Primary structure of yeast cytochrome c peroxidase. II. The complete amino acid sequence

The complete amino acid sequence of 293 residues in the single polypeptide chain of yeast cytochrome c peroxidase has been determined. Sequence analyses were performed on fragments obtained by cleavage with cyanogen bromide and by tryptic digestion of citraconylated protein. These fragments were aligned with sequential and compositional data as well as those obtained with intact protein, tryptic, and chymotryptic peptides (Takio and Yonetani, 1980, Arch. Biochem. Biophys.203, 605–614). Residues critical for catalysis by the enzyme were identified as arginine 48, tryptophan 51, histidine 52, and histidine 174 by fitting the sequence to the electron density map derived by others. Sequence comparison with other proteins show limited homology with horseradish peroxidase and myoglobin.     

Post-secretory events alter the peptide content of the skin secretion of Hypsiboas raniceps

A novel family of antimicrobial peptides, named raniseptins, has been characterized from the skin secretion of the anuran Hypsiboas raniceps. Nine cDNA molecules have been successfully cloned, sequenced, and their respective polypeptides were characterized by mass spectrometry and Edman degradation. The encoded precursors share structural similarities with the dermaseptin prepropeptides from the Phyllomedusinae subfamily and the mature 28-29 residue long peptides undergo further proteolytic cleavage in the crude secretion yielding consistent fragments of 14-15 residues. The biological assays performed demonstrated that the Rsp-1 peptide has antimicrobial activity against different bacterial strains without significant lytic effect against human erythrocytes, whereas the peptide fragments generated by endoproteolysis show limited antibiotic potency. MALDI imaging mass spectrometry in situ studies have demonstrated that the mature raniseptin peptides are in fact secreted as intact molecules within a defined glandular domain of the dorsal skin, challenging the physiological role of the observed raniseptin fragments, identified only as part of the crude secretion. In this sense, stored and secreted antimicrobial peptides may confer distinct protective roles to the frog.     

Proteomics as a Quality Control Tool of Pharmaceutical Probiotic Bacterial Lysate Products

Probiotic bacteria have a wide range of applications in veterinary and human therapeutics. Inactivated probiotics are complex samples and quality control (QC) should measure as many molecular features as possible. Capillary electrophoresis coupled to mass spectrometry (CE/MS) has been used as a multidimensional and high throughput method for the identification and validation of biomarkers of disease in complex biological samples such as biofluids. In this study we evaluate the suitability of CE/MS to measure the consistency of different lots of the probiotic formulation Pro-Symbioflor which is a bacterial lysate of heat-inactivated Escherichia coli and Enterococcus faecalis. Over 5000 peptides were detected by CE/MS in 5 different lots of the bacterial lysate and in a sample of culture medium. 71 to 75% of the total peptide content was identical in all lots. This percentage increased to 87–89% when allowing the absence of a peptide in one of the 5 samples. These results, based on over 2000 peptides, suggest high similarity of the 5 different lots. Sequence analysis identified peptides of both E. coli and E. faecalis and peptides originating from the culture medium, thus confirming the presence of the strains in the formulation. Ontology analysis suggested that the majority of the peptides identified for E. coli originated from the cell membrane or the fimbrium, while peptides identified for E. faecalis were enriched for peptides originating from the cytoplasm. The bacterial lysate peptides as a whole are recognised as highly conserved molecular patterns by the innate immune system as microbe associated molecular pattern (MAMP). Sequence analysis also identified the presence of soybean, yeast and casein protein fragments that are part of the formulation of the culture medium. In conclusion CE/MS seems an appropriate QC tool to analyze complex biological products such as inactivated probiotic formulations and allows determining the similarity between lots.     

