From relative (specificity) to absolute (affinity) quantification in interaction proteomics

3 May 2018

Biomolecules interact, and the strength of these interactions (i.e., their affinity) influences their molecular and cellular functions. Although many powerful techniques exist to measure binding affinities between biomolecules, mass spectrometry is unique in its ability to read out quantitative information for hundreds or thousands of proteins simultaneously.

Matthew Makowski (photo) and Cathrin Graewe, both researchers in the group of Michiel Vermeulen (Proteomics and Chromatin Biology), in a collaborative project with members of Till Bartke’s group from the Institute of Functional Epigenetics in Munich, recently described a new assay that leverages the unbiased, proteome-wide potential of the mass spectrometer to globally profile apparent binding affinities between proteins and DNA or nucleosomes. The study, titled “Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry”, was recently published in Nature Communications.

Of note, Vermeulen and colleagues quantified binding between canonical DNA motifs and transcription factors, observing that canonical motifs often bind many transcription factors with a variety of different affinities. In addition, they reported a novel high affinity interaction between chromatin associated protein complexes and a G-quadruplex DNA structure. In a final example, the authors studied how histone tail modifications regulate apparent binding affinities of chromatin associated protein complexes to nucleosomes.

In future work, the authors hope to use their assay to study how combinations of DNA motifs, DNA modifications, and histone modifications affect binding affinities of protein complexes to nucleosomes. The authors are also interested in quantitatively comparing transcription factor-DNA binding affinity with transcriptional output via next-generation sequencing and single-molecule approaches.