Substrate specificity of platypus venom L-to-D-peptide isomerase

A novel series of metazoan L/D peptide isomerases

The function of endogenous cell-cell signaling peptides relies on their interactions with cognate receptors, which in turn are influenced by the peptides' structures, necessitating a comprehensive understanding of the suite of post-translational modifications of the peptide. Herein, we report the initial characterization of putative peptide isomerase enzymes extracted from R. norvegicus, A. californica, and B. taurus tissues. These enzymes are both tissue and substrate-specific across all three organisms. Notably, the lungs of the mammalian species, and the central nervous system of the mollusk displayed the highest isomerase activity among the examined tissues. In vitro enzymatic conversion was observed for several endogenous peptides, such as the tetrapeptide GFFD in A. californica, and mammalian neuropeptide FF in R. norvegicus and B. taurus. To understand their mode of action, we explored the effects of several inhibitors on these enzymes, which suggest common active site residues. While further characterization of these enzymes is required, the investigations emphasize a widespread and overlooked enzyme activity related to the creation of bioactive peptides.

Utilisation of compounds from venoms in drug discovery

Difficult drug targets are becoming the normal course of business in drug discovery, sometimes due to large interacting surfaces or only small differences in selectivity regions. For these, a different approach is merited: compounds lying somewhere between the small molecule and the large antibody in terms of many properties including stability, biodistribution and pharmacokinetics. Venoms have evolved over millions of years to be complex mixtures of stable molecules derived from other somatic molecules, the stability comes from the pressure to be ready for delivery at a moment's notice. Snakes, spiders, scorpions, jellyfish, wasps, fish and even mammals have evolved independent venom systems with complex mixtures in their chemical arsenal. These venom-derived molecules have been proven to be useful tools, such as for the development of antihypotensive angiotensin converting enzyme (ACE) inhibitors and have also made successful drugs such as Byetta® (Exenatide), Integrilin® (Eptifibatide) and Echistatin. Only a small percentage of the available chemical space from venoms has been investigated so far and this is growing. In a new era of biological therapeutics, venom peptides present opportunities for larger target engagement surface with greater stability than antibodies or human peptides. There are challenges for oral absorption and target engagement, but there are venom structures that overcome these and thus provide substrate for engineering novel molecules that combine all desired properties. Venom researchers are characterising new venoms, species, and functions all the time, these provide great substrate for solving the challenges presented by today's difficult targets.

Advancing d-amino acid-containing peptide discovery in the metazoan

The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the homochirality of animal proteins while simultaneously revealing new analytical challenges in the structural and functional characterization of peptides. Most known DAACPs have been identified though laborious activity-guided purification studies or by homology to previously identified DAACPs. Peptide characterization experiments are increasingly dominated by high throughput mass spectrometry-based peptidomics, with stereochemistry rarely considered due to the technical challenges of identifying l/d isomerization. This review discusses the prevalence of enzyme-derived DAACPs among animals and the physiological consequences of peptide isomerization. Also highlighted are the analytical methods that have been applied for structural characterization/discovery of DAACPs, including results of several recent studies using non-targeted discovery methods for revealing novel DAACPs, strongly suggesting that more DAACPs remain to be uncovered.

D-Amino Acids in Peptides from Animals, Including Human: Occurrence, Structure, Bioactivity and Pharmacology

All life forms typically possess homochirality, with rare exceptions. In the case of peptides and proteins, only L-amino acids are known to be encoded by genes. Nevertheless, D-amino acids have been identified in a variety of peptides, synthesized by animal cells. They include neuroexcitatory and neuroprotective peptides, cardioexcitatory peptides, hyperglycemic hormones, opioid peptides, antimicrobial peptides, natriuretic and defensin-like peptides, and fibrinopeptides. This article is a review of their occurrence, structure and bioactivity. It further explores the pharmacology and potential medical applications of some of the peptides.

Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials

The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.

