Pulse radiolysis of aromatic amino acids — State of the art

Summary The pulse radiolysis method as well as the primary processes of water radiolysis and the spectroscopic characteristics of H, OH, HO₂/O₂ ^– and e _aq ^- are briefly presented. Subsequently, kinetic and spectroscopic data of the transients resulting from the resolved multi site attack on aromatic amino acids are discussed. The reactivity of H and e _aq ^- with the same substrates, as well as the effect of oxygen on the major radiolytic processes are reviewed. Finally, the formation of tryptophan radical cation is mentioned shortly. The presented radiation mechanisms are the fundamentals for radiolytic processes occurring in proteins, enzymes and hormones in the living cells.     

Using C′ deviation to study structures of central amino acids in peptide fragments

Summary. In this investigation, we attempted to study the backbone geometry of amino acids in peptides using C′ deviation. Diameters of distribution were used to describe the various atomic structures, and scatter graphs provided visual evaluation. The length of peptide fragments and the secondary structure of amino acids in the central position of the peptide fragments were also analyzed. The results showed that the atomic distribution of the central amino acids of five-residue peptide fragments was much more restricted than that of their corresponding three-residue peptide fragments. In identical three-residue fragments, atoms of central amino acids with different secondary structures, were distributed in distinct areas.     

Ethynylglycine synthon from Garner’s aldehyde: a useful precursor for the synthesis of non-natural amino acids

Summary. The ethynylglycine synthon, namely (R)-2,2-dimethyl-3-(tert-butoxycarbonyl)-4-ethynyl-oxazolidine, can be obtained through the synthetic elaboration of naturally occurring serine. This compound has been exploited as a helpful and versatile non-racemic building block to be used for the design and synthesis of biologically important compounds, mainly non-natural α-amino acids. Taking advantage of the terminal acetylene moiety several synthetic applications can be designed. Metalation followed by trapping with electrophiles or Cu/Pd catalysed coupling with aromatic halogenides are shown to deliver useful precursors of ethynylglycine derivatives. Additions of bimetallic reagents like stannyl- or silylcuprates are useful entries for the regio- and stereoselective functionalization of the lateral chain, aimed at the synthesis of modified vinylglycine precursors.An overview of our recent work in the field will be given, and the use of ethynylglycine synthon in the synthesis of non-racemic saturated and unsaturated non-natural amino acids will be briefly reviewed.     

Arabidopsis, a model to study biological functions of isoprene emission?

The volatile hemiterpene isoprene is emitted from plants and can affect atmospheric chemistry. Although recent studies indicate that isoprene can enhance thermotolerance or quench oxidative stress, the underlying physiological mechanisms are largely unknown. In this work, Arabidopsis (Arabidopsis thaliana), a natural nonemitter of isoprene and the model plant for functional plant analyses, has been constitutively transformed with the isoprene synthase gene (PcISPS) from Grey poplar (Populus x canescens). Overexpression of poplar ISPS in Arabidopsis resulted in isoprene-emitting rosettes that showed transiently enhanced growth rates compared to the wild type under moderate thermal stress. The findings that highest growth rates, higher dimethylallyl diphosphate levels, and enzyme activity were detected in young plants during their vegetative growth phase indicate that enhanced growth of transgenic plants under moderate thermal stress is due to introduced PcISPS. Dynamic gas-exchange studies applying transient cycles of heat stress to the wild type demonstrate clearly that the prime physiological role of isoprene formation in Arabidopsis is not to protect net assimilation from damage against thermal stress, but may instead be to retain the growth potential or coordinated vegetative development of the plant. Hence, this study demonstrates the enormous potential but also the pitfalls of transgenic Arabidopsis (or other nonnatural isoprenoid emitters) in studying isoprene biosynthesis and its biological function(s).     

N-Carbamoyl-β-alanine amidohydrolase from Agrobacterium tumefaciens C58: a promiscuous enzyme for the production of amino acids

The availability of enzymes with a high promiscuity/specificity relationship permits the hydrolysis of several substrates with a view to obtaining a certain product or using one enzyme for several productive lines. N-Carbamoyl-β-alanine amidohydrolase from Agrobacterium tumefaciens (Atβcar) has shown high versatility to hydrolyze different N-carbamoyl-, N-acetyl- and N-formyl-amino acids to produce different α, β, γ and δ amino acids. We have calculated the promiscuity index for the enzyme, obtaining a value of 0.54, which indicates that it is a modestly promiscuous enzyme. Atβcar presented the highest probability of hydrolysis for N-carbamoyl-amino acids, being the enzyme more efficient for the production of α-amino acids. We have also demonstrated by mutagenesis, modelling, kinetic and binding experiments that W218 and A359 indirectly influence the plasticity of the enzyme due to interaction with the environment of R291, the key residue for catalytic activity.     

