Cold ion spectroscopy for structural identifications of biomolecules

Boyarkin, Oleg V.

doi:10.1080/0144235x.2018.1547453

Cited by 46 publications

(74 citation statements)

References 110 publications

(124 reference statements)

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“…Infrared (IR) spectroscopy of gas-phase molecular ions, on the other hand, can be exquisitely sensitive to the smallest of structural details [18,19]. Carbohydrates possess hydroxy groups, amines, and other substituents that can serve as structural probes because their frequencies will be highly characteristic of their local environment.…”

Section: Introductionmentioning

confidence: 99%

Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion-Mobility Spectrometry and Cryogenic Ion Spectroscopy

Warnke

Faleh

Scutelnic

et al. 2019

J. Am. Soc. Mass Spectrom.

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The analysis of carbohydrates, or glycans, is challenging for established structure-sensitive gas-phase methods. The multitude of possible stereo-, regio-and structural isomers make them substantially more complex to analyze than DNA or proteins, and no one method is currently able to fully resolve them. While the combination of tandem mass spectrometry (MS) and ion mobility spectrometry (IMS) have made important inroads in glycan analysis, in many cases this approach is still not able to identify the precise isomeric form. To advance the techniques available for glycan analysis we employ two important innovations. First, we perform ultrahigh-resolution mobility separation using structures for lossless ion manipulations (SLIM) for isomer separation and pre-selection. We then complement this IMS-MS stage with a cryogenic IR spectroscopic dimension, since a glycan's vibrational spectrum provides a fingerprint that is extremely sensitive to the precise isomeric form. Using this unique approach in conjunction with oxygen-18 isotopic labelling, we show on a range of disaccharides how the two a and b anomers that every reducing glycan adopts in solution can be readily separated by mobility and identified based on their IR spectra. In addition to highlighting the power of our technique to detect minute differences in the structure of isomeric carbohydrates, these results provide the means to determine if and when anomericity is retained during collision-induced dissociation (CID) of larger glycans.

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Section: Introductionmentioning

confidence: 99%

Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion-Mobility Spectrometry and Cryogenic Ion Spectroscopy

Warnke

Faleh

Scutelnic

et al. 2019

J. Am. Soc. Mass Spectrom.

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“…by forming  H-bonds. The series of origin electronic transitions collected over the years for aromatic residues 327 provide useful guidelines to confirm assignments derived most of the time from IR spectroscopy. The sensitivity of electronic states to the structure became clear on the example of the L a and L b states of capped tryptophan (cf.…”

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confidence: 99%

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

et al. 2020

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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][90][91][92][93][94][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. Further aspects of peptide structure in gas phase The role of protection groupsWith 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...

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“…Since the pioneering work of the EPLF team [235], photo-fragment and photo-detachment spectroscopy in cryogenically cooled ion traps has flourished [175,245]. This method has opened the door to the high precision study of very big and "floppy" molecular systems; the characterization, for example, of decapeptide [246]-a polypeptide consisting of a chain of ten amino acids-would previously have been inconceivable.…”

Section: Discussionmentioning

confidence: 99%

Roadmap on dynamics of molecules and clusters in the gas phase

et al. 2021

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This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science. Graphic abstract

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Cold ion spectroscopy for structural identifications of biomolecules

Cited by 46 publications

References 110 publications

Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion-Mobility Spectrometry and Cryogenic Ion Spectroscopy

Separation and Identification of Glycan Anomers Using Ultrahigh-Resolution Ion-Mobility Spectrometry and Cryogenic Ion Spectroscopy

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Roadmap on dynamics of molecules and clusters in the gas phase

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