Education Corner: Robert J. Warburton, Shepherd University, West Virginia
Robert J. Warburton earned his Ph.D. in Biochemistry from Duquesne University. He is currently a Professor of Biochemistry at Shepherd University teaching courses in Biochemistry, Protein Chemistry and the non-majors course, Chemistry in Society.
Shepherd University is situated in the Shenandoah Valley, on the banks of the Potomac River, in historic Shepherdstown, West Virginia. The oldest town in the state, Shepherdstown is a quaint university community, with the town and campus combining to offer a unique learning-living environment. Located in the Eastern Panhandle of West Virginia, Shepherdstown is within 20 miles of nearby Maryland, Pennsylvania, and Virginia. It is only 65 miles from the metropolitan areas of Washington, D.C., and Baltimore, Maryland.
A Journey Out of Darkness
There's a story about a group of blind men inspecting an elephant. Each can only see a part of the whole and each is convinced they know the identity of the animal. Each is, of course wrong. This was my feeling in the 1980's as I worked in the lab of Dr. Dave Seybert at Duquesne University. My Ph.D. thesis involved the attempt to discern the three-dimensional shape of bovine mitochondrial adrenodoxin reductase (AR) by limited proteoltyic cleavage.
The structure of the enzyme was, at that time, unknown. A number of cDNA sequences had been determined and some information, with respect to glycosylation sites, had been proposed. An initial experiment using limited tryptic cleavage had been designed based on the functional similarities between a spinach ferridoxin oxidoreductase and the bovine mitochondrial enzyme. The cleavage produced fragments of approximately 30 kDa and 20 kDa and indicated the possibility of a two domain structure in the 55 kDa AR. So began a series of experiments attempting to characterize the structure and function of the two fragments within the whole...I felt that I was the blind man with an elephant.1
The experience of my graduate work cemented my interest in the relationship of subtle changes in primary structure and function. I left Duquesne in 1990 and traveled south to the lab of Dr. Jeff Frelinger at the University of North Carolina at Chapel Hill. Here was a new story for me to read. Here we actually had a "photograph" of the elephant to study in detail. The people in the lab were concerned with trying to determine how the triad of heavy chain, light chain and peptide of the Class I Major Histocompatibility Complex (MHC) molecule HLA-A*0201 would be affected by point mutations. Multiple variations of primary sequence of the heavy chain had been produced containing single and multiple point mutations by the use of saturation mutagenesis. Not only did we have the picture of the elephant, but having moved some of the parts of the beast around, could it still walk?
by Nikki Lantz
The first crystal structure of HLA-A*0201 had been solved by Dr. Pam Bjorkman and co-workers, working in the lab of the late Dr. Don Wiley at Harvard, and submitted to the PDB as 3HLA.2 The issue of Nature that contained the first images of "A2", were poured over by the folks in the Frelinger lab. As is always the case, many questions were both simultaneously answered and many more asked by the structure presented.
It was at this time that I was introduced to the Evans and Sutherland workstation.
Many hours were spent in a darkened room slowly moving the structure back and forth, zooming in and out, and drinking coffee... I still remember the thrill of seeing a "dynamic" image on the screen before me. One of my projects was to determine the effect of two point mutations on HLA-A*0201 that had disrupted a disulfide bridge. This bridge, between cysteine 101 and cysteine 164 held an extended section of α-helix to the edge of a α-sheet platform that made up one side of a peptide binding cleft. The question asked was: "could such a mutation in the primary sequence, and the consequent loss of rigidity in the tertiary structure disrupt the ability of the protein to function"...could the elephant still walk?
The answer was, yes it could walk, but it didn't leave the house much! 3
For me, the difference between seeing and not seeing the protein of interest was enormous and as fundamental to understanding as building models in organic chemistry can make stereochemistry make sense.
I moved on from UNC to my current position at Shepherd University in 1993 and began to use models and structures in the classroom as a means to get the students to think outside of the images presented in the book. My initial attempts were not as successful as I had hoped, the elusive identification of the elephant had returned. The epiphany for me here was provided by Dr. Robert Bourret during a return visit to UNC. He showed me 3HLA prepared by a program called "Prekin" and viewed on a program called "Mage." 4 All those hours in the dark with the Evans and Sutherland became hours now spent on an Apple Mac LC in my office. I expanded my lectures to include "kinemages." The veritable explosion of structures deposited at the PDB and modeling programs that became available for the personal computer allowed me to produce the pictures I needed for my classes.
by Brandon Copple
The excitement of these times was increased when I attended an education satellite session held at the University of San Francisco as part of the annual meeting of the ASBMB in 1997. The satellite session included workshops on Mage and RasMol 5, (previously discussed by Judith Voet 6 & Margaret Franzen 7) held by the developers of Mage, Jane and David Richardson of Duke University and Eric Martz of the University of Massachusetts. The participants were like grade school kids, very excited folks, as they were walked through the programs. We literally raced between the two computer labs so as to get the "best" seats!
