The G553M Mutant of Peroxisomal Carnitine Octanoyltransferase Catalyses Acetyl Transfer and Acetyl-CoA Hydrolysis

The structure of carnitine acetyltransferase revealed a putative binding site for longer acyl chains but access was blocked by methionine 564 (G. Jogl and L. Tong (2003) Cell 112, 113–122). The equivalent residue in all long chain carnitine acyltransferases is a conserved glycine. Mutation of glycine 553 to methionine in bovine COT resulted in loss of activity with all acyl-CoA substrates except acetyl-CoA, supporting the hypothesis that the methionine blocks access for longer acyl chains. The kinetic characteristics of acetyl transfer to carnitine were identical in the native and mutant enzyme. However, rapid acetyl-CoA hydrolysis in the mutant but not the wild-type indicates perturbation of the catalytic site.     

Effects of L-Carnitine and its Derivatives – Studies on Isolated Hearts

Summary. The metabolism in the heart prefers long-chain fatty acids to other substrates. L-Carnitine, a co-factor of coenzyme A, plays an essential role in the transport of long-chain fatty acids through the inner mitochondrial membrane. Without carnitine, metabolisation of long-chain fatty acids in the mitochondria is not possible. In addition, acyl groups from acyl-CoA compounds can be transferred to L-carnitine, thus influencing the enzymatic activities of important mitochondrial enzymes.The isolated heart model developed by Langendorff was used to investigate the effects of L-carnitine on the heart. During aerobic perfusion, the hemodynamic parameters of isolated hearts reacted in a very sensitive way to alterations in the external conditions (temperature, preload, composition of the perfusion solution). During postischemic perfusion, recovery of the hearts was also influenced by the composition of the perfusion. The hemodynamic parameters of the reperfused hearts increased markedly if there was a sufficiently high supply of long-chain fatty acids and/or glucose. The insufficient recovery of hearts perfused without glucose and at low fatty acid concentrations could be improved by adding L-carnitine. Determination of carnitine levels in heart tissue found that the heart loses about 30% of its carnitine content during ischemia, and that exogenous carnitine is taken up by the heart during reperfusion. There it effects the restoration of sufficient concentrations of creatine phosphate and ATP, a fact that was confirmed by ³¹P NMR spectroscopy. NMR spectroscopy also established that L-carnitine lessens the harmful effects of ischemia-induced metabolic acidosis.The favourable influence of L-carnitine on the heart in the reperfusion period could be due to a reduction in oxygen radicals (lowering of MDA concentrations during reperfusion, raising of GP_x and SOD activities).The findings of these experiments on isolated hearts as well as the favourable results of two placebo-controlled and double-blind clinical studies (investigating the effects of carnitine in cardiomyopathy patients and the effects of L-carnitine in hemodialysis patients) demonstrate that L-carnitine produces positive therapeutic effects, particularly in heart and circulatory diseases.     

MO Study of flavin–protein interactions in flavodoxin catalysis

MINDO /3 calculations have been performed on the Clostridium MP flavodoxin active site (a complex of the redox active coenzyme flavin mononucleotide sandwiched between the side chains of methionine and tryptophan) at various redox levels using coordinates derived from x-ray diffraction studies of the holoenzyme. Frontier orbital indices were calculated and indicate that reduction of the flavin is accompanied by induced polar states in the amino acid side chains. This stabilization of charge by the amino acid side chains could account for the reaction rate enhancement of flavin reduction catalyzed by flavodoxin. Frontier orbitals for free flavin, for the flavodoxin bound flavin without the amino acid side chains, and for the oxidized Desulfovibrio vulgaris flavodoxin active site were computed for comparison.     

