Hydrolysis of primary amide groups in Asn/Gln-containing peptides

Peptides Boc-Ala-Asn/Gln-OH and Boc-Asn/Gln-Ala-OH were saponified with barium hydroxide to corresponding Asp/Glu-containing peptides. Under the conditions of saponification, Boc-Asn-Ala-OH additionally afforded Boc-Asp-OH, isopeptide Boc-Asp(Ala)-OH, and Boc-NHSuc > Ala-OH, with the third being the key intermediate in these transformations. Boc-Asp(OMe)-Ala-OMe underwent similar transformations under treatment with diazomethane or triethylamine. Saponification with barium hydroxide was accompanied by a high epimerization of N-terminal amino acid residues, whereas the products of the diazomethane treatment of Boc-Asp(OMe)-Ala-OMe had a low degree of epimerization.     

Molecular and crystal structures of three monothiated analogues of the terminally blocked ala-aib-ala sequence of peptaibol antibiotics

The molecular and crystal structures of three monothiated analogues of the blocked L -Ala-Aib-L -Ala sequence of peptaibol antibiotics, t-Boc-L -Ala-Aib-ψ(CSNH)-L -Ala-OMe, Ac-L -Ala-Aib-ψ(CSNH)-L -Ala-OMe, and Ac-ψ(CSNH)-L -Ala-Aib-L -Ala-OMe, determined by x-ray diffraction analyses, are reported. In all cases the peptide chain is folded with φ,ψ angles close to or slightly distorted from those expected for a type II β-bend conformation. However, the 4 → 1 H-bond distance falls within the accepted limits only for Ac-L -Ala-Aib-ψ(CSNH)-L -Ala-OMe. The structures are compared with those already published for their two oxygenated analogues.     

Resolution of DL-2-aminosuberic acid via protease-catalyzed ester hydrolysis

Summary Papain-catalyzed regioselective cleavage of-methyl ester in Z-DL-Asu(OMe)-OMe leads to Z-L-Asu(OMe)-OH and Z-D-Asu(OMe)-OMe. Subsequent saponifications yield Z-L-Asu-OH and Z-D-Asu-OH. The enzymatic-ester hydrolysis was also achieved by subtilisin BPN in organic solvent with low water content.Abbreviations Asu 2-aminosuberic acid - Z benzyloxycarbonyl - OMe methyl ester - DCHA dicyclohexylamine     

Apoptosis-specific protein (ASP 45 kDa) is distinct from human Apg5, the homologue of the yeast autophagic gene apg5

We have examined whether the apoptosis-specific protein p45ASP and human Apg5 are identical proteins. Like p45ASP, myc-hApg5 cross-reacted with a c-Jun antibody and approximately 50% of myc-hApg5 was bound to a Triton X-100-insoluble fraction in HeLa cells. However, soluble myc-hApg5 was degraded during apoptosis induced by staurosporine or TNFalpha/cycloheximide whilst expression of soluble p45ASP was stabilised. Furthermore, myc-hApg5 degradation was blocked by the caspase inhibitor Boc-Asp(OMe)FMK whilst p45ASP expression was eliminated. Moreover, myc-hApg5 ( approximately 32 kDa) never assumed the size of p45ASP (45 kDa). It is therefore likely that p45ASP and human Apg5 are distinct proteins although they do share some common characteristics.     

p38 MAPK mediates TNF-induced apoptosis in endothelial cells via phosphorylation and downregulation of Bcl-x(L)

