Crystal structure of the human recombinant nucleosome (PDB ID: 2CV58), with cross-linked amino acids marked in red (close to DNA) and orange (distant to DNA).
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Atomic-resolution mapping of transcription factor-DNA interactions

Together with colleagues from the Department of Proteomics and Signal Transduction at the Max-Planck Institute of Biochemistry and several other academic institutions, ACP principal scientist Stefan Nolte has contributed with a femtosecond-laser-induced method to a recently published original research article titled "Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry" in Nature Communications (Reim et al, Nature Commun. 11, 3019 (2020).
Crystal structure of the human recombinant nucleosome (PDB ID: 2CV58), with cross-linked amino ...
Illustration: Nature Publishing Group.
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Published: 22 June 2020, 09:51 | By: Christian Helgert

Together with colleagues from the Department of Proteomics and Signal Transduction at the Max-Planck Institute of Biochemistry and several other academic institutions, ACP principal scientist Stefan Nolte has contributed with a femtosecond-laser-induced method to a recently published original research article titled "Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry" in Nature Communications (Reim et al, Nature Commun. 11, 3019 (2020).

In their work, the interdisciplinary team investigated how transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. The paper presents a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, the method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.

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