(Quasi‐)Racemic X‐ray Structures of Glycosylated and Non‐Glycosylated Forms of the Chemokine Ser‐CCL1 Prepared by Total Chemical Synthesis

Our goal was to obtain the X‐ray crystal structure of the glycosylated chemokine Ser‐CCL1. Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. We used glycosylated Ser‐CCL1 that had been prepared by total chemical synthesis as a homogeneous compound containing an N‐linked asialo biantennary nonasaccharide glycan moiety of defined covalent structure. Facile crystal formation occurred from a quasi‐racemic mixture consisting of glycosylated L ‐protein and non‐glycosylated‐D ‐protein, while no crystals were obtained from the glycosylated L ‐protein alone. The structure was solved at a resolution of 2.6–2.1 Å. However, the glycan moiety was disordered: only the N‐linked GlcNAc sugar was well‐defined in the electron density map. A racemic mixture of the protein enantiomers L ‐Ser‐CCL1 and D ‐Ser‐CCL1 was also crystallized, and the structure of the true racemate was solved at a resolution of 2.7–2.15 Å. Superimposition of the structures of the protein moieties of L ‐Ser‐CCL1 and glycosylated‐L ‐Ser‐CCL1 revealed there was no significant alteration of the protein structure by N‐glycosylation.     

Chemical Synthesis of Native S‐Palmitoylated Membrane Proteins through Removable‐Backbone‐Modification‐Assisted Ser/Thr Ligation

The preparation of native S‐palmitoylated (S‐palm) membrane proteins is one of the unsolved challenges in chemical protein synthesis. Herein, we report the first chemical synthesis of S‐palm membrane proteins by removable‐backbone‐modification‐assisted Ser/Thr ligation (RBM^GABA‐assisted STL). This method involves two critical steps: 1) synthesis of S‐palm peptides by a new γ‐aminobutyric acid based RBM (RBM^GABA) strategy, and 2) ligation of the S‐palm RBM‐modified peptides to give the desired S‐palm product by the STL method. The utility of the RBM^GABA‐assisted STL method was demonstrated by the synthesis of rabbit S‐palm sarcolipin (SLN) and S‐palm matrix‐2 (M2) ion channel. The synthesis of S‐palm membrane proteins highlights the importance of developing non‐NCL methods for chemical protein synthesis.     

Selective Inhibition of Aggregation and Toxicity of a Tau‐Derived Peptide using Its Glycosylated Analogues

Protein glycosylation is a ubiquitous post‐translational modification that regulates the folding and function of many proteins. Misfolding of protein monomers and their toxic aggregation are the hallmark of many prevalent diseases. Thus, understanding the role of glycans in protein aggregation is highly important and could contribute both to unraveling the pathology of protein misfolding diseases as well as providing a means for modifying their course for therapeutic purposes. Using β‐O‐linked glycosylated variants of the highly studied Tau‐derived hexapeptide motif VQIVYK, which served as a simplified amyloid model, we demonstrate that amyloid formation and toxicity can be strongly attenuated by a glycan unit, depending on the nature of the glycan itself. Importantly, we show for the first time that not only do glycans hinder self‐aggregation, but the glycosylated peptides are capable of inhibiting aggregation of the non‐modified corresponding amyloid scaffold.     

Delineating Binding Modes of Gal/GalNAc and Structural Elements of the Molecular Recognition of Tumor‐Associated Mucin Glycopeptides by the Human Macrophage Galactose‐Type Lectin

The human macrophage galactose‐type lectin (MGL) is a key physiological receptor for the carcinoma‐associated Tn antigen (GalNAc‐α‐1‐O‐Ser/Thr) in mucins. NMR and modeling‐based data on the molecular recognition features of synthetic Tn‐bearing glycopeptides by MGL are presented. Cognate epitopes on the sugar and matching key amino acids involved in the interaction were identified by saturation transfer difference (STD) NMR spectroscopy. Only the amino acids close to the glycosylation site in the peptides are involved in lectin contact. Moreover, control experiments with non‐glycosylated MUC1 peptides unequivocally showed that the sugar residue is essential for MGL binding, as is Ca²⁺. NMR data were complemented with molecular dynamics simulations and Corcema‐ST to establish a 3D view on the molecular recognition process between Gal, GalNAc, and the Tn‐presenting glycopeptides and MGL. Gal and GalNAc have a dual binding mode with opposite trend of the main interaction pattern and the differences in affinity can be explained by additional hydrogen bonds and CH–π contacts involving exclusively the NHAc moiety.     