The role of p38 mitogen-activated protein kinase (MAPK) in apoptosis is a matter of debate. Here, we investigated the involvement of p38 MAPK in endothelial apoptosis induced by tumor necrosis factor alpha (TNF). We found that activation of p38 MAPK preceded activation of caspase-3, and the early phase of p38 MAPK stimulation did not depend on caspase activity, as shown by pretreatment with the caspase inhibitors z-Val-Ala-Asp(OMe)-fluoromethylketone (zVAD-fmk) and Boc-Asp(OMe)-fluoromethylketone (BAF). The p38 MAPK inhibitor SB203580 significantly attenuated TNF-induced apoptosis in endothelial cells, suggesting that p38 MAPK is essential for apoptotic signaling. Furthermore, we observed a time-dependent increase in active p38 MAPK in the mitochondrial subfraction of cells exposed to TNF. Notably, the level of Bcl-x(L) protein was reduced in cells undergoing TNF-induced apoptosis, and this reduction was prevented by treatment with SB203580. Immunoprecipitation experiments revealed p38 MAPK-dependent serine-threonine phosphorylation of Bcl-x(L) in TNF-treated cells. Exposure to lactacystin prevented both the downregulation of Bcl-x(L) and activation of caspase-3. Taken together, our results suggest that TNF-induced p38 MAPK-mediated phosphorylation of Bcl-x(L) in endothelial cells leads to degradation of Bcl-x(L) in proteasomes and subsequent induction of apoptosis.     

Studies on peptides CLVIII. Model experiments for the synthesis of open-chain unsymmetrical cystine-peptides

Treatment of a mixture of Cys(R)(O) and Cys(R) with an acid was found to generate cystine in fairly good yields, when suitable R, R, and an acid were selected. An unsymmetrical cystine peptide was prepared by treatment of a mixture of Z(OMe)-Cys(R) (0)-Ala-NH₂ (R=Acm or MBzl) and Z(OMe)-Cys(MBzl)-Gly-OBzl with TFA or 1 M TFMSA/TFA.³ Oxytocin was obtained in an excellent yield by TFA treatment of the protected peptide containing Cys(Acm)(0) and Cys(MBzl). Thus, formation of the disulfide bond was found feasible at the position of Cys(R) (0).The following abbreviations are used Boc t-butyloxycarbonyl - Z(OMe) p-methoxybenzyloxycarbonyl - MBzl p-methoxybenzyl - Acm acetamidomethyl - Bzl benzyl - Ad l-adamantyl - tBu t-butyl - TFA trifluoroacetic acid - TFMSA trifluoromethanesulfonic acid - TMSOTf trimethylsilyl trifluoromethane sulfonate     

Conformations of helical Aib peptides containing a pair of l‐amino acid and d‐amino acid

A pair of l ‐leucine (l ‐Leu) and d ‐leucine (d ‐Leu) was incorporated into α‐aminoisobutyric acid (Aib) peptide segments. The dominant conformations of four hexapeptides, Boc‐l ‐Leu‐Aib‐Aib‐Aib‐Aib‐l ‐Leu‐OMe (1a), Boc‐d ‐Leu‐Aib‐Aib‐Aib‐Aib‐l ‐Leu‐OMe (1b), Boc‐Aib‐Aib‐l ‐Leu‐l ‐Leu‐Aib‐Aib‐OMe (2a), and Boc‐Aib‐Aib‐d ‐Leu‐l ‐Leu‐Aib‐Aib‐OMe (2b), were investigated by IR, ¹H NMR, CD spectra, and X‐ray crystallographic analysis. All peptides 1a,b and 2a,b formed 3₁₀‐helical structures in solution. X‐ray crystallographic analysis revealed that right‐handed (P) 3₁₀‐helices were present in 1a and 1b and a mixture of right‐handed (P) and left‐handed (M) 3₁₀‐helices was present in 2b in their crystalline states. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

N-banding in Triticum aestivum following feulgen hydrolysis

Summary Terminal and/or interstitial N-bands were produced on the seven B-genome chromosomes and chromosomes 4 and 7 of the A-genome of Triticum aestivum cv. Chinese Spring by a modified BSG technique following a standard Feulgen preparation. The banding was accomplished by modifying the barium hydroxide treatment.     

