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Characterization of autoantigenic epitopes on platelet glycoprotein IIb/IIIa using random peptide libraries.

Most patients with chronic immune thrombocytopenic purpura (ITP) have autoantibodies directed against the glycoprotein (GP) IIb/IIIa complex. We have used a filamentous phage library that displays random linear hexapeptides to identify peptide sequences recognized by these autoantibodies. Plasma antibody eluates from two patients were used to select for phage displaying autoantibody-reactive peptides. From patient ITP-1 (known to have two distinct autoantibodies), we identified anti-GPIIb/IIIa antibody-specific phage encoding the peptide sequences Arg-Glu-Lys-Ala-Lys-Trp (REKAKW) and Pro-Val-Val-Trp-Lys-Asn (PVVWKN). Patient ITP-2 bound phage encoding the hexapeptide sequence Arg-Glu-Leu-Leu-Lys-Met. Each phage showed saturable dose-dependent binding to immobilized autoantibody, and binding could be blocked with purified GPIIb/IIIa. Patient ITP-1 autoantibody recognition of phage encoding REKAKW could be blocked with a synthetic peptide derived from the GPIIIa cytoplasmic tail; however, the PVVWKN was not. Using sequential overlapping peptides from the GPIIIa cytoplasmic region, an epitope for ITP-1 was localized to the sequence Arg-Ala-Arg-Ala-Lys-Trp (GPIIIa 734-739). Inhibition studies using synthetic peptides showed that phage REKAKW and PVVWKN were recognized by distinct autoantibodies from patient ITP-1. To determine whether individual patients with ITP possessed autoantibodies that recognize similar antigenic determinants on GPIIb/IIIa, the three phage were tested for binding to five other ITP patient autoantibodies. The phage encoding the peptide PVVWKN was found to bind ITP-1 and one other patient autoantibody. This result suggests that ITP patients recognize a limited number of shared epitopes.

Amino Acid Sequence↗

A peptide isolated from a random phage peptide library is a structural mimic to the P1, P4-diadenosine 5'-tetraphosphate binding site on its receptor.

We have previously demonstrated that a monoclonal antibody (mAb TL4), which inhibits P1, P4-diadenosine 5'-tetraphosphate (Ap4A) binding to its receptor, selected a consensus RGS tripeptide from a random phage hexapeptide library. RGS interfered with Ap4A binding to its membrane receptor [Liu, G., Bryant, R. T. & Hilderman, R. H. (1996) Biochemistry 35, 197-201]. However the mechanism by which RGS interfered with Ap4A binding to its receptor was not determined. In this communication, we demonstrate that RGS interacts with Ap4A to prevent [3H]Ap4A binding to the Ap4A membrane receptor. To further characterize the mechanism by which RGS inhibits Ap4A binding to its receptor, we used mAb TL4 to screen a 15-residue random peptide phage library and DNAs from 24 clones were sequenced. 20 clones contain a RGSSS sequence while 17 of these clones contained an identical 15-amino-acid insert (clone A). Gel-filtration studies of previously equilibrated clone A phage and [3H]Ap4A support the idea that [3H]Ap4A interacts specifically with clone A phage while RGS effectively competes for [3H]Ap4A interaction on clone A phage. These data are consistent with RGS mimicking a sequence on the receptor essential for Ap4A binding.

Amino Acid Sequence↗

Selection of novel nickel-binding peptides from flagella displayed secondary peptide library.

Nickel (Ni) performs its biological or toxic functions in nickel-protein coordination form. Novel Ni-binding peptides were isolated from a random dodecapeptide library displayed on the flagella of Escherichia coli against immobilized ions. On the basis of isolated sequences rich in histidine residues, two secondary libraries were constructed respectively. By consequent selection, more Ni-chelating peptides were identified and the consensus motif RHXHR (where X was always H) was deduced. The result suggested that not only histidine, but also arginine, play an important role in Ni-binding. Furthermore, two selected clones (1035 and 2022) were chosen for further identification. They exhibited similar relative binding affinity, which was about nine times that of the original library derived clones and statistically much more significant than the positive control with polyhistidine insert. Free nickel ions could almost completely inhibit the binding of the clones 1035 and 2022 to immobilized nickel, implicating that the peptides were able to chelate nickel ions. These studies reveal that bacterial surface displayed peptide libraries may have promising future potential for the development of metal bioadsorbents. Furthermore, novel Ni-binding peptides may provide lead molecules for Ni-chelation and applications thereof.

