Fritz-Haber-Institut der Max-Planck-Gesellschaft
Department of Molecular Physics
Infrared excitation of gas-phase molecules and clusters
|AC CP MP PC TH MPG|
Biomolecules in the Gas Phase
Publication in Nature Communications: Unravelling the structure of glycosyl cations via cold-ion infrared spectroscopy
Glycosyl cations are the key intermediates during the glycosylation reaction that covalently links building blocks during the synthetic assembly of carbohydrates. The exact structure of these ions remained elusive due to their transient and short-lived nature. Structural insights into the intermediate would improve our understanding of the reaction mechanism of glycosidic bond formation. Here, we report an in-depth structural analysis of glycosyl cations using a combination of cold-ion infrared spectroscopy and first-principles theory. Participating C2 protective groups form indeed a covalent bond with the anomeric carbon that leads to C1-bridged acetoxonium-type structures. The resulting bicyclic structure strongly distorts the ring, which leads to a unique conformation for each individual monosaccharide. This gain in mechanistic understanding fundamentally impacts glycosynthesis and will allow to tailor building blocks and reaction conditions in the future.
E. Mucha, M. Marianski, F.-F. Xu, D. A. Thomas, G. Meijer, G. von Helden, P. H. Seeberger, and K. Pagel Nat. Commun., 9, 4174 (2018). http://dx.doi.org/10.1038/s41467-018-06764-3
Polyoxometalate clusters possess unique catalytic and electromagnetic properties. The structure and function of polyoxometalates is dictated by complex oligomerization processes, which in turn depend on the solution conditions. In this work, small gas-phase polyoxomolybdate nanoclusters (HMonO3n+11–, n = 1–8, and MonO3n+12–, n = 2–8) were investigated after nanoelectrospray of an acidified solution of ammonium heptamolybdate heptahydrate by ion mobility spectrometry–mass spectrometry (IMS–MS), infrared multiple photon dissociation (IRMPD) spectroscopy, and infrared action spectroscopy in helium nanodroplets. The spectra and collision cross sections obtained were matched to predictions from density-functional theory (DFT) to unravel the structural progression of nanoclusters with increasing size. For doubly charged clusters, transitions among chain (n = 2–3), ring (n = 4–5), and compact (n ≥ 6) structures are observed in IMS–MS and IR spectroscopy experiments, in agreement with low-energy structures from DFT calculations. For singly charged clusters, reduced Coulombic repulsion and hydrogen bonding interactions are found to strongly influence the most stable cluster structure. Notably, a noncovalent ring structure is observed for HMo3O101–, stabilized by a strong intramolecular hydrogen bond, and a compact structure is observed for HMo5O161–, in contrast to the ring structure favored for Mo5O162–.
M. Marianski, J. Seo, E. Mucha, D. A. Thomas, S. Jung, R. Schlögl, G. Meijer, A. Trunschke, and G. von Helden, J. Phys. Chem. C, , Article ASAP (2018). http://dx.doi.org/10.1021/acs.jpcc.8b06985
The proton‐bound dicarboxylate motif, RCOO−⋅H+⋅−OOCR, is a prevalent chemical configuration found in many condensed‐phase systems. The proton‐bound formate dimer HCOO−⋅H+⋅−OOCH was studied utilizing cold‐ion IR action spectroscopy in the range 400–1800 cm−1. The spectrum obtained at ca. 0.4 K of ions captured in He nanodroplets was compared to that measured at ca. 10 K by photodissociation of Ar‐ion complexes. Similar band patterns are obtained by the two techniques that are consistent with calculations for a C2 symmetry structure with a proton shared equally between the two formate moieties. Isotopic substitution experiments point to the nominal parallel stretch of the bridging proton appearing as a sharp, dominant feature near 600 cm−1. Multidimensional anharmonic calculations reveal that the bridging proton motion is strongly coupled to the flanking −COO− framework, an effect that is in line with the expected change in −C=O bond rehybridization upon protonation.
D. A. Thomas, M. Marianski, E. Mucha, G. Meijer, M. A. Johnson, and G. von Helden, Angew. Chem., Int. Ed., 57, 10615-10619 (2018). http://dx.doi.org/10.1002/anie.201805436
Fucose is an essential deoxysugar that is found in a wide range of biologically relevant glycans and glycoconjugates. A recurring problem in mass spectrometric analyses of fucosylated glycans is the intramolecular migration of fucose units, which can lead to erroneous sequence assignments. This migration reaction is typically assigned to activation during collision‐induced dissociation (CID) in tandem mass spectrometry (MS). In this work, we utilized cold‐ion spectroscopy and show for the first time that fucose migration is not limited to fragments obtained in tandem MS and can also be observed in intact glycan ions. This observation suggests a possible low‐energy barrier for this transfer reaction and generalizes fucose migration to an issue that may universally occur in any type of mass spectrometry experiment.
