RCSB PDB Newsletter #20: PDB Education Corner by Katherine Kantardjieff

No. 20
Winter 2004


Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank

Downloadable PDB_EXTRACT Makes Deposition Easier

Biological Unit Tutorial Now Available from the RCSB PDB

Ligand Depot--a Small Molecule Information Resource

PDB Focus: Deposition and Release Policies

PDB Deposition Statistics

Lucene Keyword Search Released on the RCSB PDB Web Site

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

PDB Focus: Searching for Experimental Data Files

Updates of mmCIF Files on the RCSB PDB FTP Site

RCSB PDB Web Site Statistics

NIGMS News: PSI-2 and Structural Biology Roadmap RFA

RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

Related Links: FTP Resources

RCSB PDB Job Listings

RCSB PDB Members & Statement of Support

Questions? info@rcsb.org

© 2004 RCSB PDB


PDB Education Corner by Katherine Kantardjieff

PDB'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 Prof. Katherine Kantardjieff, Professor of Chemistry and Biochemistry at California State University Fullerton:

The California State University (CSU) is the largest, most diverse, and one of the most affordable university systems in the country. For the majority of students seeking baccalaureate education in California, as well as those seeking professional training, the CSU is the gateway institution, significantly impacting education and the economy of our state. The CSU campuses are predominantly undergraduate institutions, where a majority of undergraduates in the sciences conduct laboratory-based research as part of their baccalaureate degree requirements. My campus, CSU Fullerton, became the 12th state college in California to be authorized by the Legislature in 1957. Today, CSUF has an enrollment of more than 32,000 students, making it the third largest in the 23-campus CSU system.

Protein Crystallography

Within the CSU, there is a vibrant California Program for Education and Research in Biotechnology (CSUPERB), which promotes system-wide biotechnology education and training, and supports several core research facilities. One such facility, based at CSUF, is the W.M. Keck Foundation Center for Molecular Structure (CMolS), which I direct. CMolS is the first comprehensive facility dedicated to research and education in both small and macromolecular structure determination and analysis using the science of crystallography, which is located at a predominantly undergraduate institution. Undergraduates and Masters' level students learn about macromolecular structure determination methods in our classrooms and our training facilities, they learn about archiving and mining structural information in the Protein Data Bank, and they actually solve protein structures in our own research laboratories. Since 1997, our facilities have been available by remote access system-wide, and we annually host workshops for undergraduate faculty who wish to incorporate structure determination methods and molecular modeling into their curriculum.

A Comprehensive Biochemistry Laboratory

A contemporary experiment in macromolecular structure/function analysis must cover not only advanced

crystallographic techniques and methods, but also the front end aspects of protein crystal- lography, protein production, purification, and crystallization, as well as the back end aspects of structure validation and analysis. At CSU Fullerton, the majority of the upper division biochemistry laboratory (CHEM 422) is devoted to the study of the enzyme lactate dehydrogenase (LDH), from chicken breast muscle. With funding from CSUPERB, we have recently expanded the laboratory into a comprehensive structure determination and analysis by adding an X-ray crystallography component.

LDH is a well-studied essential enzyme in carbohydrate metabolism for which extensive amino acid data are available for orthologous homologs, and for which some atomic resolution structure information is available (bacterial and human). In the laboratory, students isolate LDH-A from chicken breast muscle using standard techniques of tissue homogenization, centrifugation and ammonium sulfate precipitation, and LDH activity is later assayed spectrophotometrically using established protocols. Using their purified LDH-A, students gain experience in methods used in modern biotechnology to crystallize proteins for structure determination by X-ray diffraction analysis. This involves setting up 24-48 crystallization trials using commercially available random screens and vapor diffusion methods. In parallel, students also set up lysozyme crystallization trials using published procedures, and they are given an introduction to microbatch techniques, using saturated sodium chloride solutions under paraffin or mineral oil. Our students have succeeded in producing crystals of LDH-A from chicken breast muscle under a variety of screening conditions not previously reported for crystallizing either bacterial or human LDHs. We hope to have diffraction data collected before the end of this fall term, with the ultimate goal of making these data available for any biochemistry laboratory course. Students would be able to solve the structure by molecular replacement, and build models into electron density using available software, such as XtalView.

To complement the wet lab work, we have the students spend several laboratory sessions conducting related bioinformatics exercises that include visualization of the atomic resolution structural details of LDH homologs in the PDB. Students examine the details of the active site chemistry, looking at substrate and cofactor binding interactions and, using either DeepView or ICM-Pro, students make a homology model of their enzyme from chicken and conduct in silico mutagenesis experiments. Based on students' laboratory reports and general feedback, these bioinformatic and computational exercises using information in the PDB have greatly enhanced our students' understanding of protein biochemistry.

Contemporary Biology and the Art of Science

The Department of Biological Science at CSUF has designed and implemented a new curriculum that builds on a core program with themes and perspectives to connect and integrate major concepts, principles and facts. In one of the four freshman core courses, Cellular Basis of Life (BIOL 172), Dr. MerriLynn Casem has integrated the PDB into her teaching through use of the Art of Science exhibit, which CSUF has hosted during the Fall 2003 semester. In the beginning, Dr. Casem asked her students to view the images strictly as art, in whatever initial context the students brought with them. She asked them to critique the works first from an artistic perspective, and then with regard to information conveyed, to determine whether the models and graphics informed the students' understanding. Dr. Casem has since used the exhibit and the PDB as "an excellent reference point" for the themes emphasized in the course: order and organization, properties of life, and energy usage. The students have been particularly impressed by the fact that cells are not at all "empty", but rich with the molecules of life.

What we have been surprised and pleased to note is that, in addition to our own biochemistry and biology majors, students from outside the College of Natural Science and Mathematics have been sent to view the exhibit as part of their coursework, including student teachers and art majors. Thus, at CSUF, the PDB is being used to educate the broader campus community about molecular science.

Structural Bioinformatics

As part of the CSU mission to strengthen the California workforce, CSUF Extended Education offers many courses for continuing development of working professionals, including several certificate programs. Our Certificate in Bioinformatics, one of two granted system-wide, is distinguished by its capstone advanced course in sequence, structure and function analysis, which makes extensive use of structural information in the PDB. Students learn about structure-guided drug-design and explore protein-protein interactions. The Pasadena Bioscience Center-- a joint endeavor between California State University, Caltech, Huntington Medical Research Institute, Pasadena City College, City of Pasadena, and bioscience industry representatives--also offers continuing education courses in protein structure and drug design, which make extensive use of the PDB.

Cytochrome c' from Rhodobacter sphaeroides, the first protein structure to be published in the Journal of Chemical Crystallography. This structure was the Masters' thesis of Prof. Kantardjieff's student, Laura Ramirez, who was supported by the NIH-MSD program. Ms. Ramirez is now Chair of the Science Department at East Los Angeles College. This image was rendered with ICM-Pro v3.0.24a, Molsoft LLC.

PDB ID: 1gqa

L.M. Ramirez, H.L. Axelrod, S.R. Herron, B. Rupp, J.P. Allen, K.A. Kantardjieff (2003): High resolution crystal structure of ferricytochrome c' from Rhodobacter sphaeroides. Journal of Chemical Crystallography 33(5-6), pp. 413-24.