Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics Simulation Study

Sever, Alexander I M; Konermann, Lars

doi:10.1021/acs.jpcb.0c01934

Cited by 16 publications

(30 citation statements)

References 96 publications

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“…Radius of gyration vs. time plots revealed that relaxation was complete after ∼30 ns (Figure 3B). In agreement with previous work, 59,88 heatunfolded chains were relatively compact, highly dynamic, showed occasional loose clustering of hydrophobic side chains but did not possess any persistent secondary or tertiary structure. In other words, the relaxation runs of Figure 3 did not cause refolding, which would require much longer time scales (microseconds to seconds) and lower temperatures.…”

Section: ■ Results and Discussionsupporting

confidence: 93%

“…The temperature was then ramped from 300 to 1000 K over 100 ns. As demonstrated previously, 88 the highly charged (33+) chains adopted near-linear conformations that did not retain any memory of the native state (Figure 3A, t = 0). Heme was not included, reflecting the labile nature of heme-protein contacts under denaturing conditions, 5 specifically during thermal unfolding.…”

Section: ■ Results and Discussionsupporting

confidence: 70%

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Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin

Tajoddin

Scrosati

et al. 2021

J. Phys. Chem. B

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Proteins that encounter unfavorable solvent conditions are prone to aggregation, a phenomenon that remains poorly understood. This work focuses on myoglobin (Mb) as a model protein. Upon heating, Mb produces amorphous aggregates. Thermal unfolding experiments at low concentration (where aggregation is negligible), along with centrifugation assays, imply that Mb aggregation proceeds via globally unfolded conformers. This contrasts studies on other proteins that emphasized the role of partially folded structures as aggregate precursors. Molecular dynamics (MD) simulations were performed to gain insights into the mechanism by which heat-unfolded Mb molecules associate with one another. A prerequisite for these simulations was the development of a method for generating monomeric starting structures. Periodic boundary condition artifacts necessitated the implementation of a partially immobilized water layer lining the walls of the simulation box. Aggregation simulations were performed at 370 K to track the assembly of monomeric Mb into pentameric species. Binding events were preceded by multiple unsuccessful encounters. Even after association, protein−protein contacts remained in flux. Binding was mediated by hydrophobic contacts, along with salt bridges that involved hydrophobically embedded Lys residues. Overall, this work illustrates that atomistic MD simulations are well suited for garnering insights into protein aggregation mechanisms.

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Section: ■ Results and Discussionsupporting

confidence: 93%

Section: ■ Results and Discussionsupporting

confidence: 70%

Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin

Tajoddin

Scrosati

et al. 2021

J. Phys. Chem. B

Self Cite

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“…Equilibrium gas-phase structures of native like proteins give an "inside-out" orientation, with the hydrophobic interior being refolded to the surface of the protein and the external, more hydrophilic portion towards the interior. 67 Therefore, our results, along with of other gas-phase evidence, suggest that kinetically trapped solution-like states are preserved over a typical MS timescale and that inside-out gas-phase equilibrium structures are not populated. The application of a mobility separation prior to ECD allows HDX to be determined as a function of conformational family, a key aspect of this workflow versus workflows that employ fragmentation prior to mobility separation, perform HDX in the mobility cell itself, require post-mobility trapping, or do not have ion mobility.…”

Section: Discussionsupporting

confidence: 62%

Multiplexed Conformationally-Selective, Localized Gas-Phase Hydrogen Deuterium Exchange of Protein Ions Enabled by Transmission-Mode Electron Capture Dissociation

