Model Mélange

Physical Models of Peptides and Proteins

In the Model Mélange activity, you will visit different stations – each featuring a variety of different physical models of peptides or proteins. The learning objectives for this activity are:

 Explore and analyze levels of protein structure – secondary, tertiary and quaternary structure. Primary structure will be explored briefly in the context of secondary structure.

 Compare and contrast different model formats. Each format provides useful, but different, information regarding the structure.

The worksheets that follow will guide your exploration of each protein structure. Stations 1 and 2 can be done in any order, and stations 3 and 4 can also be done in any order.

The CPK Color Scheme

The standard colors of different atom types….established by Corey, Pauling (as in Linus) and Kolton. Note that hydrogen atoms are typically NOT Carbon is grey (or black) displayed in these models. There are two reasons for this: Oxygen is red  X-ray crystallography, which has been Nitrogen is blue used to determine the structure of many of the models, does not resolve the Hydrogen is white position of hydrogen atoms.

Phosphorus is orange  Because there are so many hydrogen atoms in many structures, if they were Sulfur is yellow displayed, most of the rest of the structure would be obscured. Zinc is green Station 1: Secondary Structure: α Helices

There are three different depictions of the α helix at this station:

1. An α helix construction kit: standard CPK colors, hydrogen bonds are depicted by metal posts with white balls. The green dots are on the central carbon atom (the α carbon) of each amino acid. This is the carbon atom to which the sidechain, amino and carboxyl groups are attached. Amino acid subunits are joined by magnets.

2. A static α helix without sidechains: CPK colors with green dot on α carbon.

3. A static α helix with sidechains: this is the same model as #2, but the sidechains have been added. Note that the backbone atoms are colored in light CPK colors (light grey is carbon, pale blue is nitrogen, pink is oxygen). Sidechains are in normal CPK colors. Alpha carbon atoms are identified by a green dot.

Use these models to work through the activities below and answer the questions.

1. Begin by constructing your α Helix Construction Kit©. Identify the amino (N-terminal) and carboxy (C-terminal) ends of the α helix. How are they depicted in the models? See if you can find them on the two static models as well.

2. Compare all 3 α helix models. a. How many amino acids are depicted in each structure? ___

b. How many hydrogen bonds stabilize each structure? ___

3. Go back to examining the α Helix Construction Kit©. a. What are the four atoms that make up the repeating structural unit of the α helix?

b. Which of those atoms comprise the continuous backbone chain?

4. Describe (or draw) the path the backbone takes in 3D space.

5. What feature contributes most to the stability of the α helix? Why do you think this?

6. Using the static α helix with sidechains and beginning at the N-terminal end, determine the amino acid sequence of this peptide.

7. Examine the model and predict which “face” of the helix is directed toward the center of the protein. (Recall that: 1. Due to the helix shape, the “face” will exist on a curved plane, and 2. the protein folds in the aqueous environment of the cell.) Identify the amino acids on this “face”. Also identify the amino acids which are on the “face” exposed to the outside of the protein.

a. Amino acids directed toward the inside:

b. Amino acids directed toward the outside:

c. What principles of chemistry influenced your selection of these amino acids?

8. Summarize what you have learned about α helices. Station 2: Secondary Structure: β Sheets

There are three different depictions of the β sheet at this station:

1. 2-stranded β Sheet Construction Kit©: standard CPK colors, hydrogen bonds are depicted by metal posts with white balls. The yellow dots are on the central carbon atom (the α carbon) of each amino acid. This is the carbon atom to which the sidechain, amino and carboxyl groups are attached.

2. Static, 3-stranded β sheet without sidechains: CPK colors, yellow dot on α carbon.

3. Static, 3-stranded β sheet with sidechains: this is the same model as #2, but the sidechains have been added. Note that the backbone atoms are colored in light CPK colors (light grey is carbon, pale blue is nitrogen, pink is oxygen). Sidechains are in normal CPK colors. Alpha carbon atoms are identified by a yellow dot.

Use these models to work through the activities below and answer the questions.

First analyze and compare the two static models, and use them to answer questions 1-8.

1. Identify the N-terminal and C-terminal ends of the peptides that make up the static three- stranded β sheet, without sidechains. How did you determine their identity?

2. β sheets can be either parallel (all strands running in the same direction from N-terminus to C-terminus) or antiparallel (alternating strands are oriented in the opposite direction). Which type of β sheet is represented in the static model without sidechains? Justify your answer.

