This section allows users to quickly find if a gene is within the surfaceome set

d methyltransferase fold, closes like a lid on the bound cofactor, but in the absence of SAM or SAH, this helix is partially disordered, which again alters the geometry and electrostatics of the cofactor pocket.18 Cell-penetrant SAM analogs that exploit this altered geometry may be able to inhibit CARM1 or other PRMTs. A sequential mechanism of substrate binding has been proposed for SET-domain HKMTs, whereby cofactor binding is necessary PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19812251 for proper folding of the Post-SET domain and formation of the substrate binding groove.16 A striking parallel can be made for PRMTs and DOT1L, where cofactor binding stabilizes the catalytically competent conformation of the secondary element immediately adjacent to the conserved methyltransferase fold. Whether this similarity in structural mechanism is driven by related evolutionary pressures remains an open question. Europe PMC Funders Author Manuscripts Europe PMC Funders Author Manuscripts 4. Conclusion We have shown here that addition of a single halogen atom can dramatically increase the potency of DOT1L inhibitors, and improve their selectivity versus other lysine, arginine, DNA and small molecule methyltransferases. The structural mechanism underlying these improved properties was dissected. This discovery, combined with chemical modifications at the homocystein end, provide a framework for future developments of DOT1L inhibitors. 5 Materials and Methods 5.1. Protein expression and purification A construct of human DOT1L covering residues 1-420 was subcloned into a modified pET28-MHL vector with an N-terminal His tag. The protein was overexpressed in E.coli BL21 V2R-pRARE in Terrific Broth medium in the presence of 50 g/ml of Bioorg Med Chem. Author manuscript; available in PMC 2016 March 07. Yu et al. Page 6 kanamycin and chloramphenicol. Cells were grown at 37C to an OD600 of 1.5, induced by isopropyl-1-thio-D-galactopyranoside and incubated overnight at 15C. The cell pellets were frozen in liquid nitrogen and stored at -80C. For purification, the cell paste was thawed and resuspended in lysis buffer with 1mM phenylmethyl sulfonyl fluoride. DOT1L was purified by Ni-NTA column and processed by TEV protease to remove the His tag. The protein was then incubated in 50 mM Tris-HCl pH 8.0, 0.1 mg/ml BSA, 1 mM MgCl2 with benzonase nuclease for 2 hours at room temperature. Filtered protein sample was diluted with 50 mMK2HPO4/ KH2PO4 pH 7.0, and further purified by HiTrap-SP. The protein was further purified by gel filtration. 5.2. Virtual screening Receptor preparation–The DOT1L-SAM complex structure was used. The receptor was prepared with Maestro Protein Preparation Wizard using default settings. One important structural water molecule W1025 was DMXB-A retained and included during docking. Protonation states were set at pH 7.4 using Epik. H-bond assignment was optimized by Protassign, including exhaustive sampling and minimization of hydrogens of altered species at neutral pH. Water orientation was also sampled for the conserved water molecule. The receptor was refined during Impref minimization with RMSD=0.3 Angstrom set for heavy atoms convergence under OPLS2005 forcefield. A receptor grid was centered on bound SAM. All hydroxyl groups accessible from the cofactor binding site were set rotatable. Chemical library–the ZINC clean-drug-like set containing 3.7 million commercially available compounds was used as ligand library for docking. The library was prepared with LigPrep during which protonation st