Helen M. Berman

Last updated
Helen Berman
Berman-photo.jpg
Helen Berman in 2008.
Born
Helen Miriam Berman

1943 (age 79–80)
Chicago, Illinois
Alma mater
Spouses
  • Victor Berman
  • Peter Young (1976–1999)
ChildrenJason Asher Young[ citation needed ]
Awards
Scientific career
Fields
Institutions Rutgers University
Thesis The Crystal Structures of Alpha Prime and Beta-D-Mannitol, Galacticol, Methyl Aalpha-D-Glucopyranoside and Hydroxyurea  (1967)
Doctoral advisor George A. Jeffrey[ citation needed ]
Other academic advisors Barbara Low, Jenny Glusker
Website rutchem.rutgers.edu/berman-helen-m

Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank (one of the member organizations of the Worldwide Protein Data Bank). 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 led the Protein Structure Initiative Structural Genomics Knowledgebase. [1] [2] [3]

Contents

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 research fellow.

Career

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. [4] That meeting led to the creation of the Protein Data Bank (PDB) at Brookhaven National Laboratory. [5] [6]

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. [7] At Rutgers, she continued to study nucleic acids, their interactions with proteins, [8] and also researched the structure of collagen in collaboration with Barbara Brodsky and Jordi Bella. [9] 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. [10] 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. [11] In 2006 the BioMagResData (BMRB) databank for Nuclear Magnetic Resonance (NMR) structures [12] became the fourth member of the wwPDB. [13] As of July, 2018, the NDB holds over 9600 nucleic acid structures and the PDB holds more than 142,000 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. [14]

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 Science Foundation, and serving on the editorial board of several journals. Her work has been widely published in peer reviewed scientific journals. [8] [9] [15] [16] [17]

Berman was the executive producer and creator of the documentary series Target Zero which focuses on the medical as well as the social aspects of HIV treatment and prevention. [18] The three short films interweave real-life patient stories, interviews with leading doctors, medical providers and scientists; and state of the art molecular animations. These accounts illuminate the complex history of controlling the HIV epidemic and reveal the ongoing need for compassionate, patient-centered care and a true understanding on a cellular level the science behind the treatments. [19]

Honors and awards

Personal life

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.

Related Research Articles

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

<span class="mw-page-title-main">Structural bioinformatics</span> Bioinformatics subfield

Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.

BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.

<span class="mw-page-title-main">Protein structure</span> Three-dimensional arrangement of atoms in an amino acid-chain molecule

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions, such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, cryo-electron microscopy (cryo-EM) and dual polarisation interferometry, to determine the structure of proteins.

<span class="mw-page-title-main">UniProt</span> Database of protein sequences and functional information

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.

The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

<span class="mw-page-title-main">Nucleoprotein</span> Type of protein

Nucleoproteins are proteins conjugated with nucleic acids. Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.

The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format.

The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.

<span class="mw-page-title-main">Protein domain</span> Self-stable region of a proteins chain that folds independently from the rest

In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.

<span class="mw-page-title-main">Philip Bourne</span>

Philip Eric Bourne is an Australian bioinformatician, non-fiction writer, and businessman. He is currently Stephenson Chair of Data Science and Director of the School of Data Science and Professor of Biomedical Engineering and was the first associate director for Data Science at the National Institutes of Health, where his projects include managing the Big Data to Knowledge initiative, and formerly Associate Vice Chancellor at UCSD. He has contributed to textbooks and is a strong supporter of open-access literature and software. His diverse interests have spanned structural biology, medical informatics, information technology, structural bioinformatics, scholarly communication and pharmaceutical sciences. His papers are highly cited, and he has an h-index above 50.

<span class="mw-page-title-main">ProtCID</span>

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.

Gerard Jacob Kleywegt is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank.

<span class="mw-page-title-main">WeNMR</span> Worldwide e-Infrastructure for NMR spectroscopy and structural biology

WeNMR is a worldwide e-Infrastructure for NMR spectroscopy and structural biology. It is the largest virtual Organization in the life sciences and is supported by EGI.

Computer Atlas of Surface Topography of Proteins (CASTp) aims to provide comprehensive and detailed quantitative characterization of topographic features of protein, is now updated to version 3.0. Since its release in 2006, the CASTp server has ≈45000 visits and fulfills ≈33000 calculation requests annually. CASTp has been proven as a confident tool for a wide range of researches, including investigations of signaling receptors, discoveries of cancer therapeutics, understanding of mechanism of drug actions, studies of immune disorder diseases, analysis of protein–nanoparticle interactions, inference of protein functions and development of high-throughput computational tools. This server is maintained by Jie Liang's lab in University of Illinois at Chicago.

<span class="mw-page-title-main">Structure validation</span> Process of evaluating 3-dimensional atomic models of biomacromolecules

Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.

Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.