Semisynthesis of a Post‐Translationally Modified Protein by Using Chemical Cleavage and Activation of an Expressed Fusion Polypeptide

Herein, we describe a new semisynthetic strategy of a post‐translationally modified protein in which the middle region is glycosylated. We designed a single‐plasmid coding for a fusion polypeptide, which can provide both an N‐terminal α‐thioester and a C‐terminal cysteine peptide of a target glycoprotein by using chemical‐cleavage and activation methods. The use of these resultant peptide derivatives resulted in the successful synthesis of N‐glycosylated‐interleukin 13.     

Effects of N‐Glycosylation Deletions on Cypridina Luciferase Activity

Cypridina luciferase (Cluc), a secreted luminescent protein identified from Cypridina noctiluca , has two N ‐glycosylation sites. In this study, we evaluated the effects of N ‐glycosylation on Cluc properties by creating site‐directed mutagenic modifications at the consensus sequence for N ‐glycosylation (Asn‐X‐Ser/Thr). Eight variants consisting of four single‐ and double‐residue mutants each were characterized. The producibility and relative specific activity were apparently reduced in mutant Cluc although the thermostability and secretion efficiency were not affected. These results suggested that N ‐glycosylation modifications and the proper amino acid sequence of the N ‐glycan binding sites of Cluc are required for the complete protein folding to form a stable catalytic center, for the proper conformation of substrate–protein interaction residues, or for both and that defects in the glycosylation modification are not related to secretion process and stability of the protein.     

Homogeneous Human Complex‐Type Oligosaccharides in Correctly Folded Intact Glycoproteins: Evaluation of Oligosaccharide Influence On Protein Folding,Stability, and Conformational Properties

The N‐glycosylation of proteins is generated at the consensus sequence NXS/T (where X is any amino acid except proline) by the biosynthetic process, and occurs in the endoplasmic reticulum and Golgi apparatus. In order to investigate the influence of human complex‐type oligosaccharides on counterpart protein conformation, crambin and ovomucoide, which consist of 46 and 56 amino acid residues, respectively, were selected for synthesis of model glycoproteins. These small glycoproteins were intentionally designed to be glycosylated at the α‐helix (crambin: 8 position), β‐sheet (crambin: 2 position) and loop position between the antiparallel β‐sheets (ovomucoide: 28 position), and were synthesized by using a peptide‐segment coupling strategy. After preparation of these glycosylated polypeptide chains, protein folding experiments were performed under redox conditions by using cysteine–cystine. Although the small glycoproteins bearing intentional glycosylation at the α‐helix and β‐sheet exhibited a suitable folding process, glycosylation at the loop position between the antiparallel β‐strands caused multiple products. The conformational differences in the isolated homogeneous glycoproteins compared with non‐glycosylated counterparts were evaluated by circular dichroism (CD) and NMR spectroscopy. These analyses suggested that this intentional N‐glycosylation did not result in large conformational changes in the purified protein structures, including the case of glycosylation at the loop position between the antiparallel β‐strands. In addition to these experiments, the conformational properties of three glycoproteins were evaluated by CD spectroscopy under different temperatures. The oligosaccharides on the protein surface fluctuated considerably; this was dependent on the increase in the solution temperature and was thought to disrupt the protein tertiary structure. Based on the measurement of the CD spectra, however, the glycoproteins bearing three disulfide bonds did not exhibit any change in their protein tertiary structure. These results suggest that the oligosaccharide conformational fluctuations were not disruptive to protein tertiary structure, and the tertiary structure of glycoproteins might be stabilized by the disulfide bond network.     

