Exploring Carbohydrate−Peptide Interactions in the Gas Phase: Structure and Selectivity in Complexes of Pyranosides with N-Acetylphenylalanine Methylamide

Exploring the interaction sites in glucose and galactose using phenol as a probe

Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.

Noncovalently Tagged Gas Phase Complex Ions for Screening Unknown Contaminant Metabolites in Plants

Screening the metabolites of emerging organic contaminants (EOCs) from complicated biological matrices is an important but challenging task. Although stable isotope labeling (SIL) is frequently used to facilitate the identification of contaminant metabolites from redundant interfering components, the isotopically labeled reagents are expensive and difficult to synthesize, which greatly constrains the application of the SIL method. Herein, a new online noncovalent tagging method was developed for screening the metabolites of 1H-benzotriazol (BT) based on the characteristic structural moieties reserved in the metabolites. By selecting β-cyclodextrin (β-CD) as a macrocyclic tagging reagent, metabolites with the reserved moiety were expected to exhibit a characteristic shift of the mass-to-charge ratio (Δm/z = 1134.3698) after being noncovalently tagged by β-CD. Based on the characteristic mass shift, the suspected features were reduced by 1 order of magnitude, as numerous interfering species that could not be effectively tagged by β-CD were excluded. From these suspected features, two metabolites of BT that have not been reported before were successfully screened out. The significant characteristic mass shift caused by the noncovalent tagging method is easier to identify with more confidence than the previously reported SIL method. Besides, noncovalent tagging reagents can be much more accessible and less expensive than isotopically labeled reagents. Hence, this online noncovalent tagging method can be an intriguing alternative to the conventional SIL method.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

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, in a controlled molecular environment, when successively adding aggregation partners. 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 bottom-up 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. Against this background, 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 behavior 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.

Sugar-peptidic bond interactions: spectroscopic characterization of a model system

Sugars are small carbohydrates which play numerous roles in living organisms such as storage of energy or as structural components. Modifications of specific sites within the glycan chain can modulate a carbohydrate's overall biological function as it happens with nucleic acids and proteins. Hence, identifying discrete carbohydrate modifications and understanding their biological effects is essential. A study of such processes requires of a deep knowledge of the interaction mechanism at the molecular level. Here, we use a combination of laser spectroscopy in jets and quantum mechanical calculations to characterize the interaction between phenyl-β-d-glucopyranoside and N-methylacetamide as a model to understand the interaction between a sugar and a peptide bond. The most stable structure of the molecular aggregate shows that the main interaction between the peptide fragment and the sugar proceeds via a C[double bond, length as m-dash]OH-O2 hydrogen bond. A second conformer was also found, in which the peptide establishes a C[double bond, length as m-dash]OH-O6 hydrogen bond with the hydroxymethyl substituent of the sugar unit. All the conformers present an additional interaction point with the aromatic ring. This particular preference of the peptide for the hydroxyl close to the aromatic ring could explain why glycogenin uses tyrosine in order to convert glucose into glycogen by exposing the O4H hydroxyl group for the other glucoses for the polymerization to take place.

Dipeptide-Based Carbohydrate Receptors and Polymers for Glycopeptide Enrichment and Glycan Discrimination

Glycoproteomics identifies and catalogs protein glycosylation and explores its impact on protein conformations and biofunctions. However, these studies are restricted by the bottleneck to enrich low-abundance glycopeptides from complex biosamples and the difficulties in analyzing glycan structures by mass spectrometry. Here, we report dipeptide as a simple but promising carbohydrate binding platform to tackle these problems. We build a hydropathy-index-based strategy for sequence optimization and screen out three optimal dipeptide sequences from 54 types of dipeptides. The optimized dipeptide-based homopolymers display excellent performance (e.g., selectivity up to ∼70% for real biosamples and strong anti-interference capacity capable of resisting 1000-fold bovine serum albumin interference) in glycopeptide enrichment. Meanwhile, our polymers exhibit high-efficiency chromatographic separation toward oligosaccharides with different compositions, polymerization degrees and even their linkage isomers. This brings another attractive feature that our materials can discriminate subtly variable glycan structures of glycopeptides, especially, isomeric glycosidic linkages. These features provide a solid foundation to analyze the complex glycan structures and glycosites simultaneously, which will benefit future development of glycoproteomics and glycobiology.

Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique

Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH₂ (SIVSF-NH₂), which is a partial sequence of a binding site in a β₂-adrenaline receptor protein.

Modeling the tyrosine–sugar interactions in supersonic expansions: glucopyranose–phenol clusters

We present here the structure of glucopyranoe–phenol complexes, as revealed by mass-resolved laser spectroscopy and DFT calculations.

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge

The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.

Carbohydrates

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide

The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.

Carbohydrate-aromatic interactions

The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition. With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units. In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process. The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy.

Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap

Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH(+) and SarSarH(+) [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual isomers to the overlapping vibrational band patterns are completely isolated using a pump-probe photochemical hole-burning scheme involving two tunable infrared lasers and two stages of mass selection (hence IR(2)MS(2)). These patterns are then assigned by comparison with harmonic (MP2/6-311+G(d,p)) spectra for various possible conformers. Both systems occur in two conformations based on cis and trans configurations with respect to the amide bond. In addition to the usual single intramolecular hydrogen bond motif between the protonated amine and the nearby amide oxygen atom, cis-SarSarH(+) adopts a previous unreported conformation in which both amino NH's act as H-bond donors. The correlated red shifts in the NH donor and C═O acceptor components of the NH···O═C linkage to the acid group are unambiguously assigned in the double H-bonded conformer.

Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol

Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.

Binding of inositol stereoisomers to model amyloidogenic peptides

The self-aggregation of proteins into amyloid fibrils is a pathological hallmark of numerous incurable diseases such as Alzheimer's disease. scyllo-Inositol is a stereochemistry-dependent in vitro inhibitor of amyloid formation. As the first step to elucidate its mechanism of action, we present molecular dynamics simulations of scyllo-inositol and its inactive stereoisomer, chiro-inositol, with simple peptide models, alanine dipeptide (ADP) and (Gly-Ala)(4). We characterize molecular interactions and compute equilibrium binding constants between inositol and ADP as well as, successively, monomers, amorphous aggregates, and fibril-like β-sheet aggregates of (Gly-Ala)(4). Inositol interacts weakly with all peptide systems considered, with millimolar to molar affinities, and displaces the conformational equilibria of ADP but not of the (Gly-Ala)(4) systems. However, scyllo- and chiro-inositol adopt different binding modes on the surface of β-sheet aggregates. These results suggest that inositol does not inhibit amyloid formation by breaking up preformed aggregates but rather by binding to the surface of prefibrillar aggregates.