The first activation study of a δ-carbonic anhydrase: TweCAδ from the diatom Thalassiosira weissflogii is effectively activated by amines and amino acids

The activation of the δ-class carbonic anhydrase (CAs, EC 4.2.1.1) from the diatom Thalassiosira weissflogii (TweCAδ) was investigated using a panel of natural and non-natural amino acids and amines. The most effective activator of TweCAδ was d-Tyr (K_A of 51?nM), whereas several other amino acids and amines, such as L-His, L-Trp, d-Trp, dopamine and serotonin were submicromolar activators (K_As from 0.51 to 0.93?µM). The most ineffective activator of TweCAδ was 4-amino-l-Phe (18.9?µM), whereas d-His, l-/d-Phe, l-/d-DOPA, l-Tyr, histamine, some pyridyl-alkylamines, l-adrenaline and aminoethyl-piperazine/morpholine were moderately potent activators (K_As from 1.34 to 8.16?µM). For any δ-CA, there are no data on the crystal structure, homology modelling and the amino acid residues that are responsible for proton transfer to the active site are currently unknown making it challenging to provide a detailed rational for these findings. However, these data provide further evidence that this class of underexplored CA deserves more attention.     

Employment of gas—liquid chromatography for the analysis of collagen amino acids in biopsy tissue

In this paper, gas—liquid chromatography, adapted for the determination of collagen amino acids, is described. This technique was attractive for its sensitivity in that only a small amount of protein such as in 0.5 mg of tissue, especially as obtained from biopsy tissue, was needed for the separation and determination of proline (Pro), 4-hydroxyproline (4-Hyp), 3-hydroxyproline (3-Hyp), lysine (Lys), hydroxylysine (Hyl) and ?-hydroxynorleucine (?-OH-Norleu), the characteristic amino acids of collagen. Thus, without purification of collagen, by determining the ratio Hyl/4-Hyp and 4-Hyp/Pro it was possible to determine some anomalies in the collagen content of biopsy tissue (skin or liver). The ratio Hyl/4-Hyp allows an estimation of the lack of hydroxylation of polypeptidic lysine as in the Ehlers-Danlos syndrome type VI; and the ratio 4-Hyp/Pro allows measurement of variations in collagen content in relation to protein, especially in the liver, as in alcoholic cirrhosis.     

Asymmetric hydrolysis of α-aminonitriles to optically active amino acids by a nitrilase of Rhodococcus rhodochrous PA-34

Summary Rhodococcus rhodochrous PA-34 isolated from soil as a propionitrile-utilizing microorganism, hydrolysed several -aminonitriles to optically active amino acids. The hydrolysis of -aminonitriles was found to be catalysed by a nitrilase. The characteristics of the purified enzyme revealed that this is a new nitrilase as it has a molecular mass of 45 kDa and acts as a monomer. The optimum pH and temperature for the activity of the purified enzyme were 7.5 and 35° C, respectively. Thiol-specific reagents caused inhibition whereas chelators did not significantly alter the activity of this enzyme. The amino acids produced were of L-form, except for alanine. In the case of leucine production from -aminoisocapronitrile, the enantiomeric ratio of L-leucine to D-leucine was about 60.     

Binding of histamine to the H1 receptor—a molecular dynamics study

Binding of histamine to the G-protein coupled histamine H₁ receptor plays an important role in the context of allergic reactions; however, no crystal structure of the resulting complex is available yet. To deduce the histamine binding site, we performed unbiased molecular dynamics (MD) simulations on a microsecond time scale, which allowed to monitor one binding event, in which particularly the residues of the extracellular loop 2 were involved in the initial recognition process. The final histamine binding pose in the orthosteric pocket is characterized by interactions with Asp107^3.32, Tyr108^3.33, Thr194^5.43, Asn198^5.46, Trp428^6.48, Tyr431^6.51, Phe432^6.52, and Phe435^6.55, which is in agreement with existing mutational data. The conformational stability of the obtained complex structure was subsequently confirmed in 2 μs equilibrium MD simulations, and a metadynamics simulation proved that the detected binding site represents an energy minimum. A complementary investigation of a D107A mutant, which has experimentally been shown to abolish ligand binding, revealed that this exchange results in a significantly weaker interaction and enhanced ligand dynamics. This finding underlines the importance of the electrostatic interaction between the histamine ammonium group and the side chain of Asp107^3.32 for histamine binding.     