Amino Acid Sequence↗

A mathematical model for biopanning (affinity selection) using peptide libraries on filamentous phage.

A mathematical model is presented for the process of selection of peptides for binding to a target. The affinity enrichment process commonly known as biopanning relies on subjecting a library of peptides on filamentous phage to a selection for binding to the target immobilized on solid support or in solution. The model is an implementation of the mass-action law to the diverse population of macromolecular assemblies. An analytical solution is presented for the enrichment process. Most parameters in the enrichment formula can be easily determined experimentally. Two examples corresponding to biopanning with epitope libraries and antibody libraries are given. The model allows for an estimation of the contribution of equilibrium and dissociative biopanning to the overall enrichment. The model can be a tool in the evaluation of the role of different biopanning parameters. Its implementation in a spreadsheet makes it possible to perform a computer simulation of a biopanning experiment.

Antibodies↗

Discovery and design of novel inhibitors of botulinus neurotoxin A: targeted 'hinge' peptide libraries.

Intoxication by the zinc protease botulinus neurotoxin A (BoNT-A) results from cleavage of a single Q-R bond in the neuronal protein SNAP-25, which disables the docking mechanism required for neurotransmitter release. In the present study, potential inhibitors of BoNT-A were assessed from their effects on the BoNT-A cleavage of a synthetic 17-mer peptide (SNAP-25, residues 187-203) spanning the Q-R cleavage site. Compounds that inhibited BoNT-A included thiols (zinc chelators) such as dithiothreitol, dimercaptopropanesulfonic acid, mercaptosuccinic acid and captopril. In addition, compounds containing multiple acidic functions, such as the SNARE motif V2 (ELDDRADALQ), the tripeptide Glu-Glu-Glu and the steroid glycoside glycyrrhizic acid, were effective inhibitors. 'Hinge' peptide mini-libraries (PMLs) having the structure acetyl-X(1)-X(2)-linker-X(3)-X(4)-NH(2) or X(1)-X(2)-linker-X(3), where X(1)-X(4) were mixtures of selected amino acids and the flexible linker was 4-aminobutyric acid, also provided effective inhibition. Targeted PMLs containing the acidic amino acids Asp and Glu, the scissile-bond amino acids Gln and Arg and the zinc chelators His and Cys produced pronounced inhibition of BoNT-A. Deconvolution of these libraries will provide novel ligands with improved inhibitory potency as leads in the design of peptide mimetics to treat BoNT poisoning.

Antitoxins↗

Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide libraries.

Two targeted chromogenic octapeptide combinatorial libraries, comprised of 38 pools each containing 361 different peptides, were used to analyze the enzyme/substrate interactions of five plasmepsins. The first library (P1 library) was based on a good synthetic aspartic peptidase substrate [Westling, J., Cipullo, P., Hung, S. H., Saft, H., Dame, J. B., and Dunn, B. M. (1999) Protein Sci. 8, 2001-2009; Scarborough, P. E., and Dunn, B. M. (1994) Protein Eng. 7, 495-502] and had the sequence Lys-Pro-(Xaa)-Glu-P1*Nph-(Xaa)-Leu. The second library (P1' library) incorporated results with the plasmepsins from the first library and had the sequence Lys-Pro-Ile-(Xaa)-Nph*P1'-Gln-(Xaa). In both cases, P1 and P1' were fixed residues for a given peptide pool, where Nph was a para-nitrophenylalanine chromogenic reporter and Xaa was a mixture of 19 different amino acids. Kinetic assays monitoring the rates of cleavage of these libraries revealed the optimal P1 and P1' residues for the five plasmepsins as hydrophobic substitutions. Extended specificity preferences were obtained utilizing liquid chromatography-mass spectrometry (LC-MS) to analyze the cleavage products produced by enzyme-catalyzed digestion of the best pools of each peptide library. LC-MS analysis of the P1-Phe and P1'-Phe pools revealed the favored amino acids at the P3, P2, P2', and P3' positions. These analyses have provided new insights on the binding preferences of malarial digestive enzymes that were used to design specific methyleneamino peptidomimetic inhibitors of the plasmepsins. Some of these compounds were potent inhibitors of the five plasmepsins, and their possible binding modes were analyzed by computational methods.