The search for and identification of peptides from the moss Physcomitrella patens

The isolation and identification of peptides from the moss Physcomitrella patens (Hedw.) B.S.G., which has been widely used in recent years as a model for studying plant biology, has been described. It was shown for the first time that protoplasts, the protonemata, and gametophores of Ph. patens contain a variety of peptides. From gametophores, 58 peptides, which are the fragments of 14 proteins, and from the protonemata, 49 peptides, the fragments of 15 proteins, were isolated and identified. It was found that the protonemata and gametophores of Ph. patens, which are the successive stages of the development of this plant, significantly differ from each other in both the peptide composition and the spectrum of precursor proteins of the identified peptides. The isolation of protoplasts during the enzymatic destruction of the protonema cell wall is accompanied by massive degradation of intracellular proteins, many of which are the proteins of the protosynthetic system, which is a characteristic response of higher plants to environmental stress factors. In all, 323 peptides, which are the fragments of 79 proteins, were isolated and identified from moss protoplasts.     

Assignment of the three disulfide Bridges of huwentoxin-I,a neurotoxin from the spiderSelenocosmia huwena

The positions of the disulfide bonds of huwentoxin-I, a neurotoxin from the spiderSelenocosmia huwena, have been determined. The existence of three disulfide bonds in the native toxin was demonstrated by mass spectroscopy and the lack of reactivity with a thiol reagent. The assignment procedure involved a combination of tryptic digestion of the native toxin and sequence analysis of both intact andin situ S-carboxymethylated toxin.In situ carboxymethylation is shown to be a useful procedure in sequencing of cysteine- and cystine-containing peptides. Sequence analysis of the intact, cross-linked toxin indicated that no amino acid phenylthiohydantoin (PTH) derivative is seen for the first half-cystine in a cross-linked pair, but that the PTH of dehydroalanine, which can be detected at 313 nm, is seen at the position of the second half-cystine. By sequencing disulfide cross-linked tryptic fragments, the three disulfide linkages in huwentoxin-I could be assigned as Cys₂-Cys₁₇, Cys₉-Cys₂₂, and Cys₁₆-Cys₂₉.     

Mass Spectral Analysis of Synthetic Peptides: Implications in Proteomics

Sequence determination of peptides is a crucial step in mass spectrometry–based proteomics. Peptide sequences are determined either by database search or by de novo sequencing using tandem mass spectrometry. Determination of all the theoretical expected peptide fragments and eliminating false discoveries remains a challenge in proteomics. Developing standards for evaluating the performance of mass spectrometers and algorithms used for identification of proteins is important for proteomics studies. The current study is focused on these aspects by using synthetic peptides. A total of 599 peptides were designed from in silico tryptic digest with 1 or 2 missed cleavages from 199 human proteins, and synthetic peptides corresponding to these sequences were obtained. The peptides were mixed together, and analysis was carried out using liquid chromatography–electrospray ionization tandem mass spectrometry on a Q-Exactive HF mass spectrometer. The peptides and proteins were identified with SEQUEST program. The analysis was carried out using the proteomics workflows. A total of 573 peptides representing 196 proteins could be identified, and a spectral library was created for these peptides. Analysis parameters such as “no enzyme selection” gave the maximum number of detected peptides as compared with trypsin in the selection. False discoveries could be identified. This study highlights the limitations of peptide detection and the need for developing powerful algorithms along with tools to evaluate mass spectrometers and algorithms. It also shows the limitations of peptide detection even with high-end mass spectrometers. The mass spectral data are available in ProteomeXchange with accession no. PXD017992.     

Fructose 1,6-diphosphate aldolase of Drosophila melanogaster: comparative sequence analyses of the cysteine-containing peptides.

Following tryptic digestion four cysteine-containing peptides per monomer have been isolated from fructose 1,6-diphosphate aldolase of Drosophila melanogaster. Sequence analyses of the peptides showed that three of the four cysteinyl residues appear to occur in homologous positions to three of the eight cysteines of rabbit muscle aldolase. Moreover they seem to be homologous also to three of the six sulfhydryl groups in sturgeon aldolase. The fourth cysteine-containing peptide of Drosophila aldolase has no homologous SH peptide either in the rabbit or in the sturgeon enzyme, but corresponds to another tryptic peptide in the rabbit aldolase. As deduced from homology all four SH peptides are localized in the buried region of the molecule. This conclusion is confirmed by the fact that all four cysteine-containing peptides have been isolated from the central cyanogen bromide fragment. Drosophila aldolase has no exposed thiol groups, thus demonstrating that these residues are not essential either in catalytic activity or for the stabilization of the three-dimensional structure.     

