Conformation Types of Ubiquitin [M+8H]<sup>8+</sup> Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

Shi, Hui; Pierson, Nicholas A.; Valentine, Stephen J.; Clemmer, David E.

doi:10.1021/jp210797x

Cited by 94 publications

(191 citation statements)

References 81 publications

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“…48,49 Another series of studies involves changing the solution conditions to favor different solution states of ubiquitin to explore the correlations between the gas-phase IMS distributions and populations of different solution structures. 39,43,44 The present work is discussed in light of these prior results.…”

Section: Introductionmentioning

confidence: 75%

“…32–37 In general, ions of low charge states show conformations of similar size to their solution states. In the case of ubiquitin, the collision cross section (1010 Å 2 ) 38 of the compact conformation of [M+7H] 7+ ions is slightly smaller than the 1090 Å 2 value 39 calculated from coordinates of the crystal structure by the rigorous trajectory method. 28 For ions of higher charge states, the structures become more extended to reduce the repulsive Coulombic interactions.…”

Section: Introductionmentioning

confidence: 83%

“…Despite variances in conformations between the gas phase ion and the solution state, solution structures can be correlated to their counterparts in the gas phase. 39,42,43 Different solution structures can generate dissimilar gas-phase geometries.…”

Section: Introductionmentioning

confidence: 99%

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Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions

Shi

Atlasevich

Merenbloom

et al. 2014

J. Am. Soc. Mass Spectrom.

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The solution dependence of gas-phase unfolding for ubiquitin [M+7H]7+ ions has been studied by ion mobility spectrometry-mass spectrometry (IMS-MS). Different acidic water:methanol solutions are used to favor the native (N), more helical (A), or unfolded (U) solution states of ubiquitin. Unfolding of gas-phase ubiquitin ions is achieved by collisional heating and newly formed structures are examined by IMS. With an activation voltage of 100 V, a selected distribution of compact structures unfolds, forming three resolvable elongated states (E1-E3). The relative populations of these elongated structures depend strongly on the solution composition. Activation of compact ions from aqueous solutions known to favor N-state ubiquitin produces mostly the E1 type elongated state, whereas, activation of compact ions from methanol containing solutions that populate A-state ubiquitin favors the E3 elongated state. Presumably, this difference arises because of differences in precursor ion structures emerging from solution. Thus, it appears that information about solution populations can be retained after ionization, selection, and activation to produce the elongated states. These data as well as others are discussed.

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Section: Introductionmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 83%

See 1 more Smart Citation

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions

Shi

Atlasevich

Merenbloom

et al. 2014

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

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“…34,35 While the compact conformations are similar in size to the N-state and some of the elongated structures are comparable in size to the A-state, many are not. 31,36 Compact states have been found to be stable in the gas phase on the timescale of drift tube IMS measurements (tens of ms); however, after storage in an ion trap for 40 ms, a significant increase in the collision cross section was observed, indicating substantial annealing had occurred. 37 Other experiments employing analyses with relatively longer timescales on the order of tens of milliseconds to seconds (i.e.…”

Section: Introductionmentioning

confidence: 99%

Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry

Ridgeway

Silveira

Meier

et al. 2015

Analyst

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The present work employs trapped ion mobility spectrometry (TIMS) for the analysis of ubiquitin ions known to display a multitude of previously unresolved interchangeable conformations upon electrospray ionization. The conformational distributions of ubiquitin [M + 6H](6+) through [M + 13H](13+) ions observed by TIMS are nearly identical to numerous drift tube ion mobility spectrometry studies reported in the literature. At an experimental resolving power up to ∼300, many of the congested conformations within the well-known compact, partially folded, and elongated [M + 7H](7+) states are separated. Minimizing the voltages (RF and DC) in the entrance funnel results in exclusive observation of compact [M + 7H](7+) conformers. However, under these conditions, the mobility-dependent pseudopotential coefficient may discriminate against ions having larger collision cross sections-a universal effect for all RF ion guides, funnels, and traps operating in the presence of a gas. The data presented underscore the complications associated with direct comparison of collision cross section values that represent an ensemble average of multiple underlying conformations. As illustrated herein, the microheterogeneity within a particular conformational family and the relative state-to-state abundance can be altered by solvent memory, energetic, and kinetic effects.

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“…21 In addition, MS offers the unique capability to isolate and characterize particular structural components of proteins. [21][22][23][24][25] For these reasons, the application of ESI-MS has been extended to the analysis of structural transitions of proteins. Charge state distributions (CSDs) in the ESI-MS spectra of a protein may serve as an indicator of its structural transition in solution.…”

Section: Introductionmentioning

confidence: 99%

Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source

Lee

Kim

2015

Analyst

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The effect of acids on the structure of lysozyme (Lyz) during electrospray ionization (ESI) was studied by comparing the solution and gas-phase structures of Lyz. Investigation using circular dichroism spectroscopy and small-angle X-ray scattering demonstrated that the folded conformation of Lyz was maintained in pH 2.2 solutions containing different acids. On the other hand, analysis of the charge state distributions and ion mobility (IM) distributions, combined with molecular dynamics simulations, demonstrated that the gas phase structures of Lyz depend on the pKa of the acid used to acidify the protein solution. Formic acid and acetic acid, which are weak acids (pKa > 3.5), induce unfolding of Lyz during ESI, presumably because the undissociated weak acids provide protons to maintain the acidic groups within Lyz protonated and prevent the formation of salt bridges. However, HCl suppressed the formation of the unfolded conformers because the acid is already dissociated in solution, and chloride anions within the ESI droplet can interact with Lyz to reduce the intramolecular electrostatic repulsion. These trends in the IM distributions are observed for all charge states, demonstrating the significance of the acid effect on the structure of Lyz during ESI.

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Conformation Types of Ubiquitin [M+8H]⁸⁺ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

Cited by 94 publications

References 81 publications

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions

Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry

Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source

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Conformation Types of Ubiquitin [M+8H]8+ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

Cited by 94 publications

References 81 publications

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]7+ Ions

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]7+ Ions

Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry

Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source

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Product

Resources

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Conformation Types of Ubiquitin [M+8H]⁸⁺ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions

Solution Dependence of the Collisional Activation of Ubiquitin [M + 7H]⁷⁺ Ions