Board of Governors Professor
Department of Chemistry and Chemical Biology
Rutgers, The State University of New Jersey

BioMaPS Institute for Quantitative Biology

Visiting Scientist
Center for Advanced Biotechnology and Medicine

Ph.D., 1967, University of Pittsburgh

Telephone: (732) 445-4667
Fax: (732) 445-4320

Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Site
Electron Microscopy Data Bank (EMDB) Site
Worldwide Protein Data Bank (wwPDB) Site
Protein Structure Initiative (PSI) Structural Genomics Knowledgebase Site
Laboratory for Structural Biology and Bioinformatics Site

Structural bioinformatics, structural biology

As a founding member of the Worldwide Protein Data Bank (wwPDB) collaboration, we support scientific research and education by providing the essential Protein Data Bank (PDB) archive of information about the experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The wwPDB organization ensures that the PDB is freely and publicly available to the global community. Members host deposition, annotation, and distribution centers for PDB data and collaborate on a variety of projects and outreach efforts, including developing tools and processes for validating and remediating structural data.

The Research Collaboratory for Structural Bioinformatics (RCSB) PDB, a collaboration between Rutgers and the University of California, San Diego, RCSB PDB maintains the central repository of the PDB archive for the wwPDB, and provides resources that promote a structural view of biology, including a relational database, molecular viewers, structure comparison tools, and educational materials such as the Molecule of the Month series.

The Electron Microscopy Data Bank (EMDB) is a joint effort of the Protein Data Bank in Europe, the RCSB, and National Center for Macromolecular Imaging that provides a global deposition and retrieval network for cryoEM map, model and associated metadata, and a portal for software tools for standardized map format conversion, map, segmentation and model assessment, visualization, and data integration.

In 2008, the PSI-Nature Structural Genomics Knowledgebase (PSI SGKB) was established to turn the products of the Protein Structure Initiative into knowledge that is important for understanding living systems and disease. A single search of the SGKB provides links to 3D structures, pre-built models, annotations, target information, protocols, and access to DNA clones. The site offers an easy way to keep abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology.

The work on these projects has been informed by our research and studies in structural biology, in particular protein-nucleic acid interactions, binary and ternary complexes with catabolite activating protein (CAP), and nucleic acids. Several studies have been focused on defining the precise molecular interactions involved in transcription activation by CAP. In a project led by Catherine Lawson, we obtained an experimental 3D map volume (shown below) of a class I CAP-dependent transcription activation complex using single particle averaging of 2D electron microscopy images. The EM map volume and fitted coordinates are deposited in the EM Databank (EMD-5127) and PDB (id 3iyd).

Figure 1. Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Electron microscopy reconstruction (20 Å resolution) of a transcription initiation complex from Escherichia coli comprising RNA polymerase holoenzyme (purple with alpha subunit C-terminal domain shown in green), catabolite activator protein (blue), and DNA (tan). The background is an electron micrograph of reconstituted complex particles in negative stain (Hudson et al., 2009).

Selected Publications

Hudson BP, Quispe J, Lara-González S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL. Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A. 2009 Nov 24; 106(47):19830-5

Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R, La Baer J. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. 2009 Jan; 37(Database Issue):D365-8

Berman H, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003 Dec; 10(12):980

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1; 28(1):235-42

Schneider B, Berman HM. Hydration of the DNA bases is local. Biophys J. 1995 Dec; 69(6):2661-9

Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992 Sep; 63(3):751-9