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The synthetic potential of phthalimide SET photochemistry.

The authors' studies in the area of phthalimide photochemistry are discussed in the context of the development of new methods for N-heterocycle synthesis. Emphasis is given to reactions which are initiated by both intermolecular and intramolecular SET from silicon-containing electron donors to excited states of phthalimides and related maleimides and conjugated imides. The photoaddition and photocyclization processes which ensue follow mechanistic pathways, in which efficient desilylation of initially formed radical cation occurs to generate radical pair and biradical intermediates that serve as precursors of the products. Several examples that demonstrate the preparative potential of these reactions are presented. These are taken from the authors' investigations of (1) phthalimido-alkylsilane photocyclization reactions, (2) azomethine ylide-forming excited-state processes of N-(trimethylsilylmethyl)phthalimide, and (3) photoaddition and photocyclization reactions of phthalimide alpha-silyl ether, thioether, amine, and amide systems.

Amides↗

Reactions and applications of titanium imido complexes.

This Account highlights aspects of the reactions and applications of titanium imido complexes. Over the past decade in particular, the Ti=NR linkage has been shown to couple stoichiometrically with a variety of unsaturated substrates including CO(2), carbodiimides, isocyanates, isocyanides, acetonitrile, phosphaalkynes, alkynes, alkenes, and allenes. Especially recently, there has been much interest in using titanium imides as catalysts for hydroamination and olefin polymerization. The advances in these areas are also reviewed.

Journal Article↗

Catalytic C-h/olefin coupling.

The cleavage and addition of ortho C-H bonds in various aromatic compounds such as ketones, esters, imines, imidates, nitrile, and aldehydes to olefins and acetlylenes can be achieved catalytically with the aid of ruthenium catalysts. The reaction is generally highly efficient and useful in synthetic methods. The coordination to the metal center by a heteroatom in directing groups such as carbonyl and imino groups is the key. The reductive elimination to form a C-C bond is the rate-determining step.

Journal Article↗

Voltage activation of reconstituted sodium channels: use of bacteriorhodopsin as a light-driven current source.

We present a general method for the development and control of transmembrane potentials (delta psi) in reconstituted vesicles. The light-driven proton pump bacteriorhodopsin (bR) from Halobacterium halobium is the current source in the system, and the intensity of light controls the magnitude of delta psi at any given time. Transmembrane potentials were determined from the equilibrium distribution of hydrophobic ions, which was monitored by using either electron paramagnetic resonance spectroscopy and spin-labeled phosphonium ions or a tetraphenylphosphonium-selective electrode. A bias or holding potential was generated by using gradients of anions of limited permeability in the presence of an impermeable cation. Using n-methylglucamine or the polymer poly(ethylene imide) as the impermeable cation, the anions NO3- and SCN- were most effective in producing large (> -60 mV) negative diffusion potentials in egg phosphatidylcholine vesicles. In the presence of a NO(3-)-based negative holding potential (approx. -65 mV), bR is capable of depolarizing the membrane to at least the 0-mV level within a few seconds. More rapid depolarizations can be achieved by the application of a brief intense illumination preceding the preset illumination level (supercharging). The technique was successfully used to activate for the first time a population of unmodified voltage-dependent sodium channels purified from eel electroplax.

Bacteriorhodopsins↗

Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2.

Uracil DNA glycosylase (UDG) cleaves the glycosidic bond of deoxyuridine in DNA using a hydrolytic mechanism, with an overall catalytic rate enhancement of 10(12)-fold over the solution reaction. The nature of the enzyme-substrate interactions that lead to this large rate enhancement are key to understanding enzymatic DNA repair. Using (1)H and heteronuclear NMR spectroscopy, we have characterized one such interaction in the ternary product complex of Escherichia coli UDG, the short (2.7 A) H bond between His187 N(epsilon)(2) and uracil O2. The H bond proton is highly deshielded at 15.6 ppm, indicating a short N-O distance and exhibits a solvent exchange rate that is 400- and 10(5)-fold slower than free imidazole at pH 7.5 and pH 10, respectively. Heteronuclear NMR experiments at neutral pH show that this H bond involves the neutral imidazole form of His187 and the N1-O2 imidate form of uracil. The excellent correspondence of the pK(a) for the disappearance of the H bond (pK(a) = 6.3 +/- 0.1) with the previously determined pK(a) = 6.4 for the N1 proton of enzyme-bound uracil indicates that the H bond requires negative charge on uracil O2 [Drohat, A. C., and Stivers, J. T. (2000) J. Am. Chem. Soc. 122, 1840-1841]. Although the above characteristics suggest a short strong H bond, the D/H fractionation factor of phi = 1.0 is more typical of a normal H bond. This unexpected observation may reflect a large donor-acceptor pK(a) mismatch or the net result of two opposing effects on vibrational frequencies: decreased N-H bond stretching frequencies (phi < 1) and increased bending frequencies (phi > 1) relative to the O-H bonds of water. The role of this H bond in catalysis by UDG and several approaches to quantify the H bond energy are discussed.