Peptidomic analysis of skin secretions demonstrates that the allopatric populations of Xenopus muelleri (Pipidae) are not conspecific

Mueller's clawed frog Xenopus muelleri (Peters 1844) occupies two non-contiguous ranges in east and west Africa. The phylogenetic relationship between the two populations is unclear and it has been proposed that the western population represents a separate species. Peptidomic analysis of norepinephrine-stimulated skin secretions from X. muelleri from the eastern range resulted in the identification of five antimicrobial peptides structurally related to the magainins (magainin-M1 and -M2), xenopsin-precursor fragments (XPF-M1) and caerulein-precursor fragments (CPF-M1 and -M2) previously found in skin secretions of other Xenopus species. A cyclic peptide (WCPPMIPLCSRF.NH₂) containing the RFamide motif was also isolated that shows limited structural similarity to the tigerinins, previously identified only in frogs of the Dicroglossidae family. The components identified in skin secretions from X. muelleri from the western range comprised one magainin (magainin-MW1), one XPF peptide (XPF-MW1), two peptides glycine-leucine amide (PGLa-MW1 and -MW2), and three CPF peptides (CPF-MW1, -MW2 and -MW3). Comparison of the primary structures of these peptides suggest that western population of X. muelleri is more closely related to X. borealis than to X. muelleri consistent with its proposed designation as a separate species. The CPF peptides showed potent, broad-spectrum activity against reference strains of bacteria (MIC 3-25 μM), but were hemolytic against human erythrocytes.     

Influence of apoproteins for enediyne production

Kedarcidin and neocarzinostatin belong to the chromoprotein family of endiyene antibiotics and have potent antitumor activity. Their structures consist of an apoprotein and a nonpeptide chromophore. Apoprotein has been known to be essential to stabilize and regulate the availability of a labile chromophore. Here, we have identified the complete kedarcidin apoprotein gene (kedA) from Streptoalloteichus sp. ATCC 53650 (Actinomycete L585-6). KedA was characterized by a comparative study with neocarzinostatin apoprotein (NcsA). Overexpression of kedA resulted in a ～ 2-fold enhanced production of kedarcidin in Streptoalloteichus sp., whereas overexpression of ncsA resulted in a ～ 1.6-fold enhanced production of neocarzinostatin in Streptomyces carzinostaticus ATCC 15944. Moreover, the apoprotein-overexpressed strain showed a high growth rate, which demonstrates that the apoprotein not only protects the labile chromophore, but also tolerates the toxicity of endiyene antibiotics in the host strain.     

Identification of a Conserved B-Cell Epitope on Duck Hepatitis A Type 1 Virus VP1 Protein

BackgroundThe VP1 protein of duck hepatitis A virus (DHAV) is a major structural protein that induces neutralizing antibodies in ducks; however, B-cell epitopes on the VP1 protein of duck hepatitis A genotype 1 virus (DHAV-1) have not been characterized.

Methods and Results

To characterize B-cell epitopes on VP1, we used the monoclonal antibody (mAb) 2D10 against Escherichia coli-expressed VP1 of DHAV-1. In vitro, mAb 2D10 neutralized DHAV-1 virus. By using an array of overlapping 12-mer peptides, we found that mAb 2D10 recognized phages displaying peptides with the consensus motif LPAPTS. Sequence alignment showed that the epitope ¹⁷³LPAPTS¹⁷⁸ is highly conserved among the DHAV-1 genotypes. Moreover, the six amino acid peptide LPAPTS was proven to be the minimal unit of the epitope with maximal binding activity to mAb 2D10. DHAV-1–positive duck serum reacted with the epitope in dot blotting assay, revealing the importance of the six amino acids of the epitope for antibody-epitope binding. Competitive inhibition assays of mAb 2D10 binding to synthetic LPAPTS peptides and truncated VP1 protein fragments, detected by Western blotting, also verify that LPAPTS was the VP1 epitope.