Comprehensive profiling of <Emphasis Type="Italic">N</Emphasis>-acylhomoserine lactones produced by <Emphasis Type="Italic">Yersinia pseudotuberculosis</Emphasis> using liquid chromatography coupled to hybrid quadrupole–linear ion trap mass spectrometry

A method for the comprehensive profiling of the N-acylhomoserine lactone (AHL) family of bacterial quorum-sensing molecules is presented using liquid chromatography (LC) coupled to hybrid quadrupole–linear ion trap (QqQLIT) mass spectrometry. Information-dependent acquisition (IDA), using triggered combinations of triple-quadrupole and linear ion trap modes in the same LC-MS/MS run, was used to simultaneously screen, quantify and identify multiple AHLs in a single sample. This MS method uses common AHL fragment ions attributed to the homoserine moiety and the 3-oxo-, 3-hydroxy- or unsubstituted acyl side chains, to identify unknown AHLs in cell-free culture supernatants in an unbiased manner. This LC-MS technique was applied to determine the relative molar ratios of AHLs produced by Yersinia pseudotuberculosis and the consequences of inactivating by mutation either or both of the AHL synthase genes (ypsI and ytbI) on AHL profile and concentration. The Y. pseudotuberculosis wild type but not the ypsI ytbI double mutant produced at least 24 different AHLs with acyl chains ranging from C4 to C15 with or without 3-oxo or 3-hydroxy substituents. YtbI, in contrast to YpsI, could direct the synthesis of all of the AHLs identified. The most abundant and hence most biologically relevant Y. pseudotuberculosis AHLs were found to be the 3-oxo-substituted C6, C7 and C8 AHLs and the unsubstituted C6 and C8 compounds. The LC-QqQLIT methodology is broadly applicable to quorum-sensing signal molecule analysis and can provide comprehensive AHL profiles and concentrations from a single sample and simultaneously collect confirmatory spectra for each AHL identified. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Catharine A. Ortori and Steve Atkinson made an equal contribution to the paper.     

Sulfur Deficiency Changes Mycosporine-like Amino Acid (MAA) Composition of Anabaena variabilis PCC 7937: A Possible Role of Sulfur in MAA Bioconversion

In the present investigation we show for the first time that bioconversion of a primary mycosporine-like amino acid (MAA) into a secondary MAA is regulated by sulfur deficiency in the cyanobacterium Anabaena variabilis PCC 7937. This cyanobacterium synthesizes the primary MAA shinorine (RT = 2.2 min, λ_max = 334 nm) under normal conditions (PAR + UV-A + UV-B); however, under sulfur deficiency, a secondary MAA palythine-serine (RT = 3.9 min, λ_max = 320 nm) appears. Addition of methionine to sulfur-deficient cultures resulted in the disappearance of palythine-serine, suggesting the role of primary MAAs under sulfur deficiency in recycling of methionine by donating the methyl group from the glycine subunit of shinorine to tetrahydrofolate to regenerate the methionine from homocysteine. This is also the first report for the synthesis of palythine-serine by cyanobacteria which has so far been reported only from corals. Addition of methionine also affected the conversion of mycosporine-glycine into shinorine, consequently, resulted in the appearance of mycosporine-glycine (RT = 3.6 min, λ_max = 310 nm). Our results also suggest that palythine-serine is synthesized from shinorine. Based on these results we propose that glycine decarboxylase is the potential enzyme that catalyzes the bioconversion of shinorine to palythine-serine by decarboxylation and demethylation of the glycine unit of shinorine.     

Current Methods for Determination of <Emphasis Type="Italic">L</Emphasis>-Carnitine and Acylcarnitines

Summary. L-Carnitine as endogenous compound plays an important role within several metabolic pathways and a deficiency of L-carnitine can cause adverse effects in physiological and/or mental state of health and disease. The prevention of diseases related to carnitine deficiency requires, first of all, the exact determination of L-carnitine and its esters in biological material at pmol/cm³ level. A series of analytical procedures based on biochemical assays as well as on physical methods are available today. Determination of free and total carnitine is sometimes sufficient for a clinical diagnosis, but in most cases, such as in newborn screening for genetic disorders, detailed qualitative and quantitative L-carnitine/acylcarnitine profiling is needed. Technological progress has also revolutionized the determination of carnitines. Today, comprehensive and diagnostically relevant information can be obtained by mass spectrometry. An overview is given of the technical and methodological developments in carnitine analysis and some applications, such as in neonatal screening, diabetes mellitus, and cardiomyopathy.     

