Site-Specific Analysis of Gas-Phase Hydrogen/Deuterium Exchange of Peptides and Proteins by Electron Transfer Dissociation

Rand, Kasper D.; Pringle, Steven D.; Morris, Michael; Brown, Jeffery M.

doi:10.1021/ac202918j

Cited by 63 publications

(87 citation statements)

References 66 publications

(152 reference statements)

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“…The mass spectrometer was equipped with an ESI source operated at predefined settings for minimal H/D scrambling as described previously (11,12,(31)(32)(33)(34)(35). ETD was performed in the trap T-wave by reacting radical 1,4-dicyanobenzene anions with quadrupole-selected deuterium-labeled peptide ions.…”

Section: Methodsmentioning

confidence: 99%

“…Mass spectrometry (MS) has evolved to be a powerful technique to measure protein HDX and thus monitor protein dynamics in solution, due to tolerance to complex protein systems, buffer composition, and low sample concentration. More recently, the integration of electron transfer dissociation (ETD) into the HDX-MS workflow has enabled the mapping of conformational changes in proteins at a spatial resolution down to individual residues (11,12,(31)(32)(33)(34)(35). During HDX-ETD measurements, peptides generated from solution-phase proteolysis are further fragmented in the gas-phase by ETD, and through mass analysis of fragment ions deuterium contents can often be assigned to individual sites.…”

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confidence: 99%

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Sites Involved in Intra- and Interdomain Allostery Associated with the Activation of Factor VIIa Pinpointed by Hydrogen-Deuterium Exchange and Electron Transfer Dissociation Mass Spectrometry

Song

Olsen

Persson

et al. 2014

Journal of Biological Chemistry

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Background: Site-specific hydrogen-deuterium exchange of factor VIIa (FVIIa) was measured to elucidate the mechanism by which FVIIa is up-regulated by tissue factor (TF). Results: Individual residues in FVIIa whose interaction pattern changes when TF induces the active form are pinpointed. Conclusion: A picture of the activation signal from TF contact site to active site emerges. Significance: Guidance for future work on FVIIa allostery is provided.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Sites Involved in Intra- and Interdomain Allostery Associated with the Activation of Factor VIIa Pinpointed by Hydrogen-Deuterium Exchange and Electron Transfer Dissociation Mass Spectrometry

Song

Olsen

Persson

et al. 2014

Journal of Biological Chemistry

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“…The non-ergodic ion fragmentation techniques of electron capture dissociation (ECD)[11] and electron transfer dissociation (ETD)[12] showed utility early on as a means to locate the sites of deuterium incorporation [13, 14]. Shortly later, HDX-ETD-MS characterization was coupled with ion mobility separations using a traveling wave ion guide (TWIG) instrument [15].…”

Section: Introductionmentioning

confidence: 99%

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

Khakinejad

Kondalaji

Donohoe

et al. 2016

J. Am. Soc. Mass Spectrom.

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Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M-2H]2− ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites whereas for the more diffuse [M-3H]3− ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M-2H]2− ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M-3H]3− ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

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“…More penetrating conclusions could be drawn if it were possible to extend structural resolution to the individual amino acid level. Recently reported efforts have moved in this direction (15,(17)(18)(19)(20)(21)(22)(23)(24).…”

Section: Hdx-ms | Isotope Pattern | Protein Biophysicsmentioning

confidence: 99%

“…Fig. 1, Inset, with a common terminus, might be obtained from an electron capture/transfer dissociation (ECD/ETD) analysis of samples taken from an HX MS experiment (15,21,23,24,(28)(29)(30)(31)(32)(33)(34)(35)(36)(37). The intact protein is injected into the gas phase of the mass spectrometer and an electron is delivered that leads to the rapid nonergodic cleavage of a random main-chain NH to alpha carbon bond.…”

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confidence: 99%

Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis

Kan

Walters

Mayne

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Hydrogen exchange technology provides a uniquely powerful instrument for measuring protein structural and biophysical properties, quantitatively and in a nonperturbing way, and determining how these properties are implemented to produce protein function. A developing hydrogen exchange-mass spectrometry method (HX MS) is able to analyze large biologically important protein systems while requiring only minuscule amounts of experimental material. The major remaining deficiency of the HX MS method is the inability to deconvolve HX results to individual amino acid residue resolution. To pursue this goal we used an iterative optimization program (HDsite) that integrates recent progress in multiple peptide acquisition together with previously unexamined isotopic envelope-shape information and a site-resolved backexchange correction. To test this approach, residue-resolved HX rates computed from HX MS data were compared with extensive HX NMR measurements, and analogous comparisons were made in simulation trials. These tests found excellent agreement and revealed the important computational determinants.HDX-MS | isotope pattern | protein biophysics U nlike any other method, hydrogen exchange (HX) behavior encodes detailed quantitative information at amino acid resolution on the biophysical factors that produce protein function-structure, structure change, interactions, dynamics, and energetics. HX behavior is very sensitive to these properties, and the chemistry (1, 2) and structural physics (3, 4) of HX processes in these terms are now well understood. The ability of HX to measure protein biophysical properties and their implementation in protein function has been demonstrated over the last 30 y by many NMR studies. However, routine NMR analysis is limited to small highly soluble proteins that can be obtained in quantity (multi mgs), isotopically labeled ( 15 N, 13 C), and studied at millimolar concentration. A developing technology, HX measured and analyzed by mass spectrometry (HX MS) (5-16) can extend this proven capability to the much larger and more complex protein systems that make biology work. The method requires only picomoles of protein at submicromolar concentrations; it can be used to study the properties and functioning of proteins at any condition one chooses, and the experimental protein need not even be very pure.For HX MS analysis, a protein sample taken from any H-D exchange experiment is quenched into slow HX conditions, proteolytically fragmented, and the peptide fragments are separated and analyzed by HPLC and mass spectrometry. The number of D atoms carried on each peptide fragment is given by its measurable increase in mass, usually calculated as the increment in the peptide mass centroid. These results provide structural information resolved to the level of individual fragments and are broadly able to indicate where in the protein important behavior occurs (5-16). More penetrating conclusions could be drawn if it were possible to extend structural resolution to the individual amino acid level. Re...

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Site-Specific Analysis of Gas-Phase Hydrogen/Deuterium Exchange of Peptides and Proteins by Electron Transfer Dissociation

Cited by 63 publications

References 66 publications

Sites Involved in Intra- and Interdomain Allostery Associated with the Activation of Factor VIIa Pinpointed by Hydrogen-Deuterium Exchange and Electron Transfer Dissociation Mass Spectrometry

Sites Involved in Intra- and Interdomain Allostery Associated with the Activation of Factor VIIa Pinpointed by Hydrogen-Deuterium Exchange and Electron Transfer Dissociation Mass Spectrometry

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis

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