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Ion Mobility-Mass Spectrometry to Evaluate the Effects of Protein Modification or Small Molecule Binding on Protein Dynamics

  • Lauren J. Tomlinson
  • Claire E. EyersEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2084)

Abstract

Ion mobility-mass spectrometry (IM-MS) of intact protein complexes under native conditions is a powerful tool for the analysis of protein complexes and protein–ligand interactions, permitting insight into ligand-induced changes in protein conformation. Here we describe a procedure for analyzing the effects of phosphorylation and/or inhibitor binding on protein kinase conformational flexibility using Protein Kinase A (PKA) as a model system. By calculating the protein collision cross section (CCS) before and after inhibitor binding, and additionally by performing collision-induced unfolding (CIU), we can establish the effects of protein modification or small molecule binding on protein dynamics.

Key words

Ion mobility-mass spectrometry Native mass spectrometry Collision cross section Collision-induced unfolding 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Biochemistry, Centre for Proteome Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK

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