Dynamics of Intact Immunoglobulin G Explored by Drift‐Tube Ion‐Mobility Mass Spectrometry and Molecular Modeling

Pacholarz, Kamila J.; Porrini, Massimiliano; Garlish, Rachel A.; Burnley, Rebecca J.; Taylor, Richard J. K.; Henry, Alistair J.; Barran, Perdita E.

doi:10.1002/anie.201402863

Cited by 97 publications

(130 citation statements)

References 29 publications

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“…45 Briefly optimized structures often have CCS values matching well with the experiments. 42,[46][47][48] Fabris and co-workers have recently underlined the difficulties in transposing to DNA the MD and CCS calculation protocols traditionally used for proteins. 43 As a way out they proposed to calibrate all traveling wave IMS data using short MD simulation results, but our study shows why this approach would lead to a misrepresentation of nucleic acid structures in the gas phase.…”

Section: Discussionmentioning

confidence: 99%

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Porrini

Rosu

Rabin

et al. 2017

Preprint

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ABSTRACT:Native mass spectrometry coupled to ion mobility spectrometry is a promising tool for structural biology. Intact complexes can be transferred to the mass spectrometer and, if native conformations survive, collision cross sections give precious information on the structure of each species in solution. Based on several successful reports for proteins and their complexes, the conformation survival becomes more and more taken for granted. Here we report on the fate of nucleic acids conformation in the gas phase. Disturbingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥ 100 mM aqueous NH 4 OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for short (12-bp) and long (36-bp) duplexes, and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semi-empirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb-driven expansion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.

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Section: Discussionmentioning

confidence: 99%

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Porrini

Rosu

Rabin

et al. 2017

Preprint

Self Cite

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“…Although many reports have demonstrated a strong correlation between experimental CCS measurements and CCS values extracted from solution-phase protein models, the strength of this correlation can depend on the domain structure and globularity of the protein analyte in question. [42,43] Moreover, the magnitude and nature of the errors incorporated into IM-MS multiprotein models through the coarse-graining process are currently unknown. In order to investigate such coarse-graining errors, we extracted a non-redundant set of 191 high-resolution protein complex structures from the 3D complex set database,[44] and developed a method for the rapid generation of CG structures based on these entries where the extent of coarse graining can be treated as a variable.…”

Section: Assessing Coarse-graining Errors In Multiprotein Models Genementioning

confidence: 99%

Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment

Eschweiler

Frank

Ruotolo

2017

J. Am. Soc. Mass Spectrom.

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Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analyze by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies.

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“…19 Overall, gas-phase methods appear uniquely suited to meet the challenge of describing the conformations and dynamics of flexible proteins as evidenced by the increasing number of publications in this area in recent years. [20][21][22][23][24] Nevertheless, recent studies describing the collapse of disordered structures in the absence of solvent have raised questions over the fidelity to which gas-phase methods can capture the solution conformations of these proteins. 25,26 Recent shifts in our understanding of how flexible species escape electrospray droplets during ESI also add to the complexity of describing the solution to gas-phase transfer of IDPs.…”

Section: Introductionmentioning

confidence: 99%

Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins

et al. 2015

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Intrinsically disordered proteins (IDPs) are important for health and disease, yet their lack of net structure precludes an understanding of their function using classical methods. Gas-phase techniques provide a promising alternative to access information on the structure and dynamics of IDPs, but the fidelity to which these methods reflect the solution conformations of these proteins has been difficult to ascertain. Here we use state of the art ensemble techniques to investigate the solution to gas-phase transfer of a range of different IDPs. We show that IDPs undergo a vast conformational space expansion in the absence of solvent to sample a conformational space 3-5 fold broader than in solution. Moreover, we show that this process is coupled to the electrospray ionization process, which brings about the generation of additional subpopulations for these proteins not observed in solution due to competing effects on protein charge and shape. Ensemble methods have permitted a new definition of the solution to gas-phase transfer of IDPs and provide a roadmap for future investigations into flexible systems by mass spectrometry.

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Dynamics of Intact Immunoglobulin G Explored by Drift‐Tube Ion‐Mobility Mass Spectrometry and Molecular Modeling

Cited by 97 publications

References 29 publications

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment

Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins

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