PDB EDUCATION CORNER: USING VISUALIZATION TOOLS BY J. RICKY FOX, MURRAY STATE UNIVERSITY
DB's Education Corner features a different teacher each quarter,
offering an account of how he or she uses the PDB to educate
students. This quarter's column is by J. Ricky Cox, an associate
professor of chemistry at Murray State University in Murray, KY.
While a graduate student, I developed my love and passion for
macromolecular structure, especially protein structure. It was also
during this time that I fully realized the importance of noncovalent
interactions in chemistry and biology. One of my favorite quotes
while in graduate school was a paper from the lab of Professor Alan
Fersht(1): "Biology is dominated by the chemistry of the noncovalent
bond." This quote is on the wall of my office and my students would
certainly agree that I emphasize noncovalent interactions in molecular
systems. In the case of inter- and intramolecular interactions in
biological molecules, it is very difficult for textbooks to present
the diverse array of possible noncovalent interactions that can exist
between functional groups and the role they play in the structure and
function of macromolecular systems. This is why computer-based
molecular visualization programs such as Protein Explorer, RasMol,
Kinemage and Deep View have opened many doors for instructors and
students to explore the structural nature of small and large systems.
These programs allow the user to gain access to the wealth of
information contained in the PDB. Although the structures in the PDB
were not strictly obtained for educational purposes, chemistry and
biology instructors can tap into this tremendous resource for
pedagogical purposes. Currently, my students and I use Protein
Explorer(2) to access the PDB, although one can visit the World Index of
Biomolecular Visualization Resources (www.molvisindex.org) and choose
a suitable program.
Molecular Visualization in the Classroom
I have been thoroughly impressed with how my colleagues have
integrated the use of molecular visualization software and the PDB
into the biochemistry and biology classroom.(3) Like many instructors
that teach macromolecular structure, I utilize the PDB to teach the
structural nature of these systems and to support material covered in
the textbook. I also use Protein Explorer and the PDB to emphasize
the nature and importance of noncovalent interactions that exist in
proteins and protein complexes. Along with the normal classifications
given to amino-acid side chains, I also categorize amino acids by
their ability to form the various types of noncovalent interactions,
especially the interactions involving aromatic systems (pi-pi
interactions). pi-Type interactions in protein systems are not widely
discussed in the biochemistry textbooks, even though they are an area
of interest among the research community.
Over the last several years, through my own mining of the PDB and
student exploration projects, I have cataloged several examples of the
different types of noncovalent interactions that exist between protein
side chains and in protein-ligand complexes. I show these
interactions during class when teaching protein structure and when I
discuss the different types of complexes proteins can make with other
biomolecules such as nucleic acids, carbohydrates and lipids. Even in
the metabolism chapters, I try to show the structure of metabolic
enzymes to support the discussion of the mechanistic features of these
enzymes and the structure-function relationship that is so important
in these chapters.
In one biochemistry course I teach, the focus is on medicinal
biochemistry, membrane structure and signal transduction. The
students in this course have already completed a previous biochemistry
course and are familiar with macromolecular structure. One might
expect that the use of Protein Explorer and the PDB might be limited;
however, this is certainly not the case. When teaching this course, I
often find myself before lecture searching through the PDB looking for
structures that can contribute to that day's lecture. I am usually
successful at finding at least one structure in the PDB that can be
shown and dissected via Protein Explorer that has direct application
to the topic of the lecture. This type of approach leads to a
balanced lecture period where there is an appropriate mix of lecture,
student discussion and computer-based visualization. For example, a
few days ago I was discussing the role of lipid tags (anchors) in the
structure and function of peripheral membrane proteins. One method by
which these proteins are associated with membranes is prenylation of
C-terminal cysteine residues. This involves covalent modification
with a farnesyl or geranylgeranyl group to produce a thioether linkage
to the side chain of the cysteine residue. While looking through the
PDB for a structure to discuss in class, I came across the PDB record
(PDB ID: 1o1r) of a Protein Farnesyltransferase with bound
geranylgeranyl diphosphate.(4) This alpha-helical dimer is a truly
interesting and beautiful protein structure that caught my eye right
away. I used Protein Explorer to visualize this structure in class as
it was quite complementary to the discussion of lipid tags and it
sparked a discussion on the structure and function of Ras proteins. I
may have been able to show an image of this enzyme in class; however,
the ability to manipulate this structure in Protein Explorer allowed
me to show subtle aspects of the structure (three small beta-sheet
regions) and to highlight some of the residues (Lys-164, Lys-294 and
Arg-291 and Trp-303) involved in ligand binding. The basic residues
interact with the phosphate groups of the geranylgeranyl diphosphate
ligand via ionic interactions and the Trp side chain seems to be
interacting with the hydrocarbon moiety of the ligand through CH-p
interactions. The involvement of specific amino-acid residues in the
structure and function of protein systems is always an important
aspect of my biochemistry courses even though macromolecular structure
might not be the major focus.
