The overarching goal of this project is to elucidate the molecular mechanism governing the catalysis and regulation of histone modification enzymes. We will use our Chaperone-Enabled Biology and Structure (CEBS) technology platform to study an important, but challenging group of epigenetic regulating enzymes. The lysine-specific histone methyltransferases (HMT) and their complementary partners, lysine demethylases (KDM) function as key mediators of epigenetic signaling through their actions as """"""""writers and erasers"""""""" of post-translational modifications on histone proteins. Numerous recent studies have highlighted the importance of lysine methylation of histones leading to direct impact on DNA replication, repair, recombination, gene silencing, imprinting and RNA processes making these enzymes potential key targets for drug development. However, progress in gaining fundamental knowledge about structure-function relationships governing their modes of operation has been slow because they are multidomain proteins and have been recalcitrant to both structural and functional analyses. To overcome the existing barriers, we will generate specialized reagents called """"""""synthetic affinity binders"""""""" or sABs that will be used as chaperones for crystallization, as well as customized affinity reagents for cell biologically applications. To accomplish our objectives we have assembled a world-class team of investigators that will exploit sAB reagents for both structure determination and high level biological assays. A major emphasis of our approach is to identify and structurally/biochemically characterize the molecular complexes in which the HMTs and KDMs function by using sABs that stabilize and enhance crystallization of the complexes. Thus, CEBS effort will rely on close ties to the large high throughput centers for protein production and structure determination of individual enzymes in multiple conformational states, enzyme-substrate complexes and multiprotein complexes. A unique strength of our approach is that we will provide crystallization chaperones and the information on interaction partners to the high throughput centers to greatly increase the probability of success of structure determination.

Public Health Relevance

Lysine-specific histone methyltransferases and histone demethylases are critical enzymes in the epigenetic regulation of DNA replication and repair, as well as recombination and gene expression and repression. Mutations in these enzymes have been implicated in a number of diseases. These studies will provide the biological rationale and structural basis for drug development.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-CBB-0 (BC))
Program Officer
Edmonds, Charles G
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Chicago
Schools of Medicine
United States
Zip Code
Bailey, Lucas J; Sheehy, Kimberly M; Dominik, Pawel K et al. (2018) Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J Mol Biol 430:337-347
Mukherjee, Somnath; Griffin, Dionne H; Horn, James R et al. (2018) Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins. J Biol Chem 293:2815-2828
Sun, Jian; Paduch, Marcin; Kim, Sang-Ah et al. (2018) Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Proc Natl Acad Sci U S A 115:10010-10015
Schaefer, Zachary P; Bailey, Lucas J; Kossiakoff, Anthony A (2016) A polar ring endows improved specificity to an antibody fragment. Protein Sci 25:1290-8
Dominik, Pawel K; Borowska, Marta T; Dalmas, Olivier et al. (2016) Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure 24:300-9
Galilee, Meytal; Britan-Rosich, Elena; Griner, Sarah L et al. (2016) The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Structure 24:1936-1946
Stuwe, Tobias; Correia, Ana R; Lin, Daniel H et al. (2015) Nuclear pores. Architecture of the nuclear pore complex coat. Science 347:1148-52
Dominik, Pawel K; Kossiakoff, Anthony A (2015) Phage display selections for affinity reagents to membrane proteins in nanodiscs. Methods Enzymol 557:219-45
Stuwe, Tobias; Bley, Christopher J; Thierbach, Karsten et al. (2015) Architecture of the fungal nuclear pore inner ring complex. Science 350:56-64
Borowska, Marta T; Dominik, Pawel K; Anghel, S Andrei et al. (2015) A YidC-like Protein in the Archaeal Plasma Membrane. Structure 23:1715-1724

Showing the most recent 10 out of 29 publications