Molecular Phylogeny, Classification and Evolution of Conopeptides

Surface properties of ovalbumin and of its putative signal sequence, and their interactions with phospholipids at an air-water interface, have been studied. The mature protein can form an interfacial film spontaneously from its bulk solution, whereas the signal sequence cannot. Mature ovalbumin also penetrates phospholipid monolayers from the subphase (independently of the type of phospholipid present), whereas its signal sequence does not. The surface stability of a spread film of the signal sequence is, however, higher than that of a film of mature ovalbumin. Above specific threshold concentrations of signal peptide and of mature ovalbumin in mixed films with phospholipids, two separate phases are formed. In such immiscible films, the signal sequence peptide is also able to support a higher lateral surface pressure than mature ovalbumin, at corresponding areas of peptide and mature protein in the mixed monolayers. It is suggested that the differing lateral stabilities of ovalbumin and of its putative signal sequence may be relevant to the translocation of ovalbumin across the membrane of the endoplasmic reticulum, and a scheme for its translocation is proposed that is based on these properties.

The vaccine efficacy of the gene sequence encoding the signal peptide of the antigen known as antigen 2 or proline-rich antigen (Ag2/PRA), an immunodominant antigen present in the cell wall of the fungal pathogen Coccidioides immitis, was investigated in a murine model of coccidioidomycosis. Expression plasmids for Ag2/PRA(1-18) DNA (signal sequence), Ag2/PRA(19-194) DNA (lacking the signal sequence), and Ag2/PRA(1-194) DNA (full length) were inserted in the pVR1012 vector, and the constructs were used to vaccinate the highly susceptible BALB/c mouse strain. Immunization with the signal gene sequence significantly reduced the fungal burden in the lungs and spleens of mice 12 days after intraperitoneal challenge with a lethal dose of 2,500 C. immitis arthroconidia, to a level comparable to the protection induced in mice immunized with the full-length Ag2/PRA(1-194) DNA. The Ag2/PRA(19-194) gene protected mice but to a significantly lower level than the signal sequence or the full-length Ag2 gene. The immunizing capacity of Ag2/PRA(1-18) was not attributable to a nonspecific immunostimulatory effect of DNA, as evidenced by the fact that mice immunized with a frameshift mutation of Ag2/PRA(1-18) were not protected against challenge. Furthermore, a synthetic peptide corresponding to the translated sequence of Ag2/PRA(1-18) DNA protected mice, albeit at a lower level than the Ag2/PRA(1-18) DNA vaccine. The protection induced with the signal gene vaccine correlated with the production of gamma interferon when splenocytes from Ag2/PRA(1-18)-immunized mice were stimulated with recombinant full-length Ag2 and was not associated with the production of anti-Coccidioides immunoglobulin G antibody. This is the first study to establish that a signal peptide sequence alone, administered as a gene vaccine or synthetic peptide, can induce protective immunity against a microbial pathogen.

