Gaseous Conformational Structures of Cytochrome <i>c</i>

McLafferty, Fred W.; Guan, Ziqiang; Haupts, Ulrich; Wood, Troy D.; Kelleher, Neil L.

doi:10.1021/ja9728076

Cited by 254 publications

(294 citation statements)

References 36 publications

(75 reference statements)

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“…This indicates that these conformations either are stable and do not interconvert over the ϳ1 to 30 ms timescales of these experiments; or, if interconversion occurs, it must do so rapidly compared with our experimental timescales. The present results are consistent with those found in FTICR experiments where structures do not appear to interconvert over very long time periods (several minutes) [8,9,12].…”

Section: H/d Exchange Kineticssupporting

confidence: 92%

“…As discussed previously [36,39], it is impossible to calculate the total ion energy for all possible charge site assignments for each structure [20a, 36]. Here, we assume formal charges of ϩ3 on the heme iron atom and -1 on each heme carboxylate group [12,40] Added protons from the electrospray process are confined to basic Arg, His, or Lys residues. The total number (n) possible charge site configurations for a protein is given by…”

Section: Charge Placement In Simulated Structuresmentioning

confidence: 99%

“…Ion scattering [25,26] and ion mobility studies [27][28][29][30] show that high charge states of the protein adopt elongated conformations, presumably to reduce high coulomb repulsion energies [25, 28]. It is somewhat surprising that isotopic exchange levels as a function of charge state do not show a corresponding increase [8,9,11,12].Our initial interest in this system arose from early work by McLafferty and coworkers, who used fourier …”

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confidence: 99%

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Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Valentine

Clemmer

2002

J. Am. Soc. Mass Spectrom.

109

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Isotopic exchange reactions of compact and elongated conformations of gaseous cytochrome c ions (ϩ5 and ϩ9 states) with D 2 O have been measured as a function of temperature (from 300 to ϳ440 K) using ion mobility techniques. Rate constants for those sites that exchange at high temperatures (Ͼ400 K) are about an order of magnitude smaller than rate constants for sites that exchange at 300 K. Although the exchange rates decrease, the maximum exchange levels for rapidly exchanging sites increase with temperature. At 300 K, exchange levels of 53 Ϯ 3 and 63 Ϯ 3 are measured for the compact and elongated states, respectively. From 300 to 335 K, the exchange levels increase slightly to ϳ60 to 70 hydrogens. Above 335 K, the levels increase to a value of ϳ200 for the ϩ5 state and ϳ190 for the ϩ9 state, near the maximum possible levels, 200 and 204 for these respective charge states. Molecular dynamics simulations have been carried out on structures having calculated cross sections that are near the experimental values in order to explore the exchange process. Overall, it appears that charge site and exchange site proximities are important factors in the exchange profiles for the elongated ϩ9 ion and the compact ϩ5 ion. (J Am Soc Mass Spectrom 2002, 13, 506 -517) © 2002 American Society for Mass Spectrometry I t is well known that the structures of proteins are influenced by environmental factors such as solution composition, pH, and temperature. However, the degree to which environment and intrinsic properties influence structure is not well understood. Structural domains such as ␣-helices, which are stable in a wide range of environments, were predicted theoretically without considering effects of solvation [1]. More subtle features, such as tertiary structure in different environments, are difficult to predict. Recently, efforts have been made to gather information about the degree to which solvent-free protein conformations resemble their native solution structures [2]. Several studies of lyophilized protein powders have shown that removal of solvent can cause structural changes [3], and the extent of differences between lyophilized and solution states is an active area [4]. New ion sources [5,6] make it possible to isolate biomolecules in the gas phase as ions, and a number of mass spectrometry (MS) based strategies for examining solvent-free conformations are being developed . The new information from these technologies is beginning to be evaluated by theoretical methods [33, 34,35]. There is now substantial evidence that, under some experimental conditions, anhydrous protein and peptide ions may retain elements of solution conformation.The conformations of cytochrome c ions have been examined previously by a number of MS techniques [8, 28]. Ion mobility (for reviews of ion mobility studies see [30]) and isotopic exchange studies [7-10, 11, 12] provide information about the overall shape and number of accessible exchange sites, respectively. These studies indicate the presence of multiple conformations within ind...

