The Access Excellence Periodic Tableau

Pliable Proteins

Toby Mogollon Horn, Ph.D.
Thomas Jefferson High School for Science and Technology
Alexandria, VA
thorn@lan.tjhsst.edu


N.B. The inspiration for this model comes from Grace Hopper, who brought 11 cm lengths of trash computer wire to her lectures to show the distance that light travels in a nanosecond. For several months I played with the wire that students did not pick up. Then this idea arose (in 1988).

Background

Proteins are chains of amino acids. Proteins vary in amino acid sequence, length, overall size, structure and function. Scientists have discovered that short stretches of amino acids form motifs and that combinations of motifs in the protein chain give rise to particular patterns that give proteins form, structure, and function. Information about protein structure comes from amino acid and DNA sequencing and from the X-ray diffraction patterns of crystals grown from highly purified protein. Motifs or patterns may be conserved throughout evolution and provide clues to the possible function of a particular protein sequence. When researchers obtain a protein sequence, they now contribute the sequence information to international databases. By accessing the databases, today's scientists can compare their new sequence to others. One of the most recent discoveries is the similarity of a protein that is important in fruit-fly development and a protein that is associated with the most common form of human skin cancer, basal cell carcinoma. Zinc-finger transcription factors, serine proteases, tubulins and collagens are among the different types of proteins we can model on our own. Look through a recent Science or Nature magazine and you will see 2- and 3-D ribbon renditions like the one you will soon hold in your hand. You can make and name a protein, possibly even making a model of a protein whose structure and function are known. The wire represents the peptide backbone, the connected amino acids.

Primary structure is the order (sequence) of the amino acids in the protein. The protein sequence is a particular order of 20 amino acids.

Secondary structure conformation of the backbone's coils (alpha helix) or pleats (beta sheets) or random areas. These are stabilized via disulfide bonds between distant regions of the protein.

Tertiary structures arise from the alignments of pleats and coils that are stabilized by hydrogen bonds and ionic interactions of the amino acid side chains.

Quaternary structures result from the interactions of subunits. For example hemoglobin has 4 subunits of 2 types, and collagen has 3 subunits. Fibers like tubulin, keratin, and actin are composed of many repeating units of a protein lined up (not hooked up) by non-covalent interactions such as hydrogen and ionic bonds. Because the bonds in the higher order structures are almost all non-covalent (except for disulfide bonds), proteins are intrinsically unstable. Heat, pH, salt, soap, and ions can denature proteins so they no longer maintain their native (or active) form.

Some proteins can renature (return to their active conformation) after denaturation; most others cannot. This is why many vaccines can be made. Poisonous proteins treated with heat or denaturing agents like formaldehyde lose their toxic activity yet remain similar enough to the native form to be recognized by the immune system.

Materials

  1. Trash wire or rolls of trash wire from dollar stores
  2. A stick pen or pencil
  3. Small paper clips
  4. Marker
  5. DecoWhirl or POLYFORM Nomadeco (styrofoam-covered wire) available at store decorating outlets (expensive, but worth the shock value!)

Instructions

Creative outlet
  1. Give each student a piece of wire and 2 or 3 paper clips.
  2. Ask that they spend a minute folding the wire any way they like. They may include the paper clips in the design (without distorting the clips).
  3. Ask students to rotate their creations and write about what they see from different angles. Include a drawing of each of 3 aspects.
  4. Have students show their creations to each other--for a laugh or two.

    Rules of protein creation

    Amino acids have 3 chemical parts: the amino end, the carboxyl end and the naming residue that is also attached to the a-carbon. Proteins have three basic structural elements.
    alpha-helix
    beta-sheet and
    random coil

    Proteins are synthesized by stepwise addition of amino acids on ribosomes. The first amino acid (the N-terminus) is always methionine. Methionine and additional amino acids near the N-terminus may get removed as the protein is synthesized. Sequence information near the N-terminus provides address "zip codes" for localization within, or secretion from, the cell. The last amino acid is the C-terminus, named for the free carboxyl group of the last amino acid.