Molecular recognition in carnitine acyltransferases

We are designing and synthesizing rigid guests to probe the topography of the carnitine acyltransferases, regulatory enzymes in lipid metabolism. Our designs are based on structural studies of substrates and possible molecular mechanisms of enzymatic activity. Recent X-ray,¹H NMR, and force-field computational studies on carnitine and acetylcarnitine, coupled with the known stereospecificity for activity in carnitine acyltransferases, have led us to propose a molecular mechanism for acyl transfer in these enzymes. The folded conformation of an acylcarnitine is most populated and should be preferred for binding to these enzymes, because, in this conformation, the acyloxy is the most sterically accessible. There are four key recognition sites on the enzymes: I, carboxylate; II, trimethylammonium; III, coenzyme A; IV, acyl. Sites, I, II and III serve as the three loci required to create a chiral environment on the enzymes for carnitine. An addition-elimination reaction involving the formation of a tetrahedral intermediate is suggested as the mechanism for O-to-S acyl transfer. This proposed tetrahedral intermediate is chiral and the enzymes should prefer theR configuration at this center. Based on this proposal, conformationally rigid tetrahedral-intermediate analogues have been designed, synthesized and assayed. Morpholinium and 2-hydroxymorpholinium derivatives inhibit carnitine acetyltransferase and palmitoyltransferase. Because of rigidity at their two chiral centers, these inhibitors serve as probes of molecular topography of recognition sites, I, II, and IV.     

Dependence of the main phase transition temperatures of diacyl phospolipids with mixed and identical saturated acyl chains on the chain volumes

Statistical analysis of quantitative structure—property relationships (QSPR) for the phase transition gel—liquid crystal (main phase transition) temperatures (T _m) in hydrated vesicle bilayers of diacyl phosphatidylcholines (PC) and diacyl phosphatidylethanolamines (PE) with saturated acyl chains was carried out. Multiple regression equations relating the T _m values to the volumes of the hydrocarbon fragments of the sn-1 and sn-2 acyl chains show that the acyl groups influence the transiton temperatures T _m in different manner, the effect of the sn-2 group being predominant. The transition temperatures T _m of saturated phosphatidylethanolamines and diacyl phosphatidylglycerols can be predicted using the T _m values calculated for the corresponding diacyl phosphatidylcholines.     

Pragmatic Studies on Protein-Resistant Self-Assembled Monolayers

Summary. The present study describes new synthetic routes to oligo(ethylene glycol)-terminated alkanethiols (OEG-ATs), starting from α,ω-dibromoalkanes, which are reacted either with OEG or with trityl mercaptan in the first step. In addition to these ether conjugates of OEG and AT, analogous ester and amide conjugates were prepared by established procedures. All thiols were used to form self-assembled monolayers (SAMs) on cleaned gold surfaces and these were stored for 1–2 weeks under water at 4°C before the extent of nonspecific protein adsorption was tested with IgG, BSA, and lysozyme at 1 mg cm⁻³ protein concentration in phosphate-buffered saline. Under these practice-oriented testing conditions, SAMs with tri(ethylene glycol) chains (EG ₃) exhibited nonsatisfactory protein resistance, in sharp contrast to EG ₄ or longer OEG chains. The effectiveness of EG ₃ was partially restored when they were linked to a long acyl chain (16-mercaptohexadecanoic acid) instead of 12-mercaptododecane or 11-mercaptoundecane. Furthermore it was found that (i) SAM formation at 20 μM thiol versus 500 μM OEG-AT gave identical results, (ii) gel-filtered proteins were much less adsorbed than the unpurified commercial products, and (iii) the method for gold-precleaning was very critical. In conclusion, this study offers convenient synthetic routes to OEG-AT and helps to choose molecules and procedures for reliable preparation of protein-resitant SAMs with prolonged stability during storage.     

High‐energy collision‐induced dissociation of [M+Na]+ ions desorbed by fast atom bombardment of ceramides isolated from the starfish Distolasterias nipon

