Stereoselective disulfide formation stabilizes the local peptide conformation in nisin mimics

Nisin is a polymacrocyclic peptide antimicrobial with high activity against Gram-positive bacteria. Lanthionine and methyllanthionine bridges, closing the macrocycles, are stabilized by thioether bonds, formed between cysteines and dehydrated serine or threonine. The role of polypeptide backbone conformation in the formation of macrocycles A and B within cysteine mutants of nisin residues 1?12 is investigated here by molecular dynamics simulations. Enantiomeric combinational space of Cys3 and Cys7 and of Cys8 and Cys11 is examined for the preference of disulfide bond formation over helical turn formation within this region. A clear preference for spontaneous disulfide formation and closure of rings 3,7 and 8,11 is demonstrated for the D-Cys3, D-Cys7, L-Cys8, L-Cys11 nisin homologue, while interlinked rings A and B are obtained through disulfide bridges between L-Cys3 and D-Cys8 and between D-Cys7 and D-Cys11. This study offers a simple designer approach to solid phase synthesis of macrocyclic peptides and lantibiotic analogues.     

Tetrachromacy in a butterfly that has eight varieties of spectral receptors

This paper presents the first evidence of tetrachromacy among invertebrates. The Japanese yellow swallowtail butterfly, Papilio xuthus, uses colour vision when foraging. The retina of Papilio is furnished with eight varieties of spectral receptors of six classes that are the ultraviolet (UV), violet, blue (narrow-band and wide-band), green (single-peaked and double-peaked), red and broad-band classes. We investigated whether all of the spectral receptors are involved in colour vision by measuring the wavelength discrimination ability of foraging Papilio. We trained Papilio to take nectar while seeing a certain monochromatic light. We then let the trained Papilio choose between two lights of different wavelengths and determined the minimum discriminable wavelength difference Deltalambda. The Deltalambda function of Papilio has three minima at approximately 430, 480 and 560nm, where the Deltalambda values approximately 1nm. This is the smallest value found for wavelength discrimination so far, including that of humans. The profile of the Deltalambda function of Papilio can be best reproduced by postulating that the UV, blue (narrow-band and wide-band), green (double-peaked) and red classes are involved in foraging. Papilio colour vision is therefore tetrachromatic.     

Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes

D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the beta-carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyzes metal removal. To investigate the structural basis for this difference, we solved the crystal structure of carboxypeptidase A complexed with D-cysteine (D-Cys) at 1.75-A resolution. D-Cys binds the active site zinc with a sulfur ligand and forms additional interactions with surrounding side chains of the enzyme. The structure explains the difference in potency between D-Cys and L-Cys and provides insight into the mechanism of D-penicillamine inhibition. D-Cys binding induces a concerted motion of the side chains around the zinc ion, similar to that found in other carboxypeptidase-inhibitor crystal structures and along a limited path. Analysis of concerted motions of CPD and CPD-inhibitor crystal structures reveals a clustering of these structures into distinct groups. Using the restricted conformational flexibility of a drug target in this type of analysis could greatly enhance efficiency in drug design.     

Conformational features responsible for binding of cyclic analogues of enkephalin to opioid receptors. I. Low-energy peptide backbone conformers of analogues containing Phe4

Low-energy peptide backbone conformers were found by means of energy calculation for several cyclic analogues of enkephalin in an attempt to assess models for receptor-bound conformations for opioid receptors of the mu- and delta-types. They included [D-Cys2, L-Cys5]- and [D-Cys2, D-Cys5]-enkephalinamides showing moderate preference for mu-receptors, the delta-selective compounds [D-Pen2, L-Pen5] and [D-Pen2, D-Pen5]-enkephalins and Tyr-D-Lys-Gly-Phe- analogue possessing very high affinity to receptors of the mu-type. The low-energy conformers obtained for these analogues were in good agreement with the results of calculations by other authors and with experimental evidence. All of the analogues contain a Phe residue in position 4 of the peptide chain which facilitates the eventual search for geometrical similarity between the low-energy backbone conformers of different analogues in question.     

