PROTEIN DEGRADATION

DIFFERENT PATHWAYS FOLLOWED BY PROTEIN FOR DEGRADATION

1. PROTEIN DEGRADATION 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 1

2. NAME:SWETA KUMARI REG NO.-16BBT0124 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 2

3. Turnover of protein is NOT constant Half lives of proteins vary from minutes to infinity “Normal” proteins – 100-200 hrs Short-lived proteins-regulatory proteins enzymes that catalyze committed steps transcription factors Long-lived proteins-Special cases (dentin, crystallins ) 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 3

4. Proteins are not degraded at the same rate :- ENZYME Half-life Ornithine decarboxylase 11 minutes delta- Aminolevulinate synthetase 70 minutes Catalase 1.4 days Tyrosine aminotransferase 1.5 hours Tryptophan oxygenase 2 hours Glucokinase 1.2 days Lactic dehydrogenase 16 days 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 4

5. May depend on tissue distribution: Example: Lactic Acid Dehydrogenase Tissue Half-life Heart -1.6 days Muscle - 31 days Liver -16 days Protein degradation is a regulated process: Example: Acetyl CoA carboxylase Nutritional state Half-life Fed-48 hours Fasted -18 hours 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 5

6. Ubiquitin/Proteasome Pathway: 80-90% Most intracellular proteins Lysosomal processes: 10-20% Extracellular proteins Cell organelles Some intracellular proteins Proteasomes: Large (26S) multiprotein complex (28 subunits) Degrades ubiquitinated proteins Lysosomes: Basal degradation – non-selective Degradation under starvation – selective for “KFERQ” proteins 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 6

7. The Ubiquitin/Proteasome PATHWAY: Small peptide that is a “TAG ” 76 amino acids C-terminal glycine - isopeptide bond with the e-amino group of lysine residues on the substrate Attached as monoubiquitin or polyubiquitin chains Three genes in humans: Two are stress genes (B and C) One, UbA as a fusion protein 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 7

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9. Four Main Steps: UBIQUITINATION RECOGNITION DEGRADATION DEUBIQUITINATION 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 9

10. UBIQUITINATION: First, Ubiquitin is activated by forming a link to “enzyme 1” (E1). Then, ubiquitin is transferred to one of several types of “enzyme 2” (E2). Then, “enzyme 3” (E3) catalizes the transfer of ubiquitin from E2 to a Lys e-amino group of the “condemned” protein. Lastly, molecules of Ubiquitin are commonly conjugated to the protein to be degraded by E3s & E4s 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 10

11. Ubiquitinated proteins are degraded by the proteasome: Ubiquitinated proteins are degraded in the cytoplasm and nucleus by the proteasome . Proteasomal protein degradation consumes ATP. The proteasome degrades the proteins to ~8 amino-acid peptides. Access of proteins into the proteasome is tightly regulated. The peptides resulting from the proteasome activity diffuse out of the proteasome freely. 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 11

12. DEUBIQUITINATION 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 12

13. LYSOSOMES: Digestive System of the Cell Digests – ingested materials – obsolete cell components • Degrades macromolecules of all types – Proteins – Nucleic acids – Carbohydrates – Lipids • Heterogeneous 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 13

14. Protein degradation in the lysosomes Lysosomes degrade extracellular proteins that the cell incorporates by endocytosis. Lysosomes can also degrade intracellular proteins that are enclosed in other membrane-limited organellas . In well-nourished cells, lysosomal protein degradation is non-selective (non-regulated). In starved cells, lysosomes degrade preferentially proteins containing a KFERQ “signal” peptide. The regression of the uterus after childbirth is mediated largely by lysosomal protein degradation 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 14

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16. AUTOPHAGY Macroautophagy – inducible (autophagy) Microautophagy - constitutive Chaperone-mediated autophagy (CMA) – KFERQ motif 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 16

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18. Conclusions and future perspectives: Only a few targeting signals have been identified, and the mechanisms that underlie the regulation of the system are still largely unknown？ While the system has been implicated in the pathogenesis of several diseases, the underlying mechanisms, as well as its potential involvement in many other diseases, are still an enigma？ Why are there so many ubiquitinating enzymes if prior modifications such as phosphorylation or damage are triggering events? Do DUBs show substrate specificity, perhaps by regulating the levels of ubiquitination of specific subsets of proteins? What are the binding sites for polyubiquitin chains on the microtubules and on the proteasome itself? 3/11/2018 Sweta kumari,16BBT0124,CELL BIOLOGY AND BIOCHEMISTRY 18