Prohormonal cleavage sites are associated with omega loops

Secretory peptides are generated from larger precursor proteins, or prohormones, by proteolytic cleavage at sites consisting of one or more basic amino acids. We have investigated the association of these cleavage sites with the various classes of secondary structure in the prohormones. In particular, we determined the association of cleavage sites with the newly defined category of omega loops. We developed an algorithm for predicting the occurrence of such loops from the primary structure of the precursor and validated this procedure by comparison to crystallographic data. When this method was applied to prohormones, we found that about one-third of the cleavage sites previously assigned to reverse turns were actually associated with omega loops. Moreover, sites that delimit secreted peptides are most often associated with loops and are concentrated in the neck regions of the loops. These data are interpreted in terms of a model in which the processing endoprotease interacts with two sites on the prohormone: a recognition site in the middle of a loop and the cleavage site at its neck.     

Purification and characterization of a paired basic residue-specific prohormone-converting enzyme from bovine pituitary neural lobe secretory vesicles

The neuropeptides arginine vasopressin and oxytocin are generated from their prohormones in the hypothalamoneurohypophysial system by enzymatic cleavages at paired basic residues (i.e. Lys-Arg). This study describes the purification of an enzyme from bovine neural lobe secretory vesicles, the putative site of this processing, which is capable of cleaving several prohormones at paired basic residues. The enzyme is a glycoprotein of Mr approximately 70,000 and has an acidic pH maximum. It processes the heterologous precursors pro-opiomelanocortin and insulin at paired basic residues in a manner similar to a pro-opiomelanocortin-converting enzyme derived from bovine intermediate lobe secretory vesicles which has been described previously. In addition, the neural lobe-derived converting enzyme cleaves the human vasopressin prohormone in vitro to yield arginine vasopressin-Gly10-Lys11-Arg12 as the major vasopressin cleavage product. This indicates that the enzymatic cleavage in the vasopressin precursor occurred primarily on the carboxyl side of the arginine in the pair of Lys-Arg basic residues separating the vasopressin peptide from the neurophysin moiety in the precursor. The properties of the neural and intermediate lobe-derived enzymes are virtually identical, raising the possibility that a family of similar enzymes may be responsible for cleaving a number of prohormones at paired basic residues in different tissues.     

Characterization of endothelin-converting enzyme-2. Implication for a role in the nonclassical processing of regulatory peptides

Most neuroendocrine peptides are generated by proteolysis of the precursors at basic residue cleavage sites. Prohormone convertases belonging to the subtilisin family of serine proteases are primarily responsible for processing at these "classical sites." In addition to the classical cleavages, a subset of bioactive peptides is generated by processing at "nonclassical" sites. The proteases responsible for these cleavages have not been well explored. Members of several metalloprotease families have been proposed to be involved in nonclassical processing. Among them, endothelin-converting enzyme-2 (ECE-2) is a good candidate because it exhibits a neuroendocrine distribution and an acidic pH optimum. To examine the involvement of this protease in neuropeptide processing, we purified the recombinant enzyme and characterized its catalytic activity. Purified ECE-2 efficiently processes big endothelin-1 to endothelin-1 by cleavage between Trp(21) and Val(22) at acidic pH. To characterize the substrate specificity of ECE-2, we used mass spectrometry with a panel of 42 peptides as substrates to identify the products. Only 10 of these 42 peptides were processed by ECE-2. A comparison of residues around the cleavage site revealed that ECE-2 exhibits a unique cleavage site selectivity that is related to but distinct from that of ECE-1. ECE-2 tolerates a wide range of amino acids in the P1-position and prefers aliphatic/aromatic residues in the P1'-position. However, only a small fraction of the aliphatic/aromatic amino acid-containing sites were cleaved, indicating that there are additional constraints beyond the P1- and P1'-positions. The enzyme is able to generate a number of biologically active peptides from peptide intermediates, suggesting an important role for this enzyme in the biosynthesis of regulatory peptides. Also, ECE-2 processes proenkephalin-derived bovine adrenal medulla peptides, and this processing leads to peptide products known to have differential receptor selectivity. Finally, ECE-2 processes PEN-LEN, an endogenous inhibitor of prohormone convertase 1, into products that do not inhibit the enzyme. Taken together, these results are consistent with an important role for ECE-2 in the processing of regulatory peptides at nonclassical sites.     

