Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins

Brodmerkel, Maxim N.; Santis, Emiliano De; Uetrecht, Charlotte; Caleman, Carl; Marklund, Erik

doi:10.1016/j.crstbi.2022.10.001

Cited by 8 publications

(21 citation statements)

References 79 publications

(123 reference statements)

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“…Longer rehydration time could lower the differences between rehydration and the control solution simulations. Consequently, as these structural changes are shown to be largely reversible, as published in literature [28,29], this study finds that dipole-orientation with EF up to a well-chosen strength does not on its own introduce irreversible conformational rearrangements and changes.…”

Section: Average Collision Cross Section (Ccs) [å 2 ]supporting

confidence: 67%

“…trol solution simulations (figures S1-S4); both in vacuum and in the control solution most elements are close to one or zero, indicating stable contacts, whereas the rehydrated systems have features from both the vacuum and control solution simulations, but often at intermediate occupancy. One can see that the rehydrated proteins have lost some vacuum-specific features, but not yet fully recovered all contacts characteristic solution, and also that the structures might still be changing.Earlier MD studies of protein rehydration have seen rapid partial recovery on short timescales, but not complete recovery for all proteins on timescales similar to our 200-ns simulations[29,28].At first glance, an obvious difference can be seen between the triangular matrices for each data set of Trp-cage. In the bottom matrix, showing the results of the subtraction of the vacuum contacts from the rehydration data, several contacts with a value of -1 can be seen, indicating that these contacts are predominantly present in the gas phase.…”

supporting

confidence: 58%

“…Moreover, our results suggest that differences between different protein conformations persist after time spent in vacuo and after rehydration. Here, rehydration MD simulations displayed the potential to reverse the vacuum-induced structural changes, demonstrating MD as an powerful means to refine structures acquired from gas-phase experiments [28,29].…”

Section: Introductionmentioning

confidence: 95%

“…As such, the oriented structures undergo more structural changes than observed in solution. This might be due to a compaction of the protein structure upon vacuum exposure, which is reverted by placing the protein again in an aqueous environment [28,29]. Moreover, the data suggests that In the upper plots, the RMSD was calculated using to the initial structure of each trajectory as reference.…”

Section: Proteins Depart From Their Vacuum Structures Upon Rehydrationmentioning

confidence: 99%

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Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

et al. 2023

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Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our findings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray diffraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.

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Section: Average Collision Cross Section (Ccs) [å 2 ]supporting

confidence: 67%

supporting

confidence: 58%

Section: Introductionmentioning

confidence: 95%

Section: Proteins Depart From Their Vacuum Structures Upon Rehydrationmentioning

confidence: 99%

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Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

et al. 2023

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“…23 In addition, molecular dynamics (MD) studies suggest that proteins adopt kinetically-trapped, compacted gas-phase structures that preserve the native secondary structure to a large extent. 17,[24][25][26][27][28][29] In particular, formation of additional intramolecular hydrogen bonds, also known as self-solvation, following dehydration has been proposed. 30 Together, these findings suggest that near-native structures can be retained in the gas phase.…”

Section: Main Textmentioning

confidence: 99%

Cryo-EM of soft-landedβ-galactosidase: Gas-phase and native structures are remarkably similar

Esser,

Böhning,

Önür

et al. 2023

Preprint

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Native mass spectrometry (native MS) is a powerful technique that provides information on stoichiometry, interactions, homogeneity and shape of protein complexes. However, the extent of deviation between protein structures in the mass spectrometer and in solution remains a matter of debate. Here, we uncover the gas-phase structure of β-galactosidase using single particle electron cryomicroscopy (cryo-EM) down to 2.6 A resolution, enabled by soft-landing of mass-selected protein complexes onto cold TEM grids and in-situ ice coating. We find that large parts of the secondary and tertiary structure are retained from solution, with dehydration-driven subunit reorientation leading to consistent compaction in the gas phase. Our work enables visualizing the structure of gas-phase protein complexes from numerous experimental scenarios at side-chain resolution and demonstrates the possibility of more controlled cryo-EM sample preparation.

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High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method

Persson,

Sahin,

Landreh

et al. 2024

Anal. Chem.

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Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. ( J. Chem. Theory Comput., 2020 , 16 , 6938–6949), showing that it significantly enhances the performance of gas-phase simulations of large proteins. We assess how to achieve adequate accuracy and optimal performance with FMM, finding that it expands the accessible size range and time scales dramatically. Additionally, we simulate a 460 kDa ferritin complex over microsecond time scales, alongside complementary ion mobility (IM)-MS experiments, uncovering conformational changes that are not apparent from the IM-MS data alone.

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Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins

Cited by 8 publications

References 79 publications

Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

Cryo-EM of soft-landedβ-galactosidase: Gas-phase and native structures are remarkably similar

High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method

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