Stimulation of mucosal uptake of selenium from selenite byl-cysteine in sheep small intestine

The influence of cysteine (Cys) on mucosal uptake of 75Se-labeled selenite in sheep midjejunum was investigated using a short-term uptake technique. L-Cys (concn.: 1.0 mmol/L) significantly stimulated uptake of Se from selenite (concn.: 10 mumols/L). The stimulatory effect of L-Cys on mucosal uptake of Se from selenite was Na(+)- and pH-dependent. In the absence of Na+, or at an acidic pH (5.0), the stimulatory effect of L-Cys was abolished. L-alanine and L-lysine, but not L-glutamic acid inhibited uptake of Se from selenite in the presence of L-Cys. Preincubation of mucosal preparations with 10 mmol/L L-Cys produced enhanced mucosal uptake of Se from selenite. It is concluded from these results that L-Cys stimulates absorption of Se from selenite probably by generation of selenodicysteine and maybe cysteine selenopersulfide that are subsequently transported across the intestinal brush border membrane by Na(+)-dependent amino acid carriers. Furthermore, intracellular generation of selenodicysteine might contribute to the uptake of Se from selenite by maintaining the concentration gradient for diffusive uptake of selenite.     

Methylmercury accumulation and fluxes across the intestine of channel catfish,Ictalurus punctatus

The excised intestines of channel catfish, Ictalurus punctatus, were perfused at 20 or 4 degrees C for 1 h 45 min, with methylmercury (CH(3)HgCl) alone, or in the presence of excess L-cysteine (L-Cys), D-cysteine (D-Cys), L-methionine (L-Met); or with ouabain or probenecid to identify the potential CH(3)Hg(II) uptake pathways in fish intestines. A temperature effect was noted, with CH(3)Hg(II) concentrations in tissues perfused at 20 degrees C being higher than at 4 degrees C, substantiating the idea that mechanisms requiring metabolic energy are involved in CH(3)Hg(II) uptake in fish intestines. The results indicate that, when CH(3)Hg(II) is complexed as the CH(3)Hg-L-Cys complex, it is taken up via an L-neutral amino acid carrier and rapidly transported to the serosal side of the intestine. Methylmercury uptake could be inhibited by probenecid and ouabain, although probenecid had less impact on CH(3)Hg(II) uptake than ouabain. Our results for CH(3)Hg(II) uptake in the presence of D-Cys, L-Met in excess of L-Cys, or with a metal mixture further established that CH(3)Hg(II) uptake across fish intestines occurs via a variety of pathways, including an energy-dependent L-neutral amino acid carrier, and that the route and amount of accumulation were a function of CH(3)Hg(II) speciation in the digestive tract of the fish.     

Synchronous fluorescence, UV-visible spectrophotometric, and voltammetric studies of the competitive interaction of bis(1,10-phenanthroline)copper(II) complex and neutral red with DNA

Constant wavelength synchronous fluorescence spectroscopy (CW-SFS), UV-visible absorption spectroscopy, and cyclic and differential pulse voltammetry were applied to investigate the competitive interaction of DNA with the bis(1,10-phenanthroline)copper(II) complex cation ([Cu(phen)(2)](2+)) and a fluorescence probe, neutral red dye (NR), in a tris-hydrogen chloride buffer (pH 7.4). The results show that both the [Cu(phen)(2)](2+)and the NR molecules can intercalate competitively into the DNA double-helix structure. The cyclic voltammetry method showed that both anodic and cathodic currents of [Cu(phen)(2)](2+) decreased on addition of the DNA and the intercalated [Cu(phen)(2)](2+)-DNA complex formed (beta = (4.14 +/- 0.24) x 10(3)). CW-SFS measurements were facilitated by the use of the three-way resolution of the CW-SFS for NR, [Cu(phen)(2)](2+), and NR-DNA. The important constant wavelength (CW) interval, Deltalambda, was shown to vary considerably when optimized (135, 58, and 98 nm for NR, NR-DNA, and [Cu(phen)(2)](2+), respectively). This approach clearly avoided the errors that otherwise would have arisen from the common assumption that Deltalambda is constant. Furthermore, a chemometrics approach, parallel factor analysis (PARAFAC), was applied to resolve the measured three-way CW-SFS data, and the results provided simultaneously the concentration information for the three reaction components, NR, [Cu(phen)(2)](2+), and NR-DNA, for the system at each equilibrium point. The PARAFAC analysis indicated that the intercalation of the [Cu(phen)(2)](2+) molecule into the DNA proceeds by exchanging with the NR probe and can be attributed to two parallel reactions. Comprehensive information was readily obtained; the replacement of the intercalated NR commenced immediately on introduction of [Cu(phen)(2)](2+), approximately 50% of NR was replaced by [Cu(phen)(2)](2+) at a concentration of 0.45 x 10(-5) mol L(-1), and nearly all of the NR was replaced at a [Cu(phen)(2)](2+) concentration of 2.50 x 10(-5) mol L(-1). This work has the potential to improve extraction of information from the fluorescence intercalator displacement (FID) assay.     