E. Mucha, M. Lettow, M. Marianski, D. A. Thomas, W. B. Struwe, D. J. Harvey, G. Meijer, P. H. Seeberger, G. von Helden, and K. Pagel, Angew. Chem., Int. Ed., 57, 7440-7443 (2018). http://dx.doi.org/10.1002/anie.201801418
Fluoroformate, also known as carbonofluoridate, is an intriguing molecule readily formed by the reductive derivatization of carbon dioxide. In spite of its well-known stability, a detailed structural characterization of the isolated anion has yet to be reported. Presented in this work is the vibrational spectrum of fluoroformate obtained by infrared action spectroscopy of ions trapped in helium nanodroplets, the first application of this technique to a molecular anion. The experimental method yields narrow spectral lines, providing experimental constraints on the structure that can be accurately reproduced using high-level ab initio methods. In addition, two notable Fermi resonances between a fundamental and combination band are observed. The electrostatic potential map of fluoroformate reveals substantial charge density on fluorine as well as on the oxygen atoms, suggesting multiple sites for interaction with hydrogen bond donors and electrophiles, which may in turn lead to intriguing solvation structures and reaction pathways.
D. A. Thomas, E. Mucha, S. Gewinner, W. Schöllkopf, G. Meijer, G. von Helden, J. Phys. Chem. Lett., 9 2305-2310 (2018). http://dx.doi.org/10.1021/acs.jpclett.8b00664
The amino acid serine has long been known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser8H+ structure that is in agreement with all experimental observations. Here, we present the structure of Ser8H+ determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol–1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.
V. Scutelnic, M. A. S. Perez, M. Marianski, S. Warnke, A. Gregor, U. Rothlisberger, M. T. Bowers, C. Baldauf, G. von Helden, T. R. Rizzo, J. Seo, J. Am. Chem. Soc., 140 7554-7560 (2018). http://dx.doi.org/10.1021/jacs.8b02118
The article was highlighted in JACS spotlight as 'Serine Octamer: Possible Key to Biomolecule Handedness' https://pubs.acs.org/doi/10.1021/jacs.8b05773
The hexapeptide NFGAIL is a highly amyloidogenic peptide, derived from the human islet amyloid polypeptide (hIAPP). Recent investigations indicate that presumably soluble hIAPP oligomers are one of the cytotoxic species in type II diabe-tes. Here we use Thioflavin T staining, transmission electron microscopy as well as ion mobility-mass spectrometry coupled to infrared (IR) spectroscopy to study the amyloid formation mechanism and the quaternary- and secondary-structure of soluble NFGAIL oligomers. Our data reveal that at neutral pH NFGAIL follows a nucleation-dependent mechanism to form amyloid fibrils. During the lag phase, highly polydisperse, polymorph, and compact oligomers (oligomer number n=2-13) as well as extended intermediates (n=4-11) are present. IR secondary structural analysis reveals that compact conformations adopt turn-like structures, whereas extended oligomers exhibit a significant amount of β-sheet content. This agrees well with previous molecular dynamic simulations and provides direct experimental evidence that unordered off-pathway NFGAIL aggregates up to the size of at least the 13-mer as well as partially folded β-sheet containing oligomers are coexisting.
W. Hoffmann, K. Folmert, J. Moschner, X. Huang, H. von Berlepsch, B. Koksch, M. T. Bowers, G. von Helden, K. Pagel, J. Am. Chem. Soc., 140, 244–249 (2018). http://dx.doi.org/10.1021/jacs.7b09510
The amino acid serine is known to form a very stable octamer that has properties that set it apart from serine complexes of different sizes or from complexes composed of other amino acids. For example, both singly protonated serine octamers and anionic octamers complexed with two halogen ions strongly prefer homochirality, even when assembled from racemic D,L mixtures. Consequently, the structures of these complexes are of great interest, but no acceptable candidates have so far been identified. Here, we investigate anionic serine octamers coordinated with two chloride ions using a novel technique coupling ion mobility spectrometry–mass spectrometry with infrared spectroscopy, in combination with theoretical calculations. The results allow the identification of a unique structure for (Ser8Cl2)2− that is highly symmetric, very stable and homochiral and whose calculated properties match those observed in experiments.
