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Assignments

Note:
B&T = Branden and Tooze. Introduction to Protein Structure. 2nd ed.

 

ASSIGNMENTS READINGS / HANDOUTS ASSIGNMENTS DUE

Assignment #1

1. Give the ranges of backbone Phi/PSi angle ranges found for alpha helical regions in proteins. For beta strand conformations.

2. What are the origins of the values in B&T figures 1.7a and 1.7b?

3. What is the average length of alpha helices found in crystal structures of globular proteins? Beta-strands?

4. What is the handedness of the helices shown in Pauling, Corey and Branson? The handedness of the alpha helices in the B&T reading?

Readings:

1. Branden and Tooze. Chapter 1 (2nd edition).

2. Alpha Helices:

  • Pauling, Linus, Robert B. Corey, and H. R. Branson. "The Structure of Proteins: Two Hydrogen Bonded Helical Configurations of the Polypeptide Chain." Proc. Nat. Acad. Sci. 37 (1951): 205-210.
  • Branden and Tooze. pp. 13-26.

3. Overview of X-ray diffraction methods:

  • Branden and Tooze. Chapter 18, pp. 373-386.
Ses #2

Assignment #2

Reading assignment only.

Reading:

Anfinsen, C. B., E. Haber, M. Sela, and F. H. White Jr. "The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain." PNAS 47 (1961): 1309-1314.

Ses #3

 

Assignment #3

1. Pauling, Corey and Branson (1951) concluded that two helical models satisfied their chemical/steric criteria. Please construct a Table with values of the following features for the two helices proposed.
H-bond length: Residues per turn: Rise per residue: Pitch: (rise/helical turn):

2. Draw, copy, or trace a version of figure 2(e) of B&T, with the alpha carbons and Nitrogen atoms clearly labeled or colored (N=blue, C= black). Label the N-and C-termini of this short peptide.

3. Anfinsen, et. al. (1961) show a set of experimental curves in which the regain of Rnase activity lags behind the regain of helicity and S-S bond formation. Which of their models is offered as an explanation of these phenomena?

4. Create a single image* that shows the molecular structure of bovine pancreatic ribonuclease A (PDB-ID 1FS3). The image should show:

  • the entire molecule as a ribbon colored by secondary structure,
  • all 4 disulfide bonds: CYS 26-CYS84, CYS40-CYS95, CYS58-110, and CYS 65-CYS72 as solid cylinders,
  • one disulfide bond: CYS40-CYS95 as space-filled.

5. Choose a point of view in which all three alpha helices and the one space-filled disulfide bond are completely visible, i.e. not obscured by beta-strands.

* Nothing fancy is required for the image. Using the 'PrintScreen' button and pasting the screen image into a text editing program is sufficient. Similarly, color hard copy is not essential. A monochrome image will do.

Readings:

Perutz, Max F. "A Passion for Crystals." I Wish I'd Made you Angrier Earlier: Essays on Science, Scientists & Humanity. Cold Springs Harbor Lab Press, 1998, pp. 209-212.

In Branden and Tooze:

  • Chapters 2 and 3.
  • Chapter 18: X-ray diffraction. Pp. 373-386.

Previously Handed out:

Pauling, Linus, Robert B. Corey, and H. R. Branson. "The Structure of Proteins: Two Hydrogen Bonded Helical Configurations of the Polypeptide Chain." Proc. Nat. Acad. Sci., USA 37 (1951): 205-210.

Anfinsen, C. B., E. Haber, M. Sela, and F. H. White, Jr. "The Kinetics of Formation of Native Ribonuclease During Oxidation of the Reduced Polypeptide Chain." PNAS 47 (1961): 1309-1314.

Ses #4

 

Assignment #4

1. Protein Data Bank tasks from Assign 3.

2. Draw (copy) the strand/sheet topology for g-crystallin. Draw the strand/sheet topology for the jelly roll fold under it.

3. What are the relative frequencies in beta sheet proteins of the various possible pairwise arrangements of of beta-hairpin motifs (Chapter 2)?

4. What are the dominant water clusters thought to be interacting with the surfaces of proteins?

Grad Students:

5. Are the hydrogen bonding patterns between the strands of the jelly roll fold equivalent for all pairs of strands? If not, where do they differ?

Reading:

Branden and Tooze. Chapter 5: "Beta Structures." Pp. 67-80.

Handout:

Liu, K., J. D. Cruzan, and R. J. Saykally. "Water Clusters." Science 217 (1996): 920-933.

