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Studying Protein–DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry

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Multiprotein Complexes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2247))

Abstract

Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein–DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.

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Acknowledgments

Czech Science Foundation projects 16-24309S and 16-20860S are gratefully acknowledged. Additional support was obtained from EU/MEYS projects BioCeV (CZ.1.05/1.1.00/02.0109) and NPU II (LQ1604). R.F. also thanks Charles University Grant Agency (project 1618218) and SVV260427/2019.

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Correspondence to Petr Man .

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Filandrova, R., Kavan, D., Kadek, A., Novak, P., Man, P. (2021). Studying Protein–DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry. In: Poterszman, A. (eds) Multiprotein Complexes. Methods in Molecular Biology, vol 2247. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1126-5_11

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  • DOI: https://doi.org/10.1007/978-1-0716-1126-5_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1125-8

  • Online ISBN: 978-1-0716-1126-5

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