Michael J. Trnka

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading

This paper investigates the G9a-GLP heterodimer's feedback mechanism, showing that both ANK domains are required for H3K9 dimethylation and nucleosome binding, suggesting intranucleosomal feedback.

Liver CYP4A autophagic-lysosomal degradation (ALD): A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site

The paper identifies SQSTM1/p62 as a key autophagic receptor for CYP4A degradation, showing its role in preventing proinflammatory metabolite production and insoluble aggregates in liver cells.

An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA

This study identifies an intrinsically disordered region in KDM5A that binds the nucleosome's acidic patch and DNA, enabling catalytic activity through multivalent interactions.

A community audit of error control in crosslinking mass spectrometry

The paper audits error control in twelve crosslinking mass spectrometry pipelines using ground-truth designs, finding some pipelines exceed false discovery rates by up to 29-fold.