Anions↗

Intramolecular catalysis of a proline isomerization reaction in the folding of dihydrofolate reductase.

The cis/trans isomerization of the peptide bond preceding proline residues in proteins can limit the rate at which a protein folds to its native conformation. Mutagenic analyses of dihydrofolate reductase (DHFR) from Escherichia coli show that this isomerization reaction can be intramolecularly catalyzed by a side chain from an amino acid which is distant in sequence but adjacent in the native conformation. The guanidinium NH2 nitrogen of Arg 44 forms one hydrogen bond to the imide nitrogen and a second to the carbonyl oxygen of Pro 66 in wild-type DHFR. Replacement of Arg 44 with Leu results in a change of the nature of the two slow steps in refolding from being limited by the acquisition of secondary and/or tertiary structure to being limited by isomerization. The simultaneous replacement of Pro 66 with Ala (i.e., the Leu 44/Ala 66 double mutant) eliminates this isomerization reaction and once again makes protein folding the limiting process. Apparently, one or both of the hydrogen bonds between Arg 44 and Pro 66 accelerate the isomerization of the Gln 65-Pro 66 peptide bond. The replacement of Arg 44 with Leu affects the kinetics of the slow folding reactions in a fashion which indicates that the crucial hydrogen bonds form in the transition states for the rate-limiting steps in folding.

Arginine↗

Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy.

Methylglyoxal synthase (MGS) and triosephosphate isomerase (TIM) share neither sequence nor structural similarities, yet the reactions catalyzed by both enzymes are similar, in that both initially convert dihydroxyacetone phosphate to a cis-enediolic intermediate. This enediolic intermediate is formed from the abstraction of the pro-S C3 proton of DHAP by Asp-71 of MGS or the pro-R C3 proton of DHAP by Glu-165 of TIM. MGS then catalyzes the elimination of phosphate from this enediolic intermediate to form the enol of methylglyoxal, while TIM catalyzes proton donation to C2 to form D-glyceraldehyde phosphate. A competitive inhibitor of TIM, phosphoglycolohydroxamic acid (PGH) is found to be a tight binding competitive inhibitor of MGS with a K(i) of 39 nM. PGH's high affinity for MGS may be due in part to a short, strong hydrogen bond (SSHB) from the NOH of PGH to the carboxylate of Asp-71. Evidence for this SSHB is found in X-ray, 1H NMR, and fractionation factor data. The X-ray structure of the MGS homohexamer complexed with PGH at 2.0 A resolution shows this distance to be 2.30-2.37 +/- 0.24 A. 1H NMR shows a PGH-dependent 18.1 ppm signal that is consistent with a hydrogen bond length of 2.49 +/- 0.02 A. The D/H fractionation factor (phi = 0.43 +/- 0.02) is consistent with a hydrogen bond length of 2.53 +/- 0.01 A. Further, 15N NMR suggests a significant partial positive charge on the nitrogen atom of bound PGH, which could strengthen hydrogen bond donation to Asp-71. Both His-98 and His-19 are uncharged in the MGS-PGH complex on the basis of the chemical shifts of their Cdelta and C(epsilon) protons. The crystal structure reveals that Asp-71, on the re face of PGH, and His-19, on the si face of PGH, both approach the NO group of the analogue, while His-98, in the plane of PGH, approaches the carbonyl oxygen of the analogue. The phosphate group of PGH accepts nine hydrogen bonds from seven residues and is tilted out of the imidate plane of PGH toward the re face. Asp-71 and phosphate are thus positioned to function as the base and leaving group, respectively, in a concerted suprafacial 1,4-elimination of phosphate from the enediolic intermediate in the second step of the MGS reaction. Combined, these data suggest that Asp-71 is the one base that initially abstracts the C3 pro-S proton from DHAP and subsequently the 3-OH proton from the enediolic intermediate. This mechanism is compared to an alternative TIM-like mechanism for MGS, and the relative merits of both mechanisms are discussed.