J. Seo, S. Warnke, K. Pagel, M. T. Bowers, G. von Helden, Nat. Chem., 9, 1263–1268 (2017). http://dx.doi.org/10.1038/nchem.2821
The diversity of stereochemical isomers present in glycans and glycoconjugates poses a formidable challenge for comprehensive structural analysis. Typically, sophisticated mass spectrometry (MS)-based techniques are used in combination with chromatography or ion-mobility separation. However, coexisting structurally similar isomers often render an unambiguous identification impossible. Other powerful techniques such as gas-phase infrared (IR) spectroscopy have been limited to smaller glycans, since conformational flexibility and thermal activation during the measurement result in poor spectral resolution. This limitation can be overcome by using cold-ion spectroscopy. The vibrational fingerprints of cold oligosaccharide ions exhibit a wealth of well-resolved absorption features that are diagnostic for minute structural variations. The unprecedented resolution of cold-ion spectroscopy coupled with tandem MS may render this the key technology to unravel complex glycomes.
E. Mucha, A. I. González Flórez, M. Marianski, D. A. Thomas, W. Hoffmann, W. B. Struwe, H. S. Hahm, S. Gewinner, W. Schöllkopf, P. H. Seeberger, G. von Helden, K. Pagel, Angew. Chem. Int. Ed., 56, 11248–11251 (2017). http://dx.doi.org/10.1002/anie.201702896
Amyloidogenic peptide oligomers are responsible for a variety of neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Due to their dynamic, polydisperse, and polymorphic nature, these oligomers are very challenging to characterize using traditional condensed-phase methods. In the last decade, ion mobility-mass spectrometry (IM-MS) and related gas-phase techniques have emerged as a powerful alternative to disentangle the structure and assembly characteristics of amyloid forming systems. This review highlights recent advances in which IM-MS was used to characterize amyloid oligomers and their underlying assembly pathway. In addition, we summarize recent studies in which IM-MS was used to size- and mass-select species for a further spectroscopic investigation and outline the potential of IM-MS as a tool for the screening of amyloid inhibitors.
W. Hoffmann, G. von Helden, and K. Pagel, Curr. Opin. Struct. Biol., 46, 7-15 (2017). http://dx.doi.org/10.1016/j.sbi.2017.03.002
Amphiphilic porphyrins are of great interest in the field of supramolecular chemistry because they can be fabricated into highly ordered architectures that are stabilized by π–π stacking of porphine rings as well as by non-covalent interactions between their hydrophilic substituents. Protoporphyrin IX (PPIX) has two flexible propionic acid tails and is one of the most common amphiphilic porphyrins. However, unlike other PPIX analogues, PPIX does not form stable extended nanostructures, and the reason for this is still not understood. Here, we employ ion mobility mass spectrometry in combination with infrared multiple photon dissociation spectroscopy to investigate early aggregates of PPIX. The ion mobility results show that growth occurs via single-stranded face-to-face stacking of PPIX. From the infrared spectroscopy on well-defined aggregates, it can be concluded that pairing of the carboxylic acid groups of the tails is a stabilizing element and that such a pairing occurs across a third residue from residue n to residue n+2. The tetramer appears to be especially stable, because all of its propionic acid tails are optimally paired and no free tails to promote further growth are present, which possibly prevents PPIX from forming larger, well-ordered assemblies.
J. Seo, J. Jang, S. Warnke, S. Gewinner, W. Schöllkopf, and G. von Helden, J. Am. Chem. Soc., 138, 16315-16321 (2016). http://dx.doi.org/10.1021/jacs.6b08700
In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.
S. Warnke, W. Hoffmann, J. Seo, E. De Genst, G. von Helden and K. Pagel, J. Am. Soc. Mass Spectrom., 28, 638-646 (2017). http://dx.doi.org/10.1007/s13361-016-1551-5
Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, polydisperse folding intermediates, which occur during fibril formation, are the toxic species in the amyloid-related diseases. Traditional condensed-phase methods are of limited use for characterizing these states because they typically only provide ensemble averages rather than information about individual oligomers. Here we report the first direct secondary-structure analysis of individual amyloid intermediates using a combination of ion mobility spectrometry–mass spectrometry and gas-phase infrared spectroscopy. Our data reveal that oligomers of the fibril-forming peptide segments VEALYL and YVEALL, which consist of 4–9 peptide strands, can contain a significant amount of β-sheet. In addition, our data show that the more-extended variants of each oligomer generally exhibit increased β-sheet content.