Glycosylated Cell‐Penetrating Poly(disulfide)s: Multifunctional Cellular Uptake at High Solubility

The glycosylation of cell‐penetrating poly(disulfide)s (CPDs) is introduced to increase the solubility of classical CPDs and to achieve multifunctional cellular uptake. With the recently developed sidechain engineering, CPDs decorated with α‐d ‐glucose (Glu), β‐d ‐galactose (Gal), d ‐trehalose (Tre), and triethyleneglycol (TEG) were readily accessible. Confocal laser scanning microscopy images of HeLa Kyoto cells incubated with the new CPDs at 2.5 μm revealed efficient uptake into cytosol and nucleoli of all glycosylated CPDs, whereas the original CPDs and TEGylated CPDs showed much precipitation into fluorescent aggregates at these high concentrations. Flow cytometry analysis identified Glu‐CPDs as most active, closely followed by Gal‐CPDs and Tre‐CPDs, and all clearly more active than non‐glycosylated CPDs. In the MTT assay, all glyco‐CPDs were non‐toxic at concentrations as high as 2.5 μm . Consistent with thiol‐mediated uptake, glycosylated CPDs remained dependent on thiols on the cell surface for dynamic covalent exchange, their removal with Ellman's reagent DTNB efficiently inhibited uptake. Multifunctionality was demonstrated by inhibition of Glu‐CPDs with d ‐glucose (IC₅₀ ca. 20 mm ). Insensitivity toward l ‐glucose and d ‐galactose and insensitivity of conventional CPDs toward d ‐glucose supported that glucose‐mediated uptake of the multifunctional Glu‐CPDs involves selective recognition by glucose receptors at the cell surface. Weaker but significant sensitivity of Gal‐CPDs toward d ‐galactose but not d ‐glucose was noted (IC₅₀ ca. 110 mm ). Biotinylation of Glu‐CPDs resulted in the efficient delivery of streptavidin together with a fluorescent model substrate. Protein delivery with Glu‐CPDs was more efficient than with conventional CPDs and remained sensitive to DTNB and d ‐glucose, i.e., multifunctional.     

15N NMR spectroscopy of 3‐substituted 5‐trichloromethyl‐1,2‐dimethyl‐1H‐pyrazolium chlorides

¹⁵N NMR data of a series of 3‐alkyl[aryl] substituted 5‐trichloromethyl‐1,2‐dimethyl‐1H‐pyrazolium chlorides (where the 3‐substituents are H, Me, Et, n‐Pr, n‐Bu, n‐Pe, n‐Hex, (CH₂)₅CO₂Et, CH₂Br, Ph and 4‐Br‐C₆H₄), are reported. The ¹⁵N substituent chemical shifts (SCS) parameters are determined and these data are compared with the ¹³C SCS values and data obtained by MO calculations. Copyright © 2002 John Wiley & Sons, Ltd.     

Charakterisierung der Protonen in polykristallinen Parawolframaten durch 1H‐MAS‐NMR‐Untersuchungen

Characterization of the Protons in Polycrystalline Paratungstates using ¹H MAS NMR Investigations ¹H MAS NMR experiments are used to characterize the non‐acid protons of the anions in polycrystalline paratungstates by means of the measured isotropic chemical shift values. The investigation of various hydrates of ammonium paratungstate allows a direct proof of protons in NH₄ ions and in water molecules while protons of the anions are not detectable. However, for both the potassium and the sodium paratungstates ¹H MAS NMR investigations detected the protons of water molecules and the non‐acid protons of the paratungstate anions. Additional ¹H broad‐line NMR experiments at 173 K support the interpretation of the results obtained by the ¹H MAS NMR investigations. For the NMR signal of the non‐acid protons of the paratungstate anion in the ¹H MAS NMR spectra of the potassium salt line‐splitting appears. This refers to the existence of two nonidentical positions of the protons in the crystal lattice and is in agreement with the results of the X‐ray structural analysis.     