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Section: H/d Exchange Kineticssupporting

confidence: 92%

Section: Charge Placement In Simulated Structuresmentioning

confidence: 99%

mentioning

confidence: 99%

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Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Valentine

Clemmer

2002

J. Am. Soc. Mass Spectrom.

109

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“…Different conformations/protonation motifs sometimes have different fragmentation patterns, as recently demonstrated for an aspartic acid containing fixed charge derivative peptide [7]. Both ion mobility and hydrogen/deuterium (H/D) exchange have been used to investigate gas phase isomers [8][9][10][11]. Ion mobility relies on different collisional cross-sections to separate different conformers, while H/D exchange relies on a difference in the rate of exchange with a deuterated reagent.…”

Section: Introductionmentioning

confidence: 99%

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD3OD

Herrmann

Kuppannan

Wysocki

2006

International Journal of Mass Spectrometry

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Doubly-protonated bradykinin (RPPGFSPFR) and an angiotensin III analogue (RVYIFPF) were subjected to hydrogen/deuterium (H/D) exchange with CD 3 OD in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. A bimodal distribution of deuterium incorporation was present for bradykinin after H/D exchange for 90 s at a CD 3 OD pressure of 4 × 10 −7 Torr, indicating the existence of at least two distinct populations. Bradykinin ion populations corresponding to 0-2 and 5-11 deuteriums (i.e., D 0 , D 1 , D 2 , D 5 , D 6 , D 7 , D 8 , D 9 , D 10 , and D 11 ) were each monoisotopically selected and fragmented via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID). The D 0 -D 2 ion populations, which correspond to the slower exchanging population, consistently require lower SORI amplitude to achieve a similar precursor ion survival yield as the faster-reacting (D 5 -D 11 ) populations. These results demonstrate that conformation/ protonation motif has an effect on fragmentation efficiency for bradykinin. Also, the partitioning of the deuterium atoms into fragment ions suggests that the C-terminal arginine residue exchanges more rapidly than the N-terminal arginine. Total deuterium incorporation in the b 1 /y 8 and b 2 /y 7 ion pairs matches very closely the theoretical values for all ion populations studied, indicating that the ions of a complementary pair are likely formed during the same fragmentation event, or that no scrambling occurs upon SORI. Deuterium incorporation into the y 1 /a 8 pseudo-ion pair does not closely match the expected theoretical values. The other peptide, doubly-protonated RVYIFPF, has a trimodal distribution of deuterium incorporation upon H/D exchange with CD 3 OD at a pressure of 1 × 10 −7 Torr for 600 s, indicating at least three distinct ion populations. After 90 s of H/D exchange where at least two distinct populations are detected, the D 0 -D 7 ion populations were monoisotopically selected and fragmented via SORI-CID over a range of SORI amplitudes. The precursor ion survival yield as a function of SORI amplitude falls into two distinct behaviors corresponding to slower-and faster-reacting ion populations. The slower-reacting population requires larger SORI amplitudes to achieve the same precursor ion survival yield as the faster exchanging population. Total deuterium incorporation into the y 2 /b 5 ion pairs matches closely the theoretical values over all ion populations and SORI amplitudes studied. This result indicates the y 2 and b 5 ions are likely formed by the same mechanism over the SORI amplitudes studied.

