Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization (original) (raw)
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The Journal of Physical Chemistry B, 2010
Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H] + ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross-sections for the [M + H] + ions of Ac-(AAKAA) n Y-NH 2 (n = 3-6) and Ac-Y (AEAAKA) n F-NH 2 (n = 2-5) are reported and correlated with candidate structures generated obtained using molecular modeling techniques. The [M + H] + ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H] + ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e. the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments.
Charge location on gas phase peptides
International Journal of Mass Spectrometry, 2002
Studying biological systems to determine structure has been performed by a number of analytical techniques, including electrospray ionization (ESI)/ion mobility spectrometry (IMS) with mass spectrometry (MS) detection. ESI/IMS/MS enables the determination of gas phase ionic molecular size and can be correlated to computational modeling for structural evaluation. In this study, a molecular modeling program (CHARMm) coupled with a novel method of experimentally determining ion radii with ambient pressure IMS/MS was utilized to determine the charge position on gas phase peptides. Molecular modeling predicted the relative sizes of several isomeric peptides previously separated by IMS in a nitrogen buffer gas, although the modeled radii were smaller than the experimental radii due to the large polarizability of the drift gas. To correct for the polarization of the ambient pressure gas through which the ions migrate in the ion mobility experiment, ionic radii in drift gases of differing polarizability were plotted as a function of drift gas polarizability. To compare with the zero-polarizability ionic radii (y-intercept of the linear regression), the modeling experiment mimicked conditions of the actual experiment and the modeled and measured ionic size matched well. Moreover, when all possible charge locations on the peptides were modeled, only one modeled structure matched the experimental data, indicating that the combination of modeled and mobility data can determine charge location on gas phase peptides. (Int J Mass Spectrom 219
A collision cross-section database of singly-charged peptide ions
Journal of the American Society for Mass Spectrometry, 2007
A database of ion-neutral collision cross-sections for singly-charged peptide ions is presented. The peptides included in the database were generated by enzymatic digestion of known proteins using three different enzymes, resulting in peptides that differ in terms of amino acid composition as well as N-terminal and C-terminal residues. The ion-neutral collision crosssections were measured using ion mobility (IM) spectrometry that is directly coupled to a time-of-flight (TOF) mass spectrometer. The ions were formed by a matrix-assisted laser desorption ionization (MALDI) ion source operated at pressures (He bath gas) of 2 to 3 torr. The majority (63%) of the peptide ion collision cross-sections correlate well with structures that are best described as charge-solvated globules, but a significant number of the peptide ions exhibit collision cross-sections that are significantly larger or smaller than the average, globular mobility-mass correlation. Of the peptide ions having larger than average collision crosssections, ϳ71% are derived from trypsin digestion (C-terminal Arg or Lys residues) and most of the peptide ions that have smaller (than globular) collision cross-sections are derived from pepsin digestion (90%). (J Am Soc Mass Spectrom 2007, 18, 1232-1238 I on mobility (IM) spectrometry separates ions on the basis of ion-neutral collision cross-section or apparent surface area, and several groups have combined IM spectrometry with high-performance mass spectrometers to provide accurate mass measurements of ions exiting the IM drift cell [1]. More recently, IM-MS instruments that operate as tandem mass spectrometry instruments (IM-MS/MS) have also been developed . Potential advantages of IM-MS and IM-MS/MS for proteomics research are postionization separation, which facilitates direct analysis of complex mixtures, increased sample throughput afforded by rapid data acquisition (s-ms), and reduction of chemical noise by separation of molecular classes owing to differences in intrinsic gas-phase packing efficiencies of the ions . We refer to the separation of molecular classes in the mobility-mass dimension in terms of "conformation space," which is realized by plotting collision crosssection versus m/z ratio of the ion [1].
International Journal of Mass Spectrometry, 2018
Highlights Candidate structures by thermodynamic reweighting of molecular dynamics simulations Averaging yields theoretical collision cross sections of synthetic peptides Good agreement of experimental and theoretical collision cross sections Peptide sequence and charge determine the structure and thus the cross section Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3,310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF).