Animals↗

Potent inhibitory ligands of the GRB2 SH2 domain from recombinant peptide libraries.

We cloned and expressed the SH2 domain of human GRB2 as glutathione S-transferase and maltose binding protein fusion proteins. We screened three phagemid-based fd pVIII-protein phage display libraries against SH2 domain fusion proteins. Sequence analysis of the peptide extensions yielded a variety of related peptides. By examining the ability of the phage clones to bind other SH2 domains, we demonstrated that the phage were specific for the SH2 domain of GRB2. Based on the sequence motif identified in the "random" library screening experiment, we also built and screened a phage display library based on a Tyr-X-Asn motif (X5-Tyr-X-Asn-X8). To examine the affinity of the phage derived peptides for GRB2, we set up a radioligand competition binding assay based on immobilized GRB2 and radiolabelled autophosphorylated EGFR ICD as the radioligand. Results obtained with peptide competitors derived from the phage sequences demonstrated that nonphosphotyrosine-containing peptides identified with the phage display technology had an affinity for the receptor similar to tyrosine-phosphorylated peptides derived from the EGFR natural substrate. Interestingly, when the phage display peptides were then phosphorylated on tyrosine, their affinity for GRB2 increased dramatically. We also demonstrated the ability of the peptides to block the binding of the GRB2 SH2 domain to EGFR in a mammalian cell-based binding assay.

Adaptor Proteins, Signal Transducing↗

Development of antiangiogenin peptide using a phage-displayed peptide library.

Angiogenesis is essential for tumor growth and metastasis. Here, we have developed a peptide antagonist of human angiogenin, which is a potent and tumor-associated angiogenic factor. ANI-E peptide was derived from the phage clone, which binds to angiogenin via the disulfide-constrained octapeptide epitope that is displayed on its surface, and is displaced by actin. Disulfide-constrained ANI-E peptide inhibits the interaction of angiogenin with actin, which is regarded as the angiogenin-binding protein on the surface of endothelial cells, without any visible effect on the ribonucleolytic activity of angiogenin. The peptide also inhibits the neovascularization that is induced by angiogenin in the chick chorioallantoic membrane assay. The antiangiogenic activity of the peptide is specific for angiogenin because the peptide does not have any apparent effect on embryonic angiogenesis or the preexisting blood vessels. The disulfide bond and the glutamic acid inside the disulfide ring of ANI-E peptide are indispensable for its antiangiogenin activity. Furthermore, ANI-E peptide blocks the angiogenesis that is induced by the angiogenin-secreting PC3 human prostate adenocarcinoma cells, without any direct effect on the proliferation, as well as the adhesion of PC3 cells to angiogenin. Therefore, the inhibition of the tumor-induced angiogenesis by ANI-E peptide is most likely caused by the neutralization of the extracellular angiogenin that is secreted by PC3 cells. On the basis of our results, ANI-E peptide may be effective for the treatment of various human tumors that secrete angiogenin. Our results also strongly support the hypothesis that the interaction of angiogenin with the cell surface actin-like protein is essential for the biological action of angiogenin, and angiogenin has an essential role in tumor-induced angiogenesis.

Actins↗

Use of Peptide library screening to detect a previously unknown linear diagnostic epitope: proof of principle by use of lyme disease sera.

Diagnostic peptides previously isolated from phage-displayed libraries by affinity selection with serum antibodies from patients with Lyme disease were found to give reproducible serum reactivity patterns when tested in two different enzyme-linked immunosorbent assay formats. In addition, the hypothetical possibility that peptides selected by this type of "epitope discovery" technique might identify the original antigens eliciting antibody responses was tested by searching for sequence similarities in bacterial protein databases. In support of this hypothesis, our search uncovered similarities between peptides representing two different sequence motifs and sequences in the VlsE and BBA61 antigens of Borrelia burgdorferi. Utilizing synthetic peptides, we verified that the sequence KAASKETPPALNK, located at the C terminus of the VlsE antigen, had the same reactivity pattern to sera from patients with extracutaneous Lyme disease as the diagnostic peptide SKEKPPSLNWPA, with which it shared a 7-amino-acid-residue match (consensus residues are underlined). A peptide with conservative mutations of five of the consensus residues was nonreactive, strongly suggesting that the VlsE sequence represents the epitope that originally elicited antibody responses in these patients. The diagnostic sensitivity of this new VlsE epitope was relatively low (30%) compared to that (100%) of the well-documented C6 diagnostic peptide of VlsE when tested in our small cohort of 10 patients with Lyme disease. Nonetheless, the identification of this previously unknown epitope serves as a proof of the principle of the hypothetical ability of "epitope discovery" techniques to detect specific microbial antigens with diagnostic relevance in infectious diseases.