Terminal effect of chiral residue on helical screw sense in achiral peptides

To understand the terminal effect of chiral residue for determining a helical screw sense, we adopted five kinds of peptides I – V containing N‐ and/or C‐terminal chiral Leu residue(s): Boc–L ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( I ), Boc–(Aib–ΔPhe)₂–L ‐Leu–OMe ( II ), Boc–L ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( III ), Boc–D ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( IV ), and Boc–D ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( V ). The segment –(Aib–ΔPhe)₂– was used for a backbone composed of two “enantiomeric” (left‐/right‐handed) helices. Actually, this could be confirmed by ¹H‐nmr [nuclear Overhauser effect (NOE) and solvent accessibility of NH resonances] and CD spectroscopy on Boc–(Aib–ΔPhe)₂–Aib–OMe, which took a left‐/right‐handed 3₁₀‐helix. Peptides I – V were also found to take 3₁₀‐type helical conformations in CDCl₃, from difference NOE measurement and solvent accessibility of NH resonances. Chloroform, acetonitrile, methanol, and tetrahydrofuran were used for CD measurement. The CD spectra of peptides I – III in all solvents showed marked exciton couplets with a positive peak at longer wavelengths, indicating that their main chains prefer a left‐handed screw sense over a right‐handed one. Peptide V in all solvents showed exciton couplets with a negative peak at longer wavelengths, indicating it prefers a right‐handed screw sense. Peptide IV in chloroform showed a nonsplit type CD pattern having only a small negative signal around 280 nm, meaning that left‐ and right‐handed helices should exist with almost the same content. In the other solvents, peptide IV showed exciton couplets with a negative peak at longer wavelengths, corresponding to a right‐handed screw sense. From conformational energy calculation and the above ¹H‐nmr studies, an N‐ or C‐terminal L ‐Leu residue in the lowest energy left‐handed 3₁₀‐helical conformation was found to take an irregular conformation that deviates from a left‐handed helix. The positional effect of the L ‐residue on helical screw sense was discussed based on CD data of peptides I – V and of Boc–(L ‐Leu–ΔPhe)_n–L ‐Leu–OMe (n = 2 and 3). © 1999 John Wiley & Sons, Inc. Biopoly 49: 551–564, 1999     

Toxin profile of Alexandrium catenella from the Chilean coast as determined by liquid chromatography with fluorescence detection and liquid chromatography coupled with tandem mass spectrometry

The profile of tetrahydropurine neurotoxins associated with paralytic shellfish poisoning (PSP) was determined from a Chilean strain of the marine dinoflagellate Alexandrium catenella. The toxin composition was compared with that of toxic shellfish, presumably contaminated by natural blooms of A. catenella from the same region in southern Chile. Ion pair-liquid chromatography with post-column derivatization and fluorescence detection (LC-FD) was employed for relative quantitative analysis of the toxin components, whereas unambiguous identification of the toxins was confirmed by tandem mass spectrometry (LC–MS/MS). In the dinoflagellate strain from Chile, the N-sulfocarbamoyl derivatives (C1/C2, B1) and the carbamoyl gonyautoxins GTX1/GTX4 comprise >90% of the total PSP toxin content on a molar basis. This toxin composition is consistent with that determined for A. catenella populations from the Pacific coast in the northern hemisphere. The characteristic toxin profile is also reflected in the shellfish, but with evidence of epimerization and metabolic transformations of C1 and C2 to GTX2 and GTX3, respectively. This work represents the first unequivocal identification and confirmation of such PSP toxin components from the Chilean coast.     

