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Although nanopores can be used for single-molecule sequencing of nucleic acids using low-cost portable devices, the characterization of proteins and their modifications has yet to be established. Here, we show that hydrophilic or glycosylated peptides translocate too quickly across FraC nanopores to be recognized. However, high ionic strengths (i.e., 3 M LiCl) and low pH (i.e., pH 3) together with using a nanopore with a phenylalanine at its constriction allows the recognition of hydrophilic peptides, and to distinguish between mono- and diglycosylated peptides. Using these conditions, we devise a nanopore method to detect, characterize, and quantify post-translational modifications in generic proteins, which is one of the pressing challenges in proteomic analysis. ispartof: NANO LETTERS vol:22 issue:13 pages:5357-5364 ispartof: location:United States status: published

Selective modification of carbohydrate residues in glycopeptides is highly relevant as a tool in glycobiology. In particular, oxidation allows for subsequent ligation with a label or handle and can be effectuated enzymatically or chemically. Chemical oxidation of carbohydrate residues in glycopeptides is nearly invariably done using periodate cleavage, leading to aldehydes. In this work, we applied palladium-catalyzed oxidation for the same purpose. The catalyst, [(neocuproine)PdOAc]2OTf2, developed for the site-selective oxidation of mono- and oligosaccharides on preparative scale, proved suitable for the oxidation of glucose residues in a series of glucopeptides. Careful optimization of the reaction conditions is necessary to get acceptable conversions without excessive over-oxidation of amino acid side-chains, in particular threonine. The resulting carbonyl function can be used for an oxime-ligation to biotin. A protocol for the analysis of the products using mass spectrometry is also reported.

Processivity is an important feature of enzyme families such as DNA polymerases, polysaccharide synthases, and protein kinases, to ensure high fidelity in biopolymer synthesis and modification. Here, we reveal processive character in the family of cytoplasmic protein N-glycosyltransferases (NGTs). Through various activity assays, intact protein mass spectrometry, and proteomics analysis, we established that NGTs from nontypeable Haemophilus influenzae and Actinobacillus pleuropneumoniae modify an adhesin protein fragment in a semiprocessive manner. Molecular modeling studies suggest that the processivity arises from the shallow substrate binding groove in NGT, which promotes the sliding of the adhesin over the surface to allow further glycosylations without temporary dissociation. We hypothesize that the processive character of these bacterial protein glycosyltransferases is the mechanism to ensure multisite glycosylation of adhesins in vivo, thereby creating the densely glycosylated proteins necessary for bacterial self-aggregation and adherence to human cells, as a first step toward infection.

For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates., For bacterial arginine rhamnosylation, the rhamnosyltransferase EarP specifically recognizes a β-hairpin structure in the acceptor substrate.

Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.

Here we report a novel method of site-selective oxidation of glucose moieties on individual glycopeptides and on a mixture of tryptic glycopeptides. The organometallic catalyst [(neocuproine)PdOAc]2OTf2, that was previously shown to perform regioselective C3-oxidation of glucosides, was used in the scope of this work. The selectivity of the catalyst towards glucose and the sensitivity of specific amino acid residues to oxidation was explored by screening a select panel of glycopeptides in the oxidation reactions. We reveal that glucosylated peptides are more readily oxidized compared to galactosylated peptides, and Thr/Ser-oxidation is a concomitant side-reaction. The oxidation methodology was also applied to the complex mixture of tryptic glucopeptides that was generated from the fragment of Haemophilus influenzae adhesin glycoprotein. The resulting keto-group of the glucose was further transformed into an oxime functionality, which allows introduction of various groups of interest. The methodology outlined in this work will allow to perfrom late-stage modification of glucopeptides as well as selective oxidation and functionalization of tryptic glucopeptides for proteomics analysis.

Here we report a novel method of site-selective oxidation of glucose moieties on individual glycopeptides and on a mixture of tryptic glycopeptides. The organometallic catalyst [(neocuproine)PdOAc]2OTf2, that was previously shown to perform regioselective C3-oxidation of glucosides, was used in the scope of this work. The selectivity of the catalyst towards glucose and the sensitivity of specific amino acid residues to oxidation was explored by screening a select panel of glycopeptides in the oxidation reactions. We reveal that glucosylated peptides are more readily oxidized compared to galactosylated peptides, and Thr/Ser-oxidation is a concomitant side-reaction. The oxidation methodology was also applied to the complex mixture of tryptic glucopeptides that was generated from the fragment of Haemophilus influenzae adhesin glycoprotein. The resulting keto-group of the glucose was further transformed into an oxime functionality, which allows introduction of various groups of interest. The methodology outlined in this work will allow to perfrom late-stage modification of glucopeptides as well as selective oxidation and functionalization of tryptic glucopeptides for proteomics analysis.