Amino Acid Substitution↗

Demethylation of protein carboxyl methyl esters: a nonenzymatic process in human erythrocytes?

We have compared the demethylation rate of protein carboxyl methyl esters from isolated human erythrocyte membranes with the corresponding rate of metabolic turnover of these same methyl groups in the intact erythrocyte. Surprisingly, the apparent spontaneous demethylation of these membrane protein methyl esters was significantly faster at physiological pH than the corresponding rate determined by pulse-chase analysis of intact cells incubated with L-[methyl-3H]methionine. Readdition of erythrocyte lysate to purified membranes did not increase the rate of demethylation, as might be expected if there were cytosolic or membrane-bound protein methylesterase activity, but resulted instead in an apparent stabilization of these methyl esters. Thus, the metabolic lability of these protein methyl esters in intact cells may be quantitatively explained by spontaneous, rather than enzymatic, demethylation reactions. A model is presented in which a rapid but nonenzymatic intramolecular demethylation reaction results in the formation of a polypeptide imide or anhydride intermediate. The metabolic fate of these hypothetical intermediates is unknown but may lead to the repair or degradation of protein D-aspartyl and L-isoaspartyl residues, which appear to be the substrates for the initial transmethylation reaction.

Erythrocyte Membrane↗

Slow refolding kinetics in yeast iso-2 cytochrome c.

In refolding of iso-2 cytochrome c from Saccharomyces cerevisiae, there are two slow folding reactions, tau 1a and tau 1b. The slower of the slow reactions, tau 1a = 100-200 s, is observed only by absorbance changes, while tau 1b (10-20-fold faster) is detected by fluorescence changes. The temperature dependence of the rates of these reactions has been measured: for kinetic experiments ending below the folding-unfolding transition zone (pH 7.2, 0.3 M guanidine hydrochloride, 5-30 degrees C), the activation enthalpies are delta H++ = 27 kcal/mol for tau 1a and 21 kcal/mol for tau 1b. Double-jump (unfolding, then refolding) experiments demonstrate that the two sets of species responsible for the slow folding reactions are generated slowly but at different rates under unfolding conditions (3 M guanidine hydrochloride, pH 7.2, 20 degrees C). Finally, as a test for changes in the population of the slow refolding species under different unfolding conditions, the amplitudes for slow refolding have been measured as a function of the initial unfolding conditions with the final refolding conditions held constant. Over the range accessible to measurement in the absence of interference from other reactions, the amplitudes for fluorescence-detected (alpha 1b) and absorbance-detected (alpha 1a) slow folding are independent of guanidine hydrochloride concentration and pH in the initial conditions. Although a full description requires a more complex explanation, many of the properties of the slow folding species are those expected for proline imide bond isomerization.

Cytochrome c Group↗

pH dependence of hydrogen exchange from backbone peptide amides in apamin.

The kinetics of hydrogen exchange of the 11 most protected backbone amides of bee venom apamin have been measured between pH 1 and pH 8.5 by using time-resolved and saturation-transfer NMR spectroscopy. The five amides most protected from base-catalyzed exchange, those of residues 5 and 12-15, show highly correlated exchange behavior in the base-catalyzed regime. It is proposed that the intramolecular hydrogen bonds stabilizing these amides define a stable cooperative unit of secondary structure in apamin (a C-terminal helix and an N-terminal beta-turn). This conformational unit is further stabilized (by 5-6 kJ mol-1) on titration of the Glu-7 side-chain carboxyl group. The relative contributions of specific intramolecular interactions to this conformational stabilization are estimated. The pHminima in the pH-dependent single amide exchange curves are compared with values predicted by correcting for sequence-dependent contributions to amide exchange rates [Molday, R. S., Englander, S. W., & Kallen, R. G. (1972) Biochemistry 11, 150-158]. The lack of correlation suggests that the "open" conformers from which amide exchange occurs are nonrandom. This conclusion is dependent on the assumption that acid-catalyzed exchange occurs via N-protonation so that residual conformational effects on exchange rates in the open conformers will affect acid- and base-catalyzed rates in approximately equal and opposite ways. A strong correlation between the measured pHminima and the amide proton chemical shifts is observed, however, and this may be most easily accommodated if acid-catalyzed exchange occurs by the imidic acid mechanism (via amide O-protonation).