Ten ceramides and four cerebrosides were extracted from the starfish Distolasterias nipon by solvent extraction, silica gel column chromatography and reversed‐phase high‐performance liquid chromatography. Structural identification was conducted using tandem mass spectrometry of monosodiated ions desorbed by fast atom bombardment. The complete structures of four cerebrosides were determined by a previously reported method. The high‐energy collision‐induced dissociation (CID) spectral characteristics of ceramides with various structures depend on the number and positions of double bonds on both the N‐acyl and sphingoid chains, the presence of a hydroxyl group or a double bond at the C‐4 position of the sphingoid chain and the presence of an α‐hydroxy group on the N‐acyl chain. The high‐energy CID of the monosodiated ion, [M+Na]⁺, of each ceramide molecular species generated abundant ions, providing information on the composition of the fatty acyl chains and sphingoid long‐chain bases. Each homologous ion series along the fatty acyl group and aliphatic chain of the sphingoid base was used for locating the double‐bond positions of both chains and hydroxyl groups on the sphingoid base chain. The double‐bond positions were also confirmed by the m/z values of abundant allylic even‐ and odd‐electron ions, and the intensity ratio of the T ion peak relative to the O ion peak. This technique could determine the complete structures of ceramides and cerebrosides in an extract mixture and has great potential for determining other sphingolipids isolated from various biological sources. Copyright © 2013 John Wiley & Sons, Ltd.     

Chiral DMAP‐N‐oxides as Acyl Transfer Catalysts: Design,Synthesis, and Application in Asymmetric Steglich Rearrangement

A DMAP‐N‐oxide, featuring an α‐amino acid as the chiral source, was developed, synthesized and applied in asymmetric Steglich rearrangement. A series of O‐acylated azlactones afforded C‐acylated azlactones possessing a quaternary stereocenter in high yields (up to 97 % yield) and excellent enantioselectivities (up to 97 % ee). Compared to the widespread use of pyridine nitrogen, which serves as the nucleophilic site in the asymmetric acyl transfer reaction, we discovered that chiral DMAP‐N‐oxides, in which the oxygen now acts as the nucleophilic site, are efficient acyl transfer catalysts. Our finding might open a new door for the development of chiral DMAP‐N‐oxides for asymmetric acyl transfer reactions.     

Chiral DMAP‐N‐oxides as Acyl Transfer Catalysts: Design,Synthesis, and Application in Asymmetric Steglich Rearrangement

A DMAP‐N‐oxide, featuring an α‐amino acid as the chiral source, was developed, synthesized and applied in asymmetric Steglich rearrangement. A series of O‐acylated azlactones afforded C‐acylated azlactones possessing a quaternary stereocenter in high yields (up to 97 % yield) and excellent enantioselectivities (up to 97 % ee). Compared to the widespread use of pyridine nitrogen, which serves as the nucleophilic site in the asymmetric acyl transfer reaction, we discovered that chiral DMAP‐N‐oxides, in which the oxygen now acts as the nucleophilic site, are efficient acyl transfer catalysts. Our finding might open a new door for the development of chiral DMAP‐N‐oxides for asymmetric acyl transfer reactions.     

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

CHARMM‐GUI Membrane Builder, http://www.charmm‐gui.org/input/membrane , is a web‐based user interface designed to interactively build all‐atom protein/membrane or membrane‐only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance‐based algorithm for faster initial ion displacement, (5) CHARMM inputs for P₂₁ image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM‐GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.     

An Improved Synthetic Procedure for the Preparation of N‐Acyl (2‐aminoethyl)‐β‐d‐glycopyranoside Lipids and Characterization of Their Mesogenic Properties

Abstract

A modified synthetic procedure was used for the synthesis of N‐acyl (2‐aminoethyl) glycosides bearing lactose, maltose, and melibiose carbohydrate headgroups and different acyl chains. The lipid glycosides were prepared in gram scale and investigated for their liquid crystalline properties. It was found that the polar spacer suppresses polymorphism, and the resulting simplified phase behavior was found in the pure state upon heating, as well as for the lyotropic phases     

Profiling of ornithine lipids in bacterial extracts of Rhodobacter sphaeroides by reversed-phase liquid chromatography with electrospray ionization and multistage mass spectrometry (RPLC-ESI-MS)