Conclusions and Significance

We identified LPAPTS as a VP1-specific linear B-cell epitope recognized by the neutralizing mAb 2D10. Our findings have potential applications in the development of diagnostic techniques and epitope-based marker vaccines against DHAV-1.     

Rule of antibody structure: the primary structure of a human monoclonal IgA1-immunoglobulin (myeloma protein Tro), III. Isolation and characterization of the tryptic peptides of the H-chain (author's transl)]

The reduced and either aminothylated or carboxymethylated H-chain of the monoclonal IgA1 immunoglobulin Tro was digested with trypsin. The tryptic peptides were isolated by gel and ion-exchange chromatography. Because of different methods of alkylation, the cysteine-containing peptides could be obtained in two forms and showed additional overlaps. Sequence studies performed with these fragments elucidated the primary structure of the protein.     

Biophysical studies of the membrane location of the voltage-gated sensors in the HsapBK and KvAP K channels

The membrane location of two fragments in two different K⁺-channels, the KvAP (from Aeropyrum pernix) and the HsapBK (human) corresponding to the putative “paddle” domains, has been investigated by CD, fluorescence and NMR spectroscopy. Both domains interact with q = 0.5 phospholipid bicelles, DHPC micelles and with POPC vesicles. CD spectra demonstrate that both peptides become largely helical in the presence of phospholipid bicelles. Fluorescence quenching studies using soluble acrylamide or lipid-attached doxyl-groups show that the arginine-rich domains are located within the bilayered region in phospholipid bicelles. Nuclear magnetic relaxation parameters, T₁ and ¹³C-¹H NOE, for DMPC in DMPC/DHPC bicelles and for DHPC in micelles showed that the lipid acyl chains in the bicelles become less flexible in the presence of either of the fragments. An even more pronounced effect is seen on the glycerol carbons. ²H NMR spectra of magnetically aligned bicelles showed that the peptide derived from KvAP had no or little effect on bilayer order, while the peptide derived from HsapBK had the effect of lowering the order of the bilayer. The present study demonstrates that the fragments derived from the full-length proteins interact with the bilayered interior of model membranes, and that they affect both the local mobility and lipid order of model membrane systems.     

Effects of three vasoactive peptides isolated from the plasma of the snake Bothrops jararaca

Incubation of plasma from the snake Bothrops jararaca (BJP) with trypsin generated two hypotensive peptides. The primary structure of the peptides was established for three sequences as: Asn-Pro-Phe-Val-Asp-Ala (fraction 13), Ser-Lys-Pro-Asn-Met-Ser-Asp-Glu-Ser-Leu-Ala-Val-Ala-Ile (fraction 14), Asn-Pro-Phe-Val-Asp-Ala (fraction 15). These peptides display homology with fragments of albumin from Trimeresurus flavoviridis. A bolus intra-arterial injection of the purified or the synthetic peptide produced a strong and sustained vasopressor response in the anaesthetized snake B. jararaca and Wistar rats; this hypotensive effect was also potentiated by captopril, an angiotensin-converting enzyme inhibitor (0.1 mg/kg). The natural concentrations of these peptides in plasma need to be determined and could play a physiological role in snake blood pressure regulation.     

Lipolysis of ApoC-II deficient very low density lipoproteins: enhancement of lipoprotein lipase action by synthetic fragments of apoC-II.

Enzymic hydrolysis of triacylglycerol has been studied with very low density lipoproteins from an individual with a genetically determined absence of apoC-II, the activator apoprotein for lipoprotein lipase. Normal rates of ester cleavage by purified bovine milk lipoprotein lipase can be achieved $\text{in}\text{vitro}$ with native apoC-II and by three shorter synthetic peptides, apoC-II(55–78), apoC-II(50–78) and apoC-II(43–78), which contain part of the carboxyl terminal third of the native apoprotein. At 0.5 μM concentration, all peptides produced a 7-fold activation. ApoC-II(43–78), but not apoC-II(50–78) or apoC-II(55–78), could bind VLDL as shown by separation of unbound ¹²⁵I peptides and the lipoproteins. Thus, residues 43–50 of apoC-II are part of a lipid binding region. High affinity binding of apoC-II peptides to the lipoprotein substrate is not obligatory for activation of lipoprotein lipase.     

