Protein Degradation & Turnover

Protein Degradation

  • Proteases

    • Two categories exist: specific and non-specific proteases.

    • Large number of proteases facilitates protein degradation within cells.

  • Ubiquitin

    • small protein that tags other proteins for degradation, playing a crucial role in the cellular process of protein turnover. This tagging allows the specific recognition of substrates by the proteasome, which subsequently breaks down the marked proteins into smaller peptides.

  • Intracellular Protein Degradation Pathways

    • Two main pathways responsible:

    • Ubiquitin-Proteasome Pathway

      • The ubiquitin-proteasome pathway is a crucial cellular mechanism that targets unwanted or damaged proteins for degradation. It involves the tagging of these proteins with a small protein called ubiquitin, which signals them for transport to the proteasome, a large protein complex located in the cytoplasm and nucleus, where they are broken down into smaller peptides.

    • Autophagy-Lysosomal System

      • The autophagy-lysosomal system is a cellular degradation process that recycles cytoplasmic components, including damaged organelles and misfolded proteins, through the formation of autophagosomes that fuse with lysosomes, leading to the breakdown and recycling of these materials. This system primarily occurs in the cytoplasm, where it plays a critical role in maintaining cellular homeostasis, especially during stress conditions or nutrient deprivation.

    • Additionally, both intracellular and extracellular proteases play roles in protein degradation.

Ubiquitin-Proteasome Pathway

  • Components: Enzymes involved include E1, E2, and E3.

    • E1 (Activation): Initiates ubiquitin activation process.

    • E2 (Conjugation): Transfers ubiquitin from E1.

    • E3 (Ligation): Catalyzes transfer of ubiquitin to substrate protein.

  • Steps:

    • Ubiquitin (Ub) activation by E1.

    • Conjugation of Ub to E2.

    • Ligation of Ub to substrate protein via E3.

    • Recognition of ubiquitinated substrates by proteasome for degradation.

    • Role of Proteasome:

    • Substrate protein unfolds and is degraded by the 26S proteasome into peptides and amino acids.

    • Ubiquitin is recycled for further use.

Autophagy-Lysosomal System

  • Macroautophagy Process:

    • Initiation: Triggered by conditions such as nutrient starvation affecting mTORC1.

    • Key Proteins:

    • Beclin1, VPS34, VPS15, ATG14, ULK1/2, ATG13, ATG101, FIP200 are integral to the formation and maturation of autophagosomes.

  • Mechanism:

    • Formation of phagophore for bulk uptake of cellular components.

    • Nucleation and expansion of the double-membraned autophagosome.

    • Lysosomal Fusion: Autophagosome fuses with lysosome for degradation.

    • Substrate Proteins: Hsc70 aids in mediated autophagy and ensures proper substrate recognition and degradation.

    • Endocytosis: Role of ESCRT in the formation of multivesicular bodies (MVB).

Amino Acid Catabolism

  • Dependency Factors:

    • Largely determined by intracellular amino acid concentrations.

    • Effective utilization for protein synthesis requires all proteinogenic amino acids and sufficient ATP and insulin levels.

  • Process:

    • Separation of amino groups from carbon skeletons.

    • Carbon skeletons are converted into intermediates for entry into the citric acid cycle or involved in gluconeogenesis and glycolysis.

Amino Acids Pathways and Intermediates

  • Amino acid catabolism leads to various intermediates:

    • Leucine and lysine are the only two purely ketogenic amino acids

    • These intermediates participate in crucial metabolic pathways.

Nonprotein Nitrogenous Compounds from Amino Acids

  • Amino acids are precursors for several nitrogenous and sulfur-containing compounds:

    • Alanine, Arginine, Aspartate, Asparagine, Cysteine

    • Derived Compounds: Creatine, nitric oxide, polyamines, pyrimidines, purines, glutathione, taurine, etc.

  • Detailed examples include:

    • Histidine produces carnosine and doesn’t actively donate carbon units.

    • Methionine acts as a sulfur donor and aids in multiple biosynthetic pathways.

    • Tyrosine and its derivatives play roles in synthesizing dopamine, melanin, and hormones.

Protein Turnover

  • Definition: Continuous degradation of body proteins by intracellular and extracellular proteases.

  • Significance: Enables renewal and repair of proteins, ensuring optimal cellular function

  • Turnover Process: Covers both synthesis and breakdown of proteins:

    • Involves the interaction between dietary amino acids, body proteins, and mechanisms for oxidation and nitrogen excretion.

  • Stomach and small intestine turn over most per day

Regulation of Protein Metabolism

  • Nitrogen Balance: Influenced by nitrogen intake and loss via urine and feces.

  • Fatigue and Dietary Intake: The graph suggesting protein synthesis and breakdown correlates with nutrition levels.

  • Influence of Protein Intake on Turnover:

    • Levels of dietary protein and their effects on synthesis rates in specific tissues like the liver and muscle vary with nutrition status.

    • Dietary proteins seem to be preferential during protein synthesis, suggesting that higher quality proteins can lead to increased rates of muscle recovery and growth.

  • Hormonal Effects:

    • mTORC1: a serine/threonine protein kinase

      • Integrates insulin, growth factors, and nutrient signals to regulate protein synthesis.

    • Promotes synthesis while inhibiting autophagy.

  • Hormones Relation:

    • Insulin: Reduces protein degradation and enhances synthesis when amino acid levels are high.

    • Glucagon: Promotes protein breakdown in the liver while enhancing gluconeogenesis.

    • IGF-1: Increases protein synthesis and reduces degradation in various tissues, particularly muscle, thereby playing a crucial role in growth and development.

    • Growth Hormone (GH): Stimulates muscle protein synthesis in animals and affects different metabolic pathways.

      • Acts through IGF-1, which mediates many of its anabolic effects and contributes to the regulation of protein turnover by balancing synthesis and degradation.

  • Correlation of Insulin Treatment: Studies showing effects of insulin and IGF-1 on muscle protein synthesis indicate significant outcomes in muscle health.