Deciphering the Non‐Equivalence of Serine and Threonine O‐Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an anti‐MUC1 Antibody

The structural features of MUC1‐like glycopeptides bearing the Tn antigen (α‐O‐GalNAc‐Ser/Thr) in complex with an anti MUC‐1 antibody are reported at atomic resolution. For the α‐O‐GalNAc‐Ser derivative, the glycosidic linkage adopts a high‐energy conformation, barely populated in the free state. This unusual structure (also observed in an α‐S‐GalNAc‐Cys mimic) is stabilized by hydrogen bonds between the peptidic fragment and the sugar. The selection of a particular peptide structure by the antibody is thus propagated to the carbohydrate through carbohydrate/peptide contacts, which force a change in the orientation of the sugar moiety. This seems to be unfeasible in the α‐O‐GalNAc‐Thr glycopeptide owing to the more limited flexibility of the side chain imposed by the methyl group. Our data demonstrate the non‐equivalence of Ser and Thr O‐glycosylation points in molecular recognition processes. These features provide insight into the occurrence in nature of the APDTRP epitope for anti‐MUC1 antibodies.     

On the long‐range relativistic effects in the 15N NMR chemical shifts of halogenated azines

Long‐range β‐ and γ‐relativistic effects of halogens in ¹⁵N NMR chemical shifts of 20 halogenated azines (pyridines, pyrimidines, pyrazines, and 1,3,5‐triazines) are shown to be unessential for fluoro‐, chloro‐, and bromo‐derivatives (1–2 ppm in average). However, for iodocontaining compounds, β‐ and γ‐relativistic effects are important contributors to the accuracy of the ¹⁵N calculation. Taking into account long‐range relativistic effects slightly improves the agreement of calculation with experiment. Thus, mean average errors (MAE) of ¹⁵N NMR chemical shifts of the title compounds calculated at the non‐relativistic and full 4‐component relativistic levels in gas phase are accordingly 7.8 and 5.5 ppm for the range of about 150 ppm. Taking into account solvent effects within the polarizable continuum model scheme marginally improves agreement of computational results with experiment decreasing MAEs from 7.8 to 7.4 ppm and from 5.5 to 5.3 ppm at the non‐relativistic and relativistic levels, respectively. The best result (MAE: 5.3 ppm) is achieved at the 4‐component relativistic level using Keal and Tozer's KT3 functional used in combination with Dyall's relativistic basis set dyall.av3z with taking into account solvent effects within the polarizable continuum solvation model. The long‐range relativistic effects play a major role (of up to dozen of parts per million) in ¹⁵N NMR chemical shifts of halogenated nitrogen‐containing heterocycles, which is especially crucial for iodine derivatives. This effect should apparently be taken into account for practical purposes.     

The Implications of (2S,4S)‐Hydroxyproline 4‐O‐Glycosylation for Prolyl Amide Isomerization

The conformations of peptides and proteins are often influenced by glycans O‐linked to serine (Ser) or threonine (Thr). (2S,4R)‐4‐Hydroxyproline (Hyp), together with L ‐proline (Pro), are interesting targets for O‐glycosylation because they have a unique influence on peptide and protein conformation. In previous work we found that glycosylation of Hyp does not affect the N‐terminal amide trans/cis ratios (K_trans/cis) or the rates of amide isomerization in model amides. The stereoisomer of Hyp—(2S,4S)‐4‐hydroxyproline (hyp)—is rarely found in nature, and has a different influence both on the conformation of the pyrrolidine ring and on K_trans/cis. Glycans attached to hyp would be expected to be projected from the opposite face of the prolyl side chain relative to Hyp; the impact this would have on K_trans/cis was unknown. Measurements of ³J coupling constants indicate that the glycan has little impact on the C^γ‐endo conformation produced by hyp. As a result, it was found that the D ‐galactose residue extending from a C^γ‐endo pucker affects both K_trans/cis and the rate of isomerization, which is not found to occur when it is projected from a C^γ‐exo pucker; this reflects the different environments delineated by the proline side chain. The enthalpic contributions to the stabilization of the trans amide isomer may be due to disruption of intramolecular interactions present in hyp; the change in enthalpy is balanced by a decrease in entropy incurred upon glycosylation. Because the different stereoisomers—Hyp and hyp—project the O‐linked carbohydrates in opposite spatial orientations, these glycosylated amino acids may be useful for understanding of how the projection of a glycan from the peptide or protein backbone exerts its influence.     