J. Seo, W. Hoffmann, S. Warnke, X. Huang, S. Gewinner, W. Schöllkopf, M. T. Bowers, G. von Helden and K. Pagel, Nat. Chem., 9, 39-44 (2017). http://dx.doi.org/10.1038/NCHEM.2615
Can the structures of small to medium-sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion-mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β-lactoglobulin, which are prototypical examples of helical and β-sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved.
J. Seo, W. Hoffmann, S. Warnke, M. T. Bowers, K. Pagel, and G. von Helden, Angew. Chem. Int. Ed., 55, 14173-14176 (2016).
The charge distribution in a molecule is crucially determining its physical and chemical properties. Aminobenzoic acid derivatives are biologically active small molecules, which have two possible protonation sites: the amine (N-protonation) and the carbonyl oxygen (O-protonation). Here, we employ gas-phase infrared spectroscopy in combination with ion mobility-mass spectrometry and density functional theory calculations to unambiguously determine the preferred protonation sites of p-, m-, and o-isomers of aminobenzoic acids as well as their ethyl esters. The results show that the site of protonation does not only depend on the intrinsic molecular properties such as resonance effects, but also critically on the environment of the molecules. In an aqueous environment, N-protonation is expected to be lowest in energy for all species investigated here. In the gas phase, O-protonation can be preferred, and in those cases, both N- and O-protonated species are observed. To shed light on a possible proton migration pathway, the protonated molecule-solvent complex as well as proton-bound dimers are investigated.
J. Seo, S. Warnke, S. Gewinner, W. Schöllkopf, M. T. Bowers, K. Pagel, and G. von Helden, Phys. Chem. Chem. Phys., 18, 25474-25482 (2016).
In this study the gas-phase structure of ubiquitin and its lysine-to-arginine mutants was investigated using ion mobility-mass spectrometry (IM-MS) and electron transfer dissociation-mass spectrometry (ETD-MS). Crown ether molecules were attached to positively charged sites of the proteins and the resulting non-covalent complexes were analyzed. Collision induced dissociation (CID) experiments reveal relative energy differences between the wild type and the mutant crown-ether complexes. ETD-MS experiments were performed to identify the crown ether binding sites. Although not all of the binding sites could be revealed, the data confirm that the first crown ether is able to bind to the N-terminus. IM-MS experiments show a more compact structure for specific charge states of wild type ubiquitin when crown ethers are attached. However, data on ubiquitin mutants reveal that only specific lysine residues contribute to the effect of charge microsolvation. A compaction is only observed for one of the investigated mutants, in which the lysine has no proximate interaction partner. When the lysine residues are involved in salt bridges on the other hand, attachment of crown ethers has little effect on the structure.
M. Göth, F. Lermyte, X. J. Schmitt, S. Warnke, G. von Helden, F. Sobott, K. Pagel, Analyst, 141, 5465-5466 (2016).
Polyalanine based peptides that carry a lysine at the C-terminus ([Ac-AlanLys + H]+) are known to form α-helices in the gas phase. Three factors contribute to the stability of these helices: ɪ) the interaction between the helix macro dipole and the charge, ɪɪ) the capping of dangling C=O groups by lysine and ɪɪɪ) the cooperative hydrogen bond network. In previous studies, the influence of the interaction between the helix dipole and the charge as well as the impact of the capping was studied intensively. Here, we complement these findings by systematically assessing the third parameter, the H-bond network. In order to selectively remove one H-bond along the backbone, we use amide-to-ester substitutions. The resulting depsi peptides were analyzed by ion-mobility and m/z-selective infrared spectroscopy as well as theoretical calculations. Our results indicate that peptides which contain only one ester bond still maintain the helical conformation. We conclude that the interaction between the charge and the helix macro-dipole is most crucial for the formation of the α-helical conformation and a single backbone H-bond has only little influence on the overall stability.
W. Hoffmann, M. Marianski, S. Warnke, J. Seo, C. Baldauf, G. von Helden, and K. Pagel, Phys. Chem. Chem. Phys., 18, 19950-19954 (2016).
Differentiating the structure of isobaric glycopeptides represents a major challenge for mass spectrometry-based characterisation techniques. Here we show that the regiochemistry of the most common N-acetylneuraminic acid linkages of N-glycans can be identified in a site-specific manner from individual glycopeptides using ion mobility-mass spectrometry analysis of diagnostic fragment ions.
In our newest publication we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed-phase proteins. For high charge states a new band appears, substantially red-shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb-driven transitions in secondary structures from mostly helical to extended C5-type hydrogen-bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments.