A novel prohormone processing site in Aplysia californica: the Leu-Leu rule

Neuropeptides are a complex set of signaling molecules produced through enzymatic cleavages from longer prohormone sequences. The most common cleavage sites in prohormones are basic amino acid residues; however, processing is observed at non-basic sites. Cleavage at Leu-Leu sequences has been observed in three Aplysia californica prohormones. To further investigate this unusual event, native and non-native synthetic peptides containing Leu-Leu residues are incubated with homogenates of Aplysia californica ganglia and the resulting products monitored with MALDI MS. Cleavage near and between Leu-Leu residues is observed in the abdominal and buccal ganglia homogenates, confirming the presence of an unidentified peptidase. In addition, fractions from an HPLC separation of buccal ganglia homogenates also produce cleavages at Leu-Leu residues. Products resulting from cleavage at Leu-Leu sites are observed and are produced in larger amounts in acidic and neutral pH ranges, and cleavage is inhibited by the addition of EDTA, suggesting a metal is required for activity.     

Biosynthesis and posttranslational processing of site-directed endoproteolytic cleavage mutants of pro-neuropeptide Y in mouse pituitary cells

Although pairs of basic amino acids are common endoproteolytic sites in prohormones, the enzymes responsible for these cleavages have not yet been characterized. To investigate the specificity of these endoproteases, cDNAs encoding pro-neuropeptide Y (pro-NPY) containing all four pairs of basic amino acids were expressed in AtT-20 cells. Pro-NPY was selected as a model substrate because it undergoes a single cleavage at the sequence -Lys-Arg- during posttranslational processing. AtT-20 cells, a mouse anterior pituitary corticotrope line, were selected because they synthesize pro-adrenocorticotropic hormone (pro-ACTH)/endorphin and cleave a well characterized subset of the eight pairs of basic amino acids in the precursor. Altered cDNAs encoding pro-NPY with -Arg-Arg-, -Arg-Lys-, or Lys-Lys- at the cleavage site were used to generate stable cell lines. The production of NPY and the carboxyl-terminal peptide was studied using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gel filtration, reversed-phase high performance liquid chromatography, ion-exchange high performance liquid chromatography, tryptic peptide mapping, and microsequencing. Direct amino acid labeling confirmed the identity of the pair of basic amino acids at the cleavage site. Even when the four pairs of basic amino acids were presented in the same structural context, the rate, extent, and type of cleavage was substrate-specific. Pro-NPY(-Arg-Arg-) was cleaved at a rate similar to that observed for the wild-type pro-NPY(-Lys-Arg-). In contrast, pro-NPY(-Arg-Lys-) was cleaved at a much lower rate, and pro-NPY (-Lys-Lys-) was cleaved very poorly. Following endoproteolytic cleavage, the pair of basic amino acids present did not alter the production of mature NPY with a COOH-terminal Tyr-NH2. While two of the three mutant pro-NPY molecules were processed to wild-type carboxyl-terminal peptide, the carboxyl-terminal peptide derived from pro-NPY(-Arg-Lys-) contained an amino-terminal lysine residue, indicating that biosynthetic endoproteolysis occurred in the middle or at the amino terminus of the pair of basic amino acid residues at the cleavage site. Expression of wild-type or mutant pro-NPY inhibited cleavages within the endogenous pro-ACTH/endorphin; poorly cleaved pro-NPY mutants (Lys in the second position of the cleavage site) were the most potent inhibitors of pro-ACTH/endorphin cleavage.     

