Nucleosome Binding by the Lysine Specific Demethylase 1 (LSD1) Enzyme Enables Histone H3 Demethylation.

The essential human enzyme lysine specific demethylase 1 (LSD1) silences genes by demethylating mono- and dimethylated lysine 4 in histone H3 (H3K4me1/2). Studies of the minimal requirements for LSD1 activity are complicated by the heterogeneity of histone modification states in cells. We overcame this challenge by generating homogeneous mononucleosome substrates containing semisynthetic H3K4me2. Biophysical and biochemical assays with full-length LSD1 revealed its ability to bind and demethylate nucleosomes. Consistent with a requirement for nucleosome binding prior to demethylation, a competing nucleosome-binding peptide from the high-mobility group protein effectively inhibited LSD1 activity. Thus, our studies provide the first glimpse of nucleosome demethylation by LSD1 in the absence of other scaffolding proteins.

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells.

The regulation of fundamental processes such as gene expression or cell differentiation involves chromatin states, demarcated by combinatorial histone post-translational modification (PTM) patterns. The subnuclear organization and dynamics of chromatin states is not well understood, as tools for their detection and modulation in live cells are lacking. Here, we report the development of genetically encoded chromatin-sensing multivalent probes, cMAPs, selective for bivalent chromatin, a PTM pattern associated with pluripotency in embryonic stem cells (ESCs). cMAPs were engineered from a set of PTM-binding (reader) proteins and optimized using synthetic nucleosomes carrying defined PTMs. Applied in live ESCs, cMAPs formed discrete subnuclear foci, revealing the organization of bivalent chromatin into local clusters. Moreover, cMAPs enabled direct monitoring of the loss of bivalency upon treatment with small-molecule epigenetic modulators. cMAPs thus provide a versatile platform to monitor chromatin state dynamics in live cells.

Why are the Interaction Energies of Charge-Transfer Complexes Challenging for DFT?

The description of ground state charge-transfer complexes is highly challenging. Illustrative examples include large overestimations of charge-transfer by local and semilocal density functional approximations as well as inaccurate binding energies. It is demonstrated here that standard density functionals fail to accurately describe interaction energies of charge-transfer complexes not only because of the missing long-range exchange as generally assumed but also as a result of the neglect of weak interactions. Thus, accounting for the missing van der Waals interactions is of key importance. These assertions, based on the evaluation of the extent of stabilization due to dispersion using both DFT coupled with our recent density-dependent dispersion correction (dDsC) and high-level ab initio computations, reflect the imperfect error-cancellation between the overestimation of charge-transfer and the missing long-range interactions. An in-depth energy decomposition analysis of an illustrative series of four small ambidentate molecules (HCN, HNC, HF, and ClF) bound together with NF3 provides the main conclusions, which are validated on a prototypical organic charge-transfer complex (i.e., tetrathiafulvalene-tetracyanoquinodimethane, TTF-TCNQ). We establish that the interaction energies for charge-transfer complexes can only be properly described when using well-balanced functionals such as PBE0-dDsC, M06-2X, and LC-BOP-LRD.