Voltage-gated ion channels are physiologically important transmembrane proteins involved in several pathologies including cardiac, muscular and neuronal disorders. Efforts are underway to develop potent and selective modulators of voltage-gated ion channels for the purposes of probing the pharmacology of these channels, and for the development of safe, efficacious therapeutics.Gating modifier toxins (GMTs) are a class of peptide toxins (30–40 amino acid residues in length) that modulate the gating mechanism of voltage-gated ion channels and are being pursued as probes and drug leads for these transmembrane proteins. GMTs can be isolated from the venom of various animals including cone snails, scorpions and spiders. GMTs that contain a conserved inhibitor cystine knot (ICK) motif in which disulfide bridges are arranged in a Cys I–IV, Cys II–V, Cys III–VI pattern, typically display a surface profile including a hydrophobic patch and a charged ring. This amphipathic structure putatively facilitates interactions between GMTs and lipid membranes giving rise to a tri-molecular complex formed when GMTs interact with the lipid bilayer during modulation of voltage-gated ion channels.The first aim of this thesis is to examine GMT–lipid bilayer interactions and to investigate how these interactions influence potency and selectivity for voltage-gated sodium channels. Secondly, the objective is to determine whether GMT–lipid bilayer interactions can be included in the design of potent and selective GMT modulators of NaV1.7. The third aim is to explore the pharmacological relevance of GMTs in terms of their stability, and as tools that can be used to derive novel insight about voltage-gated sodium channel pharmacology. Given that voltage-gated sodium channel pharmacology is currently a widely pursued field, bivalent GMTs, known as double-knottins, were designed and produced semi-enzymatically, in order to examine the possibility of bimodal modulation of NaV1.7.Disulfide-rich GMTs were obtained using optimized conditions for thermodynamic and regioselective oxidative folding. Double-knottins were produced via chemoenzymatic ligation using sortase A, a bacterial enzyme. Solution state NMR was used to examine structural integrity of the peptides and previously unsolved three-dimensional NMR structures were also completed. Cell-based biological FLIPRTETRAassays were conducted to analyze the activity of GMTs in the study and these assays were complemented by electrophysiological studies conducted by collaborators. Membrane binding affinity of peptides was studied with model lipid bilayers using surface plasmon resonance and the in-depth location of tryptophan residues into model lipid bilayers was examined using fluorescence spectroscopy methodologies.Through these studies, it was determined that not all native GMTs have affinity for lipid bilayers, but those with affinity bind preferentially to model membranes with anionic charge, primarily via electrostatic interactions. HwTx-IV, a GMT with weak affinity for lipid bilayers was re-engineered to form gHwTx-IV, an analogue with a higher electropositive potential and this peptide showed higher affinity for model membranes combined with a higher potency at NaV1.7 compared to HwTx-IV. Unconventionally, selectivity of gHwTx-IV was improved by modifications to important pharmacophore residues with the rationale that affinity for the lipid bilayer would compensate for potency whereas pharmacophore modifications would improve selectivity. [R26A]gHwTx-IV, [K27A]gHwTx-IV and [R29A]gHwTx-IV had lower affinity for the lipid bilayer compared to gHwTx-IV but higher affinity compared to HwTx-IV. The three analogues were more selective for NaV1.7 compared to off target NaVs, and the lipid bilayer had thus been included in the design of potent, selective modulators of NaV1.7. Stability of GMTs in physiologically relevant conditions was established using stability assays, and the versatility of these peptides as pharmacological tools was shown in their chemoenzymatic conversion to double-knottins that revealed cooperative modulation of NaV1.7, a feature that provides a novel bivalent approach to the modulation of NaVs for the design of therapeutics.

The cerato-platanin family is a group of small cysteine-rich fungal proteins new to science. They usually are abundantly secreted extracellularly and are involved in fungus-host interactions. With the advance of available fungal genome sequences, we performed a genomewide study of the distribution of this family in fungi and analyzed the common characteristics of the protein sequences. A total of 55 fungal genomes, including 27 from Ascomycota and 28 from Basidiomycota, were used. A total of 130 cerato-platanin homolog protein sequences were obtained and analyzed. Our results showed that cerato-platanin homologs existed in both Ascomycota and Basidiomycota but were lost in early branches of jelly fungi as well as in some groups with yeast or yeast-like forms in their life cycle. Homolog numbers varied considerably between Ascomycota and Basidiomycota. Phylogenetic analysis suggested that the ancestor of the Dikarya possessed multiple copies of cerato-platanins, which sorted differently in Ascomycota and Basidiomycota, and that this gene family might have expanded in the Basidiomycota. Almost all homologs contained signal peptide sequences, and the length of mature proteins were mainly 105–134 amino acids. Four cysteines involved in forming two disulfide bridges and signature sequences (CSD or CSN) were highly conserved in most homologs. These results indicated a higher diversity of the cerato-platanin family in Basidiomycota than Ascomycota.

