Isopeptide bond formation mediated by δ-selenolysine for chemical ubiquitination.

Protein ubiquitination is involved in nearly all biological processes in Eukaryotes. To gain precise insights into the function of ubiquitination in these processes, researchers frequently employ ubiquitinated protein probes with well-defined structures. While chemical protein synthesis has afforded a variety of ubiquitinated protein probes, there remains a demand for efficient synthesis methods for complex probes, such as ubiquitinated glycoproteins and ubiquitinated cysteine-containing proteins. In this study, we introduce a new method to obtain ubiquitinated proteins through isopeptide bond formation mediated by δ-selenolysine residues. We synthesized δ-selenolysine derivatives in both L- and D-forms starting from DL-δ-hydroxy-DL-lysine, accomplished by substituting the δ-mesylate with KSeCN and by enzymatic optical resolution with L- and D-aminoacylase. We synthesized ubiquitin (46-76)-α-hydrazide with a δ-seleno-L-lysine residue at position 48, as well as ubiquitin (46-76)-α-thioester, using solid-phase peptide synthesis. Subsequently, the δ-selenolysine-mediated ligation of these peptides, followed by one-pot deselenization, provided the desired isopeptide-linked ubiquitin peptide. The new δ-selenolysine-mediated isopeptide bond formation offers an alternative method to obtain complex ubiquitin- and ubiquitin-like probes with multiple post-translational modifications. These probes hold promise for advancing our understanding of ubiquitin biology.

Isolation and characterization of high-mannose type glycans containing five or six mannose residues from hen egg yolk.

High-mannose type glycans play important roles in biosynthesis of glycoproteins including glycoprotein quality control system. In the endoplasmic reticulum (ER), α1,2-mannosidases cleave several mannose (Man) residues to give small high-mannose type glycans, such as glycans containing five or six mannose residues (M5-glycan or M6-glycan). These glycans are reported to act as a signal for degradation processes of glycoproteins in the ER. In this work, we isolated the M5-glycan and the M6-glycan from delipidated egg yolk and confirmed that their structures were identical to human type glycans based on rigorous NMR experiments, suggesting the potential use for semisynthesis of glycoconjugates and glycan analysis.

The phototroph-specific ß-hairpin structure of the γ subunit of FoF1-ATP synthase is important for efficient ATP synthesis of cyanobacteria.

The FoF1 synthase produces ATP from ADP and inorganic phosphate. The γ subunit of FoF1 ATP synthase in photosynthetic organisms, which is the rotor subunit of this enzyme, contains a characteristic ß-hairpin structure. This structure is formed from an insertion sequence that has been conserved only in phototrophs. Using recombinant subcomplexes, we previously demonstrated that this region plays an essential role in the regulation of ATP hydrolysis activity, thereby functioning in controlling intracellular ATP levels in response to changes in the light environment. However, the role of this region in ATP synthesis has long remained an open question because its analysis requires the preparation of the whole FoF1 complex and a transmembrane proton-motive force. In this study, we successfully prepared proteoliposomes containing the entire FoF1 ATP synthase from a cyanobacterium, Synechocystis sp. PCC 6803, and measured ATP synthesis/hydrolysis and proton-translocating activities. The relatively simple genetic manipulation of Synechocystis enabled the biochemical investigation of the role of the ß-hairpin structure of FoF1 ATP synthase and its activities. We further performed physiological analyses of Synechocystis mutant strains lacking the ß-hairpin structure, which provided novel insights into the regulatory mechanisms of FoF1 ATP synthase in cyanobacteria via the phototroph-specific region of the γ subunit. Our results indicated that this structure critically contributes to ATP synthesis and suppresses ATP hydrolysis.

Antiparkinsonian drugs as potent contributors to nocturnal sleep in patients with Parkinson's disease.

