Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry. INTRODUCTIONLarge-scale interaction maps suggest a complex interplay of proteins within a myriad of functional assemblies 1,2 . A critical step in assigning functions to these assemblies is to determine their structure 3 . This goal is challenging, as many of these assemblies exist in low-copy numbers within cells, are frequently heterogeneous and may interact only transiently. Consequently, structural information for many protein complexes is not readily accessible by using the classical tools of structural biology (e.g., X-ray crystallography, nuclear magnetic resonance spectroscopy). New approaches are being developed that involve integrating data from a number of lower-resolution experimental methods and by combining distance and interaction restraints from these methods with homology modeling, architectural or even atomic models are being generated 4 . These restraints can be derived from a variety of experimental measurements including MS of intact complexes, chemical cross-linking, fluorescence resonance energy transfer, small angle X-ray scattering, and analytical ultracentrifugation 5,6 . One very recent addition to this series of biophysical tools is ion mobility separation coupled to mass spectrometry (IM-MS). IM is an established technique for studying shape and conformation in small molecules and individual proteins in the gas phase 7-10 but has only recently been applied to intact protein complexes 11,12 . When IM is coupled with MS, mass and consequently subunit composition can be determined simultaneously with the overall topology of protein complexes 10,12,13 .IM-MS analysis is performed by first ionizing the protein complex of interest. In our experiments, nano-electrospray ionization is used, typically requiring careful preparation procedures for most protein complexes. These procedures, as well as general practical aspects of sample preparation, are detailed in a protocol by Hernández and Robinson 14 . Although they are not discussed in detail here, knowledge of the materials and protocol steps described in that work are critical to the success of the protocol described below.After ionization, ions are injected into a region containing neutral gas at a controlled pressure (e.g., 0.5 mBar of nitrogen gas). Under the influence of a relatively weak electric field, injected ions undergo IM separation [7]...

Despite the significance of Alzheimer's disease, the link between metal-associated amyloid-β (metal-Aβ) and disease etiology remains unclear. To elucidate this relationship, chemical tools capable of specifically targeting and modulating metal-Aβ species are necessary, along with a fundamental understanding of their mechanism at the molecular level. Herein, we investigated and compared the interactions and reactivities of the green tea extract, (−)-epigallocatechin-3-gallate [(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate; EGCG], with metal [Cu(II) and Zn(II)]-Aβ and metal-free Aβ species. We found that EGCG interacted with metal-Aβ species and formed small, unstructured Aβ aggregates more noticeably than in metal-free conditions in vitro. In addition, upon incubation with EGCG, the toxicity presented by metalfree Aβ and metal-Aβ was mitigated in living cells. To understand this reactivity at the molecular level, structural insights were obtained by ion mobility-mass spectrometry (IM-MS), 2D NMR spectroscopy, and computational methods. These studies indicated that (i) EGCG was bound to Aβ monomers and dimers, generating more compact peptide conformations than those from EGCGuntreated Aβ species; and (ii) ternary EGCG-metal-Aβ complexes were produced. Thus, we demonstrate the distinct antiamyloidogenic reactivity of EGCG toward metal-Aβ species with a structurebased mechanism.amyloid-β peptide | metal ions | natural products | amyloidogenesis T he brain of individuals with Alzheimer's disease (AD) has protein aggregates composed of misfolded amyloid-β (Aβ) peptides (1-4). The Aβ peptides are produced endogenously through enzymatic cleavage of amyloid precursor protein. Aβ monomers can misfold and oligomerize into various intermediates before the formation and elongation of fibrils that exhibit a characteristic cross-β-sheet structure (1-4). The accumulation of aggregated Aβ species has been a key feature of the amyloid cascade hypothesis, which cites that these aggregates are possible causative agents in AD. In addition, transition metals, such as Cu and Zn, whose misregulation leads to aberrant neuronal function, have a suggested link to AD pathology (1,(3)(4)(5)(6)(7)(8). In vitro and in vivo studies have provided evidence for the direct interactions of metal ions with Aβ and their presence within Aβ plaques, indicating the formation of metal-associated Aβ (metal-Aβ) species. These metal-Aβ species have been implicated in processes that could lead to neurotoxicity (e.g., metal-induced Aβ aggregation and metal-Aβ-mediated reactive oxygen species generation) (1, 3-8). The involvement of metal-Aβ species in AD pathogenesis, however, has not been clearly elucidated. To advance our understanding of the potential neurotoxicity of metal-Aβ species, efforts to develop chemical tools capable of interacting directly with metal-Aβ species and modulating their reactivity in vitro and in biological systems are under way (1,(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)...