Time-resolved fluorescent chirality sensing and imaging of malate in aqueous solution

Chiral discrimination of malates in aqueous solutions at near-neutral pH is achieved through fluorescence measurement and imaging using the europium-tetracycline complex (EuTc) as a fluorescent probe. The method is based on the significantly different fluorescence properties of the ternary complexes (Eu-Tc-malate) formed between EuTc and the enantiomeric malates. The enantiomeric excess (ee) of chiral malates can be quantified by both steady-state and time-resolved fluorescence, using either a conventional fluorescence microplate reader or fluorescence imaging. It offers a facile and sensitive method for high-throughput chiral discrimination.     

pH对马铃薯‘转心乌’块茎花色苷颜色变化及降解速率的影响

用分光光度法在体外研究了不同pH条件下马铃薯'转心乌'块茎花色苷颜色呈现和降解速率的变化,以探讨马铃薯'转心乌,块茎颜色呈现的机理.结果显示:在pH 2.0时,该花色苷呈现最强烈的红色.随着pH从0增加到13.0,该花色苷在可见光区的最大吸收波长(λvis max)依次出现红移、蓝移,然后消失,在可见光区的最大吸收波长处的吸光值(Aλ,vis max)呈现为一条单峰曲线,峰值在pH 2.0处.当原始pH值被恢复到2.0后,如果原始pH小于或等于5.0,花色苷的红色均被恢复得更浓烈,λvis max不同程度地趋向537 nm,Aλ,vis max增加;如果原始pH大于或等于6.0,花色苷的红色根本不能被恢复,λvis max几乎不变,Aλ,vis max仍然维持低水平.在15℃、黑暗中,该花色苷在pH 0～5.0条件下均随时间推移而降解,在pH 2.0时的降解速度最慢;当pH小于或等于3.0时,该花色苷总体上降解缓慢,而且降解过程基本符合一级反应动力学.研究表明,'转心乌'块茎花色苷在可见光区的吸收光谱和在15℃、黑暗中的降解速度均具pH依赖性.     

Unfolding-refolding behaviour of chicken egg white ovomucoid and its correlation with the three domain structure of the protein

