7.88J | Spring 2015 | Graduate
Protein Folding and Human Disease

Readings and Assignments

Students should complete the assigned readings before class and be prepared for meaningful discussion. For the first four weeks students will be guided by specific questions. Students will be asked to prepare the presentation and discussion of the original research articles they have read. Assigned readings are from the course textbook:

[BT] = Branden, Carl, and John Tooze. Introduction to Protein Structure. 2nd ed. Garland Science, 1999. ISBN: 9780815323051. [Preview with Google Books]

Supplemental Reading: Overview of the Etiologies of Major Human Diseases

The Etiologies of Major Human Diseases (PDF) - A slide deck with descriptions and histories of different human diseases and their prominence around the world.

READINGS READING QUESTIONS DUE IN

Reading in Branden and Tooze:

[BT] Chapter 1.

[BT] Chapters 2 and 3: “Motifs of Protein Structure” and “Alpha-Domain Structures.”

Papers to Read:

Pauling, Linus, Robert B. Corey, et al. “The Structure of Proteins: Two Hydrogen Bonded Helical Configurations of the Polypeptide Chain.” Proceedings of the National Academy Science of the U.S.A. 37, no. 4 (1951): 205–11.

Sela, M., F. H. White, et al. “Reductive Cleavage of Disulfide Bridges in Ribonuclease.” Science 125, no. 3250 (1957): 691–92.

Anfinsen, C. B., E. Haber, et al. “The Kinetics of Formation of Native Ribonuclease During Oxidation of the Reduced Polypeptide Chain.” Proceedings of the National Academy Science of the U.S.A. 47, no. 9 (1961): 1309–14.

Perutz, Max F. I Wish I’d Made you Angry Earlier: Essays on Science, Scientists and Humanity. Cold Springs Harbor Lab Press, 1998, pp. 173–5. ISBN: 9780879695248.

  1. On a schematic helix, label the rise per residue, helical pitch and residues / turn for Pauling / Corey alpha helices. Use the values from the paper or from B&T.
  2. The Beta-alpha-beta motif that is common in globular proteins can be left-handed or right handed. Do they occur with equal frequency in proteins of known structure?
  3. Drawing on your undergraduate or graduate biochemistry draw the pathways for the reduction and oxidation of a pair of peptidyl cysteines capable of forming an S-S bond, with a) DTT as the redox agent, and b) Mercaptoethanol.
  4. Anfinsen et al present and discuss a series of possible models for the refolding pathways followed by the RNase chains refolding in vitro in their experiments. Summarize briefly their A1, A2, A3 & A4 models and their rationales for rejecting models A1, A2 and A3 on the basis of the Figure 1 data.

Assignment 1: due in Ses 2

Reading in Branden and Tooze:

[BT] Chapters 4 and 5: Alpha / Beta Structures and Beta Sheet Structures.

As the protein structures considered get more complex, the information content of the chapter gets more densely packed with 3-D information. Give yourself additional time to examine and assimilate the images, particularly of the physiologically and enzymatically important barrels.

Paper to Read:

O’Shea, Erin, Rheba Rutkowski, et al. “Evidence that the Leucine Zipper is a Coiled Coil.” Science 27, no. 4890 (1989): 538–42.

This is not the paper reporting the X-ray structure of the GCN4 coiled coil, but its precursor. The methodology has subsequently been used for ongoing investigations of the sequence determinants of the coiled coil fold.

  1. Alpha / beta proteins represent a common structural motif, found among proteins with diverse enzymatic activities. Describe the relationship between the location of the active sites of these subclasses of alpha / beta proteins and their 3-D folds.
    1. Describe the experimental evidence showing that the helical sequences studied in O’Shea et al are organized as parallel dimers.
    2. Can you determine from the data presented whether monomers are α-helical?

Assignment 2: due in Ses 3

Reading in Branden and Tooze:

[BT] Chapter 15: Immunoglobulins.