Arthropod venoms: Biochemistry, ecology and evolution

Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.

Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs)

Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.

Theoretical Investigations of the Chiral Transition of α-Amino Acid Confined in Various Sized Armchair Boron-Nitride Nanotubes

We computationally study the chiral transition process of the α-Ala molecule under confined different sizes of armchair SWBNNTs to explore the confinement effect. We find that the influence of a confinement environment (in armchair SWBNNTs) on the α-Ala molecule would lead to different reaction pathways. Meanwhile, the preferred reaction pathway is also different in various sizes of armchair SWBNNTs, and their energy barriers for the rate-limiting step decrease rapidly with the decreasing of the diameters of the nanotubes. It is obvious that significant decrease of the chiral transition energy barrier occurs compared with the isolated α-Ala molecule chirality conversion mechanism, by ∼15.6 kcal mol^-1, highlighting the improvement in the activity the enantiomers of α-Ala molecule. We concluded that the confinement environment has a significant impact at the nanoscale on the enantiomer transformation process of the chiral molecule.

Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis

Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing C_α-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.

Exploring the Potential of (99m)Tc(CO)3-Labeled Triazolyl Peptides for Tumor Diagnosis

In recent years the authors have reported on (99m)Tc(CO)3-labeled peptides that serve as carriers for biomolecules or radiopharmaceuticals to the tumors. In continuation of that work they report the synthesis of a pentapeptide (Met-Phe-Phe-Gly-His; pep-1), a hexapeptide (Met-Phe-Phe-Asp-Gly-His; pep-2), and a tetrapeptide (Asp-Gly-Arg-His; pep-3) and the attachment of 3-amino-1,2,4-triazole to the β carboxylic function of the aspartic acid unit of pep-2 and pep-3. The pharmacophores were radiolabeled in high yields with [(99m)Tc(CO)3(H2O)3](+) metal aqua ion, characterized for their stability in serum and saline, as well as in His solution, and found to be substantially stable. B16F10 cell line binding studies showed favorable uptake and internalization. In vivo behavior of the radiolabeled triazolyl peptides was assessed in mice bearing induced tumor. The (99m)Tc(CO)3-triazolyl pep-3 demonstrated rapid urinary clearance and comparatively better tumor uptake. Imaging studies showed visualization of the tumor using (99m)Tc(CO)3-triazolyl pep-3, but due to high abdominal background, low delineation occurred. Based on the results further experiments will be carried out for targeting tumor with triazolyl peptides.

Centipede venoms as a source of drug leads

INTRODUCTION

Centipedes are one of the oldest and most successful lineages of venomous terrestrial predators. Despite their use for centuries in traditional medicine, centipede venoms remain poorly studied. However, recent work indicates that centipede venoms are highly complex chemical arsenals that are rich in disulfide-constrained peptides that have novel pharmacology and three-dimensional structure. Areas covered: This review summarizes what is currently known about centipede venom proteins, with a focus on disulfide-rich peptides that have novel or unexpected pharmacology that might be useful from a therapeutic perspective. The authors also highlight the remarkable diversity of constrained three-dimensional peptide scaffolds present in these venoms that might be useful for bioengineering of drug leads. Expert opinion: Like most arthropod predators, centipede venoms are rich in peptides that target neuronal ion channels and receptors, but it is also becoming increasingly apparent that many of these peptides have novel or unexpected pharmacological properties with potential applications in drug discovery and development.