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“…H /D exchange (HDX) is one of the most popular techniques for the structural elucidation of biomolecules in mass spectrometry and has been widely implemented for both solution [1][2][3][4] and gas phase studies [5][6][7][8][9][10][11][12][13][14][15][16][17][18]. In solution, the extent of HDX can be directly related to the solvent accessibility of amino acid residues in proteins.…”

mentioning

confidence: 99%

Observation of zwitterion formation in the gas-phase H/D-exchange with CH₃OD: Solution-phase structures in the gas phase

Polfer

Dunbar

2007

J. Am. Soc. Mass Spectrom.

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Infrared spectroscopy of gas-phase singly deuterated [Trp ϩ K] ϩ (formed by H/D exchange with CH 3 OD) shows that some (ϳ20%) kinetically stable zwitterionic (ZW) conformer is formed, based on the diagnostic antisymmetric CO stretch of the deprotonated carboxylate moiety, as (CO 2 Ϫ ), at 1680 cm Ϫ1 . A majority of the deuterated [Trp ϩ K] ϩ is found to be in the charge solvation (CS) conformation, with deuterium exchange occurring on both the acid and amino groups, which is consistent with H/D scrambling. Interestingly, H/D exchange with the more basic ND 3 reagent did not result in the stabilization of a kinetically stable zwitterion, although it is not clear yet what causes this observation. The result for CH 3 OD shows that H/D exchange can in fact alter the structure of the analyte and, hence, care needs to be taken when interpreting gas-phase H/D exchange studies. Moreover, this result shows the possibility of forming solution-phase structures that are thermodynamically disfavored in the gas phase, thus opening a new area of study. (HDX) is one of the most popular techniques for the structural elucidation of biomolecules in mass spectrometry and has been widely implemented for both solution [1][2][3][4] and gas phase studies [5][6][7][8][9][10][11][12][13][14][15][16][17][18]. In solution, the extent of HDX can be directly related to the solvent accessibility of amino acid residues in proteins. However, in the gas phase there are many structural parameters apart from the surface availability that affect the HDX rates, as illustrated in a recent HDX study on ion-mobilityselected charge states of bovine ubiquitin [17]. Systematic studies on small peptide systems showed that the difference in proton affinity of the biomolecules and deuterated donor reagent plays a crucial role in the HDX mechanism [7][8][9][10]19]. Beauchamp and coworkers [9] suggested that lower basicity reagents, such as D 2 O and CH 3 OD, proceed via a "relay" mechanism [20] for protonated peptides, while the higher basicity ND 3 reagent gives rise to an "onium" mechanism [21]. In the case of amino acids cationized by an alkali metal ion rather than a proton, polar deuterating ligands such as D 2 O can exchange via a similar relay mechanism involving charge solvation-zwitterion (CS-ZW) isomerization [18]. Modeling of observed HDX processes and quantum chemical calculations of the potential surfaces have made a strong circumstantial case that ZW structures are traversed in many cases during HDX with basic partners like D 2 O, CH 3 OD, and ND 3 [14,16,18]. Nevertheless, computations also generally indicate that the bare ZW is sufficiently disfavored energetically that its equilibrium presence in the M ϩ /amino acid would be negligible [22,23].Here, we show unambiguous spectroscopic evidence that bare ZW can in fact be kinetically trapped as a result of the HDX of [Trp ϩ K] ϩ with CH 3 OD. Infrared multiple-photon dissociation (IR-MPD) spectroscopy of metal-tagged amino acids and peptides has already been shown to be a powerful probe for CS ...

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Gaseous Conformational Structures of Cytochrome c

Cited by 254 publications

References 36 publications

Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD3OD

Observation of zwitterion formation in the gas-phase H/D-exchange with CH₃OD: Solution-phase structures in the gas phase

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Gaseous Conformational Structures of Cytochrome c

Cited by 254 publications

References 36 publications

Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD3OD

Observation of zwitterion formation in the gas-phase H/D-exchange with CH3OD: Solution-phase structures in the gas phase

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Observation of zwitterion formation in the gas-phase H/D-exchange with CH₃OD: Solution-phase structures in the gas phase