Chaturvedi

Webb

2021

Preprint

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In this article, we present an approach for conformationally multiplexed localized hydrogen deuterium exchange (HDX) of gas-phase protein ions facilitated by ion mobility (IM) followed by electron capture dissociation (ECD). A quadrupole-ion mobility-time of flight instrument previously modified to enable ECD in transmission mode (without ion trapping) immediately following a mobility separation was further modified to allow for deuterated ammonia (ND3) to be leaked in after m/z selection. Collisional activation was minimized to prevent deuterium scrambling from giving structurally irrelevant results. This arrangement was demonstrated with the extensively studied protein folding models ubiquitin and cytochrome c. Ubiquitin was ionized from conditions that stabilize the native state and conditions that stabilize the partially-folded A-state. IM of deuterated ubiquitin 6+ ions allowed the separation of more compact conformers from more extended conformers. ECD of the separated subpopulations revealed that the more extended (later arriving) conformers had significant, localized differences in the amount of HDX observed. The 5+ charge state showed greater protection against HDX than the compact 6+ conformer, and the 11+ charge state, ionized from conditions that stabilize the A-state, showed much greater deuterium incorporation. The 7+ ions of cytochrome c ionized from aqueous conditions showed greater HDX with exterior and more unstructured regions of the protein, while interior, structured regions, especially those involved in heme binding, were more protected against exchange. These results, as well as potential future methods and experiments, are discussed herein.

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“…25,28 Thus, the question of whether gas-phase protein structures correlate with those in solution has been widely investigated. 29 The loss of water molecules may disrupt the balance between hydration and intramolecular protein interactions during transfer of proteins from solution to the gas phase. Soft ionization of ESI has been reported to generate desolvated protein ions whose solution structure features are retained by kinetic trapping.…”

Section: Introductionmentioning

confidence: 99%

“…Ion mobility mass spectrometry (IM-MS) coupled with electrospray ionization (ESI) enables the characterization of ion structures in the gas phase. − The experimental collisional cross section (CCS) supported by theoretical three-dimensional modeling is the principal means of characterizing gas-phase ion structures. Electrostatic interactions, which are substantially moderated in high dielectric solvents such as water, dominate protein structures in the gas phase. , Thus, the question of whether gas-phase protein structures correlate with those in solution has been widely investigated . The loss of water molecules may disrupt the balance between hydration and intramolecular protein interactions during transfer of proteins from solution to the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Ion Mobility Mass Spectrometry Analysis of Oxygen Affinity-Associated Structural Changes in Hemoglobin

Heo

Kim

Son

et al. 2021

J. Am. Soc. Mass Spectrom.

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Hemoglobin (Hb) is a major oxygen-transporting protein with allosteric properties reflected in the structural changes that accompany binding of O2. Glycated hemoglobin (GHb), which is a minor component of human red cell hemolysate, is generated by a nonenzymatic reaction between glucose and hemoglobin. Due to the long lifetime of human erythrocytes (∼120 days), GHb is widely used as a reliable biomarker for monitoring long-term glucose control in diabetic patients. Although the structure of GHb differs from that of Hb, structural changes relating to the oxygen affinity of these proteins remain incompletely understood. In this study, the oxygen-binding kinetics of Hb and GHb are evaluated, and their structural dynamics are investigated using solution small-angle X-ray scattering (SAXS), electrospray ionization mass spectrometry equipped with ion mobility spectrometry (ESI-IM-MS), and molecular dynamic (MD) simulations to understand the impact of structural alteration on their oxygen-binding properties. Our results show that the oxygen-binding kinetics of GHb are diminished relative to those of Hb. ESI-IM-MS reveals structural differences between Hb and GHb, which indicate the preference of GHb for a more compact structure in the gas phase relative to Hb. MD simulations also reveal an enhancement of intramolecular interactions upon glycation of Hb. Therefore, the more rigid structure of GHb makes the conformational changes that facilitate oxygen capture more difficult creating a delay in the oxygen-binding process. Our multiple biophysical approaches provide a better understanding of the allosteric properties of hemoglobin that are reflected in the structural alterations accompanying oxygen binding.

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Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics Simulation Study

Cited by 16 publications

References 96 publications

Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin

Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin

Multiplexed Conformationally-Selective, Localized Gas-Phase Hydrogen Deuterium Exchange of Protein Ions Enabled by Transmission-Mode Electron Capture Dissociation

Ion Mobility Mass Spectrometry Analysis of Oxygen Affinity-Associated Structural Changes in Hemoglobin

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