No. 21
Spring 2004


Message from the RCSB PDB

PDB Chemical Component Dictionary Format Description Available

Validation of Protein Structures for the PDB

PDB Deposition Statistics

Release of New Deposition Tool at BMRB

Website Statistics

QuickSearch Available on RCSB PDB Site

Accessing and Understanding Biological Units

The PDB: A Case Study in Management of Community Data

Molecular Machinery Poster Available as PDF

Art of Science Exhibit Visits the University of Wisconsin-Madison

Molecules of the Quarter: Carbonic Anhydrase, Glycolytic Enzymes, Calcium Pump

PDB Community Focus: Helen M. Berman

PDB Education Corner by Tommie S. Hata

Related Links: File Formats

RCSB PDB Job Listing

RCSB PDB Members & Statement of Support

Questions? info@rcsb.org

© 2004 RCSB PDB

PDB Education Corner by Tommie S. Hata

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 Tommie Hata, a biology teacher at The Pingry School in Martinsville, NJ.

The Protein Data Bank has become a significant and popular website to supplement our curriculum within molecular biology. Despite attempts by textbooks to invigorate material with animations and CD-ROM presentations, the material in a book is often static and disconnected from the real world of science. The PDB has given life to molecules, the people behind them, and the process of discovering them.

The Pingry School is a special place. It is a country day school that offers many opportunities to the student body. The students are involved in a number of diverse activities from glass blowing to biomolecular modeling in addition to the standard academic rigor. Our students have a variety of backgrounds and interests, yet have a unifying theme in a motivated attitude towards learning and achieving. The ninth grade biology program at our school has made a distinct effort to reduce the breadth of the curriculum and improve the depth of knowledge. This concept has led away from copious note taking on many broad topics within biology and deeper exploration of the process of science. The PDB has truly made this possible.
Annotator Kyle Burkhardt discusses protein structure with Tommie Hata and his class at the RCSB PDB site at Rutgers.

The first unit within our curriculum is the structure and function of macromolecules. When students are learning the specifics of protein structure, they predict a structure of a retinol binding protein (RBP) and use the PDB (1aqb) to compare their predicted structure to an actual RBP. The students look specifically for the hydrophobic nature in amino acids within the "carrying" portion of the molecule, as compared to hydrophilic portion of the molecule, using computer programs such as MDL Chime and RasMol.

The reality of seeing the amino acids in a three dimensional form, comparing different records of RBP, and manipulating the molecule using chime led to many to exclaim "Ahaa!" or "I was right!" and facilitate discussions on the other possibilities of structure.

Using Boolean commands in RasMol, such as "sidechain and alpha" or "backbone and helix," further increases the students' awareness of protein structure. On separate occasions, students have generated RasMol scripts to highlight individual amino acid sidechains in hemoglobin that interact with the heme group and to highlight cAMP bound within catabolite activator protein (CAP). The educator is simply a tool in the learning process; the students are given the resources to facilitate learning.

The Molecule of the Month feature by Dr. David Goodsell has been integral to deepening knowledge of other biological molecules and processes. Almost every unit is supplemented by having the students read a feature and then answer questions developed by the teachers. Topics such as cellular respiration, photosynthesis, gene regulation, and membrane transport relate to Molecule of the Month features. Some students take the next step to view and analyze the PDB files referenced in the features and compared different records.

In September, The Pingry School established a Students Modeling A Research Topic (SMART) team under the guidance of Dr. Tim Herman at the Milwaukee School of Engineering (see PDB Education Corner from Summer 2003 issue). With help from Dr. Richard Ebright (HHMI/Waksman Institute/Rutgers), Dr. Helen Berman, and other scientists at the PDB, my seven students have been able to design a physical model of a class I transcription-activation complex (www.mybiology.com/smartteam.htm).

College-level concepts such as protein structural motifs have become part of our discussions, which would not have been possible without the PDB. Through their interaction with Dr. Berman and the PDB, the students also gain a better understanding and appreciation for both the science and scientists involved in crystallography.

In addition to becoming a tool used in our classroom, the PDB has made scientists and their work tangible to our students. At Pingry, the PDB has morphed from a tool exclusive to the science community to a shortcut on the students' computer desktops.