Amino Acid Sequence↗

Assessment of purity and screening of peptide libraries by nested ion mobility-TOFMS: identification of RNase S-protein binders.

Combinatorial peptide synthesis in combination with affinity selection and high-resolution ion mobility/time-of-flight mass spectrometry (IM/TOFMS) analysis has been used to investigate the binding of a series of 96 related eight-residue peptides (with the general sequence NH2-GX1X2FX3X4X5G-CO2H, where X1 = L, F, V, Y; X2 = N, F; X3 = E, V, T; X4 = V, L; X5 = V, L) to the ribonuclease S protein. A key advantage of this strategy is that the IM/ TOFMS approach allows the relative abundances of individual library components (including numerous sequence and structural isomers) to be characterized before and after screening. The relative binding interactions of different sequences are assessed by comparing IM/TOFMS data for those components that pass through the column (as well as those that bind) to data for the library prior to screening. The high-affinity sequences that are found in this study are compared with those selected from much larger combinatorial libraries. The results suggest that many expected sequences in the large libraries may be missing (e.g., due to issues such as failure of specific steps during the synthesis or differences in solubility). Comparison of the binding sequences obtained in these studies and those reported previously indicates that screening results from large libraries should be interpreted with caution.

Amino Acid Sequence↗

Binding properties of SH3 peptide ligands identified from phage-displayed random peptide libraries.

Combinatorial libraries have yielded high-affinity ligands for SH3 domains of a number of different proteins. We have shown that synthetic peptides containing these SH3 ligand sequences serve as specific probes of SH3 domains. Direct binding of the N-terminal biotinylated peptide ligands was conveniently detected in ELISA, filter-blotting, and dot-blotting experiments with the use of streptavidin-conjugated enzymes. In some cases, detection of peptide-SH3 interactions required that the biotinylated peptides first were preconjugated with streptavidin to form a multivalent complex. Interestingly, these nominally tetravalent SH3 peptide ligands cross-react to varying degrees with different SH3 domains. We have used such complexes to screen lambda cDNA expression libraries and have isolated clones that encode both known and novel SH3-domain-containing proteins. Based on the success of this methodology, we propose a general strategy by which ligands of a modular domain-containing protein can be isolated from random peptide libraries and used to screen cDNA expression libraries systematically for novel modular domain-containing proteins.

Amino Acid Sequence↗

Substrate specificity of schistosome versus human legumain determined by P1-P3 peptide libraries.

Asparaginyl endopeptidases, or 'legumains' have been identified and characterized in plants, the blood fluke parasite Schistosoma, and mammals. The legumains are a novel family of cysteine proteases and display restricted specificity for peptide hydrolysis on the carboxyl side of asparagine residues. Two forms of recombinant asparaginyl endopeptidase from Schistosoma mansoni (C197 Sm32 and N197C Sm32), expressed in Pichia pastoris, have been analyzed for substrate specificity using a positional-scanning synthetic combinatorial library (PS-SCL). We first screened Sm32 using a P1-diverse library. This library demonstrated the absolute specificity of Sm32 for asparagine at P1. To determine the P2-P3 preferences of Sm32, we constructed a library with asparagine fixed at P1, and the P2-P3 positions randomized. The library was screened using the two forms of Sm32, human asparaginyl endopeptidase, and to confirm its diversity, cruzain from Trypanosoma cruzi. The schistosome legumain showed a preference for P3: Thr>Ala>Val>Ile, and P2: Ala>Thr>Val>Asn, with an overall broader specificity at P3 than at P2. Both human and schistosome legumain can accommodate Thr and Ala at P2 and P3. However, optimal substrate sequences differ, with Sm32 preferring Thr-Ala-Asn, and human legumain preferring Pro-Thr-Asn. Predictions of substrate specificity from the library screen were confirmed using single peptide substrates for kinetic assays.

