Helen M. Berman
|This biographical article relies on references to primary sources. (November 2012)|
Helen M. Berman (born 1943) is the director of the RCSB Protein Data Bank – one of the member organizations of the Worldwide Protein Data Bank and a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and leads the Protein Structure Initiative Structural Genomics Knowledgebase.
Background and education
Berman was born in Chicago, Illinois, and grew up in Brooklyn, New York. Her father, David Bernstein, was a physician and her mother, Dorothy Bernstein (née Skupsky), managed her father's office practice. Inspired by her hard-working and scholarly father, she was interested in science as a young girl and planned to become a scientist or doctor. Her mother, who was strongly involved in the community and volunteer work, influenced her to be involved in community activities throughout her life.
During high school, Berman worked in Ingrith Deyrup's laboratory at Barnard College. Deyrup encouraged Berman to attend Barnard as an undergraduate. While at college, she worked in a Columbia University College of Physicians and Surgeons laboratory with Barbara Low. There, Berman learned about crystallography, which would become a lifelong passion. She graduated from Barnard with an A.B. in chemistry in 1964.
Following college, Berman attended the University of Pittsburgh for graduate school, a place she selected because it was the only place in the country with a crystallography department, and one of the few where crystallography was offered as a subject. There she worked with George A. Jeffrey on carbohydrate structure, receiving her Ph.D. in 1967. Berman remained at the University of Pittsburgh for two more years as a postdoctoral fellow.
In 1969, Berman moved to the Fox Chase Cancer Center in Philadelphia, where she worked in Jenny P. Glusker's laboratory before starting her own independent research program as a faculty member in 1973. At Fox Chase, Berman became interested in nucleic acid structures and in bioinformatics. She knew that logical organization of data would make it useful to a variety of scientists.
In June 1971, Berman attended a symposium at Cold Spring Harbor Laboratory, where several scientists agreed that data on the expanding number of protein structures should be archived in a database. That meeting led to the creation of the Protein Data Bank (PDB) at Brookhaven National Laboratory.
In 1989, Berman moved to Rutgers and in 1992, along with other scientists, she co-founded the Nucleic Acid Database (NDB) to collect and disseminate information about nucleic acid structure. At Rutgers, she continued to study nucleic acids, their interactions with proteins, and also researched the structure of collagen in collaboration with Barbara Brodsky and Jordi Bella. She is listed as a depositor on 38 structures in the PDB from 1992 to 2011, of protein/nucleic acid complexes and their components (e.g. 1RUN, 3SSX, 2B1B), collagen fragments (e.g. 1CGD, 1EI8), and other macromolecules.
In 1998, Berman and Philip Bourne together competed for and won the contract for the Protein Data Bank and the database moved from Brookhaven to the auspices of the Research Collaboratory for Structural Bioinformatics (RCSB), currently a collaboration between Rutgers and the University of California, San Diego. With colleagues, Berman redesigned the data management system, added new user tools, and made the database searchable. Since 2003, the PDB archive has been managed by the worldwide Protein Data Bank (wwPDB), a partnership founded by Berman that consists of organizations that act as deposition, data processing and distribution centers for PDB data - the RCSB, the PDBe in Europe, and the PDBj in Japan. In 2006 the BioMagResData (BMRB) databank for Nuclear Magnetic Resonance (NMR) structures became the fourth member of the wwPDB. As of October, 2012, the NDB holds over 6000 nucleic acid structures and the PDB holds more than 85,000 macromolecular structures.
Also led by the RCSB, the Protein Structure Initiative (PSI) Structural Genomics Knowledgebase was launched in the Spring of 2008 to provide a continuously updated portal to research data and other resources from the PSI efforts.
Berman has also been active in the scientific community, serving as president of the American Crystallographic Association in 1988, advising both the National Institutes of Health and the National Scientific Foundation, and serving on the editorial board of several journals.
Berman has been married twice, to engineer Victor Berman in the 1960s, and to molecular biologist Peter Young from 1976 to 1999. From the second marriage she has a son, Jason Asher Young (born 1979), a physicist.