OBJECTIVE: To clarify whether antiparkinsonian drugs contribute to nocturnal sleep disturbances in patients with Parkinson's disease (PD). BACKGROUND: Although the major antiparkinsonian drugs L-dopa and dopamine agonists (DAs) have been found to affect sleep, little is known about the effects of specific drugs on sleep in PD patients. METHODS: The study participants consisted of 112 PD patients (median age 72.5 years [inter-quartile range: IQR 65-79]; mean disease duration 8.44 years [standard deviation: 7.33]; median Hoehn and Yahr stage 3 [IQR 2-3.75]) taking one of three types of non-ergot extended-release DAs (rotigotine 32; pramipexole 44; ropinirole 36) with or without L-dopa (median daily total dosage of antiparkinsonian drugs 525.5 mg [IQR 376.25-658] levodopa equivalent dose [LED]). Participants were assessed using the PD Sleep Scale-2 (PDSS-2). RESULTS: For the whole PD patient cohort, the PDSS-2 sleep disturbance domain score and the scores for item 1 assessing sleep quality and item 8 assessing nocturia were positively correlated with daily total dosage of antiparkinsonian drugs and dosage of L-dopa, but not with the dosage of DAs. Sub-analysis according to DA treatment revealed that DA dosage was not correlated with item 1 or 8 score in any of the subgroups. The LED ratio of rotigotine to the total dosage of antiparkinsonian drugs was inversely correlated with the item 1 score. CONCLUSIONS: These data suggest that antiparkinsonian drugs, in particular L-dopa, adversely affect nocturnal sleep in PD patients, especially in terms of sleep quality and nocturia. Thus, adjusting both the total dosage of antiparkinsonian drugs and the dose-ratio of L-dopa might be key actions for alleviating poor sleep quality in patients with PD. Among DAs, we found a clear positive correlation between the dose-ratio of rotigotine and sleep quality. Thus, partial L-dopa replacement with rotigotine could improve sleep quality in patients with PD.

Synthesis and Self-Assembly Properties of Bola-Amphiphilic Glycosylated Lipopeptide-Type Supramolecular Hydrogels Showing Colour Changes Along with Gel-Sol Transition.

Supramolecular hydrogels formed by self-assembly of low-molecular-weight amphiphiles (hydrogelators) have attracted significant attention, as smart and soft materials. However, most of the observed stimuli-responsive behaviour of these supramolecular hydrogels are limited to gel-sol transitions. In this study, we present bola-amphiphilic glycosylated lipopeptide-type supramolecular hydrogelators that exhibit reversible thermochromism along with a gel-sol transition. The bola-amphiphiles have mono-, di-, tri- or tetra-phenylalanine (F) as a short peptide moiety. We investigate and discuss the effects of the number of F residues on the gelation ability and the morphology of the self-assembled nanostructures.

Chemical Synthesis of an Erythropoietin Glycoform Having a Triantennary N-Glycan: Significant Change of Biological Activity of Glycoprotein by Addition of a Small Molecular Weight Trisaccharide.

The glycosylation of proteins contributes to the modulation of the structure and biological activity of glycoproteins. Asparagine-linked glycans (N-glycans) of glycoproteins naturally exhibit diverse antennary patterns, such as bi-, tri-, and tetra-antennary forms. However, there are no chemical or biological methods to obtain homogeneous glycoproteins via the intentional alteration of the antennary form of N-glycans. Thus, the functions of the individual antennary form of N-glycan at a molecular level remain unclear. Herein, we report the chemical synthesis of an erythropoietin (EPO) glycoform having a triantennary sialylglycan at position 83, as well as two biantennary sialylglycans at both positions 24 and 38. We demonstrated efficient liquid-phase condensation reactions to prepare a sialylglycopeptide having a triantennary N-glycan prepared by the addition of a Neu5Ac-α-2,6-Gal-ß-1,4-GlcNAc element to the biantennary glycan under semisynthetic conditions. The molecular weight of the newly added antennary element was ∼3% of the EPO glycoform, and the introduced position was the most distant from the bioactive protein. However, in vivo assays using mice revealed that the additional antennary element at position 83 dramatically increased the hematopoietic activity compared to a commercially available native EPO. These unprecedented data clearly indicate that the antennary pattern of N-glycans inherently plays a critical role in the modulation of protein functions.

Chemical Synthesis of Ubiquitinated High-Mannose-Type N-Glycoprotein CCL1 in Different Folding States.