The formation of dipeptides from amino acids and the 2′(3′)-glycyl ester of an adenylate

Summary The yields of dipeptide obtained from the reaction of 0.2M 2(3)-O-(glycyl)-adenosine-5-(O-methylphosphate) and 0.2M amino acid at pH 8.2 ranged from 0.1% to 35.5% for a group of 15 amino acids. The yields of glyser (35.3%), gly-cys (11.8%) and gly-thr (5.4%) were considerably greater than dipeptide yields obtained from any of the other 12 amino acids ( 1.7%). Aminolysis of 0.05M 2(3)-O-(glycyl)-adenosine-5-(O-methylphosphate) by 0.4M serine ethyl ester yielded 53% glycylserine diketopiperazine, via N-(glycyl)-serine ethyl ester as a transient intermediate. The prebiotic significance of these reactions is discussed.Abbreviations MepA adenosine-5-(O-methylphosphate) - MepA-gly 2(3)-O-(glycyl)-adenosine-5-(O-methylphosphate) - DKP diketopiperazine - serOEt serine ethyl ester - gly-serOEt N-(glycyl)-serine ethyl ester - Boc-gly N-tertbutyloxycarbonylglycine - cyclo-(gly-ser-) glycylserine diketo-piperazine - O-gly-ser O-glycylserine - O-(gly)-gly-ser O-(glycyl)-glycylserine - gly-ser N-glycylserine     

Do frogs use retinal elevation to measure the distance of a barrier?

Grass frogs, Rana pipiens, will detour around a barrier to reach prey on the other side. However, if the distance between prey and barrier is short, frogs attempt to push through the barrier and reach the prey directly. The relationship between the probability of detouring and the distance between prey and barrier is the same whether the frog's starting position is 4 cm or 8 cm from the barrier. This suggests that frogs measure the absolute separation between the two objects. To discover whether the retinal elevation of the bottom of the barrier contributes to measuring this distance, the relationship between the frequency of detouring and barrier-prey distance was examined in several experiments in which the retinal position of the bottom of the barrier was manipulated. No evidence was obtained that the barrier's retinal elevation helps in gauging distance.On the other hand, retinal elevation influences strongly how far a frog lunges to reach its prey. It is suggested that different cues to distance are applied to the two classes of object because, under natural circumstances, it is difficult to judge where a barrier emerges from the ground. A barrier may be hard to detect below the horizon because of the low contrast between it and the ground, or because vegetation and ground litter mask where the barrier meets the ground. In contrast, the prey's movements make it easily detectable against a stationary background and the prey's short height means that partial occlusion will have little effect on its apparent vertical position in the visual field.     

Activation studies with amines and amino acids of the β-carbonic anhydrase from the pathogenic protozoan Leishmania donovani chagasi

The activation of a β-class carbonic anhydrase (CAs, EC 4.2.1.1) from Leishmania donovani chagasi (LdcCA) was investigated using a panel of natural and non-natural amino acids and amines. The most effective activators belonged to the amine class, with histamine, dopamine, serotonin, 2-pyridyl-methylamine and 4-(2-aminoethyl)-morpholine with activation constants in the range of 0.23–0.94 µM. In addition, 2-(2-aminoethyl)pyridine and 1-(aminoethyl)-piperazine were even more effective activators (K_As of 9–12 nM). Amino acids such as L-/D-His, L-/D-Phe, L-/D-DOPA, L-/D-Trp and L-/D-Tyr were slightly less effective activators compared to the amines, but showed activation constants in the low micromolar range (1.27–9.16 µM). Many of the investigated activators are autacoids that are present in rather high concentrations in different tissues of the host mammals infected by these parasites. As CA activators have not yet been investigated for protozoan CAs, this study may be relevant for an improved understanding of the role of this enzyme in the life cycle of Leishmania.     

The effect of amino acids on the C₁₄-sphingosine-triggered germination of Nomuraea rileyi, and surface amino acids on Spodoptera litura fabricius

D-erythro-C??-Sphingosine (C??-Sph) accelerated the germination of Nomuraea rileyi in a solution containing peptone, but activity declined to a large degree in water. This suggests the presence of a co-factor in C??-Sph-triggered germination. Since the main role of peptone is to supply nitrogen constituents, we examined the effects of various nitrogen constituents. It was found that Ala and His were highly effective for C??-Sph-triggered germination.     

Identification of amino acids involved in the binding of hMIP-1α to CC-CKR1, a MIP-lα receptor found on neutrophils

Human macrophage inflammatory protein-1 (hMIP-1) and human macrophage inflammatory protein-1 (hMIP-1) are chemokines involved in a diverse range of immunological effects. Both hMIP-1 and hMIP-1 are involved in the activation of monocytes and THP-1 cells probably through a common receptor(s). However, only hMIP-1 can bind to neutrophils with high affinity, presumably through CC-CKR1 (CKR1). Since the structure of these two proteins is highly conserved, non-conserved amino acids must define the disparate binding patterns that these two proteins exhibit. Measurements of binding, chemotaxis and calcium influx conducted with hMIP-1 and hMIP-1 chimeric proteins and mutants show that two amino acids (37K and 43L) are important in the binding and signaling of hMIP-1 through CKR1. Furthermore, we also show that mutations of the three charged amino acids at the C-terminus of hMIP-1 and hMIP-1 (amino acids 61, 65 and 67), do not adversely affect the binding to THP-1 cells.     

