PDB COMMUNITY FOCUS: William L. Duax, International Union of Crystallography and Hauptman-Woodward Medical Research Institute
Dr. Duax received his Ph.D. in physical chemistry from the University of Iowa in 1967. He came to the Hauptman-Woodward Medical Research Institute in 1968 where he was head of the Molecular Biophysics Department from 1970-88, Research Director from 1988-93, Executive Vice President 1993-1999, and is currently H.A. Hauptman Distinguished Scientist. He is a Professor of the Department of Structural Biology at the State University of New York at Buffalo and the Chief Executive Officer of the American Crystallographic Association. He was a Fulbright Scholar in Yugoslavia in 1987, and received the Distinguished Scientist award from the Clinical Ligand Assay Society in 1994 and an Honorary Doctoral Degree from the University of Lodz Poland in 1999. He recently ended his term as the President of the International Union of Crystallography
Dr. Duax uses X-ray crystallographic analysis to determine the structure of biologically active molecules and correlates structures with biological activity. Early in his career he determined the structures of hundreds of steroids, published a two volume Atlas of Steroid Structure and developed an empirical model for steroid receptor binding and hormone action, (the A-ring binding/D-ring acting model) that proved valuable in the design of antiprogestational agents. More recently, together with Debashis Ghosh, he began a series of studies of steroid dehydrogenases. They determined the first crystal structure of a short chain oxidoreductase (SCOR) enzyme, elucidated of the molecular mechanism of action of SDHs, the basis for inhibition of IIβ-HSD by glycyrrhizic acid and the role of licorice in hypertension.
Recently he has begun combining information from the 3D structures of SCOR enzymes with sequence analysis of all putative SCOR genes in the gene bank to predict fold, function, cofactor, and substrate for 6000 genes. He is also engaged in a genomics project to trace the origin and evolution of the genetic code and the evolution of the amino acid composition of proteins.
Q: You were a prolific small molecule crystallographer (with ~250 entries in the Cambridge Structural Database, CSD). Why did you decide to shift your research efforts to focus on macromolecules?
A: There were two main reasons, one scientific and the other practical. The majority of our structures in the CSD are steroids. We were trying to understand how subtle changes in the shape and intermolecular interactions of steroids influenced their control of sugar metabolism, salt balance, sexual development, and fertility. Although we were able to develop empirical models for steroid structure and function, it became clear that we needed the three-dimensional structures of their protein targets to adequately test our models. Therefore, we developed collaborations with biochemists who were isolating steroid hormone receptors and enzymologists studying the biosynthesis and metabolism of steroids. We were fortunate that our first protein structure determination was of an ancient member of the short-chain oxidoreductase (SCOR) enzyme family. SCORs control the balance of active and inactive steroids involved in normal biological processes. Using that first structure, Debashis Ghosh was able to propose a model for the mechanism of action of the enzyme. This model provided the basis for understanding the activities of dozens of additional SCORs in the PDB and thousands of homologous proteins in the Swiss-Prot/TrEMBL databases. The practical reason for shifting our focus to macromolecules was that we had to go where the money was. When we published our first steroid structure in 1969, there were only a few hundred crystal structures of organic compounds in the literature. In the 1960s and 1970s, small molecule crystallography enjoyed significant support from the US National Institutes of Health (NIH). Currently, there are over 325,000 entries in the CSD, and NIH support has gradually shifted to macromolecular crystallography. Today, the macromolecular crystallographic community is facing a challenge similar to when small molecule crystallographers were unwisely relegated to the role of service crystallographers in the 1980s.
Crystallographers are well-equipped to make sense of the mass of data that the genome project has brought to light. Anticipating yet another sea change in federal funding, we have begun to utilize the explosion of macromolecular sequence data in combination with macromolecular structural data in an effort to try to predict the structure function relationship and ligand binding of thousands of hypothetical gene products.
Q: As a relatively new user of the RCSB PDB, have you found it easy to use and beneficial in your current research?
A: The PDB is absolutely essential to our current efforts to predict the structure and function of the 6,000 putative SCOR enzymes in the Swiss-Prot/TrEMBL databases. I find it very easy to access and use the PDB. This is all the more remarkable because I am totally incompetent when it comes to using computers. We use the PDB to examine the details of a billion years of molecular evolution and interactions between proteins and their cofactors and substrates in search of patterns that have predictive power. We also use the PDB to examine the nature of the interfaces among monomers in multimeric structures that are often their active forms. These studies give us insight into protein-protein interactions and allosteric behavior.
TargetDB is another reason that the RCSB PDB is critical to our research program. We use it as a resource for information on the most recently determined SCOR proteins as well as to identify new candidates to test predictions based on our proteomic research.
Q: The RCSB PDB has been involved in the creation, maintenance, and extension of the mmCIF dictionary since its commission by the IUCr in the early 1990s. The collaboration was further strengthened this year when the IUCr launched Acta Crystallographica Section F for the rapid publication of communications on structural genomics, protein structure and crystallization. What is the IUCr's perspective on this collaboration?
A: The collaboration between the RCSB PDB and the IUCr has been vitally important and extremely productive. One of the IUCr's goals is to extend the powerful technique of crystallography throughout the world. The IUCr journals are meant to be international archival journals for publication of the most accurate structure determinations. It is also essential to the mission of the IUCr to make the data available to the world community as economically and effectively as possible. The fact that the PDB is available to everyone in the world at no cost makes it an ideal resource for the IUCr community.
Q: You have traveled extensively during your tenure as IUCr President. Where have you seen the most potential for growth in new depositions to the PDB?
A: The future growth of the field of crystallography with respect to new structure determinations of all types of matter and the next generation of crystallographers is in the emerging nations of Latin America, the Asia-Pacific region, and Africa. Most emerging countries have indigenous plant, insect, and bacterial species with unique properties. Studies of the structures in these materials will provide new leads for rational drug design and disease control. We can already see the impact of the growth of a crystallographic infrastructure in these countries in the increased numbers of structure reports in Acta Crystallographica Section E that are coming from China, Malaysia and Turkey. Over 50% of the papers submitted to Acta Crystallographica Section E in 2004 came from China. It is only a matter of time before we see a similar explosion in macromolecular structure reports from these countries in Acta Crystallographica Section F.