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Biofundamentals - Protein folding and turnover


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Biofundamentals - Protein folding and turnover

  1. 1. Biofundamentals - Protein folding and turnover 9/27/08 10:53 AM Assembling Proteins printable pdf New amino acids are added to the polypeptide's C-terminus, while the N-terminus moves through a tunnel within the ribosome; about 15 amino acids are added per second. The ribosomal tunnel is approximately 10 nm long and 1.5 nm in diameter; it is narrow enough to block the folding of the newly synthesized polypeptide chain. As the polypeptide emerges from the tunnel, it encounters the crowded cytoplasmic environment; at the same time it begins to fold. As it folds, the polypeptide needs to avoid non-specific interactions with other cellular components. If it is part of a multisubunit protein, it must find its partner polypeptides. If the polypeptide does not fold correctly, it will not function correctly and may damage the cell. A number of degenerative neurological disorders are due, at least in part, to the accumulation of misfolded polypeptides. A number of enzymes, known generically as chaperones, associate with the nascent polypeptide as it emerges from the ribosome. Chaperones facilitate the proper folding of the polypeptide, primarily by suppressing or unfolding 'incorrect' structures. Chaperones bind to and stabilize polypeptides prior to their final assembly into multisubunit complexes, the final active protein One class of chaperones are known as heat shock proteins. These proteins recognize unfolded polypeptides – protein unfolding occurs with increasing frequency at higher temperatures. Heat-shock chaperones use energy from ATP hydrolysis to unfold misfolded polypeptides and allow them another chance to refold correctly. file:///Users/klymkowsky/Documents/WebSites/virtual/Biofundamentals/lectureNotes/Topic3-5_Assemblying%20Proteins.htm Page 1 of 5
  2. 2. Biofundamentals - Protein folding and turnover 9/27/08 10:53 AM How do they recognize unfolded or abnormally folded proteins? They look for hydrophobic regions on their surface. Normal soluble proteins do not have such regions and the presence of such domains can lead to non-specific protein-protein aggregation. Why does the ribosome tunnel inhibit the folding of the newly synthesized polypeptide? Why would a misfolded polypeptide pose a problem to the cell? How does a chaperone recognize a misfolded protein? Diseases of folding and misfolding: If the functional protein is in its native state, a dysfunctional misfolded protein is said to be denatured. It does not take much of a perturbation to unfold or denature most proteins. In fact, under normal conditions, proteins often become partially denatured. A number of diseases have been associated with protein misfolding. Kuru was among the first of these to be identified. Beginning in the 1950s, D. Carleton Gadjusek studied a neurological disorder common among the Fore people of New Guinea. The symptoms of kuru, which means "trembling with fear", are similar to those of scrapie, a disease of sheep, and variant Creutzfeld-Jakob disease (vCJD) in humans. Among the Fore people, kuru was linked to the ritual eating of the dead. Since this practice has ended, the disease has disappeared. Prions and protein folding: The cause of kuru, scrapie and vCJD appears to be the presence of an abnormal form of normal protein, known as a prion. We can think of prions as an anti-chaperone. The idea of proteins as infectious agents was championed by Stan Prusiner. The protein responsible for these diseases is known as PrPc . It normally exists in a largely -helical form. There is a second abnormal form of the protein, PrPsc for scrapie; it is composed primarily of ß-sheet. The two polypeptides have the same primary sequence. PrPsc acts as an anti- file:///Users/klymkowsky/Documents/WebSites/virtual/Biofundamentals/lectureNotes/Topic3-5_Assemblying%20Proteins.htm Page 2 of 5