|Structure of Protein Farnesyltransferase with bound geranylgeranyl diphosphate (PDB Code: 1O1R)|
Student Use of Visualization and PDB Tools
As a biochemistry instructor, I believe that utilizing computer-based visualization software, and data housed in the PDB, has been a tremendous asset in the teaching-learning process. I am very excited about the ability of students to use the software and the PDB data to explore macromolecular structure and search for noncovalent interactions. Over the past few years, I have had two different approaches to getting students involved in protein exploration projects. The first approach involves assigning individual students or student groups a particular macromolecule or giving them the option of finding their own structure in the PDB in which they have an interest. The students use visualization software to dissect the structure of the macromolecule and find several examples of noncovalent interactions important in stabilizing the structure of the protein or protein-ligand complex.5 The students present their findings to the class in oral presentations and field questions from me and other students in the class. Another approach I use, especially in larger classes, is to have students complete worksheets that contain questions and tasks concerning a particular structure from the PDB. These assignments are highly structured and require students to use Protein Explorer to investigate the structure of a particular protein or protein complex.3 The tasks and question for a particular assignment are provided below.
PDB Code: 1LOU
Task #1: List and describe four ionic interactions.
Task #2: List and describe three H-bonds involving the side chain of Tyr or Gln.
Task #3: Find a Ser residue forming a H-bond with a water molecule.
Interaction Question #1: Is there a cation-p interaction between Phe97 and Lys39? If yes, describe the nature of the interaction. If not, provide details on why the two side chains are not participating in a stabilizing interaction.
These assignments are designed such that students have to acquire or recall information concerning the structures of amino acids and their ability to form noncovalent interactions. The students also have to demonstrate that they understand the distance and geometrical requirements for the formation of stabilizing interactions, which can be difficult when studying a macromolecule. The description required to complete the tasks and questions in the assignments involves measuring distances and manipulating the structures in Protein Explorer. Students quickly realize that proximity of amino-acid side chains does not guarantee that they are participating in a stabilizing (or repulsive) interaction.
In my opinion, there is no way that traditional tests or quizzes can measure the ability of students to recognize and justify the existence of noncovalent interactions in protein systems. Other assignments I have used require students to comment on structural motifs that exist in proteins and to identify interactions involved in protein-ligand complexes. In some cases, students are asked to write a short paper on the biological function of protein system that is the focus of the assignment.
In some of my biochemistry courses, I ask students to give oral presentations on the molecular basis of disease. To complement the information given on the various aspects of the diseases, students have searched the PDB to find relevant structures that can be visualized in Protein Explorer during the presentation. For example, a student recently gave a presentation on Phenylketonuria, a genetic disease linked to mutations in the enzyme phenylalanine hydroxylase (PDB Codes: 1PAH and 2PAH). Protein Explorer was used to show the multimeric nature of the enzyme, the catalytic and tetramerization domains, the catalytic iron ion and its coordinating side chains and the side chain of amino acids that are mutated in the disease-causing form of the enzyme. The use of molecular visualization in the student presentations was complementary to the other material presented and enabled the students to better explain the molecular basis of disease.
1. Fersht, A. R.; Matouschek, A.; Serrano, L. The Folding of an Enzyme: Theory of Protein Engineering Analysis of Stability and Pathway of Protein Folding. J. Mol. Biol. 1992, 224, 771-782.
2. Martz, E. Protein Explorer: Easy yet Powerful Macromolecular Visualization. Trends Biochem. Sci. 2002, 27, 107-109.
3. Honey, D. W.; Cox, J. R. Lesson Plan for Protein Exploration in a Large Biochemistry Class. Biochem. Mol. Biol. Educ. 2003, 31, 356-362.
4. Turek-Etienne, T. C.; Strickland, C. L.; Distefano, M. D. Biochemical and Structural Studies with Prenyl Diphosphate Analogues Provide Insights into Isoprenoid Recognition by Protein Farnesyl Transferase. Biochemistry 2003, 42, 3716-3724.
5. Cox, J. R. Teaching Noncovalent Interactions in the Biochemistry Curriculum Through Molecular Visualization: The Search for p-Interactions. J. Chem. Educ. 2000, 77, 1424-1428.