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B5. Protease Activation and the Proteasome

Protease are potentially dangerous if their activity is not regulated. A common method to avoid unwanted protease activity is to activate the enzyme from an inactive precursor called a zymogen. The precursor is often called a proenyzme. Limited but regulated proteolysis of the proenzyme by either a different protease or by autoproteolysis leads to activation of the proteolytic activity of the zymogen. One important example is activation of procaspases to active caspases, which are calcium activated cysteine proteases that are homodimers. Activation of caspases initiates programmed cell death. Cancer cells which are immortal have found ways to inhibit procaspase activation. Hence a possible cancer therapy could involve drug-induced activation of procaspases. Wolan et used high-thoroughput screening to identify compounds that promote the activation of procaspase-3 at physiological conditions and concentrations. A dozen compounds were found to promote such activity, and their ability to activate other similar enzymes in the procaspase family were explored. Active caspases appear to be in equilibrium between an active state and an inactive one more similar to the inactive zymogen. Small drug that bind preferentially to the active state would shift the equilibrium from the inactive state to the active state. Likewise it might bind to the inactive zymogen and promote an "active" conformation of the zymogen leading to the actual activation of the zymogene by autoproteolysis. Wolan et al discovered that procaspase was able to undergo a conformational change with the addition of a specific small molecule activator (referred to as 1541) which made the “on (active)” conformation more likely, and therefore encouraged self-activation.

Proteases are found in both extracellular (digestive tract, blood, extracellular matrix), membrane, and and intracellular locations. As mentioned previously, one role of intracellular proteases is to degrade "older" and chemically damaged proteins. One of the main proteases involved in such intracellular proteolysis is the large protein complex called the proteasome. It consist of three large structures

  • one 700,000 MW 20S complex which contains 14 different subunits arranged in 4 rings of 7 subunits (2 copies of each subunit). The rings are stacked on each other. The outer two rings contain α subunits while the middle two contain β subunits. ATP-dependent cleavage of protein substrates occurs within the complex, with N terminal Ser or Thr OH groups acting as nucleophiles. 

  • two 19S complex which cap both ends of the 20S complex (not unlike the structure of the E. Coli chaperone complex GroEL/ES

Proteins destined for cleavage by the proteasome must first be chemically modified through attachment of multiple copies of the 8,500 MW protein ubiquitin, a highly conserved protein found ubiquitously in eukaryotes. (We modeled this protein in the first lab using VMD and NAMD.) The carboxyl group of the C-terminal Gly residue of ubiquitin forms an amide link to the side chain amine group of Lys residues in the protein targeted for degradation. The resulting link is an isopeptide bond since the N terminal of the target protein is not used in the amide bond. Three different proteins are involved in the ubiqutinylation of the target protein, including E1 (ubiquitin-activating enzyme which requires ATP), E2 (ubiquitin conjugating enzyme) and E3 (ubiquitin-protein lyase). Once attached, a side chain Lys of ubiquitin can form another isopeptide bond to a C-terminal carboxyl group of another ubiquitin, forming a growing ubiquitin chain on the target protein. Proteins with 4 or more linked ubiquitins are better substrates for the proteasome. Proteins with short half-lives (those with certain amino terminal amino acids like arginine or leucine, or enriched in Pro (P), Glu (E), Ser (S), and Thr (T) - (PEST) appear to be better targets for the ubiquitin pathway and subsequent degradation by the proteasome.

Proteasome activity is intimately related to health and disease. A major role of the proteasome occurs in immune recognition of self and nonself. The immune system must be able to recognize a virally infected or tumor cell (both self cells expressing foreign or aberrant proteins) as well as foreign cells like bacteria, which can be engulfed by immune cells such as macrophages. Proteasome involvement occurs when viral, tumor, or bacterial proteins are degraded to short peptides, which bind intercellular major histocompatability proteins (MHC) proteins and are translocated to the cell membrane. Peptide/MHC complexes are displayed on the cell surface and are recognized by receptors on immune cells (specifically T cells). Self cells are not recognized by T cells since the peptides in the peptide:MHC complex are self peptides derived from normal proteins. The T cell receptor recognizes determinants on both the MHC protein and the presented peptide. 

animation of protein processing and display of peptides by MHC proteins on cell surface

HHMI animation of the ubiquitin and the proteasome

Nonrecognition of self peptide:MHC complexes prevents the immune system from targeting normal healthy cells. Autoimmune diseases arise when the T cell receptor recognizes presented self peptides. 

The ubiquitin/proteasome pathways have been linked to disease manifestation in many neurodegenerative diseases like Alzheimers, Huntington's disease (which involves the aberrant folding of the Huntington protein which contains an expanded poly-Glu domain), and Parkinsons. The degradation pathway is involved in many other normal cellular functions including gene transcription and programmed cell death.

 Jmol: Updated Mammalian Proteasome - (1IRU) Jmol14 (Java) | JSMol (HTML5)