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Johns Hopkins University logoProgram in Molecular Biophysics
James BergerBerger Lab

Department of Biophysics and Biophysical Chemistry
School of Medicine

B.S. 1990, University of Utah
Ph.D. 1995, Harvard University

713 WBSB
725 N. Wolfe Street
Baltimore, MD 21205

Office: 410-955-7163


School of Medicine logo

My laboratory's research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information.  We are particularly interested in developing mechanistic models that explain how macromolecular machines transduce chemical energy into force and motion, and in determining how cells exploit these complexes and their activities for regulating the initiation of DNA replication, chromosome superstructure, and other essential nucleic acid transactions.  Our principal approaches rely on a variety of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes.  We also have extensive interests in mechanistic enzymology and the study of small-molecule inhibitors of therapeutic potential, the development of chemical approaches to trapping weak protein/protein and protein/nucleic acid interactions, and in using microfluidics for biochemical investigations of protein dynamics and structure.

Selected Publications

Strycharska, M.S., E. Arias-Palomo, A.Y. Lyubimov, J.P. Erzberger, V.L. O'Shea, C.J. Bustamante,  and J.M. Berger. (2013) Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell. 52(6):844-54.

Bleichert, F., M. Balasov, I. Chesnokov, E. Nogales, M.R. Botchan, and J.M. Berger. (2013) A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. Elife.  8;2:e00882.

Vos, S.M., N.K. Stewart, M.G. Oakley, and J.M. Berger. (2013) Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo. EMBO J. 13;32(22):2950-62.

Costa, A., I.V.Hood, and J.M. Berger. (2013) Mechanisms for initiating cellular DNA replication. Annu Rev Biochem. 82:25-54.

Arias-Palomo, E., V.L. O'Shea, I.V. Hood, and J.M. Berger. (2013) The Bacterial DnaC Helicase Loader Is a DnaB Ring Breaker. Cell. 153(2):438-48.

Wendorff, T.J., B.H. Schmidt, P. Heslop, C.A. Austin, and J.M. Berger. (2012) The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage. J Mol Biol.

Schmidt, B.H., N. Osheroff, and J.M. Berger. (2012) Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat Struct Mol Biol.

Lyubimov, A.Y., A. Costa, F. Bleichert, M.R. Botchan, and J.M. Berger. (2012) ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote. Proc Natl Acad Sci U S A. 109(30):11999-2004.

Duderstadt, K.E., K. Chuang, and J.M. Berger.  (2011) DNA stretching by bacterial initiators promotes replication origin opening. Nature. 478(7368):209-213.

Vos, S.M., E.M. Tretter, B.H. Schmidt, and J.M. Berger.  (2011) All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol. 12(12):827-841.

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