Consensus sequence for processing of peptide precursors at monobasic sites

Many regulatory peptide precursors undergo post-translational processing at mono- and/or dibasic residues. Comparison of amino acids around the monobasic cleavage sites suggests that these cleavages follow certain sequence motifs and can be described as the rules that govern monobasic cleavages: (i) a basic amino acid it present at either 3, 5, or 7 amino acids N-terminal to the cleavage site, (ii) hydrophobic aliphatic amino acids (leucine, isoleucine, valine, or methionine) are never present in the position C-terminal to the monobasic amino acid at the cleavage site, (iii) a cysteine is never present in the vicinity of the cleavage site, and (iv) an aromatic amino acid is never present at the position N-terminal to the monobasic amino acid at the cleavage site. In addition to these rules, the monobasic cleavages follow certain tendencies: (i) the amino acid at the cleavage site tends to be predominantly arginine, (ii) the amino acid at the position C-terminal to the cleavage site tends to be serine, alanine or glycine in more than 60% of the cases, (iii) the amino acid at either 3, 5, or 7 position N-terminal to the cleavage site tends to be arginine, (iv) aromatic amino acids are rare at the position C-terminal to the monobasic amino acid at the cleavage site, and (v) aliphatic amino acids tend to be in the two positions N-terminal to and the two positions C-terminal to the cleavage site, except as noted above. When compared with a large number of sequence containing single basic amino acids, these rules and tendencies are capable of not only correctly predicting the processing sites, but also are capable of excluding most of the single basic sequences that are known to be uncleaved. Many or these rules can also be applied to correctly predict the dibasic and multibasic cleavage sites suggesting that the rules and tendencies could govern endoproteolytic processing at the monobasic, dibasic and multibasic sites.     

Cloning and characterization of Xen-dorphin prohormone from Xenopus laevis: a new opioid-like prohormone distinct from proenkephalin and prodynorphin

Opioid-like peptides mediate analgesia and induce behavioral effects such as tolerance and dependence by ligand-receptor-mediated mechanisms. The classical opioid prohormones can generate several bioactive peptides, and these divergent families of prohormones share a common well conserved ancestral opioid motif (Tyr-Gly-Gly-Phe). Evidence from pharmacological and molecular cloning studies indicates the presence of multiple isoforms of opioid ligands and receptors that are as yet uncharacterized. To identify potential new members we used the opioid motif as an anchor sequence and isolated two distinct isoforms (Xen-dorphins A and B) of an opioid prohormone from Xenopus laevis brain cDNA library. Xen-dorphin prohormones can generate multiple novel opioid ligands distinct from the known members of this family. Both isoforms are present in a wide variety of tissues including the brain. Two potential bioactive peptides, Xen-dorphin-1A and -1B, that were chemically synthesized showed opioid agonist activity in frog and rat brain membranes using a [35S]GTPgammaS assay. Initial radioligand binding experiments demonstrated that Xen-dorphin-1B binds with high affinity to opioid receptor(s) and with potential preference to the kappa-opioid receptor subtype. Cloning of the Xen-dorphin prohormone provides new evidence for the potential presence of other members in the opioid peptide superfamily.     

Evidence that differentiates between precursor cleavages at dibasic and Arg-X-Lys/Arg-Arg sites.

It is well known that precursor cleavage at paired basic amino acids (e.g., Lys-Arg, Arg-Arg) within the regulated secretory pathway is one of the key steps to produce bioactive peptides. On the other hand, we have recently shown that precursors with an Arg residue at the fourth residue upstream of the cleavage site besides the basic pair, i.e. with the Arg-X-Lys/Arg-Arg (RXK/RR) motif, are cleaved within the constitutive secretory pathway. To discriminate between the precursor cleavage at RXK/RR sites within the constitutive pathway and that at dibasic sites within the regulated pathway, we examined the effects of drugs affecting the secretory process, intracellular Ca2+ depletion, and a protease inhibitor on these cleavages. Chloroquine (a weak base), depletion of intracellular Ca2+ by A23187 (a Ca2+ ionophore), and the Pittsburgh-type mutant of alpha 1-protease inhibitor differentially affected these two cleavages. Brefeldin A, which impedes protein transport from the endoplasmic reticulum to the Golgi complex, inhibited both cleavages. Colchicine (an anti-microtubular drug) had no discernible effect on either cleavage. These observations support the notion that the precursor cleavages at dibasic and RXK/RR sites occur in different subcellular compartments, and are catalyzed by different processing endoproteases.     