Multi gram-scale synthesis of galactothionolactam and its transformation into a galactonoamidine

We recently proposed to conduct selective glycosylation reactions after in situ activation of a glycosyl donor promoted by a transition metal complex immobilized in a macromolecular matrix. In order to develop this catalytic entity, a feasible multi gram-scale synthesis for 2,3,4,6-tetra-O-benzyl-d-galactothionolactam, its transformation into galactonoamidines with aromatic aglycon, and subsequent debenzylation conditions were developed. The potential for epimerization reactions at C-2 of the glycosidic ring during the transformations from the 2,3,4,6-tetra-O-benzyl-d-galactonolactam into the N-benzyl-2,3,4,6-tetra-O-benzyl-d-galactonoamidines via the 2,3,4,6-tetra-O-benzyl-d-galactothionolactam are discussed and additionally characterized by using density functional theory calculations.     

Novel teichulosonic acid from cell walls of some representatives of the genus Kribbella

Cell walls of each of five bacterial strains belonging to the genus Kribbella (family Nocardioidaceae, order Actinomycetales) contain a neutral polysaccharide (mannan) and teichulosonic acid of novel structure in different proportions. The novel teichulosonic acid found in strains VKM Ac-2500, VKM Ас-2568, VKM Ас-2572, and VKM Ас-2575 is a heteropolymer with an irregular structure where fragments I (predominant) alternate with fragments II (minor):The teichulosonic acid from Kribbella sp. VKM Ac-2527 has in general a structure similar to that above with the exception that the Pse residue is randomly glycosylated at O-4 with β-l-Rhap (along with α-d-Galp3OMe or α-d-Galp2,3OMe). The strain VKM Ac-2572 contained additionally teichuronic acid with the disaccharide repeating unit consisted of aminomannuronic acid and 2,3-diacetamido-2,3-dideoxy-α-glucopyranose. The mannan, a polysaccharide common to all of the strains, is built of (1→6)-linked α-d-mannopyranose substituted with α-d-mannopyranose at O-2. The structures of all the glycopolymers were established by a combination of chemical and NMR spectroscopic methods.     

Water unextractable polysaccharides from three milling fractions of rye grain

Water unextractable material from bran, an intermediate milling fraction and sieved flour of rye grain were sequentially extracted at room temperature with saturated barium hydroxide, water, 4 M potassium hydroxide and water followed by extraction with 2 potassium hydroxide in a boiling water bath, giving repeatable recoveries of extracts and polysaccharide residue compositions in collected fractions. Total recoveries of polysaccharide residues in extracts and residue from the different water unextractable materials were 78–88%. Extracts in which 90–93% of the carbohydrates were arabinose and xylose residues were obtained by extraction with saturated barium hydroxide. Subsequent extraction with water yielded a fraction in which 64–68% of the carbohydrates were glucose residues. The extraction with hot alkali resulted in extracts in which 85–89% of the carbohydrates were arabinose and xylose residues. The ara/xyl ratio in the collected fractions ranged from 0.1–1.3, with the lowest ratios in fractions that precipitated after neutralisation of the 4 potassium hydroxide extract and the highest ratios in the unextractable residues. Structural characterisation with ¹H-NMR spectroscopy revealed varying substitution patterns for arabinoxylans in the different extracts and that glucose residues in the extracts essentially originated from mixed-linked β-glucan. The proportion of disubstituted xylose residues was lower in barium hydroxide extracts compared to the other main extracts. A highly branched heteroxylan was extracted with hot alkali. The polysaccharides found in the corresponding extracts for all the starting materials had generally similar structural features, but the yield differed considerably.     

Arabinoxylan fractionation on DEAE-cellulose chromatography influenced by protease pre-treatment

An arabinoxylan mixture was extracted with saturated barium hydroxide from a water unextractable residue of rye bran. The mixture was fractionated on an anion exchange column which was eluted with water, 0.0025 M sodium borate, 0.025 M sodium borate and 0.4 M sodium hydroxide. It was possible to fractionate the arabinoxylan mixture into fractions with different structural features. The fractionation was repeated with prior protease treatment of the arabinoxylan mixture, but most of the arabinoxylan did not bind to the column by any mechanism that the protease treatment affected, As the largest fraction was still eluted with 0.4 M sodium hydroxide. Protease treatment affected the proportion of disubstituted xylose residues (dXyl) in the water, 0.0025 M sodium borate and 0.025 M sodium borate fractions, indicating that protein associated with arabinoxylans with a high dXyl content is more liable to the protease treatment or that protein is mainly associated with these structures. This study gives indications that protein is involved in the separation mechanism of rye arabinoxylan on a DEAE–cellulose column.     