Amphibians are, currently, considered the first vertebrates that had performed the aquatic to terrestrial transition during evolution; therefore, water balance and dehydration control were prerequisites for such environment conquering. Among anurans, Phyllomedusa is a well-studied genus, due to its peptide-rich skin secretion. Here, we have analyzed the skin secretion of Phyllomedusa distincta targeting the proteins present in the skin secretion. The major soluble protein was chromatographically isolated and utilized to immunize rabbits. Through proteomics approaches, we were able to identify such protein as being the diacylglycerol O-acyltransferase 2 (DGAT2), a crucial enzyme involved in lipid synthesis and in the skin water balance. Immunohistochemistry assays revealed the protein tissular distribution for different animal species, belonging to different branches of the phylogenetic tree. Specifically, there was positivity to the anti-DGAT2 on Amphibians' skin, and no antibody recognition on fish and mammals' skins. The DGAT2 multiple sequence alignment reveals some degree of conservation throughout the genera; however, there is a different cysteine pattern among them. Molecular modeling analyses corroborate that the different cysteine pattern leads to distinct 3D structures, explaining the different antibody recognition. Moreover, the protein phylogenetic analyses place the Xenopus DGAT2 (the available amphibian representative) next to the Coelacanthus enzyme, which have led the authors to term this a 'paleo-protein'. DGAT2 would be, therefore, an ancient protein, crucial to the terrestrial environment conquest, with a unique folding-as indicated by the molecular models and immunohistochemistry analyses-a consequence of the different cysteine pattern but with conserved biological function.

BackgroundEvolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar core promoter regions and signal sequence, we adopted an integrated approach utilizing whole genome, transcriptome and proteome database BLAST queries, other bioinformatics tools, and molecular analyses.ResultsOur data, in combination with database analyses showed evidences of expression of these genes both at the mRNA and protein levels exclusively in all developmental stages of S. japonicum. The signal sequence motif was identified in 27 distinct S. japonicum UniGene entries with multiple mRNA transcripts, and in 34 genome contigs distributed within 18 scaffolds with evidence of genome-wide dispersion. No homolog of these genes or similar domain was found in deposited data from any other organism. We observed preponderance of flanking repetitive elements (REs), albeit partial copies, especially of the RTE-like and Perere class at either side of the duplication source locus. The role of REs as major mediators of DNA-level recombination leading to dispersive duplication is discussed with evidence from our analyses. We also identified a stepwise pathway towards functional selection in evolving genes by alternative splicing. Equally, the possible transcription models of some protein-coding representatives of the duplicons are presented with evidence of expression in vitro.ConclusionOur findings contribute to the accumulating evidence of the role of REs in the generation of evolutionary novelties in organisms’ genomes.

Neuroactive peptides derived from venomous species have proven to be used as a lead compound for treating neurological diseases. In the present study, the primary structure of the peptide toxins of snakes, scorpions, spiders, cone snails, honey bees, and sea anemones was recovered from different toxin databases. The 3-D structures of the peptide toxins were analyzed with respect to secondary structural elements such as cysteine patterns and disulfide connectivity’s using PYMOL. Their interaction with ion channels/receptors was studied because of its pharmacological importance. The toxins retrieved were found to have – C–Xn–C–Xn–CC–Xn–C–Xn–C-- cysteine pattern for n≥1 that was the same --C---C---CC---C---C— cysteine pattern of ω-conotoxin and hanatoxin, but with a varying intervening non-cysteine residue between cysteines. Hence, these provide insight for structure-based drug design using these peptide toxin scaffolds. Given the optimal molecular weight and specificity of peptides compared to conventional small molecule drugs, peptides are considered future next-generation drug candidates.

The Platygastroidea are a diverse group of mostly small to tiny wasps, the common biology for which is endoparasitism of insect and spider eggs. No analytically-based phylogeny exists for the superfamily, and the current suprageneric classification is flawed in part because of its reliance on homoplasious and pleisiomorphic morphological characters. To determine platygastroid relationships as a basis for investigating host and ovipositor evolution, phylogenies of > 70 in-group species (representing 55 genera) were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial cytochrome oxidase I and the nuclear genes 28S and 18S rRNA. The results strongly support the monophyly of the superfamily and one of the two families, Platygastridae, but the Scelionidae are most likely polyphyletic. However, within the Scelionidae, there is a well supported ‘main scelionid clade’ that contains the majority of genera assigned to the family. At the subfamilial level, both putative subfamilies of Platygastridae, the Platygastrinae, and Sceliotrachelinae, are likely to be polyphyletic. Within the Scelionidae, both the Teleasinae and Telenominae are monophyletic, but the Scelioninae is clearly not so. The current tribal classification for the Scelionidae is in need of major reassessment because no tribes, with the exception of the Scelionini s.s., were found to be monophyletic. Further illustrating the problems associated with the current classification is the nonmonophyly of a number of genera, namely Opisthacantha Caloteleia, Telenomus, Trimorus, Teleas and Idris. Analysis of ovipositor evolution in the superfamily revealed that the Ceratobaeus-type ovipositor system is ancestral; however, this trait was lost prior to the evolution of the main scelionid clade, for which the Scelio-type ovipositor system is ancestral and defines a mostly paraphyletic assemblage. Ancestral state analysis indicates that the Ceratobaeus-type ovipositor was subsequently re-evolved in the main scelionid clade, representing a possible contradiction of Dollo's law. Previously, the tribal placement has been used to predict the host associations of genera for which host data were unavailable. However, the fact that most tribes are not monophyletic throws into doubt any such speculation based on the current classification.

