Collision-Induced Unfolding Is Sensitive to the Polarity of Proteins and Protein Complexes
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J. Am. Soc. Mass Spectrom. (2019) DOI: 10.1007/s13361-019-02326-z
RESEARCH ARTICLE
Collision-Induced Unfolding Is Sensitive to the Polarity of Proteins and Protein Complexes Seoyeon Hong, Matthew F. Bush Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
Abstract. Collision-induced unfolding (CIU) uses ion mobility to probe the structures of ions of proteins and noncovalent complexes as a function of the extent of gas-phase activation prior to analysis. CIU can be sensitive to domain structures, isoform identities, and binding partners, which makes it appealing for many applications. Almost all previous applications of CIU have probed cations. Here, we evaluate the application of CIU to anions and compare the results for anions with those for cations. Towards that end, we developed a “similarity score” that we used to quantify the differences between the results of different CIU experiments and evaluate the significance of those differences relative to the variance of the underlying measurements. Many of the differences between anions and cations that were identified can be attributed to the lower absolute charge states of anions. For example, the extents of the increase in collision cross section over the full range of energies depended strongly on absolute charge state. However, over intermediate energies, there are significant difference between anions and cations with the same absolute charge state. Therefore, CIU is sensitive to the polarity of protein ions. Based on these results, we propose that the utility of CIU to differentiate similar proteins or noncovalent complexes may also depend on polarity. More generally, these results indicate that the relationship between the structures and dynamics of native-like cations and anions deserve further attention and that future studies may benefit from integrating results from ions of both polarities. Keywords: Ion mobility, Collision-induced unfolding, Protein structure Received: 24 April 2019/Revised: 11 August 2019/Accepted: 16 August 2019
Introduction
I
n native mass spectrometry (MS), native-like ions are generated using electrospray ionization of proteins, nucleic acids, lipids, and/or other biological molecules in aqueous solutions. Native-like ions can retain noncovalent interactions that were present in solution, and therefore, native MS can probe the oligomeric state [1], topology [2], and stability [3] of biomolecular complexes in solution. This information can be particularly valuable when the biomolecular complex is too
Electronic supplementary material The online version of this article (https:// doi.org/10.1007/s13361-019-02326-z) contains supplementary material, which is available to authorized users. Correspondence to: Matthew Bush; e-mail: [email protected]
large or small, heterogeneous, or dynamic for other structural tools such as nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy. For example, native MS of hepatitis B virus capsid proteins provides evidence for complete c
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