Degradation of misfolded glycoproteins by the ubiquitin-proteasome system (UPS) is a very important process for protein homeostasis. To demonstrate the accessibility toward a ubiquitinated glycoprotein probe for the study of glycoprotein degradation by UPS, we synthesized ubiquitinated glycoprotein CC motif chemokine 1 (CCL1) bearing a high-mannose-type N-glycan, starting from six peptide segments. A native isopeptide linkage was constructed using δ-thiolysine (thioLys)-mediated chemical ligation. CCL1 glycopeptide with a high-mannose-type N-glycan as well as a δ-thioLys residue was synthesized chemically. The chemical ligation between δ-thioLys-containing glycopeptide and ubiquitin-α-thioester successfully yielded a ubiquitinated glycopeptide with a native isopeptide bond after desulfurization, even in the presence of a large N-glycan. In vitro folding experiments under reduced and redox conditions gave the desired two types of ubiquitinated glycosylated CCL1s, consisting of unfolded CCL1 and folded ubiquitin, and the folded form of both CCL1 as well as ubiquitin. We achieved the chemical synthesis of a complex protein molecule that contains not only the two major post-translational modifications, ubiquitination and glycosylation, but also controlled folding states of ubiquitin and CCL1. These chemical probes could have useful applications in the study of complex ubiquitin biology and glycobiology.

Structural diversification of bola-amphiphilic glycolipid-type supramolecular hydrogelators exhibiting colour changes along with the gel-sol transition.

We diversified the structures of bola-amphiphilic glycolipid-type supramolecular hydrogelators that exhibited reversible thermochromism along with a gel-sol transition. The hydrogelators were designed and synthesized to have homo- or hetero-saccharides on each end of their molecules. Herein, the effects of the saccharides' structure on the gelation ability are discussed.

Acceleration and Deceleration Factors on the Hydrolysis Reaction of 4,6-O-Benzylidene Acetal Group.

The benzylidene acetal group is one of the most important protecting groups not only in carbohydrate chemistry but also in general organic chemistry. In the case of 4,6-O-benzylidene glycosides, we previously found that the stereochemistry at 4-position altered the reaction rate constant for hydrolysis of benzylidene acetal group. However, a detail of the acceleration or deceleration factor was still unclear. In this work, the hydrolysis reaction of benzylidene acetal group was analyzed using the Arrhenius and Eyring plot to obtain individual parameters for glucosides (Glc), mannosides (Man), and galactosides (Gal). The Arrhenius and Eyring plot indicated that the pre-exponential factor (A) and ΔS⧧ were critical for the smallest reaction rate constant of Gal among nonacetylated substrates. On the other hand, both Ea/ΔH⧧ and A/ΔS⧧ were influential for the smallest reaction rate constant of Gal among diacetylated substrates. All parameters obtained suggested that the rate constant for hydrolysis reaction was regulated by protonation and hydration steps along with solvation. The obtained parameters support wide use of benzylidene acetal group as orthogonal protection of cis- and trans-fused bicyclic systems through the fast hydrolysis of the trans-fused benzylidene acetal group.

Paeonol, an Ingredient of Kamishoyosan, Reduces Intracellular Lipid Accumulation by Inhibiting Glucocorticoid Receptor Activity in 3T3-L1 Cells.

Excessive triglyceride accumulation in lipid-metabolizing tissues is associated with an increased risk of a variety of metabolic diseases. Kamishoyosan (KSS) is a Kampo composed of 10 constituent herbs, and contains moutan cortex (MC) and paeonol (PN) as the major ingredient of MC. Here, we demonstrate the molecular mechanism underlying the effect of KSS on the differentiation of mouse preadipocytes (3T3-L1 cells). KSS inhibited the accumulation of triglycerides in a dose-dependent manner in 3T3-L1 cells that were induced to differentiate into adipocytes. We also found that MC and PN were responsible for the anti-adipogenetic effect of KSS and significantly suppressed the expression of CCAAT/enhancer-binding proteins-δ (C/EBP-δ) mRNA 3 days after the induction of differentiation. Thus, PN may contribute to the anti-adipogenetic property of MC in 3T3-L1 cells. In addition, PN inhibited dexamethasone (Dex)-induced glucocorticoid receptor (GR) promoter activity. Taken together, these results suggest that PN suppresses C/EBP-δ expression by inhibiting Dex-induced GR promoter activity at the early stage of differentiation and, consequently, delays differentiation into mature adipocytes. Our results suggest that the habitual intake of Kampo-containing PN contributes to the prevention of the onset of metabolic diseases by decreasing the excessive accumulation of triglycerides in lipid-metabolizing tissues.