The construction of a bioactive peptide database in Metazoa

Bioactive peptides play critical roles in regulating most biological processes in animals, and have considerable biological, medical and industrial importance. A number of peptides have been discovered usually based on their biological activities in vitro or based on their sequence similarities in silico. Through searches in Swiss-Prot and Trembl protein databases using BLAST alignment tools and other in silico methods, all currently known bioactive peptides and their precursor proteins are extracted. In addition, 132 recently discovered putative peptide genes in Drosophila as well as their orthologs in other species are collected. In total, 20 027 bioactive peptides from 19 438 precursor proteins covering 2820 metazoan species are retained, and they, respectively, make up a peptide and a peptide precursor database. The peptides and peptide precursor proteins are further classified into 373 families, 178 of which are represented by Prosite Pfam or Smart motifs, or by typical peptide motifs that have been constructed recently. The remaining 195 families are novel peptide families. The motifs characterizing the 178 peptide families are saved into a peptide motif database. The peptide, peptide precursor and peptide motif databases (version 1.0) are the most complete peptide, precursor and peptide motif collection in Metazoa so far. They are available on the WWW at http://www.peptides.be/.     

Bridging neuropeptidomics and genomics with bioinformatics: Prediction of mammalian neuropeptide prohormone processing

Neuropeptides are an important class of cell to cell signaling molecules that are difficult to predict from genetic information because of their large number of post-translational modifications. The transition from prohormone genetic sequence information to the determination of the biologically active neuropeptides requires the identification of the cleaved basic sites, among the many possible cleavage sites, that exist in the prohormone. We report a binary logistic regression model trained on mammalian prohormones that is more sensitive than existing methods in predicting these processing sites, and demonstrate the application of this method to mammalian neuropeptidomic studies. By comparing the predictive abilities of a binary logistic model trained on molluscan prohormone cleavages with the reported model, we establish the need for phyla-specific models.     

A molecular dynamics strategy for CSαβ peptides disulfide-assisted model refinement

Many cysteine-stabilized antimicrobial peptides from a variety of living organisms could be good candidates for the development of anti-infective agents. In the absence of experimentally obtained structural data, peptide modeling is an essential tool for understanding structure–activity relationships and for optimizing the bioactive moieties. Focusing on cysteine-rich peptide structures, we reproduced the case of structure predictions in the so-called midnight zone. We developed our protocol on a training set derived by clustering the available cysteine-stabilized αβ (CSαβ) structures in nine different representative families and tested it on peptides randomly selected from each family. Starting from draft models, we tested a structure-based disulfide predictor and we used cysteine distances as constraints during molecular dynamics. Finally, we proposed an analysis for final structure selection. Accordingly, we obtained a mean root mean square deviation improvement of 21% for the test set. Our findings demonstrate that it is possible to predict the network of disulfide bridges in cysteine-stabilized peptides and to use this result to improve the accuracy of structural predictions. Finally, we applied the methods to predict the structure of royalisin, a cysteine-rich peptide with unknown structure.     

生物活性肽自动查询预测系统

论述了运用生物信息学方法和计算机技术,快速从由蛋白酶模拟酶解蛋白质而产生的大量未知生物活性的系列肽中,预测有生物活性的肽,以实现生物活性肽功能的预测。主要建立了生物活性肽数据库,应用已有生物活性肽作为序列比对的标准,实行大量未知生物活性的系列肽自动无人值守的和已知生物活性的肽序列比对查询,以发现新物种中包括动物和植物的具有新的生物活性的功能肽。应用该软件系统AQS成功地预测并发现了造血细胞增殖肽、成骨细胞生长肽以及高血压押制肽。     

Using string kernel to predict signal peptide cleavage site based on subsite coupling model

