrical, compartmental protein complex of four stacked rings forming a central pore. Each ring is composed of seven individual proteins. The inner two rings are made of seven β subunits that contain three to seven protease active sites, within the central chamber of the complex.^[3] Access to these proteases is gated on the top of the 20S, and access is regulated by several large protein complexes, including the 19S Regulatory Particle forming the 26S Proteasome. In eukaryotes, proteins that are tagged with Ubiquitin are targeted to the 26S proteasome and is the penultimate step of the Ubiquitin Proteasome System (UPS). Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins.

Protein that are destined for degradation by the 26S proteasome require two main elements: 1) the attachment of a small protein called ubiquitin and 2) an unstructured region of about 25 amino acids.^[4][5] Proteins that lack this unstructured region can have another motor, cdc48 in yeast or P97 in humans, generate this unstructured region^[6] by a unique mechanism where ubiquitin is unfolded by cdc48 and its cofactors Npl4/Ufd1.^[7] The tagging of a target protein by ubiquitin is catalyzed by cascade of enzymes consisting of the Ubiquitin-activating enzyme (E1), Ubiquitin-conjugating enzyme (E2), and ubiquitin ligases (E3). Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein in an ATP dependent manner.^[8] The degradation process by the proteasome yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins.^[8]