Chemical Modification of the N Termini of Unprotected Peptides for Semisynthesis of Modified Proteins by Utilizing a Hydrophilic Protecting Group.

A simple and efficient strategy for the selective modification of the peptide N terminus with an unnatural amino acid is described. A peptide having a SUMO-HisTag-TEV sequence (SUMO: small ubiquitin-related modifier, TEV: tobacco etch virus) preceding the N terminus of the target peptide was designed. Recombinant expression in E. coli and subsequent SUMO protease cleavage yielded the HisTag-TEV-target peptide. Partial protection of the lysine side chains of this peptide with d-glucopyranosyloxycarbonyl and removal of the HisTag-TEV sequence by TEV protease yielded the partially protected peptide with a free N-terminal amine. Coupling of selenocysteine selectively at the N terminus and subsequent acidic deprotection of the carbohydrate protecting groups yielded a modified peptide that can be used for native chemical ligation (NCL). As a proof of concept, the modification of a longer recombinant peptide with selenocysteinylserine (GalNAc) at the N terminus was demonstrated.

N,N-Dimethylaminoxy Carbonyl, a Polar Protecting Group for Efficient Peptide Synthesis.

Peptide coupling with minimal protection is one of the desired methods for the synthesis of peptides and proteins. To achieve regioselective amide bond formation, side chain protection is often essential; however, protecting groups potentially diminish peptide solubility and render the polar polyamide chain amphipathic due to their apolar nature. In this manuscript, we describe a new protecting group, N,N-dimethylaminoxy carbonyl (Dmaoc), and its use in peptide coupling reactions. The Dmaoc group has a relatively polar character compared to the Boc group, which is a conventional protecting group for the N ε-amine of Lys residues. This polar protecting group is removable by reduction in the buffer containing (±)-dithiothreitol (DTT). Furthermore, the Dmaoc group proved compatible with peptide ligation strategies featuring the activation of N-acyl diaminobenzamides (Dbz) with sodium nitrate to generate the respective benzotriazole leaving group. The Dmaoc/Dbz strategy described in this manuscript provides a new method for the chemical synthesis of peptides.

Regioselective α-Peptide Bond Formation Through the Oxidation of Amino Thioacids.

Biological systems, including ribosomes and enzymes, produce peptides with an extraordinary high speed and accuracy. On the other hand, a rational and regioselective α-peptide bond formation, without involving protecting groups, is difficult to achieve in chemical synthesis. In this study, α-amino thioacids were utilized for the generation of polypeptides without using any protecting groups. We found that an α-amino thioacid could oxidatively form a diaminoacyl-disulfide moiety and undergo a subsequent intramolecular S- to N-acyl transfer to form an α-peptide bond. Even the thioacid form of lysine, which has a free ε-amino group, generated a regioselective α-peptide bond. The oxidation of amino thioacids generated the oligomers of amino acids. Interestingly, this oligomerization reaction proceeded even in the presence of iron ore, a prebiotic element, thus suggesting a plausible prebiotic peptide bond forming reaction.

Monitoring of Glycoprotein Quality Control System with a Series of Chemically Synthesized Homogeneous Native and Misfolded Glycoproteins.