The urea and heat-induced unfolding-refolding behaviours of chicken egg white ovomucoid and its four fragments representing domains I, II + III, I + II and III were systematically investigated in 0.06 M sodium phosphate buffer (pH 7.0) by difference spectral measurements. The effect of temperature on ovomucoid and its fragments was also studied in 0.05 M sodium acetate buffer (pH 5.0) and in presence of 2 M urea at pH 7.0. Intrinsic viscosity data showed that ovomucoid and its different fragments did not lose any significant amount of their structure under mild acidic conditions (pH 4.6). Difference spectral results showed extensive disruption of the native structure by urea or temperature. Isothermal transitions showed single-step for domain I, domain I + II and domain III, and two-step having one stable intermediate, for ovomucoid and its fragment representing domain II + III. However, the presence of intermediate was not detected when the transitions were studied with temperature at pH 7.0. Strikingly, the single-step thermal transitions of ovomucoid and its fragment representing domain II + III, became two-step when measured either at pH 5.0 or in presence of 2 M urea at pH 7.0. Analysis of the equilibrium data on urea and heat denaturation showed that the second transition observed with ovomucoid or domain II + III represent the unfolding of domain III. The kinetic results of ovomucoid and its fragments indicate that the protein unfolds with three kinetic phases. A comparison of three rate constants for the unfolding of intact ovomucoid with that of its various fragments revealed that domain I, II and III of the protein correspond to the three kinetic phases having rate constants 0.456, 0.120 and 0.054 min-1, respectively. These data have led us to conclude: (i) the unusual stability of ovomucoid towards various denaturants, including temperature, is due to its domain III, (ii) initiation of the folding of the ovomucoid molecule starts from its NH2-terminal region which probably provides the nucleation site for the formation of the subsequent structure and (iii) domains I and II have greater mutual recognition between them as compared to the recognition either of them have with domain III.     

Resolution of enantiomers by HPLC on tris(4-alkoxyphenylcarbamate)s of cellulose and amylose

Ten phenylcarbamate derivatives of cellulose and amylose having alkoxy groups such as ethoxy, isopropoxy, and isobutoxy at 4-position, and methyl groups at 3- and 5-positions and methoxy group at 4-position were synthesized and their chiral recognition abilities as stationary phases for high-performance liquid chromatography were investigated and compared to those with tris(4-methoxyphenylcarbamate)s of cellulose and amylose. In 4-alkoxy derivatives of cellulose, chiral recognition ability increased as the bulkiness of 4-alkoxy groups increased. 4-Isopropoxy and 4-isobutoxy derivatives showed high chiral recognition. On the other hand, chiral discrimination of amylose 4-alkoxy derivatives scarcely depended on the bulkiness of the alkoxy group, and 4-methoxy and 4-isopropoxy derivatives showed high chiral recognition. 3,5-Dimethyl-4-methoxyphenylcarbamates of cellulose and amylose possessed higher chiral recognition ability than the corresponding 4-methoxy derivatives. © 1993 Wiley-Liss, Inc.     

A colorimetric chiral sensor based on chiral crown ether for the recognition of the two enantiomers of primary amino alcohols and amines

A new colorimetric chiral sensor material consisting of three different functional sites such as chromophore (2,4-dinitrophenylazophenol dye), binding site (crown ether), and chiral barrier (3,3'-diphenyl-1,1'-binaphthyl group) was prepared and applied to the recognition of the two enantiomers of primary amino alcohols and amines. Among five primary amino alcohols and two primary amines tested, the two enantiomers of phenylalaninol show the highest difference in the absorption maximum wavelength (Δλ(max)=43.5 nm) and in the association constants (K(S)/K(R)=2.51) upon complexation with the colorimetric chiral sensor material and, consequently, the two enantiomers of phenylalaninol were clearly distinguished from each other by the color difference.     

A kinetic recognition process for tRNA at the ribosome

In order to explain the great accuracy when amino acids are selected in protein synthesis, some authors have proposed a kinetic recognition process driven out of thermodynamic equilibrium. In this work, such a process for the recognition of the tRNA anticodon at the ribosome is considered. An important feature is that the discrimination possibility is determined not only by the differences of codon-anticodon binding energy (the only specific quantity) but also by the total binding energy including non specific bonds of other tRNA groups to the ribosome. In the context of this, the effects of streptomycin, and related features of mutant ribosome proteins or tRNA's which decrease or increase the selection accuracy can be interpreted by the kinetic model.     

Studies on deoxyribonucleic acid polymerase from normal and down’s syndrome skin fibroblasts in vitro

Summary This investigation showed that: (a) hypotonic pH 5.0 extracts of normal and Down’s syndrome fibroblasts cells (DS) exhibit DNase activity which appears to be very similar in nature and extent; (b) DNA polymerase activity was generally increased in DS cells when compared with normal cells; (c) DNA polymerase activity was increased with increased passage age for both normal and DS fibroblasts, but the normal fibroblast was never found to overlap with DS cell activity; and (d) normal cells appear to have a similar DNA polymerase activity at all chronological ages, whereas DS cells exhibit a decrease in activity with increased age of the donor.     

Kinetic modeling of lipase catalyzed hydrolysis of (R/S)-1-methoxy-2-propyl-acetate as a model reaction for production of chiral secondary alcohols

The Candida antarctica lipase B catalyzed kinetic resolution of (R/S)-1-methoxy-2-propyl-acetate was studied as a model system for the biocatalytic production of chiral secondary alcohols. For this purpose, a kinetic model is proposed involving both enantiomers of this reaction using model discrimination and parameter identification. Starting from a ping-pong bi-bi mechanism, a simplified model with sensitive parameters was derived for the R- and S-enantiomer, respectively. It was validated at pH 7.0, using time-course measurements at varying temperatures (30-60 degrees C) and initial substrate conditions (0.05-1.5 M). This model was then used for mechanistic interpretation of the kinetic resolution on a biochemical level. The effect of temperature on kinetic parameters and enantiomeric ratio was investigated and compared to findings from the field of molecular modeling to obtain a better understanding of the reaction system for process design. Values of 21.2 and 9.7 kJmol-1 were determined for the enthalpic (DeltaR-S DeltaH ++ degrees) and the entropic (-T x DeltaR-S DeltaS ++ degrees) contribution of the difference in transition state energy of both enantiomers at 30 degrees C. High enantiomeric ratio's (E of 47-110) especially at lower temperatures, in addition to enzyme activity at a wide pH range, indicate this biotransformation is a promising example for the industrial production of chiral secondary alcohols.     

Tris (phenanthroline) metal complexes: probes for DNA helicity

The intercalative binding of chiral tris(phenanthroline) metal complexes to DNA is stereo-selective. The enantiomeric selectivity is based upon the differential steric interactions between the two non-intercalating phenanthroline ligands of each isomer with the DNA phosphate backbone. Gel electrophoretic assays of helical unwinding, optical enrichment studies by equilibrium dialysis and luminescence titrations with separated enantiomers of (phen)3Ru2+ all indicate that the delta isomer binds preferentially to the right-handed duplex. The chiral discrimination is governed by the DNA helical asymmetry. Complete stereospecifity is seen with isomers of the bulkier RuDIP (tris-4,7-diphenylphenanthrolineruthenium(II]. While both isomers bind to Z-DNA, a poor template for discrimination, binding of lambda-RuDIP to B-DNA is precluded. These chiral complexes therefore serve as a chemical probe to distinguish left and right-handed DNA helices in solution.     

Pulmonary alveolar epithelial uptake of S-nitrosothiols is regulated by L-type amino acid transporter

Nitric oxide (NO) effects are often mediated via S-nitrosothiol (SNO) formation; SNO uptake has recently been shown to be mediated in some cell types via system L-type amino acid transporters (LAT-1, 2). Inhaled NO therapy may exert some biological effects via SNO formation. We therefore sought to determine if pulmonary epithelial SNO uptake depended on LAT or peptide transporter 2 (PEPT2). Both LAT-1 and PEPT2 proteins were detected by immunoblot and immunocytochemistry in L2 cells and rat lung. We tested SNO uptake through the transporters by exposing rat alveolar epithelial cells (L2 and type II) to RSNOs: S-nitrosoglutathione, S-nitrosocysteinylglycine (SNO-Cys-Gly), S-nitrosocysteine (CSNO), and to NO donor diethylamine NONOate (DEA-NONOate). SNO was detected in cell lysates by ozone chemiluminescence. NO uptake was detected by fluorescence in alveolar epithelial cells loaded with 4-amino-5-methylamino-2',7'-difluorofluorescein (DAF-FM) diacetate cultured in submersion and exposed to RSNOs and DEA NONOate. Addition of L-Cys but not D-Cys to RSNOs or DEA NONOate increased SNO and DAF-FM signal that was inhibited by coincubation with LAT competitors. Incubation of cells with PEPT2 substrate SNO-Cys-Gly showed no increase in SNO or DAF-FM signal unless incubated with L-Cys. This was unaffected by PEPT2 inhibition. We conclude that RSNOs (thionitrites, S-nitrosothiols) and NO enter alveolar epithelial cells predominantly by S-nitrosation of L-Cys, which is then imported through LAT.     