Processivity is an important feature of enzyme families such as DNA polymerases, polysaccharide synthases, and protein kinases, to ensure high fidelity in biopolymer synthesis and modification. Here, we reveal processive character in the family of cytoplasmic protein N-glycosyltransferases (NGTs). Through various activity assays, intact protein mass spectrometry, and proteomics analysis, we established that NGTs from nontypeable Haemophilus influenzae and Actinobacillus pleuropneumoniae modify an adhesin protein fragment in a semiprocessive manner. Molecular modeling studies suggest that the processivity arises from the shallow substrate binding groove in NGT, which promotes the sliding of the adhesin over the surface to allow further glycosylations without temporary dissociation. We hypothesize that the processive character of these bacterial protein glycosyltransferases is the mechanism to ensure multisite glycosylation of adhesins in vivo, thereby creating the densely glycosylated proteins necessary for bacterial self-aggregation and adherence to human cells, as a first step toward infection.

Sugars are fascinating and highly diverse molecules with a myriad of roles in all living cells. Importantly, bacteria often utilize sugars in their infection strategies. They are found on the surface of bacterial cells as parts of the larger structures responsible for movement, protection, adhesion, camouflage and interactions with the host immune system. In addition, sugars also decorate the biomolecules inside the cell, influencing their properties and functions, keeping the bacterial cell running. Interestingly, bacterial sugars are frequently distinctly different from human, which means that we can potentially target infectious bacteria using these sugars without damaging our own systems. In the projects described in this thesis, the production systems of important sugar structures from infectious bacteria were investigated and their mechanism studied in detail. For example, in one project, it was elucidated how surface adhesion molecules are decorated with multiple sugars and how to manipulate this process. In another project it was uncovered why only specific proteins are decorated with a rare bacterial sugar. With these findings our understanding of bacterial sugar systems and their roles in infection was expanded. Additionally, by uncovering parts of the mechanism, useful knowledge was gained for developing molecules that can efficiently and selectively block these processes.

Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification., Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.

Processivity is an important feature of enzyme families such as DNA polymerases, polysaccharide synthases and protein kinases, to ensure high fidelity in biopolymer synthesis and modification. Here we reveal processive character in the family of cytoplasmic protein N-glycosyltransferases (NGTs). Through various activity assays, intact protein mass spectrometry and proteomics analysis, we established that NGTs from non-typeable Haemophilus influenzae and Actinobacillus pleuropneumoniae modify an adhesin protein fragment in a semi-processive manner. Molecular modeling studies suggest that the processivity arises from the shallow substrate binding groove in NGT, that promotes the sliding of the adhesin over the surface to allow further glycosylations without temporary dissociation. We hypothesize that the processive character of these bacterial protein glycosyltransferases is the mechanism to ensure multisite glycosylation of adhesins in vivo, thereby creating the densely glycosylated proteins necessary for bacterial self-aggregation and adherence to human cells, as a first step towards infection.

With the increasing resistance of bacteria to current antibiotics, novel compounds are urgently needed to treat bacterial infections. Streptozotocin (STZ) is a natural product that has broad-spectrum antibiotic activity, albeit with limited use because of its toxicity to pancreatic &beta, cells. In an attempt to derivatize STZ through structural modification at the C3 position, we performed the synthesis of three novel STZ analogues by making use of our recently developed regioselective oxidation protocol. Keto-STZ (2) shows the highest inhibition of bacterial growth (minimum inhibitory concentration (MIC) and viability assays), but is also the most cytotoxic compound. Pre-sensitizing the bacteria with GlcNAc increased the antimicrobial effect, but did not result in complete killing. Interestingly, allo-STZ (3) revealed moderate concentration-dependent antimicrobial activity and no cytotoxicity towards &beta, cells, and deoxy-STZ (4) showed no activity at all.

With the increasing resistance of bacteria to current antibiotics, novel compounds are urgently needed to treat bacterial infections. Streptozotocin (STZ) is a natural product that has broad-spectrum antibiotic activity, albeit with limited use because of its toxicity to pancreatic β cells. In an attempt to derivatize STZ through structural modification at the C3 position, we performed the synthesis of three novel STZ analogues by making use of our recently developed regioselective oxidation protocol. Keto-STZ (2) shows the highest inhibition of bacterial growth (minimum inhibitory concentration (MIC) and viability assays), but is also the most cytotoxic compound. Pre-sensitizing the bacteria with GlcNAc increased the antimicrobial effect, but did not result in complete killing. Interestingly, allo-STZ (3) revealed moderate concentration-dependent antimicrobial activity and no cytotoxicity towards β cells, and deoxy-STZ (4) showed no activity at all.