Summary. Owing to the importance of signal peptides for studying the molecular mechanisms of genetic diseases, reprogramming cells for gene therapy, and finding new drugs for healing a specific defect, it is in great demand to develop a fast and accurate method to identify the signal peptides. Introduction of the so-called {−3,−1, +1} coupling model (Chou, K. C.: Protein Engineering, 2001, 14–2, 75–79) has made it possible to take into account the coupling effect among some key subsites and hence can significantly enhance the prediction quality of peptide cleavage site. Based on the subsite coupling model, a kind of string kernels for protein sequence is introduced. Integrating the biologically relevant prior knowledge, the constructed string kernels can thus be used by any kernel-based method. A Support vector machines (SVM) is thus built to predict the cleavage site of signal peptides from the protein sequences. The current approach is compared with the classical weight matrix method. At small false positive ratios, our method outperforms the classical weight matrix method, indicating the current approach may at least serve as a powerful complemental tool to other existing methods for predicting the signal peptide cleavage site. The software that generated the results reported in this paper is available upon requirement, and will appear at http://www.pami.sjtu.edu.cn/wm. An erratum to this article is available at .     

An in vivo characterization of the cleavage site specificity of the insulin cell prohormone processing enzymes

Most peptide hormones and neurotransmitters are synthesized as larger precursor proteins, which are post-translationally processed to mature bioactive products. An early event in prohormone maturation is endoproteolytic cleavage, occurring usually at pairs of basic amino acids (e.g. Lys-Arg). Since many of the characteristics of a prohormone endoprotease are unknown, distinguishing these enzymes from other cellular proteases in vitro has been difficult. In this report, the substrate specificity of a model prohormone processing system, the insulinoma cell line Rin m5F, was characterized in vivo to establish a set of criteria by which putative proinsulin endoproteases may be assessed. To determine the role of composition of the paired basic amino acid site in directing cleavage, a series of mutant prohormones containing altered cleavage sites was constructed and expressed in Rin m5F cells. Proopiomelanocortin (POMC) was used as a substrate since this prohormone was previously shown to be processed by these cells. To control for positional effects, all four permutations of lysine and arginine (Lys-Arg, Arg-Arg, Arg-Lys, and Lys-Lys) were introduced at both the efficiently processed cleavage site separating the ACTH and beta-lipotropin (beta-LPH) domains of POMC and at the inefficiently processed site in the beta-endorphin sequence near the COOH-terminus of the precursor. His-Arg and Met-Arg sites were also introduced at the ACTH/beta-LPH junction to assess the requirement for paired lysines and arginines. Identification of POMC-derived peptides demonstrated efficient processing of Lys-Arg and inefficient processing of Lys-Lys and Arg-Lys sites at both positions in the prohormone. The Arg-Arg sequence, however, was processed in a position-dependent manner, being efficiently cleaved between ACTH and beta-LPH but only about 50% processed within beta-endorphin. His-Arg was not cleaved in Rin m5F cells, although surprisingly Met-Arg was partially processed. These results indicate a strict preference of the insulinoma prohormone endoprotease(s) for paired basic amino acids ending in arginine, but that processing efficiency of some sequences may be modulated by location within the precursor molecule.     

PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides

Among secondary structure elements, beta-turns are ubiquitous and major feature of bioactive peptides. We analyzed 77 biologically active peptides with length varying from 9 to 20 residues. Out of 77 peptides, 58 peptides were found to contain at least one beta-turn. Further, at the residue level, 34.9% of total peptide residues were found to be in beta-turns, higher than the number of helical (32.3%) and beta-sheet residues (6.9%). So, we utilized the predicted beta-turns information to develop an improved method for predicting the three-dimensional (3D) structure of small peptides. In principle, we built four different structural models for each peptide. The first 'model I' was built by assigning all the peptide residues an extended conformation (phi = Psi = 180 degrees ). Second 'model II' was built using the information of regular secondary structures (helices, beta-strands and coil) predicted from PSIPRED. In third 'model III', secondary structure information including beta-turn types predicted from BetaTurns method was used. The fourth 'model IV' had main-chain phi, Psi angles of model III and side chain angles assigned using standard Dunbrack backbone dependent rotamer library. These models were further refined using AMBER package and the resultant C(alpha) rmsd values were calculated. It was found that adding the beta-turns to the regular secondary structures greatly reduces the rmsd values both before and after the energy minimization. Hence, the results indicate that regular and irregular secondary structures, particularly beta-turns information can provide valuable and vital information in the tertiary structure prediction of small bioactive peptides. Based on the above study, a web server PEPstr (http://www.imtech.res.in/raghava/pepstr/) was developed for predicting the tertiary structure of small bioactive peptides.     

