PDB EDUCATION CORNER: "X-rays, Molecules, and You"

Speakers, from left to right: Katherine Kantardjieff, Alexander. Alexander McPherson, Tim Herman, David S. Goodsell, Karen Lipscomb, and Frank Allen, "Tommie Hata not pictured."
It seems difficult to imagine bright-eyed high-school students and their proud teachers discussing structural biology on a summer Sunday morning. Yet this was the scene at the "X-rays, Crystals, Molecules and You" workshop held on July 18th 2004 at the Hyatt Regency Chicago during the American Crystallographic Association's annual meeting. During this workshop, prominent crystallographers and structural biologists introduced high school students and teachers to basic concepts in X-ray crystallography and structural databases to promote interest in structural biology, chemistry, and general science. This workshop generated enough interest that approximately 60 students, teachers, and parents traveled from 18 different states to participate. Several ACA members also attended the lectures. The morning session introduced crystallography concepts, highlighted structural databases, and discussed representational models of structures as teaching tools. Two mini-workshops followed in the afternoon - crystallization for teachers, and modeling and visualization of structures for students.

Judith L. Flippen-Anderson, the production and outreach leader at the RCSB PDB, began the morning session with a brief welcome address. Katherine Kantardjieff, professor of physical chemistry at California State University Fullerton and director of the W.M. Keck Center for Molecular Structure, followed by introducing the concepts and procedures involved in the practice of X-ray crystallography. She described how crystals of proteins and other molecules are grown, harvested, and used for data collection. Kantardjieff then discussed how the data collected relate to electron density maps and how these these maps are used to build a model of the structure and generate 3-dimensional coordinates for each atom. Kantardjieff shared her somewhat circuitous route to becoming a crystallographer, and encouraged students and teachers to continue working towards their goals.

Tim Henman demonstrates hands-on protein folding

The second lecture discussed the data, tools and resources available at the Cambridge Crystallographic Data Center (CCDC; www.ccdc.cam.ac.uk). Frank Allen, the executive director of CCDC, explained how crystallography is used to determine the structures of molecules ranging from small metal ions to very large viruses. In all cases, this method provides an understanding of the shape, size, dimensions and interactions of the molecule being studied. He then focused on the structures present in the Cambridge Structural Database (CSD), the world repository of the small molecule crystal structures and the principle product of the CCDC. Allen described the different classes of molecules in the CSD and the ways in which the CSD can be used, including predicting where some of these small molecules may bind in an enzyme active site or binding pocket. Scientific Support Manager Karen Lipscomb then demonstrated some of the tools and resources available at the CCDC by querying the database for the Nobel Prize-winning structures solved by Dorothy Hodgkin and creating structure images.

David S. Goodsell and a SMART team at the poster session at the ACA meeting.
Then David Goodsell, associate professor in the Department of Molecular Biology at the Scripps Research Institute, discussed how the structural data present in the PDB archives are used for research and education. The growing PDB archive contains the three-dimensional coordinates and related information about biological macromolecules. These structures, including proteins, nucleic acids, and large macromolecular complexes, provide insight into these molecules? roles in fundamental biological processes. Goodsell is also the illustrator and primary author of the RCSB PDB's Molecule of Month educational feature. He presented a historic overview of how the atoms that make up proteins, nucleic acids and other molecules in the PDB have been visually represented by hand drawings, wire-frame, backbones, space-filling models and finally as ribbons. He demonstrated how each representation highlights different aspects and features of molecules.

The final lecture in the morning session was jointly presented by Tim Herman, Director of the Center for BioMolecular Modeling (CBM) at the Milwaukee School of Engineering, and Tommie Hata, a high school teacher at the Pingry School in Martinsville, NJ. Tim Herman started off by describing how physical models act as ?thinking tools? and can make molecular structures ?real? for researchers, teachers, and students alike. He briefly described how he uses the 3-D coordinates from the PDB archives to generate physical models of proteins. He also distributed a kit containing a pliable 4-foot tube and colored thumbtacks designed to demonstrate concepts in protein folding and interaction (see http://www.3dmoleculardesigns.com/). The student-teacher workshops organized by his center to promote an understanding of molecular structure through physical models were discussed. Tommie Hata had attended one of these workshops, following which he involved some of his own students in CBM's "Students Modeling A Research Topic" (SMART) team program. Hata talked about his SMART team's experiences, which included working with research scientists to create a physical model of a class I transcription activation complex.

Following lunch, teachers and students participated in different activities. Alexander McPherson, professor of molecular biology and biochemistry at University of California at Irvine, led the teachers through a hands-on exercise in crystallizing lysozyme. McPherson was awarded the ACA's prestigious Fankuchen Award later in the meeting for his many significant contributions, including his work in crystallization, and determination of various plant viruses, immunoglobulins and other molecules. Meanwhile, Goodsell, Herman, and Lipscomb led the students in various exercises. They explored the RCSB PDB, and located, downloaded and viewed a structure of a DNA-binding protein containing zinc finger domains. The students were challenged to search for and visualize estrogen and testosterone in the CSD in a short time period. They then used the tube kit to model a single zinc finger domain based on what they downloaded and examined from the PDB. The students also explored the exhibitor booths and poster presentations at the ACA meeting. Several students presented posters at the ACA meeting about their own SMART projects.

The workshop provided a great opportunity for students and teachers to learn about crystallography and structural biology alongside expert research scientists in their field.

This workshop was organized by the RCSB Protein Data Bank and co-sponsored by the ACA. This review is written by Shuchismita Dutta (RCSB PDB).