Antimicrobial activity of endogenous peptides of the moss <Emphasis Type="Italic">Physcomitrella patens</Emphasis>

Plant and animal cells contain pools of endogenous peptides, which are the degradation products of functionally active proteins. It is known that these peptides can possess biological activity; however, the functions of most of them are unknown. The goal of the present study was to estimate the antimicrobial potential of endogenous peptides resulting from the degradation of functional proteins in cells of the moss Physcomitrella patens. Earlier, 117 peptides possessing an antimicrobial potential predicted in silico have been identified in the peptidomes of three types of P. patens cells by mass spectrometry. In the present work, the antimicrobial activity of six of these peptides toward the gram-positive bacteria Bacillus subtilis SHgw and Clavibacter michiganensis pv. michiganensis and gram-negative bacteria Escherichia coli K12 and Xanthomonas arboricola 3004 has been revealed. The results have shown that three of six peptides inhibit the growth of the phytopathogenic bacteria X. arboricola and C. m. pv. michiganensis; four peptides inhibit the growth of the gram-negative bacterium E. coli K12, and one peptide inhibits the growth of the gram-positive bacterium B. subtilis. It has been found that the peptides inhibiting the bacterial growth are predominantly the fragments of ribosomal proteins. The work confirms the potential of the biological activity of peptides that are the degradation products of functional proteins.     

Primary structure of yeast cytochrome c peroxidase. I. Chemical characterization of the polypeptide chain and of tryptic and chymotryptic peptides

The amino acid composition of yeast cytochrome c peroxidase was determined and calculated assuming that the enzyme contained one protoheme per molecule. On the basis of the amino acid composition and heme content the minimum M_r was calculated to be 35,235. Gel electrophoresis in the presence of sodium dodecyl sulfate indicated the presence of a single polypeptide chain with a M_r of approximately 33,000. A single cysteinyl residue present in the molecule was shown to be resistant against reaction with iodoacetic acid in the native form of both holo- and apo-enzymes, but readily modified with the reagent in the denatured form. Automated Edman degradation yielded an aminoterminal sequence of 11 residues beginning with threonine. Twenty-eight tryptic and 47 chymotryptic peptides were isolated from the carboxymethylated apoprotein and subjected to the sequence analysis by the dansyl-Edman method. The results with these peptides confirmed and extended the amino- and carboxyl-terminal sequences and in addition provided a partial sequence covering approximately 90% of the polypeptide chain.     

Comparison of the susceptibility of porcine and human dipeptidyl-peptidase IV to inhibition by protein-derived peptides

The enzyme dipeptidyl-peptidase IV (DPP-IV) is recognized to be a promising target for the management of type 2 diabetes. Over the last decade, numerous synthetic molecules and more recently, peptides from dietary proteins, have been reported to be able to inhibit DPP-IV activity. Most studies that have investigated the in vitro effect of these inhibitors have used porcine or human DPP-IV. Although structurally alike, it is unclear whether these two species display similar inhibition patterns. Therefore, the objective of this study was to compare the effects of protein-derived peptides on the activity of porcine and recombinant human DPP-IV. The two species showed different inhibition susceptibility to 43 of the 62 peptide sequences investigated. While 37 protein-derived peptides were more effective at inhibiting the porcine DPP-IV, only six caused a stronger inhibition of the activity of the human enzyme. Although the peptides WR, IPIQY and WCKDDQNPHS were found to be among the most potent inhibitors of both species, the inhibitory effect was greater on the porcine enzyme than on human DPP-IV (αK_i or K_i = 11.5, 13.4, 13.3 μM and 31.4, 28.2, 75.0 μM for porcine and human DPP-IV, respectively). Investigation into the mode of action of the most effective inhibitory peptides revealed that both species were inhibited in a similar manner by short fragments (≤5 amino acid residues), but that some of the longer peptides acted differently on the enzymes. This study shows that porcine DPP-IV is generally inhibited with greater potency by protein-derived peptides than is the human enzyme.