Researchers can nominate targets and view the 10 most recent protein structures on the Community Nominated Targets page of the SBKB. More solved structures can be viewed in the SBKB’s new Discoveries Hub at http://sbkb.org/discoveries/.
When solving a complex problem such as elucidating the mechanisms of epigenetic regulation, many perspectives are welcome. As Principal Investigator of the PSI:Biology High-Throughput Enabled Structural
Biology Partnership, Chaperone-Enabled Studies of Epigenetic Regulation Enzymes CEBS, Anthony Kossiakoff, has assembled a team of researchers to tackle the many facets of this important biological phenomenon. Dr. Kossiakoff, Otho S. A. Sprague Professor in the Department of Biochemistry and Molecular Biology at
the University of Chicago, drew from North America
and the United Kingdom to build the CEBS Partnership. In addition to Dr. Marcin Paduch in the Kossiakoff Lab, CEBS includes Shohei Koide (University of Chicago), Sachdev Sidhu (University of Toronto), Sean
Taverna (Johns Hopkins University), Cheryl Arrowsmith (University of Toronto), Song Tan (The
Pennsylvania State University), and Udo Oppermann (Oxford University). CEBS also draws heavily on collaborative arrangements with the
Northeast Structural Genomics Center (NESG) and the Structural Genomics Consortium (SGC).
The overarching goals of the CEBS Partnership are to study the structural basis for how histone modification enzymes perform their functional roles in myriad aspects of gene regulation including DNA replication, repair, and recombination, as well as gene silencing, genomic imprinting, and RNA processes. These enzymes generally function as integral parts of large multi-protein complexes that work in concert to read, write, and erase post-translational modification on histone tails. Because of the fundamental importance of these epigenetic regulation systems in disease and virtually all aspects of cell development, extensive efforts have been made to learn how these processes work at the molecular level. Unfortunately, progress has been frustrated by the lack of suitable reagents to study them in any significant detail. To overcome this barrier, the CEBS team has assembled a high-throughput phage display pipeline that enables the generation of synthetic antibodies (sABs) that can be used as customized affinity reagents for the epigenetic modifying enzymes, as well as their associated binding partners. This sAB pipeline has been described in detail by Paduch, et al., 2012. sABs are produced using high performance phage display library selections and can target particular surface sites on a target protein, trap functionally important conformational states, and capture and stabilize specific forms of multi-protein complexes. These binders function as chaperones for crystallization and phase determination, as well as customized affinity reagents for cell biology applications. Additionally, CEBS has developed technology to allow delivery of functional sABs into live cells Rizk, et al., 2012). In vivo, they co-localize with their target proteins and can be used as highly specific imaging agents, inhibitors, and perturbers of protein-protein interactions to facilitate functional studies.
To study these various structural and biological applications, Dr. Kossiakoff has built an extensive collaborative network that includes protein engineers, structural biologists, and cell biologists from PSI:Biology Centers, NIH centers, and various research institutions. These researchers are applying the use of chaperones to their studies of various epigenetic regulation enzymes. sABs will be the focus of a larger study conducted with PSI:Biology High-Throughput Center for Structure Determination NESG to determine the optimal number of sABs needed to ensure crystallization of a target. NESG has solved four epigenetic protein target structures identified by CEBS, as well as two from community nominated target collaborations.
More information about the technology developed by the CEBS Partnership can be found in the Featured Technology article, “Chaperone-Enabled Structural Biology.” The work being done by NESG was highlighted in a 2012 Center Profile.
*Structure shown: Maltose-bound MBP with a conformationally specific synthetic antigen binder (sAB) from Rizk SS, Paduch M, Heithaus JH, Duguid EM, Sandstrom A, Kossiakoff AA. “Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.” Nat. Struct. Mol. Biol. 18: 437-442 (2011). PubMed: 21378967 | PubMedCentral Link