13C and 15N NMR spectra of high‐energy polyazidocyanopyridines

¹³C and ¹⁵N NMR spectra of high‐energy 2,4,6‐triazidopyridine‐3,5‐dicarbonitrile, 2,3,5,6‐tetraazidopyridine‐4‐carbonitrile and 3,4,5,6‐tetraazidopyridine‐2‐carbonitrile are reported. The assignment of signals in the spectra was performed on the basis of density functional theory calculations. The molecular geometries were optimized using the M06‐2X functional with the 6‐311+G(d,p) basis set. The magnetic shielding tensors were calculated by the gauge‐independent atomic orbital method with the Tao–Perdew–Staroverov–Scuseria hybrid functional known as TPSSh. In all the calculations, a polarizable continuum model was used to simulate solvent effects. This approach provided accurate predictions of the ¹³C and ¹⁵N chemical shifts for all the three compounds despite complications arising due to non‐coplanar arrangement of the azido groups in the molecules. It was found that the ¹⁵N chemical shifts of the N_α atoms in the azido groups of 2,4,6‐triazidopyridines correlate with the ¹³C chemical shifts of the carbon atoms attached to these azido groups. Copyright © 2016 John Wiley & Sons, Ltd.     

Characterization of 2‐aryl‐1,3,4‐oxadiazoles by 15N and 13C NMR spectroscopy

¹⁵N NMR chemical shifts of 2‐aryl‐1,3,4‐oxadiazoles were assigned on the basis of the ¹H–¹⁵N HMBC experiment. Chemical shifts of the nitrogen and carbon atoms in the oxadiazole ring correlate with the Hammett σ‐constants of substituents in the aryl ring (r² ≥ 0.966 for N atoms). ¹⁵N NMR data are a suitable and sensitive means for characterizing long‐range electronic substituent effects. Additionally, ¹³C NMR data for these compounds are presented. Copyright © 2003 John Wiley & Sons, Ltd.     

Long‐Range Chemical Ligation from N→N Acyl Migrations in Tryptophan Peptides via Cyclic Transition States of 10‐ to 18‐Members

Chemical ligations to form native peptides from N→N acyl migrations in Trp‐containing peptides via 10‐ to 18‐membered cyclic transition states are described. In this study, a statistical, predictive model that uses an extensive synthetic and computational approach to rationalize the chemical ligation is reported. N→N acyl migrations that form longer native peptides without the use of Cys/Ser/Tyr residues or an auxiliary group at the ligation site were achieved. The feasibility of these traceless chemical ligations is supported by the N?C bond distance in N‐acyl isopeptides. The intramolecular nature of the chemical ligations is justified by using competitive experiments and theoretical calculations.     

The Substituent Effect of 1‐Arylazonaphthen‐2‐ols on Azo‐hydrazone Tautomerization According to NMR Analysis

The substituent effect on azo‐hydrazone tautomerization of 1‐arylazonaphthen‐ols is studied by means of NMR analysis. Among the ¹³C chemical shifts, the C(2) of this series compound is the most sensitive to the variation in the nature of substituent on the phenyl ring. Therefore, the variation in the chemical shifts of C(2) is used to probe the substituent effect by using the substituent chemical shifts and free energy vs. Hammett’s constant (χρ⁺). Both methods give a negative correlation slope, indicating the electron‐with‐ drawing groups favor the hydrazone tautomer form. The effect on the chemical shifts of C(2) of compound 8 in ten solvents can be classified as the solvent with a proton‐donor, proton‐acceptor and arenes system. The substituent with electron‐donating character is more sensitive to the nature of solvent and it favors the hydrazone form. Free energy obtained from the dynamic NMR technique indicates the tautomerization favors the hydrazone‐form for the substituent with electron‐withdrawing character.     