Neuropeptide precursors in Tribolium castaneum

Neuropeptides and neurohormones are among the more diverse and functionally important classes of cell-to-cell signaling molecules involved in animal development and behavior. Less is known about the hormones and neuropeptides of the red flour beetle, Tribolium castaneum, than many other insects. However, the genomic information becoming available from this organism presents an opportunity to identify multiple neuropeptide and hormone genes, and hence their associated protein precursors. Using similarity-based prediction, we report new neuropeptides and hormone precursors from T. castaneum, bringing the number of annotated precursors to 37. We identified one prohormone (SVDPIDGDLIG-containing) having little similarity to other insect prohormones. The conversion of the protein precursors into bioactive peptides requires a suite of processing enzymes and a number of enzymatic steps; using the web-based NeuroPred application and similarity-based bioinformatics approaches, we predict 132 likely peptides that may result from the enzymatic processing of these gene products.     

From precursor to final peptides: a statistical sequence-based approach to predicting prohormone processing

Predicting the final neuropeptide products from neuropeptides genes has been problematic because of the large number of enzymes responsible for their processing. The basic processing of 22 Aplysia californica prohormones representing 750 cleavage sites have been analyzed and statistically modeled using binary logistic regression analyses. Two models are presented that predict cleavage probabilities at basic residues based on prohormone sequence. The complex model has a correct classification rate of 97%, a sensitivity of 97%, and a specificity of 96% when tested on the Aplysia dataset.     

The processing of peptide precursors. 'Proline-directed arginyl cleavage' and other monobasic processing mechanisms

The classical conversion site in precursors of regulatory peptides is a sequence of two basic amino acids. During recent years, however, a group of monobasic cleavage sites has emerged. In certain cell systems it has been shown that the monobasic cleavage mechanism is both a specific mechanism which only attacks a particular basic residue, and a distinct mechanism which can be separated from the dibasic cleaving mechanism within the same cell. The vast majority of monobasic cleavages occur at single arginines although cleavage after a lysine residue has also been demonstrated. There is no 'consensus sequence' of amino acids surrounding the single basic residue which is the apparent signal for proteolytic processing. However, in approximately one third of the cases, a proline residue is found either just before or just after the basic residue. On the basis of this 'proline-directed arginyl cleavage' it is discussed how the conformation of the peptide backbone might be important for this type of cleavage. Finally, it is suggested that tissue-specific expression of different processing enzymes, e.g. dibasic and monobasic specific forms, might explain the tissue-specific processing of precursors like the pro-opiomelanocortin and the CKK and somatostatin precursor.     

Cleavage of synthetic peptides by purified poliovirus 3C proteinase

Synthetic peptides, 14-16 residues in length, were used as substrates for purified recombinant poliovirus proteinase 3C. The sequences of the substrates correspond to the sequences of authentic cleavage sites in the poliovirus polyprotein, all of which contain Gln-Gly at the scissile bond. Specificity of cleavages was demonstrated by analysis of 3C digests of synthetic peptides. Relative rate constants for the cleavages were derived by competition experiments. The rate constants roughly correlated with the estimated half-life of the homologous precursor proteins detected in poliovirus-infected cells. The peptide most resistant to cleavage corresponded to the 3C/3D junction, a site known to be cleaved very slowly by 3C in vivo. Substitution of threonine for alanine in P4 position of this peptide, however, resulted in significant cleavage. This observation supports the hypothesis that the residue in P4 position, in addition to the Gln-Gly in P1 and P1', respectively, contributes to substrate recognition. Ac-Gln-Gly-NH2 was not a substrate for 3C.