MALDI TOF/TOF-Based Approach for the Identification of d- Amino Acids in Biologically Active Peptides and Proteins

Several biologically active peptides contain a d- amino acid in a well-defined position, which is position 2 in all peptide epimers isolated to date from vertebrates and also some from invertebrates. The detection of such D- residues by standard analytical techniques is challenging. In tandem mass spectrometric (MS) analysis, although fragment masses are the same for all stereoisomers, peak intensities are known to depend on chirality. Here, we observe that the effect of a d- amino acid in the second N-terminal position on the fragmentation pattern in matrix assisted laser desorption time-of-flight spectrometry (MALDI-TOF/TOF MS) strongly depends on the peptide sequence. Stereosensitive fragmentation (SF) is correlated to a neighborhood effect, but the d- residue also exerts an overall effect influencing distant bonds. In a fingerprint analysis, multiple peaks can thus serve to identify the chirality of a sample in short time and potentially high throughput. Problematic variations between individual spots could be successfully suppressed by cospotting deuterated analogues of the epimers. By identifying the [d-Leu2] isomer of the predicted peptide GH-2 (gene derived bombininH) in skin secretions of the toad Bombina orientalis, we demonstrated the analytical power of SF-MALDI-TOF/TOF measurements. In conclusion, SF-MALDI-TOF/TOF MS combines high sensitivity, versatility, and the ability to complement other methods.

The Unexpected Advantages of Using D-Amino Acids for Peptide Self- Assembly into Nanostructured Hydrogels for Medicine

Self-assembled peptide hydrogels have brought innovation to the medicinal field, not only as responsive biomaterials but also as nanostructured therapeutic agents or as smart drug delivery systems. D-amino acids are typically introduced to increase the peptide enzymatic stability. However, there are several reports of unexpected effects on peptide conformation, self-assembly behavior, cytotoxicity and even therapeutic activity. This mini-review discusses all the surprising twists of heterochiral self-assembled peptide hydrogels, and delineates emerging key findings to exploit all the benefits of D-amino acids in this novel medicinal area.

Post-translational Introduction of D-Alanine into Ribosomally Synthesized Peptides by the Dehydroalanine Reductase NpnJ

Ribosomally synthesized peptides are generally limited to L-amino acid building blocks. Given the advantageous properties of peptides containing D-amino acids such as stabilization of certain turns and against proteolytic degradation, methods to introduce D-stereocenters are valuable. Here we report the first in vitro reconstitution and characterization of a dehydrogenase that carries out the asymmetric reduction of dehydroalanine. NpnJA reduces dehydroalanine to D-Ala using NAPDH as cosubstrate. The enzyme displays high substrate tolerance allowing introduction of D-Ala into a range of non-native substrates. In addition to the in vitro reactions, we describe five examples of using Escherichia coli as biosynthetic host for D-alanine introduction into ribosomal peptides. A deuterium-label-based coupled-enzyme assay was used to rapidly determine the stereochemistry of the newly installed alanine.

Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition

Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of ^DAla in collagen like peptide (imino-poor region of type I collagen) on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of ^DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD). Our findings suggest that, ^DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.

Tracing monotreme venom evolution in the genomics era

The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.

Different transcription regulation routes are exerted by L- and D-amino acid enantiomers of peptide hormones

Conversion of one or more amino acids in eukaryotic peptides to the D-configuration is catalyzed by specific L/D peptide isomerases and it is a poorly investigated post-translational modification. No common modified amino acid and no specific modified position have been recognized and mechanisms underlying changes in the peptide function provided by this conversion were not sufficiently studied. The 72 amino acid crustacean hyperglycemic hormone (CHH) of Astacidea crustaceans exhibits a co-existence of two peptide enantiomers alternately having D- or L-phenylalanine in their third position. It is a pleiotropic hormone regulating several physiological processes in different target tissues and along different time scales. CHH enantiomers differently affect time courses and intensities of examined processes. The short-term effects of the two isomers on gene expression are presented here, examined in the hepatopancreas, gills, hemocytes and muscles of the astacid Pontastacus leptodactylus. Muscles and hemocytes were poorly affected by both isomers. Two CHH modes of action were elucidated in the hepatopancreas and the gills: specific gene induction by D-CHH only, elucidated in both organs and mutual targeted attenuation affected by both enantiomers elucidated in the gills. Consequently a two-receptor system is hypothesized for conveying the effect of the two CHH isomers.