Chemistry - A European Journal, 2002
Apolar, neutral peptides have been shown to ionize extremely well under the conditions used for electrospray ionization mass spectrometry (ESIMS). Peptides for which the conformations have been independently determined in solution and in crystals have been examined by ESIMS. Studies of peptide helices ranging from 7 to 18 residues reveal that shorter helices yield exclusively singly charged ions, while in larger helices multiply charged species are detectable. Multiple sites for protonation/metallation are introduced in the helix by proline insertion or by changing the chirality in the residue. The preferred site of cation binding to helices may be the C-terminus end, where three free CO groups are available for chelation. Ab initio and DFT calculations at several levels have been carried out for the binding of H , Li , Na , and K to CHO-(Gly) 3 )-OMe. The results reveal that metallation in helices is favoured by chelation to carbonyl groups at the C-terminus, while protonation involved two carbonyl groups and thus favour a 10-membered cyclic hydrogen-bonded structure. In b-strands, metallation/protonation occurs at isolated carbonyl groups. Collision induced fragmentation of hydrophobic peptides under ESI conditions reveals that helix fragmentation occurs predominantly from the C-terminus, while in b-hairpins cleavage occurs simultaneously at multiple sites.
How Cations Change Peptide Structure
Chemistry - A European Journal, 2013
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure. To do so, we compare the conformational ensembles of model peptides in isolation and in the presence of either Li + or Na + cations by state-of-the-art density-functional theory (including van der Waals effects) and gas-phase infrared spectroscopy. These monovalent cations have a drastic effect on the local backbone conformation of turn-forming peptides, by disruption of the H bonding networks and the resulting severe distortion of the backbone conformations. In fact, Li + and Na + can even have different conformational effects on the same peptide. We also assess the predictive power of current approximate density functionals for peptide-cation systems and compare to results from established protein force fields as well as to high-level quantum chemistry (CCSD(T)).
Analytical Chemistry, 2010
The selective covalent modification of singly protonated peptides in the gas-phase via ion/ion charge inversion reactions is demonstrated. Doubly deprotonated 4-formyl-1,3-benzene disulfonic acid serves as a reagent anion for forming a Schiff base via the reaction of a primary amine on the peptide and the aldehyde functionality of the reagent anion. The process is initiated by the formation of an ion/ion complex comprised to the two reactants. Ion trap collisional activation of the complex results in loss of water from the intermediate that gives rise to Schiff base formation. N-terminally acetylated peptides with no lysine residues do not undergo covalent bond formation upon reaction with the reagent anion. Rather, the adduct species simply loses the reagent either as a neutral species or as a deprotonated species. The ability to modify singly protonated peptide ions covalently and selectively opens up new possibilities for the analysis of peptides, and, possibly, other analyte species with primary amine functionalities.
Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues
Chemical Reviews, 2020
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes by successively adding aggregation partners and thus an environment to a molecule. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottomup approach was successfully applied to neutral amino acids starting around the 1990s. Ever since experimental and theoretical methods developed further and investigations could be extended to larger peptide systems. Beyond, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behaviour are presented. Beyond the linear α-peptides the main results of structural analysis on cyclic systems as well as on β-and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance. 45) , non-protected (cf. e.g. 46-48) and protected amino acids (cf. e.g. 49) up to dipeptide models (cf. e.g. 50). In this context, laser spectroscopic techniques combining IR and UV excitations, that one can consider as belonging to the so-called 'action spectroscopies', provide an isomer-selective method of choice to tackle the 87) or immunoglobulins (cf. e.g. 88), but they are also found in context with neurodegenerative diseases (cf. e.g. 89-95 and Section 12). A further structure associated with these diseases (cf. e.g. 96) is the β-helix, which presents a protein structure of several parallel β-strands in a helical arrangement with a frequently repetitive amino acid sequence. The structure is stabilized by H-bonds, sometimes ionic interactions or so called protein-protein interactions, which e.g. include electrostatic and hydrophobic effects. 2.3. Further aspects of peptide structure in gas phase The role of protection groups With the unmodified N-and C-terminus amino acids and peptides can exhibit strong preferences for intramolecular H-bonds involving the N-and C-terminus, and can also form intermolecular H-bonds leading to polymer chains. Nevertheless, in a context where the description of the properties of a protein or a long peptide (with respect to its backbone) by smaller peptides is targeted, the introduction of protecting groups at the N-and C-terminus is a useful approach. The protection groups help to get rid of edge effects due to the Nand C-terminus, especially with regard to the bottom-up approach of gas phase spectroscopy. Thus, the resulting protected or capped peptides can be considered as suitable model systems for extracts of larger polypeptide chains and their structural preferences. In many gas phase spectroscopic investigations, the acetyl group (Ac) is the preferred protection for the N-terminus, while the C-terminus is frequently esterified or amidated (also cf. Section 3). The hydroxyl group of the tyrosine residue can also be protected with a methyl group. These caps at the termini do not only reduce the 'undesired' formation of inter-and intramolecular Hbonds, but they also introduce additional amide bonds elongating the peptide backbone (e.g. Ac-Val-Tyr(Me)-NHMe is a dipeptide but can also denoted as tripeptide model 102). Beyond, certain protection groups like the Zgroup (also abbrev. by Cbz, denoted as benzyloxycarbonyl or carbobenzyloxy) introduce a UV chromophore required for R2PI (resonant 2 photon ionization) or laser induced fluorescence (LIF)-based spectroscopic methods (cf. Section 4) when no aromatic side chain is available in the peptide sequence (cf. e.g.
Peptide design. Structural evaluation of potential nonhelical segments attached to helical modules
Journal of the American Chemical Society, 1995
The conformations of three decapeptides containing a helical heptapeptide module attached to a potentially helix destabilizing tripeptide segment have been investigated in single crystals. X-ray diffraction studies of the sequence Boc-Gly-Dpg-Xxx-Val-Ala-Leu-Ab-Val-Ala-Leu-OMe (Xxx = Leu (l), Pro (2), and Ala (3); Dpg = a,a-din -propylglycine; Aib = a-aminoisobutyric acid) reveal helical conformations for the segment 2-9 in all three peptides. In 1 and 2 Gly(1) is not accommodated in the right-handed helix and adopts a left-handed helical conformation with positive 4, q!~ values. The terminal blocking group extends away from the helix in 1 and 2. In 3 the helix is continuous, encompassing residues 1-9. The Dpg residues in all three cases adopt helical conformations, even when flanked by two helix destabilizing residues as in 2. These findings suggest that the higher a,a-dialkyl residues are good helix promoters although theoretical calculations suggest the existence of a pronounced energy minimum in fully extended regions of conformational space. None of the peptides pack efficiently. The register between helices in the head-to-tail region is not good, with disordered water molecules serving as hydrogen bond bridges and as space fillers. The crystallographic parameters follow.
Physical chemistry chemical physics : PCCP, 2015
Reliable, quantitative predictions of the structure of peptides based on their amino-acid sequence information are an ongoing challenge. We here explore the energy landscapes of two unsolvated 20-residue peptides that result from a shift of the position of one amino acid in otherwise the same sequence. Our main goal is to assess the performance of current state-of-the-art density-functional theory for predicting the structure of such large and complex systems, where weak interactions such as dispersion or hydrogen bonds play a crucial role. For validation of the theoretical results, we employ experimental gas-phase ion mobility-mass spectrometry and IR spectroscopy. While unsolvated Ac-Ala19-Lys + H(+) will be shown to be a clear helix seeker, the structure space of Ac-Lys-Ala19 + H(+) is more complicated. Our first-principles structure-screening strategy using the dispersion-corrected PBE functional (PBE + vdW(TS)) identifies six distinctly different structure types competing in th...