Advanced mass spectrometry (MS) has capabilities to offer structural biologists layers of insight into the details of protein complexes. Mass measurements deliver information on stoichiometry of binding partners directly, even for multi-ligand hetero-complexes and molecular machines with masses well beyond 1 MDa. With electrospray ionization (ESI), MS can measure proteins and complexes from aqueous solution at near neutral pH, i.e., “native” MS. ESI’s gift for transforming solution-phase macromolecules into gas-phase ionized counterparts without disrupting covalent bonds and weak noncovalent interactions is key for applying MS to study protein complexes. Professor Fred McLafferty showed us how top-down mass spectrometry can be an effective tool for protein sequencing. We follow the path he cleared by using top-down high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS to probe ligand-binding sites and generate topological information for large proteins and complexes. We are using electron capture dissociation (ECD)/FT-ICR MS to investigate the molecular action of compounds that prevent amyloid fibril formation in neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. Native top-down MS generates information on the surface topology, ligand binding sites, and post-translational modifications of protein complexes and membrane proteins. We aim to relate the 3D architecture of the gas phase protein to the solution phase state as a means to further develop MS for structural biology. Native top-down MS should be one of several approaches to provide important data for an integrated approach to structural biology. Acknowledgments: Support from the US National Institutes of Health (R01GM103479, S10RR023045, S10RR028893) and the US Department of Energy is acknowledged.

Developing native top-down mass spectrometry as a tool for protein structural biology

249th National Meeting (2015)

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