Wear, M. A. | Search bioRxiv

bioRxiv2025

MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation

Methyl-CpG-binding protein 2 (MeCP2) is an epigenetic reader essential for neuronal function, but how it binds DNA methylation within chromatin is unclear. Using designer nucleosomes we observe that MeCP2 preferentially engages DNA methylation positioned at multiple sites around the nucleosome. Surprisingly, MeCP2 can bind methylated DNA in bent, histone-contacting core nucleosomal DNA. However, this activity requires additional DNA linker interactions, using MeCP2 regions beyond its canonical methyl binding domain. We mapped a novel DNA-binding region in MeCP2 required for this function. Furthermore, histone H1 antagonises the MeCP2-nucleosome interaction by competing for linker DNA. Overall, this reveals that MeCP2 combines nonspecific but essential interactions with linker DNA to aid specific binding to nucleosomal methylated DNA, independent of nucleosome structure. Our findings reveal a novel contribution to full MeCP2 function, and mechanistic insight into how this clinically important protein interacts with chromatin.

biochemistry↗

bioRxiv2017

Pushing The Limits Of Detection Of Weak Binding Using Fragment Based Drug Discovery: Identification Of New Cyclophilin Binders

Fragment Based Drug Discovery (FBDD) is an increasingly popular method to identify novel small-molecule drug candidates. One of the limitations of the approach is the difficulty of accurately characterizing weak binding events. This work reports a combination of X-ray diffraction, surface plasmon resonance (SPR) experiments and molecular dynamics (MD) simulations, for the characterisation of binders to different isoforms of the cyclophilin (Cyp) protein family. Although several Cyp inhibitors have been reported in the literature, it has proven challenging to achieve high binding selectivity for different isoforms of this protein family. The present studies have led to the identification of several structurally novel fragments that bind to diverse Cyp isoforms in distinct pockets with low millimolar dissociation constants. A detailed comparison of the merits and drawbacks of the experimental and computational techniques is presented, and emerging strategies for designing ligands with enhanced isoform specificity are described.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/136101_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@5d2d48org.highwire.dtl.DTLVardef@147f922org.highwire.dtl.DTLVardef@356562org.highwire.dtl.DTLVardef@1933853_HPS_FORMAT_FIGEXP M_FIG C_FIG Research Highlights O_LIFBDD is a popular method but weak binding is difficult to detect\nC_LIO_LIThere is a need for pushing the limits of weak binding detection\nC_LIO_LICombination of X-ray, SPR and MD methodologies increases successful characterization of weak binding events\nC_LIO_LISeveral novel Cyclophilin fragment binders were identified\nC_LI

biophysics↗