The effect of temperature and salt concentration on the circular dichroism exhibited by unionized derivatives of L-alanine in aqueous solution

The circular dichroism of Ac–Ala–NHMe, cyclo(–Ala–Ala–), Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe has been measured in water and in aqueous salt solutions as a function of temperature. Only cyclo(–Ala–Ala–) exhibits circular dichroism which is independent of temperature. Each of the linear derivatives of L -alanine exhibits a positive circular dichroism in the range 208–218 nm at 15°C in water. Heating reduces the intensity of the positive circular dichroism, and only Ac–Ala–OMe retains positive circular dichroism at 75°C in water. Isothermal addition of salts produces changes in the circular dichroism of linear derivatives of L -alanine which resemble those seen on heating. The relative effectiveness of the salts tested, at a concentration of 4M, is LiCl ? KCl = NaCl < MgCl₂ ? CaCl₂ ? NaClO₄. The circular dichroism of cyclo(–Ala–Ala–) is also affected by the salts. Extrapolation of the results obtained with Ac–Ala–OMe, Ac–Ala–Ala–OMe, and Ac–Ala–Ala–Ala–OMe to a long polypeptide with a –CH₂R side chain in the L -configuration leads to the conclusion that this polypeptide should exhibit a temperature-dependent salt-sensitive positive circular dichroism between 208 and 218 nm when it exists as a statstical coil.     

Separation of D-forms and L-forms of DL-aspartic acid derivatives by the enzyme subtilisin DY

The ability of the enzyme subtilisin DY for the synthesis of derivatives of DL-aspartic acid which are differently N and C-terminal protected and semiproducts of the peptide synthesis was investigated. The enzyme reaction was characterized by high yields and a comparatively short reaction time. Two of the substrates, Z-D,L-Asp-(OMe)₂ and PhAc-D,L-Asp-(OMe)₂, were hydrolyzed for about 15 min; the reaction time for Boc-D,L-Asp-(OMe)₂ was 2.5 h. The values for the MICHAELIS constants obtained for Z-D,L-Asp-(OMe)₂ (K_m = 0.576 mM) and PhAc-D,L-Asp-(OMe)₂ (K_m = 0.300 mM) showed a high affinity of the enzyme to the substrates. For Boc-D,L-Asp-(OMe)₂ the affinity of the enzyme is considerable lower (K_m = 14.07 mM). The results of these investigations can be effectively used for the separation of N-protected derivatives of D,L-aspartic acid and with a high probability also for other amino and racemic forms.     

New cell wall glycopolymers of the representatives of the genus Kribbella

Each of the cell walls of four representatives of the genus Kribbella (order Actinomycetales; suborder Propionibacterineae; family Nocardioidaceae) contains a neutral polysaccharide and an acidic polysaccharide with unusual structures. Common to all four strains studied is a mannan with the following repeating unit: In the cell wall of the strain VKM Ac-2541, a teichulosonic acid was identified with a monosaccharide component that has not hitherto been found in Gram-positive bacteria, viz., pseudaminic acid, and an unusual linkage type in the polymeric chain,

Full-size image (1K)

where R = Н (45%), α-d-Galp3OMe (37%) or α-d-Galp2,3OMe (18%).The anionic cell wall components of three other strains are represented by teichuronic acids with a rare constituent, viz., a diaminosugar, 2,3-diacetamido-2,3-dideoxyglucopyranose. The structures of their repeating units differ in the nature of the acidic components:→4)-β-d-Manp2,3NAcA-(1→6)-α-d-Glcp2,3NAc-(1→ (VKM Ас-2538 and VKM Ас-2540) and →4)-β-d-ManpNAcA-(1→6)-α-d-Glcp2,3NAc-(1→ (VKM Ас-2539).The structures of all the glycopolymers were established by chemical and NMR spectroscopic methods; they are identified in Gram-positive bacteria for the first time.     

