Introduction:  Proteins are organic molecules found in large quantities in most living systems.  Proteins perform a variety of functions:  structural (collagen), regulatory (insulin), contractile (actin, myosin), transport (hemoglobin), protective (antibodies), and enzymatic (pepsin).  Although proteins are used for many different functions, proteins are very similar in structure.  Proteins are generally large molecules containing hundreds of amino acids.

The amino acids which are the basic units of proteins have the same fundamental structure as shown below:
 
 
 

In living organisms, a protein is assembled into a long polypeptide chain by the linking of amino acids.  This linear sequence of amino acids is called the primary structure.

As the chain of amino acids is formed, various interactions begin to take place among the amino acids along the chain.  Linus Pauling and Robert Corey discovered that H bonds could form between the slightly positive amino hydrogen of one amino acid and the slightly negative carboxyl oxygen of another amino acid.  Due to these H bonds, two possible structures result:  an alpha helix and a beta pleated sheet.
The regular, repeated configurations caused by H bonding between atoms of the polypeptide backbone is called the secondary structure.  However, other forces counteract the formation of H bonds.  For example, disulfide bonds can form between two R groups.  These disulfide bridges lock molecules into position.
R groups with unlike charges are attracted to each other, those with like charges are repelled.  Twisting and turning occurs and an intricate three -dimensional structure occurs due to these interactions and this is referred to as the tertiary structure.

Many proteins are composed of more than one polypeptide chain.  In addition to all the interactions that occur along one polypeptide, interactions also occur between polypeptide chains.  The interactions between different polypeptides is called the quaternary structure of a protein.

The interactions at the quaternary level can make the proteins unstable and can result in an alteration of the active site.  Since the particular patterns that occur in a protein give the protein its form, structure and function, altering the shape of a protein can result in physiological changes in an organism.

Over the past 18 years, a normal cellular protein  PrP that generally exists in the alpha helix form (pN) has been known to change its shape into beta sheets  (pD) (Prusiner, 1995).  This structural change is believed to be responsible for several degenerative disorders of the central nervous system collectively known as spongiform encephalopathies.

Infectious diseases are generally considered to be caused by pathogens which contain genetic material (DNA or RNA) which enables them to reproduce.  In the case of Creutzfeldt-Jakob, Scrapies, and Mad Cow Disease, the causative agent is believed to be an altered -structure protein called a prion.  Prion stands for “proteinaceous infectious particle” (Prusiner, 1995).   Susan Lindquist, a prion researcher “hypothesized that the distorted protein could bind to other proteins of the same type and induce them to change their conformation as well, producing a chain reaction that propagates the disease and generates new infectious material” (Prusiner, 1995).

The structure of proteins becomes even more significant if they are now believed to cause disease.  At present,  the PrP protein is linked to degenerative central nervous system disorders.   However, recent research on yeast suggest that “prions unrelated in amino acid sequence to the PrP protein could exist.  Reed B. Wickner  of the NIH reports that a protein called Ure2p might sometimes change its conformation, thereby affecting its activity in the cell.”(Prusiner, 1995).  Continued research is necessary to determine if prions play a role in other common neurodegenerative conditions, such as Alzheimer’s disease, Parkinson’s and amyotrophic lateral sclerosis (Prusiner, 1995).

Activity:      Pliable Proteins
 
Source:       Toby Mogollon Horn, PhD
                   Thomas Jefferson High School for Science and Technology
                   Alexandria, VA
                   Thorn@1an.tjhsst.edu

      I have made some modifications to the original activity.
 
Objective:   To allow students to observe and manipulate the structure of a protein.

Materials:    Trash wire (for polypeptide chains)
       A stick pen or pencil
                     Paper clips (for disulfide bonds)
                     Marker
                     Velcro (for hydrogen bonds)
        Small shape (eraser)

Directions:

1. To form an alpha helix:  Wrap your wire around a thin pen or pencil.  It should wrap clockwise as the end faces you.  Call the front end the N-terminus, where the protein starts.

2. To form an beta sheet:  In between the alpha helix, fold the wire a bit to form a beta sheet.  A kink here or there can represent a proline, which does not have a free peptide bond.

3. To add disulfide bonds:  Put a paper clip or two in the structure to hold different helices together.  Gently try to pull the protein apart.  Note that the paper clips (disulfide bonds) help stablize the chain’s conformation.

4. Locate an active site:  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 promixity.
a. Pick an area of the wire model that can gently form around or over a small shape (eraser).
b. Mark all of the segments of the wire that the shape touches.  This is the binding or active site.
c. Compare your location with other students.  Note that some sites may be on the surface, near the surface, or inside the protein structure.
d. Denature your protein my stretching out the chain.  Note the variable distances between the marked areas of active site amino acids.

Extensions:

1. Make a model of a known protein.
2. Make a multimeric protein.

References for Introduction:

 Pruisner, S., 1995.  The Prion Diseases.  Scientific American 272:48-57.

Resources for Pliable Proteins:

 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.
  NY, NY
 Numerous articles in Science and Nature magazines.
 Internet search:  Protein Structure Images.