Cyclization enhances function of linear anti-arthritic peptides

This study describes the biophysical and immunomodulatory features of a cyclic peptide termed C1 which consists of alternating d-, l-amino acids and is capable of inhibiting IL-2 production in vitro and reducing the induction and extent of T-cell mediated inflammation in animal models. Solid-state nuclear magnetic resonance demonstrates that the peptide orders the lipid bilayer, suggesting a transmembrane orientation, and this is supported by surface plasmon resonance indicating strong binding affinity of C1 to model membranes. In vitro cell viability and proliferation assays show that C1 does not disrupt the integrity of cell surface membranes. Permeation studies of C1 and analogs across human epidermis cells show that the stability and skin permeability are enhanced by cyclization. Treatment with C1 in an asthma and in an arthritis animal model resulted in a suppressed immune response. Cyclization may be a useful means of enhancing biological linear peptide activity and improving delivery.

Validation of the distal effect of electron-withdrawing groups on the stability of peptide enolates and its exploitation in the controlled stereochemical inversion of amino acid derivatives

Theoretical studies had predicted that N-electron-withdrawing substituents, hydrogen bonding, and protonation at amide nitrogen selectively increase the acidity of a distal proton adjacent to the amide carbonyl to the extent that the α-carbonyl acidity of some N-substituted amides exceeds that of typical ketones. Now, in the present work, competitive, base-catalyzed hydrogen-deuterium exchange experiments, with diisopropyl ketone and a series of N-substituted acetamides and diketopiperazines, have established that there is a strong correlation between the calculated acidities and the experimental rates of deprotonation in these systems. The results show that the rates of exchange of the distal protons of N-acylated and N-sulfonylated amides are more than 4 orders of magnitude faster than those of the N-methylated analogues and that the acylated and sulfonylated amides are much more reactive in this regard than diisopropyl ketone. The magnitude and regioselectivity of the distal effect is sufficient for practical applications and has been exploited in the manipulation of N-acetyl α,α'-disubstituted diketopiperazines for the controlled α-deuteration and stereochemical inversion of N-methylamino acids, and in the production of α-deuterated (2R,3S)-N-methylalloisoleucine from the nondeuterated (2S,3S)-isoleucine diastereomer.

Substrate specificity of a peptidyl-aminoacyl-L/D-isomerase from frog skin

In the skin of fire-bellied toads (Bombina species), an aminoacyl-l/d-isomerase activity is present which catalyses the post-translational isomerization of the l- to the d-form of the second residue of its substrate peptides. Previously, this new type of enzyme was studied in some detail and genes potentially coding for similar polypeptides were found to exist in several vertebrate species including man. Here, we present our studies to the substrate specificity of this isomerase using fluorescence-labeled variants of the natural substrate bombinin H with different amino acids at positions 1, 2 or 3. Surprisingly, this enzyme has a rather low selectivity for residues at position 2 where the change of chirality at the alpha-carbon takes place. In contrast, a hydrophobic amino acid at position 1 and a small one at position 3 of the substrate are essential. Interestingly, some peptides containing a Phe at position 3 also were substrates. Furthermore, we investigated the role of the amino-terminus for substrate recognition. In view of the rather broad specificity of the frog isomerase, we made a databank search for potential substrates of such an enzyme. Indeed, numerous peptides of amphibia and mammals were found which fulfill the requirements determined in this study. Expression of isomerases with similar characteristics in other species can therefore be expected to catalyze the formation of peptides containing d-amino acids.