The glycoprotein quality control (GQC) system in the endoplasmic reticulum (ER) effectively uses chaperone-type enzymes and lectins such as UDP-glucose:glycoprotein glucosyltransferase (UGGT), calnexin (CNX), calreticulin (CRT), protein disulfide bond isomerases (ERp57 or PDIs), and glucosidases to generate native-folded glycoproteins from nascent glycopolypeptides. However, the individual processes of the GQC system at the molecular level are still unclear. We chemically synthesized a series of several homogeneous glycoproteins bearing M9-high-mannose type oligosaccharides (M9-glycan), such as erythropoietin (EPO), interferon-ß (IFN-ß), and interleukin 8 (IL8) and their misfolded counterparts, and used these glycoprotein probes to better understand the GQC process. The analyses by high performance liquid chromatography and mass spectrometer clearly showed refolding processes from synthetic misfolded glycoproteins to native form through folding intermediates, allowing for the relationship between the amount of glucosylation and the refolding of the glycoprotein to be estimated. The experiment using these probes demonstrated that GQC system isolated from rat liver acts in a catalytic cycle regulated by the fast crosstalk of glucosylation/deglucosylation in order to accelerate refolding of misfolded glycoproteins.

Semisynthesis of Complex-Type Biantennary Oligosaccharides Containing Lactosamine Repeating Units from a Biantennary Oligosaccharide Isolated from a Natural Source.

Poly-N-acetyllactosamine (poly-LacNAc) structures on glycoproteins play important roles in essential biological events such as cell-cell adhesion. Here, we report a new strategy for the semisynthesis of LacNAc-extended complex-type biantennary oligosaccharides. We found an efficient isopropylidenation reaction that selectively protects the terminal Gal-3,4-OH of a biantennary complex-type nonasaccharide isolated from a natural source. This finding enabled the conversion of the nonasaccharide into the two types of oligosaccharides containing di-LacNAc units at one or two antennae via ten-step chemical sequences.

Substrate Recognition of Glycoprotein Folding Sensor UGGT Analyzed by Site-Specifically 15N-Labeled Glycopeptide and Small Glycopeptide Library Prepared by Parallel Native Chemical Ligation.

UDP-glucose:glycoprotein glucosyltransferase (UGGT) distinguishes glycoproteins in non-native conformations from those in native conformations and glucosylates from only non-native glycoproteins. To analyze how UGGT recognizes non-native glycoproteins, we chemically synthesized site-specifically 15N-labeled interleukin 8 (IL-8) C-terminal (34-72) glycopeptides bearing a Man9GlcNAc2 (M9) oligosaccharide. Chemical shift perturbation mapping NMR experiments suggested that Phe65 of the glycopeptide specifically interacts with UGGT. To analyze this interaction, we constructed a glycopeptide library by varying Phe65 with 10 other natural amino acids, via parallel native chemical ligation between a glycopeptide-α-thioester and a peptide library consisting of 11 peptides. UGGT assay against the glycopeptide library revealed that, although less hydrophobic glycopeptides could be used as substrates for UGGT, hydrophobic glycopeptides are preferred.

Total Synthesis of O-GalNAcylated Antifreeze Glycoprotein using the Switchable Reactivity of Peptidyl-N-pivaloylguanidine.

Antifreeze glycoprotein (AFGP) is an O-glycoprotein that displays antifreeze activity through depression of the freezing point of water. GalNAc is a core sugar structure of AFGP, and contributes to induce antifreeze activity of this glycoprotein. However, the general functional role that this sugar plays at the molecular level is still unknown. To elucidate this, it is essential to determine the relationship between structure and activity of O-GalNAcylated AFGP using homogeneous glycoproteins. Thus, the total synthesis of homogeneous O-GalNAcylated AFGP was conducted by using a unique peptide derivative: peptidyl-N-pivaloylguanidine. It was found that peptidyl-N-pivaloylguanidine is an "unreactive" peptide in peptide coupling reactions but is interconvertible with a "reactive" peptide-α-thioester by means of a simple treatment under buffer condition at pH=7 to 8. The unique switchable reactivity of peptidyl-N-pivaloylguanidine enabled an efficient sequential peptide coupling strategy. By using this strategy, various lengths of homogeneous O-GalNAcylated AFGP were synthesized, including one that was 120 amino acids in length, with 40 O-GalNAcylation sites. The structural analysis by circular dichroism spectroscopy and evaluation of the antifreeze activity of the synthetic AFGP(GalNAc)s revealed that the simple O-glycosylation with GalNAc is essential for both structural and functional basis of AFGP to exhibit antifreeze activity.

