Faculty Research

Berman, Helen

helen berman2 2e9b7Board of Governors Distinguished Professor Emerita of Chemistry and Chemical Biology

Research Synopsis: X-ray crystallographic and molecular modelling studies of biological molecules

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Research Summary

Proteomics April 2016 v2

From 1998-2014, I was the Director of the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). RCSB PDB is a member of the Worldwide Protein Data Bank (wwPDB) that manages the PDB archive of information about the structures of proteins, nucleic acids, and complex assemblies. I play a leadership role for the EMDataBank and am working to develop infrastructure for the archiving of structures determined using Integrative/Hybrid Methods.

The work on these projects has been informed by our research and studies in structural biology, in particular protein-nucleic acid interactions, collagen, binary and ternary complexes with catabolite activating protein (CAP), and nucleic acids. Currently, we are working in new classification schemes for transcription factors with a focus on understanding the details of the protein-nucleic acid interface.

Most recently I am working on how to use film to communicate to a broader audience about the importance of structural biology in medicine and health.

Selected References

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. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775702/)

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. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686438)

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. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472)

Schneider B, Berman HM. Hydration of the DNA bases is local. Biophys J. 1995 Dec;69(6):2661-9. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236503)

Bella J, Eaton M, Brodsky B, Berman HM. Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution. Science 1994 266:75-81. (http://www.ncbi.nlm.nih.gov/pubmed/7695699)

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. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1262208)

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