The Proteasome

Protein degradation is as essential to the cell as protein synthesis. For example,

• to supply amino acids for fresh protein synthesis
• to remove excess enzymes
• to remove transcription factors that are no longer needed.

There are two major intracellular devices in which damaged or unneeded proteins are broken down:

• lysosomes and
• proteasomes

Lysosomes deal primarily with

• extracellular proteins, e.g., plasma proteins, that are taken into the cell, e.g., by endocytosis
• cell-surface membrane proteins that are used in receptor-mediated endocytosis.
• the proteins (and other macromolecules) engulfed by autophagosomes.

Proteasomes deal primarily with endogenous proteins; that is, proteins that were synthesized within the cell such as:

• transcription factors
• cyclins (which must be destroyed to prepare for the next step in the cell cycle)
• proteins encoded by viruses and other intracellular pathogens
• proteins that are folded incorrectly because
  • of translation errors
  • they are encoded by faulty genes

    Most cases of cystic fibrosis are caused by the accelerated degradation of a mutant version of a chloride transporter. [Link]

  • they have been damaged by other molecules in the cytosol.

Structure of the Proteasome

The Core Particle (CP)

• The core particle is made of 2 copies of each of 14 different proteins.
• These are assembled in groups of 7 forming a ring.
• The 4 rings are stacked on each other (like 4 doughnuts).

The Regulatory Particle (RP)

• There are two identical RPs, one at each end of the core particle.
• Each is made of 19 different proteins (none of them the same as those in the CP).
• 6 of these are ATPases.
• Some of the subunits have sites that recognize the protein ubiquitin.

Ubiquitin

• a small protein (76 amino acids);
• conserved throughout all the kingdoms of life; that is, virtually identical in sequence whether in bacteria, yeast, or mammals;
• used by all these creatures to target proteins for destruction.

The Process

Proteins destined for destruction

• are conjugated to a molecule of ubiquitin which binds to the terminal amino group of a lysine residue.
• Additional molecules of ubiquitin bind to the first forming a chain.
• The complex binds to ubiquitin-recognizing site(s) on the regulatory particle.
• The protein is unfolded by the ATPases using the energy of ATP.
• The unfolded protein is translocated into the central cavity of the core particle.
• Several active sites on the inner surface of the two middle "doughnuts" break various specific peptide bonds of the chain.
• This produces a set of peptides averaging about 8 amino acids long.
• These leave the core particle by an unknown route where
  • they may be further broken down into individual amino acids by peptidases in the cytosol or
  • in mammals, they may be incorporated in a class I histocompatibility molecule to be presented to the immune system as a potential antigen [see below].
• The regulatory particle releases the ubiquitins for reuse.

Antigen Processing by Proteasomes

In mammals, activation of the immune system

• leads to the release of the cytokine interferon-gamma.
• This causes three of the subunits in the core particle to be replaced by substitute subunits.
• The peptides generated in this altered proteasome are picked up by TAP (= transporter associated with antigen processing) proteins and transported from the cytosol into the endoplasmic reticulum where
• each enters the groove at the surface of a class I histocompatibility molecule.
• This complex then moves through the Golgi apparatus and is inserted in the plasma membrane where it can be "recognized" by CD8⁺ T cells.