Emodin The finding that a peptide consisting of d amino

The finding that a peptide consisting of d-amino acids binds to LSD1-CoREST1 with equal affinity as the l-amino Emodin ligand indicates that the assays detect a generally non-specific association between two highly charged molecules. Nonetheless, p53-CTD is an effective inhibitor of LSD1 and its binding to the enzyme is markedly and specifically reduced by a charge-reversal mutation (E379K), which is located on the outer rim of the LSD1 active site (Fig. 3). This protein region is rich in negatively-charged residues and was previously shown to represent the binding site for the potent polymyxin inhibitors [38]. Of notice, these peptide-like molecules feature a sequence that closely resembles the LSD1-binding sequence of p53-CTD. Collectively, these findings indicate that p53-CTD and the active site of LSD1 can be envisioned to form an encounter complex whose association is mostly mediated by non-specific electrostatic interactions. Such an encounter complex can potentially further promote more specific interactions between p53 and nucleosomal DNA and/or other proteins associated to LSD1-COREST1 core complex. This complex would also lead to the recruitment of LSD1 and associated partners such as histone deacetylases onto p53 target genes, inducing demethylation and/or other chromatin modifications in agreement with previous literature [17], [18], [19], [44]. At the same time, engagement by LSD1 can mask the positive charges on the CTD, thereby hampering the interaction of p53 with 53BP1 in agreement with published data [28]. Consistently with the idea of “association initiated by electrostatics”, the changes of post-translational modifications (i.e. change of surface charges) within the CTD represent an ideal tool to modulate binding affinities among several possible partners that can associate to the CTD. The essence of these processes is that a plethora of low-affinity binding events can occur, which are nonetheless finely tuned and all together contribute to the correct targeting.
Acknowledgments This work was supported by AIRC (IG-15208) and MIUR (Progetto Epigen).
Introduction Dynamic regulation of chromatin structure is necessary to allow for execution of processes that require access to DNA in response to physiological and environmental stimuli. Histones undergo several types of post-translational modifications, including methylation, acetylation, phosphorylation, ubiquitination, and SUMOylation, all of which can influence regulation of gene expression. Histone modifications can influence chromatin condensation, and poise genes for either transcriptional activation or repression, depending on how the modification is read and translated in a cell type specific context. While individual histone marks have been correlated with either active or silenced transcriptional states, many modifications have several, seemingly opposing roles, and the combination of marks as well as their genomic context appear to be essential for the biological output [1]. In particular, the methylation status of specific lysine residues on Histone H3 is involved in gene regulation. For instance, methylation on H3K4 and H3K36 is closely associated with transcritptional activation, whereas methylation on H3K9 and H3K27 correlates with gene silencing. Two enzyme superfamilies, lysine methyltransferases (KMTs) and demethylases (KDMs), regulate histone lysine methylation states. KDMs are currently categorized into two protein families based on the organization of their catalytic domains and the type of oxidative mechanism that underlies the demethylation reaction. The Jumonji (JmjC) domain-containing KDM family members utilize 2-oxoglutarate (2-OG; α-ketoglutarate) as a cofactor while KDM1A (LSD1, BHC110, AOF2) and KDM1B (LSD2) contain an aminoxidase domain and require FAD [2]. KDMs are usually selective for a given lysine residue and individual KDMs specifically catalyze the removal of methyl groups from tri-, di- and mono-methylated lysines. In addition to their catalytic domains, KDMs frequently harbor chromatin-, DNA- and protein–protein interaction domains and often function as part of multi-subunit protein complexes.