Amides↗

Amino acid sequence of the sex steroid binding protein of human blood plasma.

The amino acid sequence of the sex steroid binding protein (SBP) from human plasma has been determined. The SBP subunit consists of a 373-residue polypeptide chain containing two disulfide bonds and three oligosaccharide chains. The sequence was solved primarily by analysis of peptides derived by cleavage at either lysyl or methionyl residues. In our preparations, approximately half of the protein molecules have the amino-terminal sequence Arg-Pro-Val-Leu-Pro; the other half lack Arg-Pro and begin with the valine. Preparations of Hammond et al. [Hammond, G. L., Robinson, P. A., Sugino, H., Ward, D. N., & Finne, J. (1986) J. Steroid Biochem. 24, 815] have an additional leucine at the amino terminus, making a total of 373 residues in the chain. Oligosaccharide chains are placed at Thr-7 and at Asn residues 351 and 367. The two disulfide bonds connect Cys-164 to Cys-188 and Cys-333 to Cys-361. The reported heterogeneity of preparations of the molecule may result in part from the amino-terminal microheterogeneity, in part from variations in the oligosaccharide moieties, and possibly in part from rearrangements involving cyclic imide formation in two Asn-Gly sequences. Certain hydrophobic segments are suggested as possible components of the steroid-binding sites. The protein shows no homology either with the cDNA-derived sequences of the estrogen and glucocorticoid receptors found by others to be homologous with each other or with any other protein sequence in the 1986 data base.

Amino Acid Sequence↗

Replacement of proline-76 with alanine eliminates the slowest kinetic phase in thioredoxin folding.

The conformational transition observed upon addition of guanidine hydrochloride (Gdn-HCl) to solutions of oxidized Escherichia coli thioredoxin is dominated by a slow kinetic phase (time constant tau 1 = 300-800 s) that has features appropriate to a proline peptide isomerization. This observation has been interpreted as reflecting a folding pathway involving an obligatory isomerization of the imide peptide bond between isoleucine-75 and proline-76 [Kelley, R. F., & Stellwagen, E. (1984) Biochemistry 23, 5095-5102]; this peptide bond is known to have the cis configuration in the folded state [Eklund, H., Cambillan, C., Sjöberg, B.-M., Holmgren, A., Jörnvall, H., Höög, J.-O., & Brändén, C.-I. (1984) EMBO J. 3, 1443-1449]. We have tested this hypothesis by examining the conformational transitions of two thioredoxin mutants, trxA76 having an alanine substituted for proline-76 and trxA2 [Russel, M., & Model, P. (1983) J. Bacteriol. 154, 1064-1070] having proline-34 replaced with serine. Both mutant proteins display far-ultraviolet circular dichroic spectra similar to that of native wild-type thioredoxin. The tryptophan fluorescence emission of native trxA2 is equivalent to that of wild-type thioredoxin, while the emission intensity of native trxA76 at 350 nm is 2-fold greater. Tryptophan fluorescence and peptide ellipticity measurements indicate that the mutant proteins undergo two-state and reversible equilibrium unfolding transitions upon addition of guanidine hydrochloride (Gdn-HCl). These transitions are centered at 2.4 and 1.5 M Gdn-HCl for trxA2 and trxA76, respectively, as compared to a midpoint of 2.5 M denaturant for wild-type thioredoxin. As observed for wild-type thioredoxin, fluorescence measurements reveal monophasic unfolding kinetics for trxA2 at a variety of final denaturant concentrations. The tau for unfolding varies monotonically from 210 s in 2.4 M Gdn-HCl to 7 s for a final Gdn-HCl concentration of 3.5 M. Refolding of denatured trxA2 in 1.5 M Gdn-HCl detected by fluorescence measurements is described by three kinetic phases with time constants and fractional amplitudes (alpha) similar to those of wild-type thioredoxins. The fractional amplitude (alpha 1) of the slowest of these phases, tau 1 = 430 +/- 38 s in 2.0 M Gdn-HCl, decreases with final Gdn-HCl concentration. Multimixing experiments suggest that this phase results from an equilibration between denatured forms and has a tau of 34 s in 4 M denaturant, features previously observed for the wild-type protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Alanine↗

