Predicting the Shapes of Protein Complexes Through Collision Cross Section Measurements and Database Searches

Abstract

In structural biology, collision cross sections (CCS) from ion mobility mass spectrometry (IM-MS) measurements are routinely compared to computationally or experimentally derived protein structures. Here, we investigate whether CCS data can inform about the shape of a protein in the absence of specific reference structures. Analysis of the proteins in the CCS database shows that protein complexes with low apparent densities are structurally more diverse than those with a high apparent density. Using the CCS, molecular weight, and oligomeric states to mine the Protein Data Bank (PDB) for potentially similar protein structures, we find that we can distinguish oblate- and prolate-shaped protein complexes. We then apply the strategy to an integral membrane protein by comparing the shapes of a prokaryotic and an eukaryotic sodium/proton antiporter homologue. We conclude that mining the PDB with IM-MS data is a time-effective way to derive low-resolution structural models.

Mass-selective and ice-free cryo-EM protein sample preparation via native electrospray ion-beam deposition

“…This result is consistent with previous IMS data, suggesting a gas-phase collapse of the apoferritin cavity and stabilization of holoferritin by the iron core. 52,53 Fig. 3d shows a micrograph of a GroEL sample.…”

Electrospray ionization of native membrane proteins proceeds via a charge equilibration step

“…[11][12][13][14] Bush et al have reported an average density of 0.63 g cm À3 based on dri-tube ion mobility MS measurements of nearspherical globular proteins. 15,16 The relationship between size, SASA, and therefore ESI charge, is well-established and predictable for soluble proteins.…”

Collision Cross Sections for Native Proteomics: Challenges and Opportunities

“…IM-MS is commonly used to interrogate the structures of purified proteins and protein complexes, 22−24 and is increasingly being utilized to assess the conformation of protein assemblies in the context of complex mixtures that remain refractory to other structural biology approaches. 25,26 While protein CCS prediction methodologies currently lag significantly behind those currently in use for small molecules and peptides, 27 the wide availability of structural data for individual proteins and their associated assemblies 28 allows for predictions to be made concerning the effectiveness of CCS values in the identification of such biomolecules within complex mixtures. In this perspective, I explore both the potential advantages and future challenges associated with IM-MS in native proteomics, as well as suggest future routes for the development of IM-MS methods aimed at comprehensive protein complex identification.…”