Spider venom comprises a mixture of compounds with diverse biological activities, which are used to capture prey and defend against predators. The peptide components bind a broad range of cellular targets with high affinity and selectivity, and appear to have remarkable structural diversity. Although spider venoms have been intensively investigated over the past few decades, venomic strategies to date have generally focused on high-abundance peptides. In addition, the lack of complete spider genomes or representative cDNA libraries has presented significant limitations for researchers interested in molecular diversity and understanding the genetic mechanisms of toxin evolution. In the present study, second-generation sequencing technologies, combined with proteomic analysis, were applied to determine the diverse peptide toxins in venom of the Chinese bird spider Ornithoctonus huwena. In total, 626 toxin precursor sequences were retrieved from transcriptomic data. All toxin precursors clustered into 16 gene superfamilies, which included six novel superfamilies and six novel cysteine patterns. A surprisingly high number of hypermutations and fragment insertions/deletions were detected, which accounted for the majority of toxin gene sequences with low-level expression. These mutations contribute to the formation of diverse cysteine patterns and highly variable isoforms. Furthermore, intraspecific venom variability, in combination with variable transcripts and peptide processing, contributes to the hypervariability of toxins in venoms, and associated rapid and adaptive evolution of toxins for prey capture and defense.

Zootoxins are produced by venomous and poisonous species and are an important cause of poisoning in companion animals and livestock in Europe. Little information about the incidence of zootoxin poisoning is available in Europe, with only a few case reports and review papers being published. This review presents the most important zootoxins produced by European venomous and poisonous animal species responsible for poisoning episodes in companion animals and livestock. The main zootoxin-producing animal species, components of the toxins/venoms and their clinical effects are presented. The most common zootoxicoses involve terrestrial zootoxins excreted by the common toad, the fire salamander, the pine processionary caterpillar, and vipers. The lack of a centralized reporting/poison control system in Europe makes the evaluation of the epidemiology of zootoxin-induced poisonings extremely difficult. Even if there are many anecdotal reports in the veterinary community about the exposure of domestic animals to terrestrial and marine zootoxins, the number of published papers regarding these toxicoses is low. Climate change and its consequences regarding species distribution and human-mediated transportation are responsible for the emerging nature of some intoxications in which zootoxins are involved. Although new venomous or poisonous animal species have emerged in regions where they were previously unreported, zootoxins produced by native species remain the main concern in Europe. The diversity of poisonous and venomous animal species and the emerging nature of certain poisonings warrant the continuous update to such knowledge by veterinary professionals and animal owners. This review offers an overview about zootoxin-related poisonings in domestic animals in Europe and also provides important information from a health perspective.

Today, the 'obesity pandemic' is one of the biggest health issues around the world. Melanin-concentrating hormone (MCH), a hypothalamic neuropeptide, is one of the most potent, central stimulators of feeding and it also attenuates energy expenditure. Inhibitions of the MCH receptor, the melanin-concentrating hormone receptor-1 (MCHR1), has attracted considerable attention as a potential anti-obesity drug, during the last decade. Now, there are a large number of MCHR1 antagonists, pharmacological tools and clinical drug candidates that can provide clues to develop new structures with high potency and good pharmacokinetic profile. The function of MCHR1 in energy homeostasis, obesity, metabolic syndrome, mood disorders and inflammatory bowel disease is discussed. Relevant clinical trials and patent background information of the MCHR1 antagonists over the last 4 years are also reviewed.

