Proton Transfer-Induced Conformational Changes and Melting In Designed Peptides in the Gas Phase

Kohtani, Motoya; Jones, Thaddeus C.; Ramasamy, Sudha; Jarrold, Martin F.

doi:10.1021/ja056745s

Cited by 30 publications

(55 citation statements)

References 24 publications

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“…The Jarrold group has previously shown that the location of basic sites in polyalanine-based peptides has a profound impact on the gas-phase structures of the peptides, with helical structures being favored for peptides protonated at the C-terminus and globular structures being favored for peptides protonated at the N-terminus. 4, 6, 7, 56 The starting structure of monomeric melittin was taken from the protein data bank, entry 1MLT, and modified such that only three amino acids were positively charged. Because the C-terminus of melittin is naturally amidated and acidic residues are not present in the peptide, zwitterions were not considered.…”

Section: Resultsmentioning

confidence: 99%

Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry

Morrison

Brodbelt

2016

Analyst

104

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Characterization of all gas-phase charge sites of natively sprayed proteins and peptides is demonstrated using 193 nm UVPD. The high sequence coverage offered by UVPD is exploited for the accurate determination of charge sites in protein systems up to 18 kDa, allowing charge site to be studied as a function of protein conformation and the presence of disulfide bonds. Charging protons are found on both basic sidechains and on the amide backbone of less basic amino acids such as serine, glutamine, and proline. UVPD analysis was performed on the 3+ charge state of melittin, the 5+ to 8+ charge states of ubiquitin, and the 8+ charge state of reduced and oxidized β-lactoglobulin. The location of charges in gas-phase proteins is known to impact structure; molecular modeling of different charge site motifs of 3+ melittin demonstrates how placement of protons in simulations can dramatically impact the predicted structure of the molecule. The location of positive charge sites in ubiquitin and β-lactoglobulin are additionally found to depend on the presence or absence of salt-bridges, columbic repulsion across the length of the peptide, and protein conformation. Charge site isomers are demonstrated for ubiquitin and β-lactoglobulin but found to be much less numerous than previously predicted.

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Section: Resultsmentioning

confidence: 99%

Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry

Morrison

Brodbelt

2016

Analyst

104

View full text Add to dashboard Cite

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“…Gas-phase structures representing the different conformers types of [M+4H] 4+ ions filtered by the HAS-NEC model are shown in Supplementary Figure 8 It is worthwhile to mention that for the quadruply-charged ions, the elongation of the ion due to excessive charge density would not allow preservation of solution-like structures; therefore, these structures are discussed from a reference point of gas-phase structure stabilization. All three conformer types display a degree of helicity within the first peptide ion segment (Acetyl-PAAAAK) where the charge located at K(6) may stabilize the helix [44]. Significant coulomb repulsion and the presence of a positive charge at N-terminal locations of subsequent segments do not allow these portions to adopt specific secondary structure.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

Khakinejad

Kondalaji

Tafreshian

et al. 2017

J. Am. Soc. Mass Spectrom.

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Gas-phase hydrogen deuterium exchange (HDX) using D2O reagent and collision cross section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out in a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

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“…It may be argued that, for MDS simulations, one should consider the apparent gas phase acidities of different residues;[59, 60] however, estimating apparent gas phase acidities requires a knowledge of the distance between charge sites[59] which requires candidate structures from MDS. Even knowing the distance between potential charge sites may not be sufficient to accurately estimate correct locations as the most stable ion structure can dictate unique charge arrangements [61]. …”

Section: Resultsmentioning

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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Proton Transfer-Induced Conformational Changes and Melting In Designed Peptides in the Gas Phase

Cited by 30 publications

References 24 publications

Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry

Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry

Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

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

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