Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry Histone post-translational modifications (PTMs) often serve as distinct recognition sites for the recruitment of chromatin-associated proteins (CAPs) for epigenome regulation. While CAP:PTM interactions are extensively studied using histone peptides, this cannot represent the regulatory potential of multisite binding on intact nucleosomes. To overcome this limitation, we applied Nucleosome Mass Spectrometry (Nuc-MS), a native Top-Down MS approach that enables the controlled disassembly and proteoform analysis of CAP:nucleosome (CAP:nuc) complexes. As proof of principle, we show the BPTF plant homeodomain (PHD)-bromodomain (BD) native tandem reader binds synergistically to both PTM classes in fully defined ([H3K4me3K9acK14acK18ac]2) nucleosomes. We then extend to explore the engagement of BRD4 (native BD1-BD2), DNMT3A-MPP8 (chimeric PWWP-CD), and Populus trichocarpa Short Half Life (PtSHL) (native bromodomain-adjacent homology (BAH-PHD) tandem readers with endogenous HeLa nucleosomes. In the resulting enrichment profiles, BRD4 favors di- and triacetylated histone H4 proteoforms, whereas DNMT3A-MPP8 and PtSHL recover distinct hypermethylated H3 proteoforms. Of note, PtSHL enriches a potential {H3K4me3K27me3} cis combinatorial that expands the biology of this bivalent signature previously only described in trans. By directly characterizing CAP:nuc complex composition, Nuc-MS informs on the nucleoforms driving binding and thus identifies primary candidates for direct biochemical, structural, and genomic studies.

Direct Readout of Multivalent Chromatin Reader-Nucleosome Interactions by Nucleosome Mass Spectrometry #ACSCentSci pubs.acs.org/doi/10.1021/...

#RobSelects paper of the week #ACSCentSci: Systematic statistical analysis of 66,000 organic reactions from high-throughput experiments representative of pharmaceutical drug discovery. #orgchem https://doi.org/10.1021/acscentsci.5c02031

A Small Molecule Drug-Based Ru(II) Polypyridine Mass-Tag for Multimodal Imaging of Tissue Samples Mass spectrometry imaging (MSI) is a powerful tool for spatially resolved multiomics analysis of tissue samples in clinical research. However, its proteomics application is still limited due to challe...

A Small Molecule Drug-Based Ru(II) Polypyridine Mass-Tag for Multimodal Imaging of Tissue Samples #ACSCentSci #MassSpec pubs.acs.org/doi/10.1021/...

Revealing Anisotropic Growth of Liraglutide Oligomers by Native Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation Oligomerization is an intriguing problem, particularly at the early stages of soluble prefibril oligomer formation, where the growth mechanisms of these species remain difficult to study due to their ...

Revealing Anisotropic Growth of Liraglutide Oligomers by Native Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation #ACSCentSci pubs.acs.org/doi/10.1021/...

Direct (LC-)MS Identification of Regioisomers from C–H Functionalization by Partial Isotopic Labeling C–H functionalization of complex substrates is highly enabling in total synthesis and in the development of late-stage drug candidates. Much work has been dedicated to developing new methods as well as predictive modeling to accelerate route scouting. However, workflows to identify regioisomeric products are arduous, typically requiring chromatographic separation and/or nuclear magnetic resonance spectroscopy analysis. In addition, most reports focus on major products or do not assign regioisomeric products, which biases predictive models constructed from such data. Herein, we present a novel approach to complex reaction analysis utilizing partial deuterium labels, which enables direct product identification via liquid chromatography–mass spectrometry. When combined with spectral deconvolution, the method generates product ratios while circumventing chromatography altogether. Competitive kinetic isotope effects can also be determined. The resultant data are expected to be useful in the construction of predictive models across several dimensions including reaction selectivity, the impact of structure on mechanism, and mass spectral ionization patterns and expedite the identification of drug metabolites.

Direct (LC-)MS Identification of Regioisomers from C-H Functionalization by Partial Isotopic Labeling #ACSCentSci pubs.acs.org/doi/10.1021/...

#RobSelects paper of the week #ACSCentSci: Automated flow-based platform for high-throughput optimization of triplet-triplet annihilation photon upconversion of sensitizer-annihilator mixtures. #autochem https://doi.org/10.1021/acscentsci.4c02059