The Biological Magnetic Resonance Data Bank is an open access repository of nuclear magnetic resonance (NMR) spectroscopic data from peptides, proteins, nucleic acids and other biologically relevant molecules. The database is operated by the University of Wisconsin–Madison and is supported by the National Library of Medicine. The BMRB is part of the Research Collaboratory for Structural Bioinformatics and, since 2006, it is a partner in the Worldwide Protein Data Bank (wwPDB). The repository accepts NMR spectral data from laboratories around the world and, once the data is validated, it is available online at the BMRB website. The database has also an ftp site, where data can be downloaded in the bulk. The BMRB has two mirror sites, one at the Protein Database Japan (PDBj) at Osaka University and one at the Magnetic Resonance Research Center (CERM) at the University of Florence in Italy. The site at Japan accepts and processes data depositions.

<span class="mw-page-title-main">Macromolecular Crystallographic Information File</span> File format used for macromolecular structure data

The Macromolecular Crystallographic Information File (mmCIF) also known as PDBx/mmCIF is a standard text file format for representing macromolecular structure data, developed by the International Union of Crystallography (IUCr) and the Protein Data Bank It is an extension of the Crystallographic Information File (CIF), specifically for macromolecular data, such as proteins and nucleic acids, incorporating elements from the PDB file format.

References

  1. 1 2 Helen M. Berman publications indexed by Google Scholar
  2. ↑ Demasters K: ON THE MAP; A Bank Where the Currency Is Molecules. New York Times 2000-11-26. Accessed 2008-10-22.
  3. ↑ Helen Berman's story from Rutgers University Office for the Promotion of Women in Science, Engineering, and Mathematics
  4. ↑ Cold Spring Harbor Symposia on Quantitative Biology, vol. XXXVI (1972)
  5. ↑ Bernstein FC, Koetzle TF, Williams GJ, 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 (3): 535–542. doi:10.1016/S0022-2836(77)80200-3. PMID   875032.
  6. ↑ Berman H (2008). "The Protein Data Bank: a historical perspective". Acta Crystallographica A. 64 (Pt 1): 88–95. Bibcode:2008AcCrA..64...88B. doi: 10.1107/S0108767307035623 . PMID   18156675.
  7. ↑ About the Nucleic Acid Database Archived 2008-09-20 at the Wayback Machine
  8. 1 2 Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH (2002). "Structural basis of transcription activation: The CAP-αCTD-DNA complex". Science. 297 (5586): 1562–1566. Bibcode:2002Sci...297.1562B. doi:10.1126/science.1076376. PMID   12202833. S2CID   17422837.
  9. 1 2 Bella J, Eaton M, Brodsky B, Berman HM (1994). "Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution". Science. 266 (5182): 75–81. Bibcode:1994Sci...266...75B. doi:10.1126/science.7695699. PMID   7695699.
  10. ↑ 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 (1): 235–242. doi:10.1093/nar/28.1.235. PMC   102472 . PMID   10592235.
  11. ↑ Berman HM, Henrick K, Nakamura H (2003). "Announcing the worldwide Protein Data Bank". Nature Structural Biology. 10 (12): 980. doi: 10.1038/nsb1203-980 . PMID   14634627. S2CID   2616817.
  12. ↑ Doreleijers, J. F.; Mading, S; Maziuk, D; Sojourner, K; Yin, L; Zhu, J; Markley, J. L.; Ulrich, E. L. (2003). "BioMag ResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank". Journal of Biomolecular NMR. 26 (2): 139–46. doi:10.1023/a:1023514106644. PMID   12766409. S2CID   13221156.
  13. ↑ Berman HM; Henrick K; Nakamura H; John L. Markley JL (2007). "The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data". Nucleic Acids Research. 35 (Database issue): D301–D303. doi:10.1093/nar/gkl971. PMC   1669775 . PMID   17142228.
  14. ↑ 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.
  15. ↑ Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B. (1992). "The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids". Biophysical Journal. 63 (3): 751–759. Bibcode:1992BpJ....63..751B. doi:10.1016/S0006-3495(92)81649-1. PMC   1262208 . PMID   1384741.
  16. ↑ Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. (2000). "The Protein Data Bank". Nucleic Acids Research. 28 (1): 235–242. doi:10.1093/nar/28.1.235. PMC   102472 . PMID   10592235.
  17. ↑ Berman, H. M.; Kleywegt, G. J.; Nakamura, H; Markley, J. L. (2012). "The Protein Data Bank at 40: Reflecting on the past to prepare for the future". Structure. 20 (3): 391–6. doi:10.1016/j.str.2012.01.010. PMC   3501388 . PMID   22404998.
  18. ↑ "Target Zero: Official Website". targetzerofilm.org. Retrieved 17 January 2021.
  19. ↑ Posatko, Mary (1 May 2017). "Target Zero". imdb.com. Retrieved 17 January 2021.
  20. ↑ Sigma Xi Distinguished Lecturers
  21. ↑ ""Two distinguished Rutgers chemists named Biophysical Society Fellows." Bio-Medicine". Archived from the original on 2016-03-03. Retrieved 2008-10-22.
  22. ↑ Rutgers Professor Helen M. Berman to Receive the Prestigious M.J. Buerger Award, Rutgers News Release, August 16, 2006 Archived July 20, 2011, at the Wayback Machine
  23. ↑ "Berman recognized for her efforts in removing barriers to data access". Archived from the original on 22 January 2015. Retrieved 22 January 2015.
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