A. I. González Flórez, E. Mucha, D.-S. Ahn, S. Gewinner, W. Schöllkopf, K. Pagel, G. von Helden Angew. Chem. Int. Ed., 55 3295–3299 (2016).
Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility–mass spectrometry—a method that separates molecules according to their mass, charge, size, and shape—can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility–mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.
J. Hofmann, H. S. Hahm, S. Seeberger, K. Pagel Nature, 526, 241–244 (2015).
Ultracold IR spectra of the protonated five amino acid peptide leu-enkephalin (Tyr-Gly-Gly-Phe-Leu) embedded in superfluid helium droplets have been recorded using a free-electron laser as radiation source. The results show resolved spectra, which are in good agreement with theoretical calculations, as well as with the available gas-phase data indicating that the helium environment does not induce a significant matrix-shift. In addition, the effect of the interaction between the charge and the peptide backbone has been further investigated by complexing protonated leu-enkephalin with one 18-crown-6 molecule. Good agreement between the experimental and theoretical results allow for an assignment of a preferred molecular structure.
A. I. González Flórez, D.-S. Ahn, S. Gewinner, W. Schöllkopf and G. von Helden, Phys. Chem. Chem. Phys., 17, 21902-21911 (2015).
In our newest publication ion mobility-mass spectrometry was used to obtain detailed information about the kinetics of the light-induced trans/cis isomerization process of a new supramolecular azobenzene-based bolaamphiphile. Further experiments revealed that the investigated light-induced structural transition dramatically influences the aggregation behaviour of the molecule.
L. Urner, B. Thota, O. Nachtigall, S. Warnke, G. von Helden, R. Haag, and K. Pagel, Chem. Commun., 51, 8801-8804 (2015).
The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization (ESI) process. Here we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry (IM-MS) to yield gas-phase IR spectra of simultaneously m/z and drift-time resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species - the N- and O-protonated form. Density functional theory (DFT) calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation has been suggested.
S. Warnke, J. Seo, J. Boschmans, F. Sobott, J.H. Scrivens, C. Bleiholder, M.T. Bowers, S. Gewinner, W. Schöllkopf, K. Pagel and G. von Helden, J. Am. Chem. Soc., 137, 4236–4242 (2015).
We would like to cordially invite you and your co-workers to our workshop on ion mobility-mass spectrometry, which will take part from 26. to 27. March 2015 at the Fritz Haber Institute of the Max Planck Society in Berlin.
We are looking forward to seeing you there.
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 + vdWTS) identifies six distinctly different structure types competing in the low-energy regime (≈16 kJ mol−1). For these structure types, we analyze the influence of the PBE and the hybrid PBE0 functional coupled with either a pairwise dispersion correction (PBE + vdWTS, PBE0 + vdWTS) or a many-body dispersion correction (PBE + MBD*, PBE0 + MBD*). We also take harmonic vibrational and rotational free energy into account. Including this, the PBE0 + MBD* functional predicts only one unique conformer to be present at 300 K. We show that this scenario is consistent with both experiments.
F. Schubert, M. Rossi, C. Baldauf, K. Pagel, S. Warnke, G. von Helden, F. Filsinger, P. Kupser, G. Meijer, M. Salwiczek, B. Koksch, M. Scheffler and V. Blum; Phys. Chem. Chem. Phys., 17, 7373-7385 (2015).
The top-down approach in protein sequencing requires simple methods in which the analyte can be readily dissociated at every position along the backbone. In this context, ultraviolet photodissociation (UVPD) recently emerged as a promising tool because, in contrast to slow heating techniques such as collision induced dissociation (CID), the absorption of UV light is followed by a rather statistically distributed cleavage of backbone bonds. As a result, nearly complete sequence coverage can be obtained. It is well-known, however, that gas-phase proteins can adopt a variety of different, sometimes coexisting conformations and the influence of this structural diversity on the UVPD fragmentation behavior is not clear. Using ion mobility-UVPD-mass spectrometry we recently showed that UVPD is sensitive to the higher order structure of gas-phase proteins. In particular, the cis/trans isomerization of certain proline peptide bonds was shown to significantly influence the UVPD fragmentation pattern of two extended conformers of 11+ ubiquitin. Building on these results, we here provide conformer-selective UVPD data for 7+ ubiquitin ions, which are known to be present in a much more diverse and wider ensemble of different structures, ranging from very compact to highly extended species. Our data show that certain conformers fall into groups with similar UVPD fragmentation pattern. Surprisingly, however, the conformers within each group can differ tremendously in their collision cross section. This indicates that the multiple coexisting conformations typically observed for 7+ ubiquitin are caused by a few, not easily inter-convertible, subpopulations.