Chemical Synthesis of Glycoproteins with the Specific Installation of Gradient-Enriched 15 N-Labeled Amino Acids for Getting Insights into Glycoprotein Behavior.

Elucidating the effects of oligosaccharides on glycoprotein properties, such as local conformational changes, stability, and dynamics, has still been challenging. In this paper, a novel partial 15 N-labeling method for the amide backbone of a synthetic glycoprotein is proposed. Using solid-phase peptide synthesis (SPPS) and native chemical ligation (NCL), thirteen 15 N-labeled amino acids were inserted at specific positions of the protein backbone, while intentionally varying the enrichment of 15 N atoms. This idea discriminated even the same type of amino acid based on the intensities of 1 H-15 N HSQC signals, combined with classic homonuclear TOCSY and NOESY methods, thus allowing for understanding the dynamics of the local conformation of a synthetic homogeneous glycoprotein. Results suggested that the attachment of an oligosaccharide of either a bi-antennary complex-type or a high-mannose-type did not disturb protein conformation. However, T1 values suggested that the oligosaccharide influenced dynamics at the local conformation. Temperature-varied circular dichroism (CD) spectra and T1 values clearly indicated that oligosaccharides appeared to inhibit protein fluctuation or, in other words, stabilize protein structure. This insight into oligosaccharide behavior suggests some further effects on binding affinity between a glycoprotein and its receptor.

Gustatory Salivation Is Associated with Body Mass Index, Daytime Sleepiness, and Snoring in Healthy Young Adults.

The taste detection system for oral fatty acid may be related to obesity. In addition, sleep is intrinsically and closely related to food intake and metabolism. However, the association of gustatory salivation with body mass index (BMI), daytime sleepiness, or sleep habits is largely unknown. Therefore, we evaluated the relationship between gustatory salivation and BMI, Epworth sleepiness scale (ESS, a daytime sleepiness scale) or sleep habits among 26 healthy young individuals (20 males and 6 females; mean age: 26.0 ± 4.3 years). We also measured the saliva flow rate (SFR) that was induced by gum-chewing or each of three prototypical tastants (acetic acid, sucrose, and NaCl). Further, the SFR was induced by fatty acid, provided as oleic acid (OA) homogenized in non-fat milk. All participants showed normal rates of salivation during resting and gum-chewing states. The increase in the SFR induced by OA, but not by each of the three tastants, was associated with BMI. Moreover, both daytime sleepiness level and frequency of snoring were associated with the increase in the SFR induced by NaCl. These results suggest that BMI is associated with salivation induced by oral fatty acid exposure. Additionally, the regulatory mechanism for the NaCl-induced salivation reflex may have a relationship with impairments of the respiratory control system that are related to snoring during sleep and lead to daytime sleepiness because of insufficient sleep. Thus, measurement of gustatory salivation might contribute to the evaluation and prevention of obesity and sleep-related breathing disorders.

Direct assay for endo-α-mannosidase substrate preference on correctly folded and misfolded model glycoproteins.

We previously reported a unique assay system for UDP-glucose glycoprotein glucosyltransferase (UGGT) toward glycoprotein folding intermediates during the folding process. The assay involved the in vitro folding of both high-mannose type oligosaccharyl crambin, which yielded only the correctly folded glycoprotein form (M9-glycosyl-native-crambin), and its mutant, which yielded misfolded glycoproteins (M9-glycosyl-misfolded-crambin), in the presence of UGGT. The process successfully yielded both mono-glucosylated M9-glycosyl-native-crambin (G1M9-glycosyl-native-crambin) and M9-glycosyl-misfolded-crambin (G1M9-glycosyl-misfolded-crambin). Here, we report the use of our in vitro folding system to evaluate the substrate preference of Golgi endo-α-mannosidase against G1M9-native and -misfolded glycoprotein forms. In our assay Golgi endo-α-mannosidase removed Glc-α-1-3-Man unit from G1M9-native and -misfolded-crambins clearly proving that Golgi endo-α-mannosidase does not have specific preference for correctly folded or misfolded protein structure.