Recent brachiopods from New Zealand — background to the study cruises of 1977–79

Abstract

Information collected during study cruises to Stewart Island, Fiordland, and the Marlborough Sounds, New Zealand, has led, to a reappraisal of both the physical nature of living brachiopods and the habitats occupied by, them. Two widely disparate environments—steep rock walls of fiords, and floors of shallow, muddy inlets—have brachiopod species in common. Other macrobrota characteristic of these hard and soft substrates are described. Populations of species belonging to two of the genera observed and collected in these habitats form the basis for morphological, population, and behavioural studies. One conclusion from these studies—that an individual's capacity to occupy any substrate or environment is restrioted only by one variable organ, the pedlicle—is consistent with the historical record of the phylum.     

Activation studies with amines and amino acids of the α-carbonic anhydrase from the pathogenic protozoan Trypanosoma cruzi

The activation of a α-class carbonic anhydrase (CAs, EC 4.2.1.1) from Trypanosoma cruzi (TcCA) was investigated with the best known classes of activators, the amino acids and aromatic/heterocyclic amines. The best TcCA activators were l-/d-DOPA and 4-amino-l-phenylalanine, which had activation constants in the range of 0.38–0.83?µM. Low micromolar activators were also l-/d-Trp, l-/d-Tyr, l-Gln, histamine and serotonin (K_As of 1.79–4.92?µM), whereas l-/d-His, l-/d-Phe and l-Asp were less effective activators (K_As of 6.39–18.7?µM). Amines such as dopamine, pyridyl-alkylamines, aminoethyl-piperazine or l-adrenaline, were devoid of activating effects on TcCA. Since the role of autacoids as many of these compounds investigated here is not known for the life cycle of T. cruzi, our work provides new tools for further investigations of factors connected with this protozoan pathogen infection.     

How relevant is the ratio of dietary n-6 to n-3 polyunsaturated fatty acids to cardiovascular disease risk? Evidence from the OPTILIP study

PURPOSE OF REVIEW: There has been much debate over the practical utility of the dietary ratio of n-6 to n-3 polyunsaturated fatty acids in optimizing the benefits of n-3 fatty acids (C18-C22) on cardiovascular health. This review examines the supporting evidence from the OPTILIP study within the context of the emerging consensus on the value of this dietary metric. RECENT FINDINGS: The question of whether the ratio of n-6/n-3 polyunsaturated fatty acids or total amounts of dietary polyunsaturated fatty acids is of more importance to cardiovascular health has been addressed recently in a randomly controlled trial (OPTILIP) and in a stable isotope tracer study. These two studies were independently unanimous in concluding that the ratio of n-6/n-3 polyunsaturated fatty acids is of no value in modifying cardiovascular disease risk. The latter study also showed that the absolute amounts of dietary linoleic acid and alpha-linolenic acid are of relevance to the efficiency of conversion of alpha-linolenic acid to eicosapentaenoic acid and docosahexaenoic acid. SUMMARY: This review should help to settle any outstanding controversy over the dietary ratio of n-6/n-3 polyunsaturated fatty acids. It reinforces current recommendations to increase the consumption of preformed eicosapentaenoic acid/docosahexaenoic acid in fish, and supports dietary measures to increase and decrease intakes alpha-linolenic acid and linoleic acid, respectively, to promote the endogenous synthesis of these longer chain n-3 polyunsaturated fatty acids.     

The first activation studies of the η-carbonic anhydrase from the malaria parasite Plasmodium falciparum with amines and amino acids

The first activation study of a η-class carbonic anhydrase (CAs, EC 4.2.1.1) is reported. A panel of 24 natural and non-natural amino acids and amines was used to explore the activation profile of Plasmodium falciparum CA (PfACA). The most effective activators belonged to the amino acid chemotype, with d-Glu, l-Asp, l-/d-Phe and l-/d-DOPA possessing activation constant in the range of 82 nM–0.75 µM, whereas l-/d-His, l-Tyr, 4-amino-l-Phe and l-Gln were slightly less effective (K_A in the range of 1.00–2.51 µM. The only amine with submicromolar activating properties was 1-(2-aminoethyl-piperazine) with a K_A of 0.71 µM, whereas histamine, dopamine and serotonin showed K_A ranging between 7.18 and 9.97 µM. As CA activators have scarcely been investigated for their interaction with protozoan CAs, this study may be relevant for an improved understanding of the role of this enzyme in the life cycle of the malaria producing organisms belonging to the genus Plasmodium.