S. Warnke, G. von Helden, K. Pagel; Proteomics, 16, 2804–2812 (2015).
In natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β2hAla)6-LysH+ to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH+ that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, allied to state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures.
F. Schubert, K. Pagel, M. Rossi, S. Warnke, M. Salwiczek, B. Koksch, G. von Helden, V. Blum, C. Baldauf and M. Scheffler; Phys. Chem. Chem. Phys., 17, 5376-5385 (2015).
In our most recent publication we demonstrate the calibration of travelling wave ion mobility-mass spectrometer to estimate CCS of carbohydrates. Glycosylation is one of the most common post-translational modifications occurring in proteins. A detailed structural characterization of the involved carbohydrates is still challenging, since multiple regio- and stereoisomers with an identical monosaccharide composition may exist. Ion mobility-mass spectrometry (IM-MS) is a promising technique for the separation and structural analysis of complex carbohydrate. Measured drift-times can be converted into collision cross sections (CCSs), which can be compared and implemented into databases. However, most of the currently used commercial IM-MS instruments utilize a non-uniform travelling wave field to propel the ions through the IM cell. As a result, CCSs measurements cannot be performed directly. Here, we present a calibration dataset for negatively charged N-glycans and their fragments. Moreover, we show that the well defined polysaccharide dextran is also a suitable calibrant for CCS estimations. In addition, our data indicate that a considerably increased error has to be taken into account when reference CCSs acquired in a different drift gas are used for calibration.
J. Hofmann, W. B. Struwe, C. A. Scarff, J. H. Scrivens, D. J. Harvey, K. Pagel, Anal. Chem., 86 (21), 10789–10795 (2014).
In our most recent publication we investigated conformer-selected ubiquitin and their different ultraviolet photodissociation (UVPD) spectra.
S. Warnke, C. Baldauf, M. Bowers, K. Pagel, G. von Helden; J. Am. Chem. Soc., 136 (29), 10308–10314 (2014).
The article also received a spotlight by Jeffrey M. Perkel.
At the beginning of December our group measured several IR spectra of biomolecules with the new FHI free electron laser (FEL). Stephan Warnke coupled his drift tube ion mobility-mass spectrometer to the FEL and recorded an IR spectrum of a mass- and conformer-selected Ubiquitin (see left picture).
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of either Li+ or Na+, which can have different conformational effects on the same peptide, by using state-of-the-art density-functional theory (including van der Waals effects) and gas-phase infrared spectroscopy. We also assess the predictive power of current approximate density functionals for peptide-cation systems and compare to results with those of established protein force fields as well as high-level quantum chemistry calculations.
C. Baldauf, K. Pagel, S. Warnke, G. von Helden, B. Koksch, V. Blum, M. Scheffler; Chem. Eur. J. 19, 11224-11234 (2013).
Due to their immense structural diversity and complexity it is still very challenging to fully characterize the structure of complex carbohydrates. A new and very promising technique to overcome these limitations is mobility-mass spectrometry (IM-MS). Here ions with identical atomic composition and mass, but different structure can be separated according to their shape and collision cross section (CCS). With the emergence of commercially available instruments in 2006 the technology became readily available. Because of the nonhomogeneous, travelling wave (TW) field utilized in these instruments, however, CCS values currently cannot be determined directly from the drift times measured. Instead, an external calibration using compounds of known CCS and similar molecular identity is required.
K. Pagel, D. J. Harvey; Anal. Chem. 85, 5138-5145 (2013).
There is ongoing debate on the extent to which protein structure is retained after transfer into the gas phase. Here, using ion mobility-mass spectrometry (IM-MS), we investigate the impact of side-chain backbone interactions on the structure of gas-phase protein ions by non-covalent attachment of crown ethers (CE). Our results indicate that in the absence of solvent, secondary interactions between charged lysine side chains and backbone carbonyls can significantly influence the structure of a protein. Once the charged residues are capped with CEs, certain charge states of the protein are found to undergo a significant structural compaction.
S. Warnke, G. von Helden, K. Pagel; J. Am. Chem. Soc. 135, 1177-1180 (2013).
The article was highlighted in Nature Chemistry as ‘Crowning Achievement’ http://dx.doi.org/10.1038/nchem.1590
Address: Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany