Amino acid–dependent stability of the acyl linkage in aminoacyl-tRNA

Aminoacyl-tRNAs are the biologically active substrates for peptide bond formation in protein synthesis. The stability of the acyl linkage in each aminoacyl-tRNA, formed through an ester bond that connects the amino acid carboxyl group with the tRNA terminal 3′-OH group, is thus important. While the ester linkage is the same for all aminoacyl-tRNAs, the stability of each is not well characterized, thus limiting insight into the fundamental process of peptide bond formation. Here, we show, by analysis of the half-lives of 12 of the 22 natural aminoacyl-tRNAs used in peptide bond formation, that the stability of the acyl linkage is effectively determined only by the chemical nature of the amino acid side chain. Even the chirality of the side chain exhibits little influence. Proline confers the lowest stability to the linkage, while isoleucine and valine confer the highest, whereas the nucleotide sequence in the tRNA provides negligible contribution to the stability. We find that, among the variables tested, the protein translation factor EF-Tu is the only one that can protect a weak acyl linkage from hydrolysis. These results suggest that each amino acid plays an active role in determining its own stability in the acyl linkage to tRNA, but that EF-Tu overrides this individuality and protects the acyl linkage stability for protein synthesis on the ribosome.     

Heterologous expression of the acyl–acyl carrier protein thioesterase gene from the plant Umbellularia californica mediates polyhydroxyalkanoate biosynthesis in recombinant Escherichia coli

The acyl-acyl carrier protein (ACP) thioesterase cDNA from the plant Umbellularia californica was functionally expressed in various recombinant Escherichia coli strains in order to establish a new metabolic route toward medium-chain-length polyhydroxyalkanoate (PHA(MCL)) biosynthesis from non-related carbon sources. Coexpression of the PHA synthase genes from Ralstonia eutropha and Pseudomonas aeruginosa, or only the PHA synthase gene from P. aeruginosa, respectively, showed PHA(MCL) accumulation when the type II PHA synthase from P. aeruginosa was produced. Both wild-type E. coli and various fad mutants were investigated; and only when the beta-oxidation pathway was impaired PHA(MCL) accumulation from gluconate was observed, contributing to about 6% of cellular dry weight. Thus coexpression of type II PHA synthase gene with cDNA encoding the medium-chain acyl-ACP thioesterase from U. californica established a new PHA(MCL) biosynthesis pathway, connecting fatty acid de novo biosynthesis with fatty acid beta-oxidation, using a non-related carbon source.     

Cloning,characterization, and expression analysis of acyl–acyl carrier protein (ACP)-thioesterase B from seeds of Chinese Spicehush (Lindera communis)

Acyl–acyl carrier protein (ACP) thioesterases (TE EC 3.1.2.14) are fatty acid biosynthesis key enzymes that determine fatty acid carbon chain length in most plant tissues. A full-length cDNA corresponding to one of the fatty acyl–ACP thioesterase (Fat) genes, designated LcFatB, was isolated from developing Lindera communis seeds using PCR and RACE with degenerate primers based on conserved sequences of multiple TE gene sequences obtained from GenBank. The 1788 bp cDNA had an open reading frame (ORF) of 1260 bp encoding a protein of 419 amino acids. The deduced amino acid sequence showed 61–73% identity to proteins in the FatB class of plant thioesterases. Real-time quantitative PCR analysis revealed that LcFatB was expressed in all tissues of L. communis, with the highest expression in the developing seeds 75 days after flowering. Recombinant pET-MLcFatB was constructed using the pET-30a vector and transformed into Escherichia coli BL21(DE3)△ FadE, a strain that deleted the acyl-CoA dehydrogenase (FadE). SDS-PAGE analysis of proteins isolated from pET-MLcFatB E. coli cells after induction with IPTG revealed a protein band at ~ 40.5 kDa, corresponding to the predicted size of LcFatB mature protein. The decanoic acid and lauric acid contents of the pET-MLcFatB transformant were increased significantly. These findings suggest that an LcFatB gene from a non-traditional oil-seed tree could be used to function as a saturated acyl–ACP thioesterase and could potentially be used to modify the fatty acid composition of seed oil from L. communis or other species through transgenic approaches.     

Isolation and characterization of acyl homoserine lactone–producing bacteria during an urban river biofilm formation

The presence and diversity of acyl homoserine lactone (AHL)-producers in an urban river biofilm were investigated during 60-day biofilm formation. AHL biosensors detected the presence of AHL-producers in 1–60-day river biofilms. Screening for AHL-producers resulted in 17 Aeromonas spp., 3 Pseudomonas spp., 3 Ensifer spp., and 1 Acinetobacter sp. Among these isolates, six of them were closely related to Acinetobacter tjernbergiae, Aeromonas allosaccharophila, Aeromonas aquariorum, Aeromonas jandaei, Pseudomonas panipatensis, and Ensifer adhaerens and represented novel AHL-producing species. Thin layer chromatography revealed that C4-homoserine lactone was prevailing in Aeromonas spp., whereas C6- and C8-homoserine lactones and their derivatives were prevailing in other strains. Using degenerate primers, novel AHL synthetase genes from the three Ensifer spp. were successfully amplified. This study reports for the first time the diversity of AHL-producers from a river biofilm and the variety of novel AHL synthetase genes in Ensifer group.     

How does acyl chain length affect thermotropic phase behavior of saturated diacylphosphatidylcholine–cholesterol binary bilayers?

Thermotropic phase behavior of diacylphosphatidylcholine (CnPC)–cholesterol binary bilayers (n = 14–16) was examined by fluorescence spectroscopy using 6-propionyl-2-(dimethylamino)naphthalene (Prodan) and differential scanning calorimetry. The former technique can detect structural changes of the bilayer in response to the changes in polarity around Prodan molecules partitioned in a relatively hydrophilic region of the bilayer, while the latter is sensitive to the conformational changes of the acyl chains. On the basis of the data from both techniques, we propose possible temperature T–cholesterol composition X_ch phase diagrams for these binary bilayers. A notable feature of our phase diagrams, including our previous results for diheptadecanoylphosphatidylcholine (C17PC) and distearoylphosphatidylcholine (C18PC), is that there is a peritectic-like point around X_ch = 0.15, which can be interpreted as indicating the formation of a 1:6-complex of cholesterol and CnPCs within the binary bilayer irrespective of the acyl chain length. We could give a reasonable explanation for such complex formation using the modified superlattice view. Our results also showed that the X_ch value of the abolition of the main transition is almost constant for n = 14–17 (ca. 0.33), while it increases to ca. 0.50 for n = 18. By contrast, a biphasic n-dependence of X_ch was observed for the abolition of the pretransition, suggesting that there are at least two antagonistic n-dependent factors. We speculate that this could be explained by the enhancement of the van der Waals interaction with increases in n and the weakening of the repulsion between the neighboring headgroups with decreases in n.     

Native N-glycopeptide thioester synthesis through N→S acyl transfer

Peptide thioesters are important tools for the total synthesis of proteins using native chemical ligation (NCL). Preparation of glycopeptide thioesters, that enable the assembly of homogeneously glycosylated proteins, is complicated by the perceived fragile nature of the sugar moiety. Herein, we demonstrate the compatibility of thioester formation via N→S acyl transfer with native N-glycopeptides and report observations that will aid in their preparation.     

Effects of phospholipid acyl chain structure on thermotropic phase properties. 3. Phosphatidylcholines with (−), and (±)-anteiso acyl chains

We have synthesized a number of anteiso-branched fatty acids, both as racemates and as pure (?)-stereoisomers, as well as the corresponding di-anteiso-acyl phosphatidylcholines (PCs). The phase transition temperatures (_c of the hydrated PCs have been determined by differential thermal analysis (DTA). Consideration of the observed effects of acyl chain length and terminal see-butyl group configuration on anteiso acid melting points and di-anteiso-acyl PC transition temperatures leads us to the conclusion that the terminal branched portions of anteiso acyl chains interact only weakly with adjacent acyl chains in the hydrated phosphatidylcholine bilayer and probably in the anhydrous fatty acid crystal as well. In agreement with this conclusion, we observe that the DTA heating transition endotherms for hydrated di-anteiso-acyl PCs appear to be considerably less strongly endothermic, and occur at much lower temperatures, than do the major transition endotherms for the di-n-acyl PCs of like carbon number. Our findings generally support the proposal that anteiso acyl lipids tend to fluidize membranes, although they do so less effectively than do cis-unsaturated acyl lipids.     

Theoretical study to gain fundamental insight into reaction mechanism of N–S acyl transfer of N-sulfanylethylanilide-based protein labeling reagent on protein surface

