Flavin-dependent histone demethylases catalyze the posttranslational oxidative demethylation of mono- and dimethylated lysine residues, producing formaldehyde and hydrogen peroxide in addition to the corresponding demethylated protein. In vivo, the histone demethylase LSD1 (KDM1; BCH110) is a component of the multiprotein complex that includes histone deacetylases (HDACs 1/2) and the scaffolding protein CoREST. Although little is known concerning the affinities of or the structural basis for the interaction between CoREST and HDACs, the structure of CoREST286–482 bound to an alpha helical coiled-coil tower domain within LSD1 has been recently reported. Given the significance of CoREST in directing demethylation to specific nucleosomal substrates, insight into the molecular basis of the interaction between CoREST and LSD1 may suggest a new means to inhibit LSD1 activity by misdirecting the enzyme away from nucleosomal substrates. Towards this end, isothermal titration calorimetry studies (ITC) were conducted to determine the affinity and thermodynamic parameters characterizing the binding interaction between LSD1 and CoREST286–482. The proteins tightly interact in a 1:1 stoichiometry with a dissociation constant (Kd) of 15.9 ± 2.07 nM, and their binding interaction is characterized by a favorable enthalpic contribution near room temperature with a smaller entropic penalty at pH 7.4. Additionally, one proton is transferred from the buffer to the heterodimeric complex at pH 7.4. From the temperature dependence of the enthalpy change of interaction, a constant pressure heat capacity change (ΔCp) of the interaction was determined to be −0.80 ± 0.01 kcal/mol·K. Notably, structure-driven truncation of CoREST revealed that the central binding determinant lies within residues 293–380, also known as the CoREST ‘linker’ region, which is a central isolated helix that interacts with the LSD1 coiled-coil tower domain to create a triple helical bundle. Thermodynamic parameters obtained from the binding between LSD1 and the linker region293–380 of CoREST are similar to those obtained from the interaction between LSD1 and CoREST286–482. These results provide a framework for understanding the molecular basis of protein-protein interactions that govern nucleosomal demethylation.

We developed a high-throughput yeast-based assay to screen for chemical inhibitors of Ca 2+ / calmodulin-dependent kinase pathways. After screening two small libraries we identified the novel antagonist 125-C9, a substituted ethyleneamine. In vitro kinase assays confirmed that 125-C9 inhibited several CaMKs competitively with Ca 2+ /CaM. This suggested that 125-C9 acted as an antagonist for Ca 2+ /CaM rather than for CaMKs. We confirmed this hypothesis by showing that 125-C9 binds directly to Ca 2+ /CaM using isothermal titration calorimetry. We further characterized 125-C9 binding to Ca 2+ /CaM and compared its properties with those of two well-studied CaM antagonists: trifluoperazine (TFP) and W-13. Isothermal titration calorimetry revealed that 125-C9 binding to CaM is absolutely Ca 2+ -dependent, likely occurs with a stoichiometry of five 125-C9 molecules to one CaM molecule, and involves an exchange of two protons at pH 7.0. Binding of 125-C9 is driven overall by entropy and appears to be competitive with TFP and W-13, which is consistent with occupation of similar binding sites. To test the effects of 125-C9 in living cells, we evaluated mitogen-stimulated re-entry of quiescent cells into proliferation and found similaralthough slightly better -levels of inhibition by 125-C9 than TFP and W-13. Our results not only define a novel Ca 2+ /CaM inhibitor but reveal that chemically unique CaM antagonists can bind CaM by distinct mechanisms but similarly inhibit cellular actions of CaM. KeywordsCalmodulin antagonist; trifluoperazine; W-13; isothermal titration calorimetry; calmodulin binding Calcium (Ca 2+ ) is a major cell signaling transducer that links cell stimuli to specific cell responses. A ten-fold increase in cytoplasmic Ca 2+ levels from 100 nM to 1 μM is a common response to a variety of cell stimuli, resulting in Ca 2+ binding to a variety of calcium binding proteins (1). One of the most prominent calcium binding proteins is calmodulin (CaM), which is evolutionarily conserved amongst all eukaryotic organisms. CaM contains four Ca 2+ binding EF-hand motifs and undergoes conformational changes upon binding of four Ca 2+ molecules. Consequently, two hydrophobic domains of CaM become exposed to the solvent -one on the N-terminal and one on the C-terminal domain -markedly increasing the affinity of Ca 2+ /CaM means001@mc.duke.edu. SUPPORTING INFORMATION AVAILABLE Supporting information includes Extended Experimental Procedures with a description of the synthesis of 125-C9 (Scheme 1S), an example of ITC raw power output of 125-C9 with CaM ( Figure 1S), yeast growth inhibition from the screening process ( Figure 2S), ITC analysis of 125-C9 with CaMKI ( Figure 3S), summary of IC 50 values for 125-C9 on different CaMK (Table 1S), list of χ 2 values for 125-C9 binding to CaM (Table 2S), summary of thermodynamic parameters for 125-C9, TFP and W-13 (Table 3S), and summary of K a values in competition assays (Table 4S). This material is available free of charge via the Internet at http://pubs.acs.org. NIH...

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