It was as exciting for me to finally "see" the structure, as rendered by PyMol, as it had been to watch HLA-A2 come to life on the Evans and Sutherland. The structure presented supported some of the features we had been able to "glimpse" by Tryptic cutting.
Since that time, KiNG 8 has been added to compliment Mage. We now regularly use PyMol, developed by Warren DeLano. 9 This program is used in my lecture to illustrate a structural or mechanistic feature to supplement the information provided in the structures constructed by Jean-Yves Sgro in the text used in the biochemistry course (Lehninger 10), or in the laboratory course as the students explore transfection of E. coli with a plasmid coding for green fluorescent protein (1C4F). 11
In my Advanced Protein Chemistry course (taught every two years as an option within the comprehensive biochemistry track) students examine protein structure function relationships in a collaborative seminar-style course. Using the protein structure texts of Branden and Tooze,12 Petsko and Ringe,13 and Whitford14 as references to the primary literature, the students examine folding patterns, discuss nucleation and molten globular models, and investigate the relationship of structure to function in various model enzymes. As a major component of the course, the students must model structures from the PDB. The spring semester of 2006 saw the students telling a story of Rossmann folds and nucleotide binding domains in ... my own elephant, Adrenodoxin Reductase.
Since my graduate days, Ziegler and Schulz have successfully crystallized the flavoprotein (1E1L) 15
and Juergen Mueller and colleagues have prepared the flavoprotein with its companion ferredoxin and
deposited the results with PDB (1E6E).19
Currently, in my undergraduate research laboratory we are using two crystal structures from PDB. Both are of the mouse MHC molecule H-2Kb, in complex with T cell receptor proteins. The first, deposited by Garcia and co-workers (2CKB),16 the second by Reiser and co-workers (1FO0).17 We are using structures to try to predict the consequences of a point mutation that has been implicated in transplant rejection involving a restricted subset of T cells.
by Matt Wells
Both in the lecture and the laboratory, the students augment the images on the screen by use of the three-dimensional model of HLA-A*0201, based on 3HLA, available from 3-D Molecular Designs of Wauwatosa, Wis. 18 This model is a wonderful extension from the PDB file seen by computer visualization to a "hands-on" three-dimensional appreciation of the structure and function.
The structures on the computer screen still fill me with the same sense of excitement as I felt when I first sat in the darkened room with the Evans and Sutherland workstation. I see that same look on my students' faces. One of my goals is to ensure that "look" does not leave the faces of students in the future... or mine!
- Warburton, R.J., and Seybert, D.W. Structural and functional characterization of bovine adrenodoxin reductase by limited proteolysis. Biochim. Biophys. Acta 1995 1246: 39-46
- Bjorkman, P.J., et al. Structure of the human class I histocompatibility antigen, HLA-A2. Nature 1987 329: 506-512.
- Warburton, R.J., et al. Mutation of the alpha 2 domain disulfide bridge of the class I molecule HLA-A*0201. Effect on maturation and peptide presentation. Hum. Immunol 1994 39: 261-271
- Richardson, D.C., and Richardson, J.S. The kinemage: A tool for Scientific communication. Protein Sci.1992 1: 3-9.
- Sayle, R., and Milner-White, E.J. RasMol: biomolecular graphics for all. Trends Biochem. Sci. 1995 20: p. 374
- Voet, J. A Short History of Visualizing Structures in the PDB PDB Education Corner RCSB Protein Data Bank Newsletter 2005 25: 5-6
- Franzen, M.A. PDB Education Corner RCSB Protein Data Bank Newsletter 2006 28: 5-6
- See http://kinemage.biochem.duke.edu/software/king.php
- See http://pymol.sourceforge.net/
- Nelson, D.L., and Cox, M.M Lehninger: Principles of Biochemistry (4th Ed.) 2005 W.H. Freeman & Co. New York, NY.
- Elsliger, M.A., et al. Structural and spectral response of green fluorescent protein variants to changes in pH. Biochemistry 1999 38: 5296-5301.
- Branden, C., and Tooze, J Introduction to Protein Structure (2nd Ed.) 1999 Garland Publishing, Inc. New York, NY.
- Petsko, G.A., and Ringe, D. Protein Structure and Function 2004 Sinauer Associates, Inc. Sunderland, MA.
- Whitford, D. Proteins: Structure and Function 2005 John Wiley & Sons Inc. Hoboken, NJ.
- Ziegler, G.A., and Schulz, G.E. Crystal structures of adrenodoxin reductase in complex with NADP+ and NADPH suggesting a mechanism for the electron transfer of an enzyme family. Biochemistry 2000 39 10986-10995
- Garcia, K.C., et al. Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen. Science 1998 279 :1166-1172.
- Reiser, J.B., et al. Crystal structure of a T cell receptor bound to an allogeneic MHC molecule. Nat.Immunol. 2000 1 :291-297.
- See http://www.3dmoleculardesigns.com
- Muller, J.J., Lapko, A., Bourenkov, G., Ruckpaul, K., Heinemann, U. Adrenodoxin reductase-adrenodoxin complex structure suggests electron transfer path in steroid biosynthesis. J.Biol.Chem. 2001 276: 2786-2789