Elucidation of protein function is one of the central issues in the field of life sciences. To study the function of proteins not in isolation, but in a cell or its lysate, thus, it is necessary to selectively label the target protein in a mixture. Affinity labeling is one of several widely used methods for selective labeling; however, this method has the disadvantage that the labeling reagent is always activated, albeit weakly. Therefore, fine-tuning of the reactivity and/or reaction conditions is generally required for successful target-selective labeling. We previously developed a new affinity labeling reagent with N-sulfanylethylanilide (SEAlide) as a key reactive unit. It was designed based on the following hypotheses. SEAlide is less reactive and does not label in the absence of a target protein. Upon target binding, amino acid side-chain functional groups on the target surface convert SEAlide into a thioester form via N–S acyl transfer, allowing the target to be labeled. However, no evidence has been obtained so far to directly prove the hypothesis. In this study, we examine whether amino acid side-chain functional groups can activate SEAlide from the viewpoint of theoretical chemistry. The theoretical studies show that the activation free energy and enthalpy of the acyl transfer of SEAlide are reduced in the presence of methylammonium, which is a model for the protonated side chain of Lys, and acetate, which is a model for the deprotonated side chain of Asp/Glu. It suggests that Lys and Asp/Glu side chains could potentially stabilize the activation transition states to accelerate the thioester formation. Furthermore, the significant decrease in the activation enthalpy indicates that the contribution of entropy to the transition state is large. This result supports the original hypothesis that the SEAlide-based labeling reagent is efficiently activated by binding to the target protein.     

Chirality of the acyl group of β-hydroxy-β-methylglutarylhydroxyabscisic acid

The β-carbon of the acyl group of β-hydroxy-β-methylglutarylhydroxyabscisic acid was shown to possess R-configuration by HPLC analysis of the reduced product.     

Synthesis and physical properties of phosphatidylcholines containing ω-cyclohexyl fatty acyl chains

Phosphatidylcholines (PCs) with cyclohexyl fatty acids as acyl chains were synthesized from 11-cyclohexyl and 13-cyclohexyl fatty acids and their physical properties were examined. The thermotropic behavior and barrier function of liposomal membranes formed from these PCs were studied. These PCs showed about 10°C lower gel-to-liquid crystalline phase transition temperatures (T_c) than the corresponding straight-chain PCs. The properties of mixtures of these cyclohexyl acyl PCs with straight-chain PCs were rather different from those observed with mixtures of straight-chain PCs. Cyclohexyl fatty acyl PCs showed barrier functions even above the T_c unlike the corresponding straight-chain PCs. These results indicate significant differences between the overall packing of cyclohexyl fatty acyl PCs and of the corresponding straight-chain PCs both in the gel state and in the liquid crystalline state. The significance of these cyclohexyl acyl chains in polar lipids, which are abundant in the thermophilic acidophilic bacterium, Bacillus acidocaldarius, is discussed.     

Angkorensides A and B – Two anti-inflammatory acyl glycosides from Gardenia angkorensis

Two new acyl glycosides, angkorensides A and B (1 and 2) together with twelve known compounds including hedyotol C 7″-O-β-D-glucopyranoside (3), proanthocyanidin A-1 (4), (-)-epicatechin (5), (+)-lyoniresinol 3α-O-β-D-glucopyranoside (6), kaempferol-3-O-β-D-galactopyranoside (7), cuneataside E (8), 4-hydroxyacetophenone 4-O-(6′-O-β-D-apiofuranosyl)-β-D-glucopyranoside (9), cinnamtannin B-1 (10), aesculitannin B (11), quercetin 3-O-rham-(1−6)-β-D-galactopyranoside (12), quercetin 3-O-β-D-galactopyranoside (13), and proanthocyanidin A-2 (14) have been unprecedentedly isolated from Gardenia angkorensis Pit. Angkorensides A and B (1 and 2) showed moderate anti-inflammatory inhibitory effects on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW264.7 macrophages and the known compounds (4, 10-14) exhibited strong 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity.     

Long-chain acyl CoA synthetase,carnitine and β-oxidation in the pea-seed mitochondrion

Mitochondria from pea (Pisum sativum L.) seeds were separated into two fractions, mitoplasts (intact inner membrane) and the outer-membrane fraction. The mitoplasts only oxidised palmitate in the presence of carnitine and added outermembrane fraction. Mitoplasts were able to oxidise palmitoylCoA in the presence of carnitine and added outer-membrane fraction had no effect on this oxidation. It was concluded that a long-chain acylCoA synthetase (EC 6.2.1.3) was located on the outer membrane and that the activity of this enzyme in assays was more than sufficient to account for any observed rate of O₂ uptake during palmitate oxidation by pea mitochondria. The location of carnitine long-chain acyltransferase (carnitine palmitoyl transferase EC 2.3.1.21) would appear to be the mitoplast i.e. the inner mitochondrial membrane, and confirms the previous work at Newcastle.Abbreviation Tris 2-amino-2-(hydroxymethyl)-1,3-propanediol     

Diacylglycerol acyl transferase 1 overexpression detoxifies cardiac lipids in PPARγ transgenic mice

