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Credit: Nick Romanenko
Helen Berman
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Helen Berman is a busy woman. In addition to her responsibilities as a Rutgers Board of Governors Professor of Chemistry, she is the director of the Protein Data Bank (PDB), an international repository for three-dimensional protein structures housed at Busch campus. This dynamic computer library of more than 35,000 molecular structures is one of the world’s most critical resources for understanding biological processes and studying human disease. It grows continually as researchers around the world determine, and then electronically deposit, new structures. The PDB is funded by the National Science Foundation, representing one of the largest single chunks of money coming into Rutgers. The National Institutes of Health and the U.S. Department of Energy also contribute to the PDB’s support. Focus writer Brian Geldziler recently spoke with Berman about the PDB, among other topics.
Question: One next step beyond the Human Genome Project is to study the proteins encoded by genes. Many of these proteins have medical relevance, and have proven useful for the study of such diseases as HIV, influenza and SARs, for example. How is the PDB carrying this mission forward? And what is your vision of the PDB’s future role in biomedical research?
Answer: We’re heavily involved in all of the structural genomics projects under way; all of their data come to us. We understand that structure does not stand alone, however, and we need to integrate other protein information with the structures in the PDB. Our next initiative will be to create a knowledge base for all this information, annotated with interpretive and explanatory notes. These annotations help us characterize structures and allow us to predict the function of unknown proteins by comparing them to structurally similar ones with known functions in the database. The more annotated structures we have, the stronger our predictions about protein functions will be.
Question: What does the PDB and its federal funding mean to the university in research and education and to the state of New Jersey?
Answer: In the life sciences there are really only two key databases: GenBank – the NIH database of all publicly available DNA sequences – and the PDB. The PDB is a key archival resource and having the repository at Rutgers not only adds to our prestige, but also could be a wonderful thing for the New Jersey economy and for education. Its presence creates opportunities for integrating our work with education, for example, in the chemistry courses that I teach at Rutgers. We also have the opportunity to work with the pharmaceutical companies that produce many structures, potentially leading to further mutually beneficial collaborations.
Question: Do you find it difficult to keep your collaborating partners on track in this massive undertaking, given the geographic separation?
Answer: It is challenging, but also exciting. The management of the PDB consists of a fairly equal partnership between Rutgers and the University of California at San Diego. By having different points of view, you make the team richer, more interesting and create a more vibrant research tool.
Question: Men still outnumber women in the hard sciences, although this is starting to change. Do you regard yourself as a role model for the next generation of female scientists?
Answer: I don’t know if I’m a role model. I will tell you that it’s very difficult to be a woman in science. There are many issues affecting us that have nothing to do with science itself – but are more to do with how to manage your life. It’s not as straightforward as I would have hoped it would be. I think we’ve come some distance, but it’s still the case that for women in science the juggling of career and personal life is very difficult.
Question: You’ve publicly acknowledged being a breast cancer survivor. Have you been engaged in support groups for others who have been diagnosed?
Answer: Yes. I’m very involved. I’m in my 24th year of survival. I had a lot of support when I went through this myself, so I’ve always felt very strongly that I should support other women. I am always available to talk to other women in this situation and have been involved in making videos and other formal support activities for women with this disease. I think it’s very important to be open and to recognize that this is a disease that afflicts a large number of people.
Question: When you’re not doing science, what do you enjoy?
Answer: I like to cook, entertain and do all kinds of house projects. I like to go to the theater, dance performances, walking and, sometimes, I just like to do nothing. I also love to travel and, because of the travel requirements of my work, I’ve become very good at moving long distances with very little wear and tear.
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