During the 1980s, Berman was diagnosed with breast cancer. The experience made her more focused in her life and her career, and interested in supporting other women who face the same diagnosis.
Honors and awards
- New Jersey Woman of Achievement (1993)
- Fellow, American Association for the Advancement of Science (1996)
- Outstanding Woman Scientist Award, Association for Women in Science, New York Chapter (1999)
- Distinguished Lecturer, Sigma Xi: The Scientific Research Society (2007–2009)
- Distinguished Service Award, Biophysical Society (2000)
- Fellow, Biophysical Society (2001)
- M.J. Buerger Award, American Crystallographic Association (2006)
- Department of Chemistry Alumni Award from the University of Pittsburgh (2010)
- American Crystallographic Association Fellow (2011)
- "The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids." Berman HM, Olson WK, Beveridge D, Westbrook J, Gelbin A, Demeny T, Hsieh S-H, Srinivasan AR and Schneider B. Biophysical Journal 63: 751–759 (1992).
- "Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution." Bella J, Eaton M, Brodsky B and Berman HM. Science 266: 75–81 (1994).
- "The Protein Data Bank." Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN and Bourne PE. Nucleic Acids Research 28: 235–242 (2000).
- "Structural basis of transcription activation: The CAP-αCTD-DNA complex." Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM and Ebright RH. Science 297: 1562–1566 (2002).
- "The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future." Berman HM, Kleywegt GJ, Nakamura H and Markley JL. Structure 20:391-396 (2012).
- Cold Spring Harbor Symposia on Quantitative Biology, vol. XXXVI (1972)
- Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977). "Protein Data Bank: a computer-based archival file for macromolecular structures". Journal of Molecular Biology 112: 535–542. doi:10.1016/S0022-2836(77)80200-3.
- Berman H (2008). "The Protein Data Bank: a historical perspective". Acta Crystallographica A. 64 pages=88–95. doi:10.1107/S0108767307035623. PMID 18156675.
- About the Nucleic Acid Database
- Benoff B et al. (2002). "Structural basis of transcription activation: The CAP-αCTD-DNA complex". Science 297: 1562–1566. doi:10.1126/science.1076376.
- Bella J et al. (1994). "Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution". Science 266: 75–81. doi:10.1126/science.7695699.
- Berman HM, Westbrook J, Feng J, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000). "The Protein Data Bank". Nucleic Acids Research 28: 235–242. doi:10.1093/nar/28.1.235. PMC 102472. PMID 10592235.
- Berman HM, Henrick K, Nakamura H (2003). "Announcing the worldwide Protein Data Bank". Nature Structural Biology 10: 980. doi:10.1038/nsb1203-980.
- Doreleijers JF, Mading S, Maziuk D, Sojourner K, Yin L, Zhu J, Markley JL, Ulrich EL (2003). "BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank". Journal of Biological NMR 26: 139–146.
- Berman HM, Henrick K, Nakamura H, and John L. Markley JL (2007). "The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data". Nucleic Acids Research 35: D301–D303. doi:10.1093/nar/gkl971. PMC 1669775. PMID 17142228.
- Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM (2006). "The RCSB PDB information portal for structural genomics". Nucleic Acids Research 34 (Database issue): D302–D305. doi:10.1093/nar/gkj120. PMC 1347482. PMID 16381872.
- Sigma Xi Distinguished Lecturers
- "Two distinguished Rutgers chemists named Biophysical Society Fellows." Bio-Medicine
- Rutgers Professor Helen M. Berman to Receive the Prestigious M.J. Buerger Award, Rutgers News Release, August 16, 2006
- Nucleic Acid Database
- worldwide PDB (wwPDB)
- RCSB PDB, Rutgers
- PDBe, EBI Cambridge
- PDBj, Osaka
- BMRB (BioMagResBank, Wisconsin)
- Helen Berman’s page at Rutgers
- Demasters K: ON THE MAP; A Bank Where the Currency Is Molecules. New York Times 2000-11-26. Accessed 2008-10-22.
- Helen Berman’s story from Rutgers University Office for the Promotion of Women in Science, Engineering, and Mathematics