Purification and characterization of active recombinant human napsin A.

Recombinant human napsin A expressed in human embryonic kidney 293 cells was purified to homogeneity by a single-step procedure using part of napsin A propeptide as affinity ligand. N-Terminal amino-acid sequencing of the purified enzyme identified the mature form of napsin A. Treatment of purified napsin A with endoglycosidases F and H resulted in a decrease in its molecular mass from 39 kDa to approximately 37 kDa, confirming that napsin A is glycosylated. The kinetic properties were analyzed by using two fluorogenic synthetic substrates K(Dabsyl)-TSLLMAAPQ-Lucifer yellow (DS1) and K(Dabsyl)-TSVLMAAPQ-Lucifer yellow (DS3). The Km values obtained were 1.7 microM and 6.2 microM, respectively. A substrate-specificity study using a napsin A-targeted peptide library confirmed the preference of napsin A for hydrophobic residues at positions P1 and P1'. Adjacent positions, P2-P4 and P2'-P4', appeared less restricted in distribution of amino acids. A pH optimum between 4.0 and 5.5 at room temperature was determined. The purified enzyme was fully active for more than 10 h at pH 5.0 and 6.0, while a half-life of 4 h was determined at pH 7.0 and 37 degrees C.     

NMR chiral recognition of lipoic acid by cinchonidine CSA: A stereocenter beyond the organic function

Alpha-lipoic acid is a natural product that possesses distinct pharmacological properties. Lipoic acid is a short-chain fatty acid containing an asymmetric carbon at five bonds of distance to the organic function. Herein, we developed a nuclear magnetic resonance protocol to access the chiral recognition of lipoic acid in a simple and rapid procedure employing cinchonidine as a cheap chiral solvation agent in deuterated chloroform. To optimize this method, a statistical design of the experimental model was performed to produce a clear understanding of the optimal concentration, temperature, and molar ratio parameters. Based on the obtained spectra, the cinchonidine H₈-H₉ scalar coupling indicated a conformational preference in the chiral discrimination procedure. Density functional theory calculations established a proximity between the asymmetric center of lipoic acid and the aromatic moiety of cinchonidine, clarifying possible conformations in this ion-pair interaction. The described protocol demonstrates how far is far enough to chiral discrimination using a chiral solvation agent, expanding the method to compounds that contain a remote stereocenter.     

Induction, purification and molecular characterization of sulfhydryl oxidase from an Egyptian isolates of Aspergillus niger

The conditions for the sulfhydryl oxidase (SOX) production and activity from an Egyptian isolate of Aspergillus niger were optimized. Purification and determination of the kinetic properties (K(m) and V(max)) of the purified enzyme have been done. The possibility for the SOX induction using L-Cys (as a natural substrate) was studied to determine whether SOX could be produced as an inducible enzyme in addition to being a constitutive one (i.e. whether induction leads to increase SOX production and activity or not). The optimum temperature and pH for its activity were found to be 60 degrees C and 5.5, respectively. The activity of the induced intracellular SOX, was measured according to Ellman's method using the standard GSH oxidation where it reached 94% while that of non-induced one reached only 27.6%. This wide difference in activity between the induced and non-induced SOX indicates the successful L-Cys-induction of the SOX production (i.e. SOX from A. niger AUMC 4947 is an inducible enzyme). Molecular characterization of the pure SOX revealed that it is constituted of two 50-55 KDa subunits. K(m) and V(max) were found to be 6.0 mM and 100 microM/min/mg respectively.