MAPping the chiral inversion and structural transformation of a metal-tripeptide complex having ni-superoxide dismutase activity

The metal abstraction peptide (MAP) tag is a tripeptide sequence capable of abstracting a metal ion from a chelator and binding it with extremely high affinity at neutral pH. Initial studies on the nickel-bound form of the complex demonstrate that the tripeptide asparagine-cysteine-cysteine (NCC) binds metal with 2N:2S, square planar geometry and behaves as both a structural and functional mimic of Ni superoxide dismutase (Ni-SOD). Electronic absorption, circular dichroism (CD), and magnetic CD (MCD) data collected for Ni-NCC are consistent with a diamagnetic Ni(II) center. It is apparent from the CD signal of Ni-NCC that the optical activity of the complex changes over time. Mass spectrometry data show that the mass of the complex is unchanged. Combined with the CD data, this suggests that chiral rearrangement of the complex occurs. Following incubation of the nickel-containing peptide in D(2)O and back-exchange into H(2)O, incorporation of deuterium into non-exchangeable positions is observed, indicating chiral inversion occurs at two of the α carbon atoms in the peptide. Control peptides were used to further characterize the chirality of the final nickel-peptide complex, and density functional theory (DFT) calculations were performed to validate the hypothesized position of the chiral inversions. In total, these data indicate Ni-SOD activity is increased proportionally to the degree of structural change in the complex over time. Specifically, the relationship between the change in CD signal and change in SOD activity is linear.

Mammalian peptide isomerase: platypus-type activity is present in mouse heart

Male platypus (Ornithorhynchus anatinus) venom has a peptidyl aminoacyl L/D-isomerase (hereafter called peptide isomerase) that converts the second amino acid residue in from the N-terminus from the L- to the D-form, and vice versa. A reversed-phase high-performance liquid chromatography (RP-HPLC) assay has been developed to monitor the interconversion using synthetic hexapeptides derived from defensin-like peptide-2 (DLP-2) and DLP-4 as substrates. It was hypothesised that animals other than the platypus would have peptide isomerase with the same substrate specificity. Accordingly, eight mouse tissues were tested and heart was shown to have the activity. This is notable for being the first evidence of a peptide isomerase being present in a higher mammal and heralds finding the activity in man.

The distal effect of electron-withdrawing groups and hydrogen bonding on the stability of peptide enolates

Relative gas-phase carbon acidities have been computed for a series of acetamides, diketopiperazines, and linear dipeptides. The results show that N-electron-withdrawing substituents, protonation, and hydrogen bonding at amide nitrogen in these systems increase the acidity of both a C-H proton adjacent to the amide carbonyl and that of one proximal to the amide nitrogen. There is a good correlation between the magnitudes of the increases at the two positions, but the extent of the increase for the distal C-H adjacent to the carbonyl is greater than that for the proximal C-H, in most cases by a factor of about two. The effects on the stability of the distal enolate are shown to result from predominantly inductive affects. The size of these effects is such that protonation and hydrogen bonding at nitrogen increase the acidity of the distal C-H to almost the same extent as seen for the analogous interactions at the carbonyl oxygen. The effect is also seen in solution, where the computed aqueous pK(a) values are greater for the C-H adjacent to the amide carbonyl, by up to 13 units, and where preliminary experimental studies have shown that N-acetylation of an amide increases the rate of hydrogen-deuterium exchange via formation of the corresponding distal enolate by more than 3 orders of magnitude above the rates of exchange via the proximal enolate, of the nonacetylated amide and of diisopropylketone. The results also indicate that hydrogen bonding to amide nitrogen could be as important as bonding to oxygen in enzyme-catalyzed cleavage of alpha-C-H bonds.

Molecular diversity of spider venom

Spider venom, a factor that has played a decisive role in the evolution of one of the most successful groups of living organisms, is reviewed. Unique molecular diversity of venom components including substances of variable structure (from simple low molecular weight compounds to large multidomain proteins) with different functions is considered. Special attention is given to the structure, properties, and biosynthesis of toxins of polypeptide nature.