Isolation and characterization of three novel Gla-containing Conus marmoreus venom peptides, one with a novel cysteine pattern

The corticotropin-releasing factor receptor type 2a (CRF(2(a)) receptor) belongs to the family of G protein-coupled receptors. The receptor possesses a putative N-terminal signal peptide that is believed to be cleaved-off after mediating the endoplasmic reticulum targeting/insertion process, like the corresponding sequence of the homologous CRF(1) receptor. Here, we have assessed the functional significance of the putative signal peptide of the CRF(2(a)) receptor and show that it is surprisingly completely incapable of mediating endoplasmic reticulum targeting, despite meeting all sequence criteria for a functional signal by prediction algorithms. Moreover, it is uncleaved and forms part of the mature receptor protein. Replacement of residue Asn(13) by hydrophobic or positively charged residues converts the sequence into a fully functional and cleaved signal peptide demonstrating that conventional signal peptide functions are inhibited by a single amino acid residue. Deletion of the domain leads to an increase in the amount of immature, intracellularly retained receptors demonstrating that the sequence has adopted a new function in receptor trafficking through the early secretory pathway. Taken together, our results identify a novel hydrophobic receptor domain in the family of the heptahelical G protein-coupled receptors and the first pseudo signal peptide of a eukaryotic membrane protein. Our data also show that the extreme N termini of the individual CRF receptor subtypes differ substantially.

The nicotinic acetylcholine receptors of zebrafish and an evaluation of pharmacological tools used for their study

Multicyclic peptides that are constrained through covalent cross-linkers can usually maintain stable three-dimensional (3D) structures without the necessity of incorporating noncovalently interacting cores. This configuration allows for a greater utilization of residues for functional purposes compared to larger proteins, rendering multicyclic peptides attractive molecular modalities for the development of chemical tools and therapeutic agents. Even smaller multicyclic peptides, which may lack stable 3D structures due to limited sequence-driven folding capabilities, can still benefit from the specific conformations stabilized by covalent cross-linkers to facilitate target binding. Disulfide-rich peptides (DRPs) are a class of particularly significant multicyclic peptides that are primarily composed of disulfide bonds in their interior. However, the structural diversity of DRPs is limited to a few naturally occurring and designer scaffolds, which significantly impedes the development of multicyclic peptide ligands and therapeutics. To address this issue, we developed a novel method that utilizes disulfide-directing motifs to design and discover DRPs with new structures and functions in random sequence space. Compared with traditional DRPs, these new DRPs that incorporate disulfide-directing motifs exhibit more precise oxidative folding regarding disulfide pairing and demonstrate greater tolerance to sequence manipulations. Thus, we designated these peptides as disulfide-directed multicyclic peptides (DDMPs).Over the past decade, we have developed a new class of multicyclic peptides by leveraging disulfide-directing motifs, including biscysteine motifs such as CPXXC, CPPC, and CXC (C: cysteine; P: proline; X: any amino acid), as well as triscysteine motifs that rationally combine two biscysteine motifs (e.g., CPPCXC and CPXXCXC) to direct the oxidative folding of peptides. This leads to the introduction of a novel concept known as motif-directed oxidative folding, which is valuable for the construction of peptides with multiple disulfide bonds. A large diversity of DDMPs have been designed by simply altering the disulfide-directing motifs, the arrangement of cysteine residues (i.e., cysteine patterns), and the number of random residues separating them. As the oxidative folding of DDMPs is primarily determined by disulfide-directing motifs, these peptides are intrinsically more tolerant of extensive sequence manipulations compared to traditional DRPs. Consequently, multicyclic peptide libraries with an unprecedented high degree of sequence randomization have been developed by utilizing commonly used biological display systems such as phage display. We have validated the applicability of these libraries by successfully discovering DDMPs with unique protein-like 3D structures and high affinity and specificity to various cell-surface receptors, including tumor-associated antigens, immune costimulatory receptors, and G protein-coupled receptors (GPCRs). Currently, multicyclic peptides used in clinical settings are of natural origin or derived from natural DRPs. Our studies have opened up the possibility of developing multicyclic peptides without relying on natural scaffolds, representing a pivotal breakthrough in the field of peptide ligand and drug discovery. Further investigations will facilitate the application of our DDMPs in broader fields such as bioanalysis, chemical biology, and biomedicine.