In considering the immunoglobulin fold on pages 303–05 look back to chapter 5 and compare with the γ-crystallin and jellyroll folds. The MHC structures on pages 315–20 have been considered by some as a model for how some chaperonins might recognize extended sequences.

Richardson, Jane S., and David C. Richardson. “Amino Acid Preferences for Specific Locations at the Ends of α Helices.” Science 240, no. 4859 (1988): 1648–52.

S., Marqusee, Baldwin R. L. “α-Helix Formation by Short Peptides in Water.” In Protein Folding: Deciphering the Second Half of the Genetic Code. Edited by L. Gierasch and  J. King. Amer Assn for the Advancement, 1990, pp. 85–94. ISBN: 9780871683533.

P. B., Harbury, T. Zhang, et al. “A Switch Between Two-, Three-, and Four-stranded Coiled Coils in GCN4 Leucine Zipper Mutants.” Science 262, no. 5138 (1993): 1401–7.

Students will choose a few key experiments or results for short oral paper summations in class.

No written assignment to hand in.

Assignment 3: due in Ses 4

Mitraki, A., J. King. “Protein Folding Intermediates and Inclusion Body Formation.” Nature Biotechnology 7 (1989): 690–97. (Bio/technology is now Nature Biotechnology).

Brems, D. N., S. M. Plaisted, et al. “Stabilization of an Associated Folding Intermediate of Bovine Growth Hormone by Site-directed Mutagenesis.” Proceedings of the National Academy Science of the U.S.A. 85, no. 10 (1988): 3367–71.

Bovine growth hormone to be used in the cattle industry (therefore not requiring FDA approval) was one of the first cloned recombinant proteins produced on an industrial scale. This somewhat dense paper is the outcome of solving the expression and aggregation problems encountered along the way. Similar problems were encountered in the expression of many recombinant human proteins in bacteria.

Nall, Barry T. “Proline Isomerization and Folding of Yeast Cytochrome c.” In Protein Folding: Deciphering the Second Half of the Genetic Code. Edited by L. Gierasch and  J. King. Amer Assn for the Advancement, 1990, pp. 198–207. ISBN: 9780871683533.

 No written assignment to hand in. Assignment 4: due in Ses 5

Jarrett J. T., E. P. Berger, et al. “The Carboxy Terminus of the β Amyloid Protein is Critical for the Seeding of Amyloid Formation: Implications for the Pathogenesis of Alzheimer’s Disease.” Biochemistry 32, no. 18 (1993): 4693–7.

Fowler, D. M., A. V. Koulov, et al. “Functional Amyloid – from Bacteria to Humans.” TiBS 32, no. 5 (2007): 217–24.

 No written assignment to hand in. Assignment 5: due in Ses 6

Reading in Branden and Tooze:

[BT] Chapter 14.

Kuivaniemi, H., G. Tromp, et al. “Mutations in Collagen Genes: Causes of Rare and Some Common Diseases in Humans.” The FASEB Journal 5, no. 7 (1991): 2052–60.

Laganowsky, A. “Atomic View of a Toxic Amyloid Small Oligomer.” Science 335, no. 6073 (2012): 1228–31.

Schmid, F. X. “Prolyl Isomerases Join the Fold.” Current Biology 5, no. 9 (1995): 993–4.

 No written assignment to hand in. Assignment 6: due in Ses 7

Pereira, J. H., C. Y. Ralston, et al. “Cyrstal Structures of a Group II Chaperonin Reveal the Open and Closed States Associated with the Protein Folding Cycle.” The Journal of Biological Chemistry 285, no. 36 (2010): 27958–66.

Martin, J., T. Langer, et al. “Chaperonin-mediated Protein Folding at the Surface of GroEL through a ‘Molten Globule’-like Intermediate.” Nature 352 (1991): 36–42.

 No written assignment to hand in. Assignment 7: due in Ses 8
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