J-compensated PGSE: an improved NMR diffusion experiment with fewer phase distortions

Peak distortion caused by homonuclear (1)H J-coupling is a major problem in many spin-echo-based experiments such as pulsed gradient spin-echo (PGSE) experiments. Although peak phase distortions can be lessened by the incorporation of anti-phase purging sequences, the sensitivity is substantially decreased. Techniques for lessening the effect of homonuclear J-coupling evolution in spin-echo-based experiments have been investigated. Two potentially useful candidates include a J-compensated inversion sequence that is efficient over a wide range of J-coupling values and a pulse sequence that refocuses homonuclear J-evolution during the spin-echo. The latter was found to work superbly on samples containing two spin (AX or AB) systems and still provided significant advantage over the standard method on samples containing more complicated spin systems. Implementation of this J-refocusing technique into a PGSE-type experiment (J-PGSE) leads to dramatic improvement of spectra and easier data analysis. The J-PGSE sequence should find applications in many diffusion studies where the PGSE-type method is required and should be a viable alternative to PGSTE especially in dilute samples due to its enhanced sensitivity.

L-to-D-peptide isomerase in male echidna venom

The monotremes (the echidnas and the platypus) display both mammalian and reptilian features. Male monotremes have a bilateral crural gland that is connected via a duct to a spur on each hind limb. Male echidnas appear not to use their spurs as weapons in aggressive acts, but the crural system may have a role in reproductive behaviour because it appears only to be active during the breeding season. The secretions produced by the echidna’s crural gland have not hitherto been biochemically or pharmacologically characterised. We used reverse-phase high-performance liquid chromatography (RP-HPLC) to separate the components of echidna venom and compared the chromatograms with those from platypus venom. The echidna venom appears to contain fewer proteins and peptides than platypus venom; however, it appears to have defensin-like peptides that behave similarly on RP-HPLC to those in platypus venom. Like platypus venom, echidna venom has peptidyl aminoacyl l/d-peptide isomerase activity. An RP-HPLC-based assay showed that the second amino acid residue, of a probe synthetic hexapeptide, was converted into the d-form, when incubated with echidna venom.

Molecular and cellular specificity of post-translational aminoacyl isomerization in the crustacean hyperglycaemic hormone family

D-aminoacyl residues have been detected in various animal peptides from several taxa, especially vertebrates and arthropods. This unusual polymorphism was shown to occur in isoforms of the crustacean hyperglycaemic hormone (CHH) of the American lobster because a D-phenylalanyl residue was found in position 3 of the sequence (CHH and D-Phe3 CHH). In the present study, we report the detailed strategy used to characterize, in the lobster neuroendocrine system, isomers of another member of the CHH family, vitellogenesis inhibiting hormone (VIH). We have demonstrated that the fourth residue is either an L- or a D- tryptophanyl residue (VIH and D-Trp4 VIH). Furthermore, use of antisera specifically recognizing the epimers of CHH and VIH reveals that aminoacyl isomerization occurs in specialized cells of the X organ-sinus gland neurosecretory system and that the D-forms of the two neuropeptides are not only present in the same cells, but, importantly, also are co-packaged within the same secretory vesicles.

Analysis of Endogenous D-Amino Acid-Containing Peptides in Metazoa

Peptides are chiral molecules with their structure determined by the composition and configuration of their amino acid building blocks. The naturally occurring amino acids, except glycine, possess two chiral forms. This allows the formation of multiple peptide diastereomers that have the same sequence. Although living organisms use L-amino acids to make proteins, a group of D-amino acid-containing peptides (DAACPs) has been discovered in animals that have at least one of their residues isomerized to the D-form via an enzyme-catalyzed process. In many cases, the biological functions of these peptides are enhanced due to this structural conversion. These DAACPs are different from those known to occur in bacterial cell wall and antibiotic peptides, the latter of which are synthesized in a ribosome-independent manner. DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. Their serendipitous discovery has often resulted from discrepancies observed in bioassays or in chromatographic behavior between natural peptide fractions and peptides synthesized according to a presumed all-L sequence. Because this L-to-D post-translational modification is subtle and not detectable by most sequence determination approaches, it is reasonable to suspect that many studies have overlooked this change; accordingly, DAACPs may be more prevalent than currently thought. Although diastereomer separation techniques developed with synthetic peptides in recent years have greatly aided in the discovery of natural DAACPs, there is a need for new, more robust methods for naturally complex samples. In this review, a brief history of DAACPs in animals is presented, followed by discussion of a variety of analytical methods that have been used for diastereomeric separation and detection of peptides.