The regiospecific N-derivatization of histidine side chains: reinvestigation of a supposed Nτ to Nπ migration

A report claiming that AcHisOMe reacts regiospecifically with 4-fluoronitrobenzene to give AcHis[τPh(NO₂)]OMe, which on treatment with H₂/Pd(C) undergoes a partial τ–π shift to give some AcHis[πPh(NH₂)]OMe, cannot be substantiated. 4(5)-Methylimidazole, a model for AcHisOMe, gives on reaction with 4-fluoronitrobenzene a 4:1 mixture of the regioisomers 1-(4-nitrophenyl),4-methylimidazole, corresponding to τ-substitution, and 1-(4-nitrophenyl),5-methylimidazole, corresponding to π-substitution, each of which has been isolated and fully characterized, including proof of orientation. In both cases, treatment with H₂/Pd(C) gives a single product, without any change of orientation in either case. © 1997 European Peptide Society and John Wiley & Sons, Ltd. J. Pep. Sci.3: 391–394 No. of Figures: 2. No. of Tables: 0. No. of References: 9     

Investigation of α/γ hybrid peptide self‐assembled structures with antimicrobial and antibiofilm properties

The present work describes the synthesis and characterization of α/γ hybrid peptides, Boc‐Phe‐γ⁴‐Phe‐Val‐OMe, P1 ; Boc‐Ala‐γ⁴‐Phe‐Val‐OMe, P2 ; and Boc‐Leu‐γ⁴‐Phe‐Val‐OMe, P3 together with the formation of self‐assembled structures formed by these hybrid peptides in dimethyl sulfoxide (DMSO)/water (1:1). The self‐assembled structures were characterized by infrared (IR) spectroscopy, circular dichroism (CD), and scanning electron microscopy (SEM). Further, α/γ hybrid peptide self‐assembled structures were evaluated for antibacterial properties. Among all, the self‐assembled peptide P1 exhibited the antimicrobial activity against Escherichia coli and Klebsiella pneumoniae, while self‐assembled peptide P3 inhibited the biofilms of Salmonella typhimurium and Pseudomonas aeruginosa. In this study, we have shown the significance of self‐assembled structures formed from completely hydrophobic α/γ hybrid peptides in exploring the antibacterial properties together with biofilm inhibition.     

The Enzymatic Segment Condensation of Peptides on a Solid Phase in Organic Medium

The segment condensation of peptides on a solid phase (Aminosilochrom) in organic medium catalyzed by a subtilisin complex with sodium dodecylsulfate was studied. The dependence of the efficiency of the enzymatic coupling of tripeptides with the basic structure X-Ala-Ala-Y-OMe [where X = Z, Boc, or Dnp and Y = Leu or Glu(OMe)] on the spacer (Phe-Met-Gly-Gly) content on the support and on the structure of the acylating component was investigated. The tripeptide segments were successively coupled to Aminosilochrom containing the Met-Ala-Gly spacer, and the peptidylaminosilochroms Dnp-Ala-Ala-Leu-Ala-Ala-Leu-Ala-Ala-Glu(OMe)-Met-Ala-Gly-Aand Dnp-Ala-Ala-Leu-Ala-Ala-Glu(OMe)-Ala-Ala-Leu-Met-Ala-Gly-A(Ais the Aminosilochrom residue) were obtained in satisfactory yields. It was shown by these examples that the second and third segments are attached in yields higher than that for the first segment and the coupling efficiency does not depend on the amino acid composition of the acylating component.