Using three-dimensional imaging of proteins: Examples of class activities and subsequent assessments†
Support for the development of this course comes from National Science Foundation Grant NSF/HBCU-UP HRD 9908994.
This paper discusses the development of a new biochemistry course, “Biochemistry of Cellular Regulation,” which is taught at the 300 level at Tuskegee University. The chemistry of cellular signaling and the subsequent cell regulation are discussed from a molecular viewpoint with emphasis on chemical structure, reactivity, and thermodynamics. Classroom lectures are composed almost entirely of PowerPoint lectures whereby figures from the textbook and figures from current research articles are incorporated directly into the lecture notes. The incorporation of supplemental materials from the textbook, i.e. the CD-ROM and websites from the CD-ROM was especially important. Three-dimensional images of proteins can be viewed and manipulated at these websites, which is critical for understanding the structural basis of protein function. Specific examples of class activities and subsequent assessments will be presented.
This paper has two major objectives. One is to introduce the new biochemistry course, “Biochemistry of Cellular Regulation,” developed at Tuskegee University, and the other objective is to describe in detail two examples of in-class protein imaging activities developed for that course.
The new course, titled “Biol/Chem 360: Biochemistry of Cell Regulation,” was targeted for juniors from a variety of majors such as biology, medical technology, pre-veterinary medicine, nutrition and foods, chemistry, and animal science. It is a self-contained one-semester class but also serves as an introductory course for a more advanced 500 level biochemistry course. The prerequisites for the class are first-semester organic chemistry and a 200 level or higher cell biology course.
The objectives of the class were to teach the basics of protein structure and function by specifically using cell-signaling cascades as the theme upon which the concepts were developed. Thus the material taught included structure and function of proteins, lipids, and carbohydrates, etc. but focused on examples specific to the plasma membrane, surface transport proteins, surface receptors, and the subsequent cell-signaling cascades. The idea was to use G protein-coupled receptors and protein-tyrosine kinase receptors, etc. as examples to explain protein function instead of the standard proteins such as hemoglobin and chymotrypsin. Lehninger's Biochemistry, 3rd ed., was the textbook in the fall semester, and The Cell, A Molecular Approach, 2nd ed., by Geoffrey Cooper was used in the spring. Seventeen students took the course each semester.
One very important objective of the class was to utilize all of the resources in the book, especially web links from the CD-ROM that came with the book and led to websites containing protein imaging. To this end, two in-class activities were developed. The first example concerned the A2A receptor and used a web-linked site found on the CD-ROM in the Lehninger textbook, and the second example used some basic literature searching of on-line databases (American Chemical Society journals) to look at the structures of A3 receptors. The goals of these assignments were to reinforce the transition from primary structure to secondary to tertiary structure (i.e. from 1-D to 3-D), 1 and to reinforce the importance of specific amino acid residues found at the binding site of receptors and the amino acid sequences that would lead to the secondary structures such as α-helices.
In example one, which used a web-linked site found in the CD-ROM included with the Lehninger textbook, the students were given the following instructions concerning the A2A adenosine receptor:
Find its primary amino acid sequence, identify the amino acids in one of the transmembrane helices, list all of the hydrophobic, hydrophilic, charged, etc. amino acids in that helix, and explain why it forms an α-helix and why it is in the plasma membrane.
To answer these questions the students had to look up this receptor on the PIR International Protein Sequence Database site, where they could then view the whole amino acid sequence. Next, this site led them to the Protein Data Bank site where they could view the protein in 3-D using the Structure Explorer program (which requires Chime software to operate). They could then see which specific amino acids made up the transmembrane helices. This assignment, therefore, stressed the importance of the amino acid sequence in forming an α-helix and the electrostatic, hydrophobic, and hydrophilic interactions that would cause this to be a transmembrane helix. The students scored an average of 19/20 (97%), which meant that it was perhaps too easy, because all they had to do was follow a set of instructions as opposed to actually applying concepts to answer a problem. The exercise only reinforced the concepts, because essentially all the students did was view and analyze the pieces of a detailed picture.
The second assignment was a literature search using ACS journals. The Tuskegee library has access to many online, full-text, scientific literature databases, and this was another important tool for the students to utilize. To study the structures of the A3 receptors the following assignment was given:
You will carefully read the article “A3 Receptors” in Chemical and Engineering News (February 12, 2001, pp. 37–40). Within this article is a reference to a journal article (J. Med. Chem. 43, 4768 (2000) that you should also read (scan) through briefly. Using these articles (and especially the pictures within these articles), create a plausible structure for the binding site in the adenosine receptors, i.e. what types of important amino acids would be found as part of the transmembrane helices that help the binding of adenosine and the binding of the antagonists talked about within these articles?
Part of the importance of viewing articles full text on the computer is that they can be viewed in color and full size on the screen. These articles had large colorful 3-D images of the binding sites and the ligands. The students only averaged 55% on this assignment; probably because it was much more open-ended, they did not do as well. It required application of concepts (the structures and forces involved in binding), asked them to visualize in 3-D on their own, based on the what they saw in the articles, and then draw a picture of what they thought the site looked like. Perhaps the most difficult question was to explain why they thought the binding site looked the way it did.
It would appear that the easier assignment used 3-D protein imaging to reinforce concepts (albeit in a much more visual way), but the harder assignment required them to use the 3-D representations as the basis of questions that required application of the concepts.
I express my gratitude to Dr. Gregory Pritchett, Dr. Helen Benford, Dr. Roberta Troy, and Dr. Adriane Ludwick.
The abbreviations used are: 1-D, one-dimensional; 3-D, three-dimensional.