Ornithine lipids (OLs), a sub-group of the large (and of emerging interest) family of lipoamino acids of bacterial origin, contain a 3-hydroxy fatty acyl chain linked via an amide bond to the α-amino group of ornithine and via an ester bond to a second fatty acyl chain. OLs in extracts of Rhodobacter sphaeroides (R. sphaeroides) were investigated by high-performance reversed phase liquid chromatography (RPLC) with electrospray ionization mass spectrometry (ESI-MS) in negative ion mode using a linear ion trap (LIT). The presence of OLs bearing both saturated (i.e, 16:0, 17:0, 18:0, 19:0 and 20:0) and unsaturated chains (i.e., 18:1, 19:1, 19:2 and 20:1) was ascertained and their identification, even for isomeric, low abundance and partially co-eluting species, was achieved by low-energy collision induced dissociation (CID) multistage mass spectrometry (MSⁿ, n = 2–4). OLs signatures found in two R. sphaeroides strains, i.e., wild type 2.4.1 and mutant R26, were examined and up to 16 and 17 different OL species were successfully identified, respectively. OLs in both bacterial strains were characterized by several combinations of fatty chains on ester-linked and amide-linked 3-OH fatty acids. Multistage MS spectra of monoenoic amide-linked 3-OH acyl chains, allowed the identification of positional isomer of OL containing 18:1 (i.e. 9-octadecenoic) and 20:1 (i.e. 11-eicosenoic) fatty acids. The most abundant OL ([M−H]⁻ at m/z 717.5) in R. sphaeroides R26 was identified as OL 3-OH 20:1/19:1 (i.e., 3-OH-eicosenoic acid amide-linked to ornithine and esterified to a nonadecenoic chain containing a cyclopropane ring). An unusual OL (m/z 689.5 for the [M−H]⁻ ion), most likely containing a cyclopropene ester-linked acyl chain (i.e., OL 3-OH 18:0/19:2), was retrieved only in the carotenoidless mutant strain R26. Based on the biosynthetic pathways already known for cyclopropa(e)ne ring-including acyl chains, a plausible explanation was invoked for the enzymatic generation of this ester-linked chain in R. sphaeroides.     

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

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

Sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate

The title compound, Na⁺·3C₂H₆NO₂⁺·2SiF₆²⁻·3C₂H₅NO₂, arose from an unexpected reaction of glycine and HF with the glass container. It is an unusual hybrid organic–inorganic network built up from chains of vertex‐sharing NaF₄O₂ and SiF₆ octahedra. A pair of glycinium/glycine molecules bridges the chains into a sheet via a centrosymmetric O...H...O link. The other organic species interact with the network by an extensive N—H...F hydrogen‐bond network, including bifurcated and trifurcated bonds. Finally, an extremely short C—H...O interaction (H...O = 2.25 Å) is seen in the crystal structure. The Na atom has site symmetry .     

Purification and properties of carnitine acetyltransferase from citric acid producingAspergillus niger

Carnitine acetyltransferase was purified from the citric acid producingA. niger mycelium with a protein band showing a relative molecular weight of 77,000 and a pH optimum of 7.3. TheK _m values for the purified enzyme for acetyl-CoA and for carnitine were 0.1 mM and 1 mM, respectively. Carnitine acetyltransferase was located both in the mitochondria and in the cytosol. Both mitochondrial and cytosolic enzyme were purified using ammonium sulfate precipitation, Mono Q and Superose 12 separation. Regarding the localization, except for maximum velocity, there were no differences observed in substrate specificity and inhibition. Inhibition of the enzyme with micromolar concentrations of Cu²⁺ could contribute to a greater citric acid biosynthesis. Carnitine acetyltransferase can be considered as an enzyme necessary for the transport of acetyl groups through mitochondrial membrane in both directions.     

Ag clusters electrochemically reduced in stearic acid Langmuir-Blodgett films and their structural characterizations

Silver ions confined in the silver stearate Langmuir-Blodgett (L-B) films of 8-14 layers were elec-trochernically reduced into Ag clusters,which made the observation of well-ordered scanning tunneling microscope (STM) images of the films with molecular resolution.A hexagonal packing of the hydrophobic chains was obtained,which was superimposed on the two-dimensional Ag clusters of 2-3 nm m diameter.Furthermore,a (2×1) struc-time of the hexagonal packing was observed.It was attributed to a self-assembled structure of the hydrophilic surface of the L-B films through hydrogen bonding.The strong surface enhanced Raman scattering (SERS) effect of Ag clusters made it possible to record Raman spectra of two-layer steanc acid L-B films in the region of C-C stretching vibration frequencies The appearance of the bands at 1 128 0 and 1 100.7 cm-1,which correspond to the antisymmetric C-C stretching model of the acyl chains m the all-trans conformation and the C-C stretching model of the acyl chains in the gauche