An exact hard-spheres scattering model for the mobilities of polyatomic ions

Shvartsburg, Alexandre A.; Jarrold, Martin F.

doi:10.1016/0009-2614(96)00941-4

Cited by 787 publications

(955 citation statements)

References 31 publications

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“…Our molecular dynamics simulation and molecular orbital calculations also suggest that charge-solvated species represent the most stable conformations of the [M ϩ H] ϩ ions, which is consistent with Simon's studies [31]. Theoretical collision cross-sections for [M ϩ H] ϩ ions for arginine-containing di-and tripeptide and C-terminal methylated derivatives (see Table 2) were calculated by using Mobcal [49]. The theoretical crosssections of methylated species follow the trend…”

Section: Resultssupporting

confidence: 86%

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

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The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di-and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M ϩ H] ϩ ions with deuterated ammonia (ND 3 ) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and argininecontaining tri-peptide [M ϩ H] [15]. Valentine and Clemmer used ion mobility-mass spectrometry to examine the conformation dependence of H/D exchange reactions, and suggested that ion conformation has a significant effect on H/D exchange [16,17].Compared with the intensive investigations carried out on the conformational characterization of peptides and proteins using solution-phase H/D exchange reaction chemistry, the corresponding gas-phase studies are much less comprehensive. The key question regarding gas-phase H/D exchange is: does the "solvent molecule," i.e., H/D exchange reagent, sample the entire "available surface area" of the peptide/protein ion, or is H/D exchange limited by other factors? For example, are all solution phase labile hydrogen atoms exchangeable in the gas phase and are the reactivities of all exchangeable hydrogen atoms similar? Dookeran and Harrison studied the H/D exchange reactions of 18 naturally occurring amino acids and selected di-and tripeptides with ND 3 , and reported that amino acid [M ϩ H] ϩ ions containing hydroxyl, carboxyl, and amine side chains exchange all labile hydrogen atoms, whereas the side-chain hydrogen atoms of glutamine, asparagine, and histidine [M ϩ H] ϩ ions exchange less readily, and tyrosine and arginine [M ϩ H] ϩ ions do not undergo significant exchange [18]. In a separate study, Lebrilla et al. found that the carboxylic acid group of glycine and aliphatic amino acid [M ϩ H] ϩ ions (alanine, valine, leucine, isoleucine, and proline) undergo H/D exchange three to 10 times faster than the NAddress reprint requests to Dr.

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Section: Resultssupporting

confidence: 86%

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

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“…Analyzing IM-MS data with molecular modeling 21| Generate a modified version of MOBCAL 18,19 . Currently, we use two different versions of the MOBCAL code.…”

Section: | Validate This Calibration Curve Against the Trend Shown Inmentioning

confidence: 99%

“…For example, Figure 1a shows modeling data for four different protein complex topologies as a function of subunit mass and number. To generate these data, we used open source software for calculating the collision cross-section of trial structures (MOBCAL) 18,19 , and altered the code so that spherical representations of whole subunits could be used in place of all-atom models (see protocol). It is worth noting that the collision cross-sectional dependence of similar structural trends has been discussed in the atomic cluster literature previously [20][21][22] .…”

Section: Introductionmentioning

confidence: 99%

Ion mobility–mass spectrometry analysis of large protein complexes

et al. 2008

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Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry. INTRODUCTIONLarge-scale interaction maps suggest a complex interplay of proteins within a myriad of functional assemblies 1,2 . A critical step in assigning functions to these assemblies is to determine their structure 3 . This goal is challenging, as many of these assemblies exist in low-copy numbers within cells, are frequently heterogeneous and may interact only transiently. Consequently, structural information for many protein complexes is not readily accessible by using the classical tools of structural biology (e.g., X-ray crystallography, nuclear magnetic resonance spectroscopy). New approaches are being developed that involve integrating data from a number of lower-resolution experimental methods and by combining distance and interaction restraints from these methods with homology modeling, architectural or even atomic models are being generated 4 . These restraints can be derived from a variety of experimental measurements including MS of intact complexes, chemical cross-linking, fluorescence resonance energy transfer, small angle X-ray scattering, and analytical ultracentrifugation 5,6 . One very recent addition to this series of biophysical tools is ion mobility separation coupled to mass spectrometry (IM-MS). IM is an established technique for studying shape and conformation in small molecules and individual proteins in the gas phase 7-10 but has only recently been applied to intact protein complexes 11,12 . When IM is coupled with MS, mass and consequently subunit composition can be determined simultaneously with the overall topology of protein complexes 10,12,13 .IM-MS analysis is performed by first ionizing the protein complex of interest. In our experiments, nano-electrospray ionization is used, typically requiring careful preparation procedures for most protein complexes. These procedures, as well as general practical aspects of sample preparation, are detailed in a protocol by Hernández and Robinson 14 . Although they are not discussed in detail here, knowledge of the materials and protocol steps described in that work are critical to the success of the protocol described below.After ionization, ions are injected into a region containing neutral gas at a controlled pressure (e.g., 0.5 mBar of nitrogen gas). Under the influence of a relatively weak electric field, injected ions undergo IM separation [7]...

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“…ically, candidate low-energy structures are identified by using molecular mechanics or a combination of mechanics with ab initio methods, and cross sections are determined for each of these structures by either projection approximation [26], exact hard sphere scattering [23], or trajectory calculations [24,27]. The method used to obtain cross sections from ion mobility measurements has been described in detail elsewhere [68,69].…”

Section: Methodsmentioning

confidence: 99%

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

Wong

Williams

Counterman

et al. 2005

J. Am. Soc. Mass Spectrom.

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The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs. T he structure of a molecule in solution depends both on intramolecular interactions and on intermolecular interactions between the molecule and solvent. Gas-phase studies can provide information about the intrinsic properties of a molecule. From such measurements, information about solvent effects can be inferred. A number of different methods can provide information about molecular structure in the gas phase, even complex systems, such as large synthetic or biological polymers. These methods include spectroscopy [1][2][3][4][5], hydrogen/deuterium exchange [6-12], dissociation [13][14][15][16][17][18], proton transfer reactivity [19][20][21][22], and ion mobility mass spectrometry . These methods have been used to obtain information about protein conformation and folding, DNA duplex structure, and in a wide variety of other interesting applications.Of these methods, ion mobility mass spectrometry, a method pioneered by Bowers and Jarrold for ion structure characterization, has several advantages, including rapid measurement time, minimal perturbation of ground state structure, exquisite temperature control, and the ability to investigate kinetics of structural change over a limited time. With ion mobility, ions are injected into a drift tube where they thermalize through collisions with an introduced background gas, typically helium. In the presence of an applied electric field, ions are made to drift through an elevated pressure region. Based on the drift time through this tube...

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An exact hard-spheres scattering model for the mobilities of polyatomic ions

Cited by 787 publications

References 31 publications

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Ion mobility–mass spectrometry analysis of large protein complexes

Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers

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