  5. To form an a-helix, wrap your wire a few times around a thin pen or pencil. It goes around clockwise as the end faces you. Call the front end the N-terminus, where the protein sequence starts. Linus Pauling figured out that proteins could form this helix spontaneously and that the helix is stabilized by hydrogen bonds. Pauling earned a Nobel Prize in Chemistry.

  6. Form some a-helix regions. In between, fold the wire a bit to form a b-sheet. A kink here or there can represent a proline, which does not have a "free" peptide bond. Prolines in the sequence specify a turn in the chain.

  7. Hold your protein gently. Look at it in from several aspects. See if you can draw it. This is a 3-dimensional representation of a protein. To get an image of this, scientists crystallize pure proteins and take X-ray pictures. It is very difficult to crystallize a protein, which may have hundreds of atoms per molecule, compared to NaCl, which has only 2 atoms, or glucose, which has 24 atoms.

  8. Add disulfide bonds. Put a paper clip or 2 in the structure to hold different helices together. Gently try to pull the protein apart. Note that the paper clips (disulfide bonds) help stabilize the chain's conformation.

  9. Let the protein work. The active site is usually inside the protein, though sometimes it is near the surface, like the cleft of a hot-dog roll (for lysozyme). The protein glues or cuts molecules, depending on whether it is a synthetic or a degradative enzyme. Enzymes are catalysts; not used up in the process. Just squeeze the protein gently and allow it to return to its original state. Such conformation changes provide the energy to shift substrates into the transition state and form product.

  10. Denature the protein with heat. Heat provides kinetic energy. Too much heat and things go wild. Many proteins denature at high temperature (what happens when you boil an egg). Pull the protein apart. Can you get it back to its original shape?

  11. Renature your protein and denature it with detergent. Rub the protein much as you would wash socks. The protein will again form a random coil. In this state, the highly negative detergent coats the amino acids, preventing them from renaturing. Nature in her wisdom has designed proteins that are stable to detergents and to high temperatures, which is why we have enzyme detergents that remove stains without bleach!!!!

Resources:

Advertisement from the Parson's School of Design. New York Times.
Finding the Critical Shapes. 1990. Howard Hughes Medical Institute Report. Chevy Chase, MD.
Introduction to Protein Structure. 1991. Carl Branden and John Tooze. Garland Publishing, Inc. NYC, NY.
Numerous articles in Science and Nature magazines.
Internet search: Protein Structure Images.

Extensions

Origins of the Active Site

Additional materials:

Marking pen
A small shape (like a gummy bear)

The active site is the region of a protein that does what the protein is known for. Discover how protein folding brings amino acids from distant locations into proximity.

  1. Pick an area of the wire model that can gently form around or over the small shape (substrate).

  2. Mark all of the segments of the wire that the shape touches. This is the binding or active site.

  3. Compare your location with other students.' Note that ome sites may be on the surface, near the surface, or inside the protein structure.

  4. Denature your protein by stretching out the chain. Note the variable distances between the marked areas or active site amino acids.

Model a Protein Whose Structure is Known

Additional Materials:

Branden and Tooze or a protein structure report from Science or Nature

  1. Find the example and draw a copy in your own book.

  2. Follow the protein chain from N to C termini (sort of like connect the numbered dots).

  3. Form the wire to conform to the shape.

Make a Multimeric Protein

Additional Materials:

Multiple wires of the same color and length

Many active proteins come in multiples. The Lac operon repressor is a tetramer; hemogolobin is a tetramer of 2 different subunits. Multimeric proteins align via non-covalent bonds, such as H-bonds, or hydrophobic or hydrophilic amino acid residue interactions. Though these wire backbones do not enable us to see the chemistry of the interactions, we can see how the peptide backbones line up.

  1. Each student makes the same protein using a regular pencil.

  2. Try out different alignments of the subunits:
    • Same direction
    • Opposite direction
    • Top vs bottom.

  3. Align the subunits as indicated in the research article or sketch or web page.


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