Platypus venom: source of novel compounds

An anatomical feature of the platypus (Ornithorhynchus anatinus) that is seen in only one other mammal, the echidna, is that the male has a crural glandular system that produces venom that is used for defence and territorial–breeding functions; whether the echidna is similarly venomous is not yet established. Platypus venom contains many novel proteins and peptides that are different from those in reptilian venom. It also causes pain and symptoms that are not experienced by any other kind of envenomation. Five types of proteins and peptides have been isolated and identified from platypus venom, namely: defensin-like peptides (DLPs); Ornithorhynchus venom C-type natriuretic peptides (OvCNPs); Ornithorhynchus nerve growth factor; hyaluronidase; and l-to-d-peptide isomerase. The structures of DLPs and OvCNPs have already been studied and they are very similar to β-defensin-12 and mammalian C-type natriuretic peptides, respectively. A special mammalian l-to-d-peptide isomerase that is responsible for interconverting the l- and d-peptide isomers is also found in platypus venom. Isomerase activity has recently been discovered in platypus tissues other than the venom gland. It is possible that similar kinds of enzymes might exist in other mammals and play important, as yet unknown, biological roles. Considering the fact that some animal venoms have already been widely used in pharmaceutical applications, research into platypus venom may lead to the discovery of new molecules and potent drugs that are useful biomedical tools.

Platypus venom genes expressed in non-venom tissues

The venom of the platypus (Ornithorhynchus anatinus) has been poorly studied to date. The recent publication of the platypus genome heralds a new era for mammalian venom research and is a useful starting tool for functional studies of venom components. We report here the patterns of tissue expression of two venom genes, OvNGF and OvCNP, in order to provide some insight into the functions of the proteins they produce and to pave the way for further functional and pharmacological studies, which may lead to the development of novel therapeutic agents.

Antimicrobial peptides and bacteriocins: alternatives to traditional antibiotics

Antimicrobial peptides (AMPs) are ubiquitous, gene-encoded natural antibiotics that have gained recent attention in the search for new antimicrobials to combat infectious disease. In multicellular organisms, AMPs, such as defensins and cathelicidins, provide a coordinated protective response against infection and are a principal component of innate immunity in vertebrates. In unicellular organisms, AMPs, such as bacteriocins, function to suppress competitor species. Because many AMPs kill bacteria by disruption of membrane integrity and are thus thought to be less likely to induce resistance, AMPs are being extensively evaluated as novel antimicrobial drugs. This review summarizes and discusses the antibiotic properties of AMPs highlighting their potential as alternatives to conventional antibiotics.

Removal of J-coupling peak distortion in PGSE experiments

Peak distortion caused by homonuclear J-coupling is a major problem that limits the utility of the pulsed-field gradient spin-echo (PGSE) method for studying translational diffusion. This unwanted effect can be removed by incorporation of anti-phase magnetization purging pulse elements at the end of the spin-echo sequence. Three methods, namely, trim-pulse, homospoil pulse gradient and chirp based z-filter were evaluated as potential candidates for an improved NMR diffusion method that is less sensitive to J-coupling peak distortion. The chirp based z-filter was found to be excellent in suppressing anti-phase magnetization while leaving the in-phase magnetization basically intact in spin-echo and stimulated-echo based experiments. The incorporation of chirp based z-filter into PGSE could allow diffusion analysis that would otherwise be impossible by conventional means.