Synthesis of the Highly Glycosylated Hydrophilic Motif of Extensins

Extensin, the structural motif of plant extracellular matrix proteins, possesses a unique highly glycosylated, hydrophilic, and repeating Ser₁Hyp₄ pentapeptide unit, and has been proposed to include post‐translational hydroxylation at proline residue and subsequent oligo‐L ‐arabinosylations at all of the resultant hydroxyprolines as well as galactosylation at serine residue. Reported herein is the stereoselective synthesis of one of the highly glycosylated motifs, Ser(Galp₁)‐Hyp(Araf₄)‐Hyp(Araf₄)‐Hyp(Araf₃)‐Hyp(Araf₁). The synthesis has been completed by the application of 2‐(naphthyl)methylether‐mediated intramolecular aglycon delivery to the stereoselective construction of the Ser(Galp₁) and Hyp(Araf_n) fragments as the key step, as well as Fmoc solid‐phase peptide synthesis for the backbone pentapeptide.     

Hydroacridines: Part 23. 1H and 13C NMR spectra of sym‐octahydroacridine,its 9‐(3‐pyridyl) and 9‐(4‐pyridyl) derivatives and the corresponding N(10)‐oxides. An experimental approach to the diamagnetic anisotropy of the pyridine nucleus

The complete ¹H NMR chemical shift assignments of 1,2,3,4,5,6,7,8‐octahydroacridine ( 1 ), 1,2,3,4,5,6,7,8‐octahydro‐9‐(3‐pyridyl)acridine ( 2 ), 1,2,3,4,5,6,7,8‐octahydro‐9‐(4‐pyridyl)acridine ( 3 ) and the corresponding N(10)‐oxides 1a , 2a and 3a , respectively, were achieved on the basis of 400 MHz ¹H NMR spectra and proton–proton decoupling, HMQC and NOEDIFF experiments. The spectral data for the above compounds provided the first experimental evidence of the difference in the anisotropy effect of the two non‐symmetrical moieties of the pyridine nucleus, and allowed us to ascertain that the shielding effect of the moiety defined by the C(2′)—N—C(6′) atoms is weaker than that of the C(3′)—C(4′)—C(5′) moiety. The ¹³C NMR spectra of 1 – 3 and 1a – 3a and the effect of N(10)‐oxidation on the ¹³C NMR chemical shifts are also discussed. The N‐oxidation of 2 and 3 with m‐chloroperbenzoic acid occurred regiospecifically, affording the N(10)‐oxides 2a and 3a free of N(1′)‐oxide isomers. Copyright © 2002 John Wiley & Sons, Ltd.     

Imidazole‐Aided Native Chemical Ligation: Imidazole as a One‐Pot Desulfurization‐Amenable Non‐Thiol‐Type Alternative to 4‐Mercaptophenylacetic Acid

Various bioactive proteins have been synthesized by native chemical ligation (NCL) and its combination with subsequent desulfurization (e.g., conversion from Cys to Ala). In NCL, excess 4‐mercaptophenylacetic acid (MPAA) is generally added to facilitate the reaction. However, co‐elution of MPAA with the ligation product during preparative high‐performance liquid chromatography sometimes reduces its usefulness. In addition, contamination of MPAA disturbs subsequent desulfurization. Here, we report for the first time that imidazole can be adopted as an alternative to MPAA in NCL using a peptide‐alkylthioester. The efficiency of the imidazole‐aided NCL (Im‐NCL) is similar to that of traditional MPAA‐aided NCL. As model cases, we successfully synthesized adiponectin(19‐107) and [Ser(PO₃H₂)⁶⁵]‐ubiquitin using Im‐NCL with a one‐pot desulfurization.