Carboxy-terminal sequencing: formation and hydrolysis of C-terminal peptidylthiohydantoins.

Proteins and peptides can be sequenced from the carboxy terminus with isothiocyanate reagents to produce amino acid thiohydantoin derivatives. Previous studies in our laboratory indicated that the use of trimethylsilyl isothiocyanate (TMS-ITC) as a coupling reagent significantly improved the yields and reaction conditions and reduced the number of complicating side products [Hawke et al. (1987) Anal. Biochem. 166, 298]. The present study further explores the conditions for formation of the peptidylthiohydantoins by TMS-ITC and examines the cleavage of these peptidylthiohydantoin derivatives into a shortened peptide and thiohydantoin amino acid derivative. Schizophrenia-related peptide (Thr-Val-Leu) was used as a model peptide and was treated with acetic anhydride and TMS-ITC at 50 degrees C for 30 min, and the peptidylthiohydantoin derivatives were isolated by reverse-phase HPLC and characterized by FAB-MS. The purified derivatives were subjected to a variety of cleavage conditions, and rate constants for hydrolysis were determined. Hydrolysis with acetohydroxamate as reported originally by Stark [(1968) Biochemistry 7, 1796] was found to give excellent cleavage of the terminal thiohydantoin amino acid, but also led to the formation of stable hydroxamate esters of the shortened peptide which are poorly suited for subsequent rounds of degradation. Hydrolysis with 2% aqueous triethylamine under mild conditions (1-5 min at 50 degrees C) was found to be more suitable for carboxy-terminal sequence analysis by the thiocyanate method. The shortened peptide, which could be isolated and subjected to a second round of degradation, and the released thiohydantoin amino acid are formed in good yield (90-100%). Several other small peptides containing 15 different C-terminal amino acid side chains were also investigated in order to examine any interfering reactions that might occur when these side chains are encountered in a stepwise degradation using the thiocyanate chemistry. Quantitative yields of peptidylthiohydantoins were obtained for all the amino acids examined with the following exceptions: low yields were obtained for C-terminal Glu or Thr, and no peptidylthiohydantoins were obtained for C-terminal Pro or Asp. Asparagine was found to form cyclic imides (64%) at the penultimate position (C-2) during hydrolysis of the peptidylthiohydantoins by 2% aqueous triethylamine. Cleavage of C-terminal Asn under these conditions led to the formation of the expected shortened peptide (69%), but also to the formation of a shortened peptide (31%) with a C-terminal amide. Problems with Glu and Thr could be solved by minimizing the reaction time with acetic anhydride.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

Structural analysis of ribosomal protein L7/L12 by the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate.

The structure of the dimeric form of the protein L7/L12 from ribosomes from Escherichia coli was studied by using the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate. The imidate group of the cross-linker reacts very specifically with Lys-51 of L7/L12. Subsequent cross-linking of this modified L7/L12 by reductive alkylation of the aldehyde group of the cross-linker results in the formation of a covalent cross-link between both polypeptide chains of the L7/L12 dimer. This covalently cross-linked dimer is fully active in reconstitution of elongation factor G dependent GTP hydrolysis of 50S cores lacking L7/L12, suggesting a conformation of the cross-linked protein similar to the conformation of native L7/L12. Analysis of the tryptic peptides of cross-linked L7/L12 shows the points of attachment of the cross-linker to be Lys-51 in one polypeptide chain and Lys-29 in the other. On the basis of a combination of this result with published data, a structure for the N-terminal region of L7/L12 dimers is proposed. The important feature of this model is a shifted parallel alignment of both polypeptide chains resulting in one free N-terminal stretch for each L7/L12 dimer which attaches the protein to the ribosome via protein L10.