  3. 3. Biofundamentals - Protein folding and turnover 9/27/08 10:53 AM primary sequence. PrPsc acts as an anti- chaperone, catalyzing the transformation of PrPc into PrPsc. Once initiated, this leads to a chain reaction and PrPsc accumulation. As it accumulates, PrPscassembles into rod- shaped aggregates that appear to damage cells. This process occurs within the cells of the central nervous system, and leads to severe neurological defects. There is no natural defense, since the protein responsible is a normal protein. Disease transmission: When the Fore ate the brains of their beloved ancestors, the inadvertently introduced the PrPsc protein into their bodies. Genetic studies indicate that early humans evolved resistance to prion diseases, indicating that cannibalism might have been an important selective factor during human evolution. Since cannibalism is not nearly as common today, how does anyone get such diseases in the modern world? There are rare cases of iatrogenic transmission, where the disease is caused by faulty medical practice, for example through the use of contaminated surgical instruments or diseased tissue for transplantation. Where did these people get the disease? Since the disease is caused by the formation of PrPsc, any event that leads to PrPsc formation could cause the disease. Normally, the formation of PrPsc from PrPc is very rare. We all have PrPc but very few of us spontaneously develop kuru-like symptoms. There are, however, mutations in the gene that encodes PrPc that greatly enhance the frequency of the file:///Users/klymkowsky/Documents/WebSites/virtual/Biofundamentals/lectureNotes/Topic3-5_Assemblying%20Proteins.htm Page 3 of 5
  4. 4. Biofundamentals - Protein folding and turnover 9/27/08 10:53 AM mutations in the gene that encodes PrPc that greatly enhance the frequency of the PrPc to PrPsc conversion. Such mutations may be inherited (genetic) or may occur during the life of an organism (sporadic). The schematic of the brain on the left is from a person with familial fatal insomnia (FFI). FFI is due to the inheritance of a mutation in the PRNP gene; this mutation changes the normal aspartic acid 178 to an asparagine. The squares mark brain regions affected; the lower section reveals the presence of aberrant protein aggregates in these regions. When combined with a second mutation at position 129, the FFI mutation leads to Creutzfeld-Jacob disease (CJD). The circles in the right hand brain schematic indicate regions affected in CJD. There are holes or lacunae in the tissue. Both FFI and CDJ are late onset diseases. Symptoms first appear ~ 50 years of age. How is the presence of a prionsc lead to the change in the structure of prionc ? Is this a genetic change? Could this type of change be inherited? Why, do you think that FFI and CDJ are late onset diseases? What, do you think, leads to the lacunae in brain tissue? Protein degradation: An obvious question is why do these aberrant protein aggregates accumulate? We characterized the stability of a protein in the cell (or organism), by its half-life, that is, the time it takes for 50% of the protein present at time = 0 to be destroyed or degraded. There are a number of file:///Users/klymkowsky/Documents/WebSites/virtual/Biofundamentals/lectureNotes/Topic3-5_Assemblying%20Proteins.htm Page 4 of 5
  5. 5. Biofundamentals - Protein folding and turnover 9/27/08 10:53 AM There are a number of mechanisms involved in the turnover of proteins in the cell. A common one involves a macromolecular machine, the proteosome. The proteosome is a multienzyme complex that degrades polypeptides. Such enzymes are known generically as proteases. Proteases cleave peptide bonds via a hydrolysis reaction. There are many specialized proteases in the cell. They can be divided into two generic classes. Those that hydrolyze polypeptides from one end or the other, they release amino acids. These are known as exoproteases. Proteases that cleave a polypeptide chain internally are known as endoproteases - they generate two polypeptides. So why do PrPsc aggregates accumulate? To cut a peptide bond, the protease must position the target peptide bond within its catalytic active site. If the target protein's peptide bonds do not fit into the active site, they cannot be cut. Because of their structure, PrPsc aggregates are highly resistant to proteolysis. They gradually accumulate over many years, a fact that may explain the late onset of PrP- based diseases. Which do you think would be more susceptible to proteolytic degradation, a compact or an extended polypeptide? Use Wikipedia | revised 27-Sep-2008 file:///Users/klymkowsky/Documents/WebSites/virtual/Biofundamentals/lectureNotes/Topic3-5_Assemblying%20Proteins.htm Page 5 of 5