3. Look at both static, 3-stranded models. Examine if any of the strands appear to be continuous or individual. Describe your observations.

4. Which type of β sheet pattern(s) would contain a ‘hairpin turn’ (looped) structure? Why?

5. What role do sidechains play in the hydrogen-bonding that stabilizes protein secondary structure?

6. How many amino acids are there in the longest β strand in the static models? ____

7. Use the static β sheet with sidechains model and locate the N-terminal end of the continuous strand that contains the ‘hairpin turn’ loop. Beginning with the N-terminal end, what is the sequence of the first eight amino acids of this peptide?

8. What pattern do you notice about the orientation of each successive amino acid sidechain relative to the plane of the β sheet?

Use the β Sheet Construction Kit© to construct an antiparallel β sheet and answer questions 9-13.

9. How many hydrogen bonds stabilize this structure? _____

10. What are the four atoms that make up the repeating structural unit (backbone) of this model of the β sheet?

11. Describe (or draw) the path the backbone takes in 3D space.

12. Examine the static model with sidechains. Predict which “face” of the sheet is directed toward the center of the protein. (Recall that the protein folds in the aqueous environment of the cell.) Identify the amino acids on this “face”. Also identify the amino acids which are on the “face” exposed to the outside of the protein.

a. Amino acids directed toward the inside:

b. Amino acids directed toward the outside:

c. What principles of chemistry influenced your selection of these amino acids?

13. Summarize what you have learned about β sheets.

Station 3: Tertiary Structure: Zinc Fingers

This station focuses on tertiary structure by analyzing models of zinc fingers. Zinc fingers are small protein motifs, only 20-30 amino acids in length. Zinc fingers can play many roles, including assisting in protein folding and stabilization, as well as DNA recognition. Zinc finger motifs are often found in proteins that interact with DNA, like transcription factors. (You can see a zinc finger in association with DNA in one of the zinc finger models on display). Zinc fingers share a common structure which includes a two-stranded β sheet and a single α helix. A zinc atom stabilizes the secondary structure and is coordinated by four amino acids – a combination of cysteines and histidines. These particular zinc finger models have two cysteines and two histidines.

Perhaps you have heard the story of the seven blind men and the elephant? Each man felt a different part of the elephant and described it, then argued about which description was right. Another man resolved the argument by pointing out that each man had only seen a part of the elephant, and that an elephant included ALL of their descriptions.

Similar to the elephant story, there are several models of zinc fingers at this station. Each depicts different aspects of the protein. When trying to tell a story about how a protein functions, scientists determine which features of the protein they want to emphasize, then choose the depiction that best illustrates those features.

Match each physical model of the zinc finger to the correct format listed below, then list one positive and one negative feature of that format.

A. α carbon backbone format, no side chains

Advantage:

Disadvantage:

B. α carbon backbone format, with side chains

Advantage:

Disadvantage:

C. Spacefill format

Advantage:

Disadvantage:

D. Surface format

Advantage:

Disadvantage:

E. α carbon backbone format, with selected sidechains

Advantage:

Disadvantage:

If you only had one model format to use in your classroom, which format would you find most useful, and why?

Station 4: Quaternary Structure

Some, but not all, proteins contain multiple peptides. This station allows you to explore several proteins that demonstrate this quaternary structure, as well as a few that lack quaternary structure.

Examine each of these protein models, and analyze the following:

1. How many subunits are in the protein? How can you tell? 2. Based on your answer to #1, does the protein have quaternary structure? 3. Are there α helices in the protein? (If so, few or many?) 4. Are there β sheets in the protein? (If so, few or many?)

Aquaporin

GFP (Green Fluorescent Protein)

Hemoglobin

Beta-Globin

Influenza HA (Hemagglutinin)

MHC (Major Histocompatibility Complex)

F0 complex (from ATP synthase)

Station 5: Structure Challenges!

α Helices and β Sheets:

1. Numbering of a peptide begins at the N-terminus and moves toward the C-terminus. Examine the static α helix model. Complete the following statement that describes the hydrogen bond linkage pattern that stabilizes the α helix:

The carbonyl oxygen of amino acid number 1 is hydrogen-bonded to the amino nitrogen of amino acid number ___.

2. The pitch of an α helix is defined as the number of repeating units per turn. What is the pitch of the α helix? How did you determine this?

3. The pitch of a β sheet is defined as the number of repeating units per turn. What is the pitch of the β sheet? How did you determine this?

4. What patterns can you find when looking at the pitch of these structure? What could be possible research applications for this information?