Ses #6

 

Assignment #5

1. Read the following two papers carefully:

  • O'Shea, Erin, Juli D. Klem, Peter S. Kim, and Tom Alber. “X-ray Structure of the CGN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil.” Science 254 (1991): 539-544.
  • Cohen, Carolyn, and David A. D. Parry. “Alpha-Helical Coiled Coils: More Facts and better Predictions.”
    Science 263 (1994): 488-489.

2. Answer the following question:
What intra-helical ion pairs are present in the GCN4 structure in addition to the inter-helical ion pairs described in lecture?

3. Create a single image of the GCN4 (PDB-ID: 2ZTA) structure which shows:

  • the backbones of the two coils depicted as ribbons, colored by chain and,
  • the inter-helical ion pairs described in lecture depicted as space-filled models.

Readings:

Perutz, Max F. "I wish I’d made you angry earlier." From I wish I’d made you angry earlier: Essays on Science, Scientists & Humanity. Cold Springs Harbor Laboratory Press, 1998, pp. 173-175.

Read the following two papers carefully:

O'Shea, Erin, Juli D. Klem, Peter S. Kim, and Tom Alber. "X-ray Structure of the CGN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil." Science 254 (1991): 539-544.

Cohen, Carolyn, and David A. D. Parry. "Alpha-Helical Coiled Coils: More Facts and better Predictions." Science 263 (1994): 488-489.

Ses #7

Assignment #6

Reading assignment only.

Readings:

Lumb, Kevin J., and Peter S. Kim. "A Buried Polar Interaction Imparts Structural Uniquemess in a Designed Heterodimeric Coiled Coil." Biochem. 34 (1995): 8642-8648.

Shoemaker, Kevin R., Peer S. Kim, David N. Brems, Susan Marquesee, Eunice J. yourk, Irwin M. Chaiken, John M. Stewart, and Robert L. Baldwin. "Nature of the Charged-Group Effect on the Stability of the C-peptide Helix." PNAS 82 (1985): 2349-2353.

Ses #9
Assignment #7

1. Could the helices shown in Figure 4 of Marquesee & Baldwin, dock stably against each other or themselves if they occurred within a globular protein? How, why or why not?

2.

  • List the various contributions promoting the formation of alpha helices in polypeptide chains considered by Aurora et. al.
  • Would you add any additional factors from your reading or lecture notes, or eliminate or reduce the importance of any of theirs?

3. In Figure 1 of Nall, why do the signals in a and b decrease, while those in the other four panels increase with time?

 

Readings:

Marquesee, Susan, and Robert L. Baldwin. "a-Helix Formation by Short Peptides in Water." Protein Folding: Deciphering the Second Half of the Genetic Code. Edited by Lila M. Gierasch, and Jonathan King. Washington D.C.: AAAS, 1990.

Richardson, Jane S., and David C. Richardson. "Amino Acid Preferences for specific Locations at the Ends of a Helices." Science 240 (1988): 1648-1652.

Aurora, R., T. P. Creamer, R. Srinivasan, and G. D. Rose. "Local Interactions in Protein folding: Lessons from the a-Helix." JBC 272 (1997): 1413-1416.

Nall, Barry T. "Proline Isomerization and Folding of Yeast Cytochrome c." Protein Folding: Deciphering the Second Half of the Genetic Code. Edited by Lila M. Gierasch, and Jonathan King. Washington D.C.: AAAS, 1990.

Creighton, Thomas E. Proteins: Structures and Molecular Properties. 2nd ed. New York: W. H. Freeman & Co., 1993, Section 6.3, pp. 238-244.

Graduate Students:

Pain. Mechanisms of Protein Folding. Chapter 3: Section 5, pp. 84-94.

Ses #11

Assignment #8

Reading assignment only.

Reading:

Brandon and Tooze. Chapter 6: "Folding and Flexibility."

Ses #12

Assignment #9

Reading assignment only.

Reading:

Pain. "Case study 2: Folding of the Collagen Triple-helix and its Naturally Occurring Mutants." Chapter 12 in Mechanisms of Protein Folding. Edited by Jean Baum and Barbara Brodsky.

Handout:

Kuivaniemi, H., G. Tromp, and D. J. Prockop. "Mutations in Collagen Genes: Causes of Rare and Some Common Diseases in Humans." FASEB Journal 5 (1991): 2025-2060.

Ses #14