Accumulation of excess lipids is associated with heart failure. The effects of transgenic expression of diacylglycerol acyl transferase 1 (DGAT1) in cardiomyocytes is controversial. We explored whether mice expressing DGAT1 via the myosin heavy chain (MHC) promoter develop heart dysfunction with aging or after crossing with mice over expressing peroxisome proliferator-activated receptor γ (PPARγ) in the heart. MHC-DGAT1 transgenic mice had increased heart triglyceride but no evidence of heart dysfunction, even up to age 12 months. The MHC-DGAT1 transgene improved heart dysfunction and survival of MHC-PPARγ-expressing transgenic mice. Both diacylglycerol and ceramide levels in the heart were reduced by this cross, as were the levels of several mRNAs of genes involved in lipid metabolism. There were fewer large lipid droplets in MHC-DGAT1×MHC-PPARγ mice compared with MHC-PPARγ, but total lipid content was not changed. Therefore, overexpression of DGAT1 is not toxic to the heart but reduces levels of toxic lipids and improves lipotoxic cardiomyopathy. Moreover, the beneficial effects of DGAT1 illustrate the interrelationship of several lipid metabolic pathways and the difficulty of assigning benefit to an isolated change in one potentially toxic lipid species.     

Characterization and inhibition of aminopeptidase A by α-mercapto-β-amino acyl dipeptides

Summary In order to study the physiological role of aminopeptidase A(APA), several α-mercapto-β-amino acyl dipeptides were synthesized to obtain compounds having a high affinity for APA and a high selectivity versus aminopeptidase N (APN). Sulfornamide and carboxylate moieties which have been shown to be recognized by the S₁ subsite of the enzyme were introduced on the side chain of the α-mercapto-β-amino acyl sub-unit, the latter being coupled to dipeptides optimized to interact with the S'₁ and S'₂ subsites by means of combinatorial chemistry. Good affinities (16nM) were obtained, the selectivity factors being up to 160-fold versus APN.     

Reactivity of platina-β-diketones towards chelating nitrogen and sulfur donors: formation of acyl(hydrido)platinum(IV) and acyl(chloro)platinum(II) complexes

The platina-β-diketone [Pt₂{(COMe)₂H}₂(μ-Cl)₂] (1) was found to react with chelating N,N-ligands 2(R^′NCR)C₅H₄N (R/R^′=Ph/OH, H/Ph, Me/Ph) to form acyl(hydrido)platinum(IV) complexes [Pt(COMe)₂Cl(H){2-(R^′NCR)C₅H₄N}] (R/R^′=Ph/OH 2a; H/Ph 2b; Me/Ph (2c)). Reactions of complex 1 with chelating S,S- and N,S-donors (RS-CH₂-CH₂-SR, 2-(RSCH₂)C₅H₄N, R=Et, Ph, t-Bu) afforded acyl(chloro)platinum(II) complexes [Pt(COMe)Cl(RSCH₂CH₂SR)] (R=Et, 3a; Ph, 3b; t-Bu, 3c) and [Pt(COMe)Cl{2-(RSCH₂)C₅H₄N}] (R=Et, 4a; Ph, 4b; t-Bu, 4c), respectively. All complexes were fully characterized by microanalysis, IR and NMR (¹H, ¹³C) spectroscopy. Furthermore, molecular structures of complexes 3b and 4b were determined by single-crystal X-ray diffraction analyses revealing close to square-planar configuration. In complex 4b the acetyl ligand is trans to pyridine N atom (configuration index SP-4-2). The reactions are discussed in terms of consecutive oxidative addition and reductive elimination reactions.     

Inverse acyl phosph(on)ates: substrates or inhibitors of beta-lactam-recognizing enzymes?

Acyl phosph(on)ates represent a new class of inhibitors of beta-lactam-recognizing enzymes. Previously described members of this class were aroyl phosph(on)ates. These compounds have been shown to acylate and/or phosphylate the active site serine residue, leading to either transient or essentially irreversible inhibition [Li, N., and Pratt, R. F. (1998) J. Am. Chem. Soc.120, 4264-4268]. The present paper describes the synthesis and evaluation as inhibitors of an inverse pair of acyl phosph(on)ates that incorporate the amido side chain that represents a major substrate specificity determinant of these enzymes. Thus, N-(phenylacetyl)glycyl phenyl phosphate and benzoyl N-(benzyloxycarbonyl)aminomethyl phosphonate were prepared. The former of these compounds was found to be a substrate of typical class A and C beta-lactamases and of the DD-peptidase of Streptomyces R61; it thus acylates the active site serine. In contrast, the latter compound was an irreversible inhibitor of the above enzymes, probably by phosphonylation of the active site serine. With each of these enzymes therefore, the amido side chain rather than the acyl group dictates the orientation of the bound phosph(on)ate and thus the mode of reaction.     

Calculation of the Three-Dimensional Structures of Two Antigenic Sequences, Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro and Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro, of the Circumsporozoite Protein From a Malaria-Causing Plasmodium

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp)₂. We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–NHCH₃ as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro–NHCH₃. We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.