PDB Education Corner

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. Paul A. Craig, Associate Professor of Chemistry at the Rochester Institute of Technology:

The Protein Data Bank plays a critical role in teaching, learning and research in Biochemistry education at the Rochester Institute of Technology (RIT), a career-oriented comprehensive university with about 17,000 students. In the College of Science, students majoring in Biology, Chemistry, Biochemistry, Biotechnology and Clinical Chemistry all take courses in Biochemistry. The complete Biochemistry sequence consists of three courses which last a full academic year under our quarter system. The first course covers amino acids, proteins and membranes, the second is metabolism and the third is about nucleic acids and molecular genetics.

Teaching and Learning We use Biochemistry by Berg, Tymoczko and Stryer (Berg JM, Tymoczko JL, Stryer L, 5th edition, W.H. Freeman, New York, 2002) in our courses. Tim Driscoll of molvisions (molvisions.com) has developed an excellent set of Living Figures for the publisher which we use in lecture to demonstrate the structural features of proteins and nucleic acids throughout the course sequence. We believe that the students learn much more, however, when they work on developing their own structure documentaries based on PDB files. To emphasize the importance of understanding structure and function in these courses, these documentaries account for 20% of their course grades. For these projects, students are asked to select a particular type of protein (e.g., a kinase or a protease) from the PDB which includes either an inhibitor (for the first course in our sequence) or a complex with a nucleic acid (for the third course, which focuses on molecular biology). They then use the PDB Structure Explorer page to identify the primary reference for the structure. From this starting point, they go to PubMed (www.ncbi.nlm.nih.gov) to identify at least two additional referred resources. From these sources the students prepare a structure annotation that includes a brief introduction, a statement of the physiological role of the structure, a detailed description of the structure of the protein which includes general features (e.g., secondary structures) and specific features of the active site and the interaction between the protein and inhibitor (or nucleic acid), and a summary of the family relationships of the structure. Students are also required to prepare a series of molecular visualizations for the structure part of the documentary. This requires that students spend a few hours learning how to read PDB files and compare information in their files with the related publications. After earlier attempts with Kinemage and Rasmol, we spent several years helping students prepare Chime pages, with varying degrees of success. For the last two years the students have been preparing their structure documentaries using a program called BioEditor (bioeditor.sdsc.edu) that was developed at the San Diego Supercomputer Center (more on that below).

A more detailed description of the project requirements can be found at www.rit.edu/~pac8612/Biochemistry/502(702)/protein_vis.htm. A number of students have produced stellar documentaries using BioEditor and these can be viewed on the BioEditor Web site at bioeditor.sdsc.edu/documentaries.shtml.

Software Development My professional interests are at the interface between computers and biology. This has included simulations of several protein separation processes. The most successful of these is an electrophoresis simulation (www.rit.edu/~pac8612/electro/Electro_Sim.html). In communicating with the programmers, I have always found that PDB files are an effective starting point to explain sequence and structure information.

I was fortunate to spend the 2001-2002 academic year on sabbatical at the San Diego Supercomputer Center where I worked Peng Yang (a programmer), David Goodsell (a molecular biologist and a wonderful artist – see the PDB Molecule of the Month pages) and Phil Bourne on developing a software tool called BioEditor (bioeditor.sdsc.edu), which is designed to facilitate the annotation of macromolecular structure (Yang P, Craig PA, Goodsell D, Bourne PE. BioEditor – Simplifying Macromolecular Structure Annotation, Bioinformatics (2003) 19: 897-898). This tool enables users to assemble information and images they need to create documentaries about a particular structure or family of structures. It includes a number of powerful features that enable users to prepare structure documentaries: a built-in browser based on Internet Explorer which enables users to directly download and incorporate PDB structure files, a molecular visualization interface based on the Chime plug-in, a tool for cataloguing images that are created by the user or collected from other sites, and the ability to assemble references based only on their PubMed ID numbers (PMIDs).

Students in Computer Science and Bioinformatics at RIT continue to work on improving the ease of use and power of BioEditor as part of their undergraduate and M.S. degree programs.

Screenshot of a BioEditor documentary on human cyclin dependent kinase 2, created by Seth Staples, RIT