Research

Research in my laboratory is focused on understanding the molecular mechanisms and cellular functions of multisubunit assemblies that control the organization, preservation, and flow of genetic information. We are particularly interested in developing atomic-level models that explain how chemical energy is transduced into force and motion, and how dynamic assemblies control DNA replication, gene expression, chromosome superstructure, and other essential nucleic-acid transactions.

My group’s approach relies on a blend of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes. X-ray crystallography and traditional biochemistry have traditionally formed the core of our approach; however, we are increasingly merging these methods with other experimental tools such as small-angle X-ray scattering, single-molecule studies, and electron microscopy. Since the inception of the group in 1995, we have biochemically and structurally defined the range and nature of key functional intermediates and transitions for a variety of nucleotide-dependent ‘molecular machines,’ including topoisomerases, helicases, condensins, and replication initiation complexes.

Our efforts have allowed us to define how biological systems use these factors to organize, transport, and reshape target nucleic-acid substrates at a physical level, and how their actions are controlled by both protein-protein interactions and small-molecule agents. My lab has a consistent track record of bringing new concepts and fundamentally important discoveries to the field, and in innovating new approaches and technologies to studying multi-protein and protein/nucleic-acid assemblies in general. Training has been a similarly important facet of my efforts; to date, 22 doctoral students and 20 post-doctoral fellows have worked in my group. All who have left thus far have gone on to productive careers in academia (18), biotechnology/pharma (10), law (2), medicine (1), and consulting (1).

A complete list of our publications, excluding chapters and articles not accessed by PubMed, can be found at:http://www.ncbi.nlm.nih.gov/sites/myncbi/james.berger.1/bibliograpahy/40436728/public/?sort=date&direction=descending

Ongoing project areas:

Molecular control of DNA superstructure. The appropriate organization and management of chromosomal strands depends on the action of enzymes that modulate DNA supercoiling, looping, and topology. How these factors interact with target DNA segments to productively disentangle strands and actively control DNA twist and writhe is a long-standing issue in the field. We have helped establish how type IIA topoisomerases bind and cleave duplex DNA and how ATP binding and hydrolysis coordinate the passage of a second DNA segment through this break. We have also helped to define the evolution of different type II topoisomerase families, connecting one branch of this group to meiotic recombination processes, and have begun to establish how type II topoisomerases interface with SMC-family condensin type factors and are regulated by partner protein interactions.

Ring ATPase assembly and mechanism.  A myriad number of essential cellular processes, ranging from DNA replication and chromatin modeling to vesicle trafficking and proteolytic degradation, rely on oligomeric, ring-shaped ATPases for proper function. How a common class of ATPase folds can actively support such a broad number of systems and functions is a wide-ranging basic research question. My group has focused on understanding how certain hexameric members of the RecA and AAA+ ATPase superfamilies act as DNA and RNA motor proteins. We have helped define the structural basis of distinct ring-opening and ring-assembly mechanisms that permit the loading of proteins such as the Rho transcription termination factor and the E1, MCM2-7 and DnaB replicative helicases and onto target nucleic acid substrates, and we have helped defined the organization of higher-order helicase assemblies and how accessory factors assist in controlling motor function and mechanism. We also have shown how ATP binding and hydrolysis can be coupled to nucleic acid movement through a hexameric motor, and determined why RecA and AAA+-type hexameric helicases move DNA or RNA with the opposing (5′-3′ vs. 3′-5′) polarities.

Applied and Translational Research. Although a majority of my group’s research has focused on solving fundamental questions concerning the connection between macromolecular structure/function relationships and biology, we have also established a track record in developing innovative solutions to technical problems and in addressing practical issues, such as defining small molecule inhibitor mechanisms. For example, we helped co-develop (with Prof. Steve Quake, Stanford) the first microfluidic device for crystallizing nano-volume solutions of proteins and/or nucleic acids by free-interface diffusion, and have more recently (with Prof. Axel Brunger, Stanford) expanded on this method to develop microcrystal harvesting devices for use at synchrotron and XFEL sources. We created a high-throughput screening approach to trapping protein/DNA complexes through disulfide bond formation, and developed a novel fluorescent reporter for monitoring DNA supercoiling status in real time. We also have determined co-structures of certain nucleic acid-dependent motors bound to clinically used drugs. We anticipate continuing with these types of efforts as the need and opportunity arise, particularly in conjunction within the Chemical Therapeutics Program at the S. Kimmel Comprehensive Cancer Center, which I presently co-direct with Dr. Jun O. Liu.