Tandem mass spectrometry (MS) of large protein complexes has proven to be capable of assessing the stoichiometry, connectivity, and structural details of multiprotein assemblies. While the utility of tandem MS is without question, a deeper understanding of the mechanism of protein complex dissociation will undoubtedly drive the technology into new areas of enhanced utility and information content. We present here the systematic analysis of the charge state dependent decay of the noncovalently associated complex of human transthyretin, generated by collision-induced dissociation (CID). A crown ether based charge reduction approach was applied to generate intact transthyretin tetramers with charge states ranging from 15+ to 7+. These nine charge states were subsequently analyzed by means of tandem MS and ion mobility spectrometry. Three different charge-dependent mechanistic regimes were identified: (1) common asymmetric dissociation involving ejection of unfolded monomers, (2) expulsion of folded monomers from the intact tetramer, and (3) release of C-terminal peptide fragments from the intact complex. Taken together, the results presented highlight the potential of charge state modulation as a method for directing the course of gas-phase dissociation and unfolding of protein complexes.

Recent applications of mass spectrometry (MS) in structural biology have highlighted its ability to define the stoichiometry of numerous protein complexes. [1,2] When combined with tandem MS, this extra dimension has made possible 1) analysis of polydisperse assemblies, [3] 2) characterization of release of proteins from within proteasome and chaperone complexes, [4,5] and 3) identification of proteins released from intact megadalton ribosomes.[6] Tandem MS is effective because macromolecular protein-complex ions decay through a mechanism that involves a dramatic transfer of charge to monomeric subunits prior to their ejection. This asymmetric dissociation acts to distribute the product ion spectrum over a large m/z range, thus enabling separation of ions with overlapping m/z values and identification of heterocomplexes from released subunits.It has been proposed that protein unfolding events are involved in the dissociation mechanism, [7][8][9] although direct evidence pertaining to the structure of the intermediates has not been reported. Ion mobility (IM)-MS, [10,11] a gas-phase technology that separates ions based on their size and shape, has been used to explore gas-phase protein folding, [12][13][14] oligonucleotide structures, [15] and noncovalent complexes. [16][17][18] Herein, we apply IM-MS to examine the activated form of a macromolecular complex. For our studies, we used the 56-kDa complex of tetrameric transthyretin (TTR), primarily because its gas-phase dissociation behavior has been studied extensively.[19] Our experiments were performed on a quadropole-ion mobility-time of flight (Q-IM-ToF) instrument (Synapt, Waters, Milford MA, USA, see the Experimental Section) using an IM separator that employs a series of low-voltage DC waves to push ions through a drift chamber filled with neutral molecules (0.5-1 mBar N 2 ).[20] The speed with which an ion traverses the drift region depends on its collision cross section (CCS); ions with larger CCSs proceed more slowly than ions with smaller ones.These drift times are then calibrated using protein ions of known CCS.[18] Subsequently, molecular modeling is used to generate a range of possible structures, and the CCSs for these models are calculated for comparison with experimental values.Mass spectra for TTR recorded under conditions designed either to maintain or to activate the intact oligomers (80 V or 150 V accelerating voltage, respectively, in the source region of the instrument) are shown (Figure 1 A, C). At 80 V, the minimum accelerating voltage for observation of massresolved protein-complex ions, peaks in the spectrum can be assigned to TTR tetramer and octamer. At 150 V, peaks corresponding to the octamer and tetramer persist; however, under these conditions monomeric subunits are also evident (Figure 1 C). This result indicates that a population of oligomeric TTR ions is undergoing the initial stages of dissociation and is therefore at an ideal stage for analysis of activated states of the complexes.IM data shows that without activation, both tet...

High-accuracy, high-resolution ion mobility measurements enable a vast array of important contemporary applications in biological chemistry. With the recent advent of both new, widely available commercial instrumentation and also new calibration datasets tailored for the aforementioned commercial instrumentation, the possibilities for extending such high performance measurements to a diverse set of applications have never been greater. Here, we assess the performance characteristics of a second-generation traveling-wave ion mobility separator, focusing on those figures of merit that lead to making measurements of collision cross-section having both high precision and high accuracy. Through performing a comprehensive survey of instrument parameters and settings, we find instrument conditions for optimized drift time resolution, cross-section resolution, and cross-section accuracy for a range of peptide, protein and multi-protein complex ions. Moreover, the conditions for high accuracy IM results are significantly different from those optimized for separation resolution, indicating that a balance between these two metrics must be attained for traveling wave IM separations of biomolecules. We also assess the effect of ion heating during IM separation on instrument performance.