Amino Acid Sequence↗

Covalent modification of rhodopsin with imidoesters: evidence for transmembrane arragnement of rhodopsin in rod outer segment disk membranes.

The transmembrane disposition of the visual pigment rhodopsin was studied by the covalent labeling of protein amino groups with membrane-permeable and -impermeable imidoesters. A new, highly reactive permeable reagent, 2-(methylsulfonyl)ethyl acetimidate (SAI) was developed for this purpose. The permeabilities of both this compound and the "impermeable" reagent isethionyl acetimidate (IAI) across the rod outer segment disk membrane were directly measured. Our results indicate that rhodopsin contains three classes of amino groups. One class (35--55% of the total) reacts rapidly with the membrane-impermeable reagent and is presumably exposed on the outside surface of the membrane. A second class (35--55% of the total) is located on the internal surface of the disk since its rate of reaction is dependent on the relative permeabilities of the labeling reagents. The remaining 10% of the rhodopsin amino groups are inaccessible to either type of imidate and are largely accounted for by the single lysine residue which specifically binds the chromophore retinal. These findings, taken together with evidence from freeze--fracture electron microscopy, imply that rhodopsin is a transmembrane protein.

Animals↗

Superoxide dismutase, a study of the electronic properties of the copper and zinc by X-ray absorption spectroscopy.

The x-ray absorption for copper and zinc in oxidized and reduced superoxide dismutase, as well as in various model compounds, was studied. Upon reduction of the protein, the added electron affects the copper site almost exclusively, while the zinc remains virtually unchanged. Reduction decreases the charge on the copper atom [toward Cu(I)] and changes the configuration of the copper site so that it becomes less symmetric. An analysis of the copper absorption observed with the oxidized enzyme and a comparison with that for Cu(II)(imid)4 suggests that the copper is not simply ligated to four imidazoles. The addition of H2O2 to superoxide dismutase reduces the copper to Cu(I), while oxygen addition to the peroxide-reduced protein restores the copper to Cu(II).

Absorption↗

Photoactivated heterobifunctional cross-linking reagents which demonstrate the aggregation state of phospholipase A2.

Two novel heterobifunctional cross-linking reagents, which can be used to attach photoactivatable nitroaryl azides to primary amino groups of proteins, have been synthesized. The two compounds, N-5-azido-2-nitrobenzoyloxy-succinimide and ethyl N-5-azido-2-nitrobenzoylaminoacet-imidate-HCl, as well as ethyl 4-azidobenzimidate-HCl have been attached to lysine residues of cobra venom phospholipase A2 without a loss in enzymatic activity. Subsequent illumination of the modified forms of the enzyme at appropriate wavelengths under conditions in which the native enzyme exists in an aggregated state led to the formation of covalently linked dimers and large aggregates which could be separated by electrophoresis on polyacrylamide gels in the presence of sodium dodecyl sulfate.

Elapid Venoms↗

2-Imino-2-methoxyethyl 1-thioglycosides: new reagents for attaching sugars to proteins.

Cyanomethyl 1-thioglycosides ofD-galactose, D-glucose, 2-acetamido-2-deoxy-D-glucose, and D-mannose were prepared from the respective pseudothiourea derivatives and chloroacetonitrile. The nitrile group in these cyanomethyl thioglycosides can be converted to a methyl imidate group by treatment with sodium methoxide or HC1 in dry methanol to yield 2-imino-2-methoxyethyl 1-thioglycosides (IME-thioglycosides). The factors influencing the yield of IME-thioglycosides were investigated. The most convenient method of preparing IME-thioglycosides was treating 0.1 M cyanomethyl thioglycoside peracetate in dry methanol with 0.01 M sodium methoxide at room temperature for 24-48 h (50-60% yield). These IME-thioglycosides reacted readily with simple amines, amino acids, and proteins in mildly alkaline buffer solutions. Alpha-amylase and lysozyme modified with these reagents under appropriate conditions retained full activities. Thus the IME-thioglycosides constitute a new group of reagents for attaching sugars to proteins.

Acetylglucosamine↗