The Ims Paradox: A Perspective on Structural Ion Mobility‐mass Spectrometry

McCabe, Jacob W.; Hebert, Michael J.; Shirzadeh, Mehdi; Mallis, Christopher S.; Denton, Joanna K.; Walker, Thomas E.; Russell, David H.

doi:10.1002/mas.21642

Cited by 39 publications

(35 citation statements)

References 171 publications

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“…While we cannot completely rule out that some reactions may occur in the confined environment of the nano-droplets formed by ESI, evaporative cooling of the nanodroplets has been shown to be an effective mechanism for kinetically-trapping (freeze drying) 30 ions during the transition from solution to the gas-phase. 30,31 The relationships between ESI freeze drying and cryo-EM has been noted previously 18 and is supported by detection of intermediates and final products that are similar to those previously reported by Ranson et al using cryo-EM. 2 The similarities between results obtained using native MS and cryo-EM, 2, 32 underscore the potential utility of native MS for investigations of molecular machines as well as identification of key intermediates that may be involved in the chaperone-assisted protein folding cycle.…”

Section: Introductionsupporting

confidence: 84%

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Walker

Shirzadeh

Sun

et al. 2021

Preprint

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Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature-electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL/GroES complexes. The results show clear evidences for destabilization of both GroEL14 and GroES7 at temperatures of 50 oC and 45 oC, respectively, substantially below the previously reported melting temperature (Tm ~ 70 oC). This destabilization is accompanied by temperature-dependent reaction products that have previously unreport-ed stoichiometries, viz. GroEL14-GroESx-ATPy, where x = 1, 2, 8 and y = 0, 1, 2, that are also dependent on Mg2+ and ATP concentrations. Variable-temperature native mass spectrometry reveals new insights about the stability of GroEL in response to several environmental effects: (i) temperature-dependent ATP binding to GroEL (ii) effects of temperature as well as Mg2+ and ATP concentrations on the stoichiometry of the GroEL-GroES complex, with Mg2+ showing greater effects compared to ATP; and, (iii) a change in the temperature-dependent stoichiometries of the GroEL-GroES complex (GroEL14-GroES7 vs GroEL14-GroES8) between 24 to 56 oC. The similarities between results obtained using native MS and cryo-EM (Clare et al., An expanded protein folding cage in the GroEL-gp31 complex. J Mol Biol 2006, 358, 905-11; Ranson et al., Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes. Nat. Struct. Mol. Biol. 2006, 13, 147-152.) underscores the util-ity of native MS for investigations of molecular machines as well as identification of key intermediates involved in the chaperone-assisted protein folding cycle.

show abstract

Section: Introductionsupporting

confidence: 84%

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Walker

Shirzadeh

Sun

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…24 While we cannot completely rule out that some reactions may occur in the confined environment of the nano-droplets formed by ESI, evaporative cooling of the nanodroplets has been shown to be an effective mechanism for kinetically-trapping (freeze-drying) 29 ions during the transition from solution to the gas-phase. 29,30 The relationships between ESI freeze-drying and cryo-EM has been noted previously 17 and is supported by detection of intermediates and final products that are similar to those previously reported by Ranson et al using cryo-EM. 2 The similarities between results obtained using native MS and cryo-EM, 2,31 underscores the potential utility of native MS for investigations of molecular machines as well as identification of key intermediates that may be involved in the chaperone-assisted protein folding cycle.…”

Section: Introductionsupporting

confidence: 74%

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Walker

Shirzadeh

Sun

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature-electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL/GroES complexes. The results show clear evidences for de-stabilization of both GroEL14 and GroES7 at temperatures of 50 oC and 45 oC, respectively, substantially below the pre-viously reported melting temperature (Tm ~ 70 oC). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL14-GroESx-ATPy, where x = 1, 2, 8 and y = 0, 1, 2, that are also dependent on Mg2+ and ATP concentrations. Variable-temperature native mass spectrometry re-veals new insights about the stability of GroEL in response to several environmental effects: (i) temperature-dependent ATP binding to GroEL (ii) effects of temperature as well as Mg2+ and ATP concentrations on the stoichiome-try of the GroEL-GroES complex, with Mg2+ showing greater effects compared to ATP; and, (iii) a change in the temper-ature-dependent stoichiometries of the GroEL-GroES complex (GroEL14-GroES7 vs GroEL14-GroES8) between 24 to 56 oC. The similarities between results obtained using native MS and cryo-EM (Clare et al., An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-11; Ranson et al., Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes. Nat. Struct. Mol. Biol. 2006, 13, 147-152.) underscores the utility of native MS for investiga-tions of molecular machines as well as identification of key intermediates involved in the chaperone-assisted protein folding cycle.

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“…IM coupling with native MS can offer structural information, including stoichiometry and conformational change at the global level, for conformationally heterogeneous protein samples in the gas phase. Several reviews are available describing IM development, guidelines, and applications in structural studies [ 48 , 49 , 50 , 51 ]. IM-MS has been employed to study conformational changes induced by metal ion binding on α-synuclein [ 52 ], metallothionein [ 53 ], β2-microglobulin [ 54 ] and tau protein [ 55 ], among others.…”

Section: Qualitative Studies and Stoichiometry Determination By Ms-based Methodsmentioning

confidence: 99%

Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies

Yan-chun

Gross

2022

Biomolecules

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Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), “fast photochemical oxidation of proteins” (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including “protein–ligand interactions by mass spectrometry, titration and HD exchange” (PLIMSTEX) and “ligand titration, fast photochemical oxidation of proteins and mass spectrometry” (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.

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The Ims Paradox: A Perspective on Structural Ion Mobility‐mass Spectrometry

Cited by 39 publications

References 171 publications

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes

Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies

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