Amino Acid Sequence↗

Solid-phase synthesis of a farnesylated CaaX peptide library: inhibitors of the Ras CaaX endoprotease.

A solid-phase method, based on Kaiser's p-benzophenone oxime resin, was developed for the synthesis of a series of N-acetyl-S-(E, E-farnesylated) Ca(1)a(2)X tetrapeptides as potential inhibitors of recombinant Ras and a-factor converting enzyme (RCE). N-Acetyl-S-(E, E-farnesyl)-L-cysteine was coupled to resin-bound a(1)a(2) dipeptide using HOBt/DCC activation in conjunction with N-BOC chemistry. The protected farnesylated tripeptide was cleaved from the resin with simultaneous addition of the X residue by treating the resin-bound farnesylated Ca(1)a(2) tripeptide with L-amino acid benzyl ester tosylates under mildly acidic conditions. The benzyl ester was saponified, and the resulting carboxylate precipitated by ether to afford a library of tetrapeptides as a mixture of diastereomers at the cysteine center. The peptides were evaluated as inhibitors of recombinant yeast RCE endoprotease (yRCE) to obtain information about the affinity of the enzyme for the a(1)a(2)X portion of the Ca(1)a(2)X moiety.

Amino Acid Sequence↗

Identification of novel inhibitors of Pseudomonas aeruginosa MurC enzyme derived from phage-displayed peptide libraries.

OBJECTIVES: The machinery of peptidoglycan biosynthesis is an ideal site at which to look for novel antimicrobial targets. Phage display was used to develop novel peptide inhibitors for MurC, an essential enzyme involved in the early steps of biosynthesis of peptidoglycan monomer. METHODS: We cloned and overexpressed the murA, -B and -C genes from Pseudomonas aeruginosa in the pET expression vector, adding a His-tag to their C termini. The three proteins were overproduced in Escherichia coli and purified to homogeneity in milligram quantities. MurA and -B were combinatorially used to synthesize the MurC substrate UDP-N-acetylmuramate, the identity of which was confirmed by mass spectrometry and nuclear magnetic resonance analysis. Two phage-display libraries were screened against MurC in order to identify peptide ligands to the enzyme. RESULTS: Three rounds of biopanning were carried out, successively increasing elution specificity from round 1 to 3. The third round was accomplished with both non-specific elution and competitive elution with each of the three MurC substrates, UDP-N-acetylmuramic acid (UNAM), ATP and L-alanine. The DNA of 10 phage, selected randomly from each group, was extracted and sequenced, and consensus peptide sequences were elucidated. Peptides were synthesized and tested for inhibition of the MurC-catalysed reaction, and two peptides were shown to be inhibitors of MurC activity with IC(50)s of 1.5 and 0.9 mM, respectively. CONCLUSION: The powerful selection technique of phage display allowed us to identify two peptide inhibitors of the essential bacterial enzyme MurC. The peptide sequences represent the basis for the synthesis of inhibitory peptidomimetic molecules.

Amino Acid Sequence↗

A peptide library expressed in yeast reveals new major epitopes from human immunodeficiency virus type 1.

In order to characterize novel human immunodeficiency virus type 1 (HIV-1) continuous epitopes, we designed a simple method, based on recombinant DNA, providing a complete set of peptides derived from HIV-1. A library (4 x 10(4) clones) was first constructed in a new expression/secretion vector, using as inserts small fragments of HIV-1 DNA (50-150 bp) generated by random DNAse I cleavage. This peptide library, expressed in the yeast Saccharomyces cerevisiae, was screened with sera of HIV-1 infected individuals and human and murine anti-HIV-1 monoclonal antibodies. Plasmids from immunoreactive colonies were recovered and the sequences of the HIV-1 derived inserts were determined. By using human sera, we have detected classical HIV-1 epitopes and identified two novel major epitopes, which may be used to improve diagnostic tests, localized in the p24 core protein and in the endonuclease. In addition, four minor epitopes were also defined by screening the library with monoclonal antibodies: in the protease, in the p17 core protein, in gp120 and near the C-terminal of gp41. This method is general and can be used for any protein from which a cloned cDNA is available.

Amino Acid Sequence↗

The use of phage-peptide libraries to define the epitope specificity of a mouse monoclonal anti-Der p 1 antibody representative of a major component of the human immunoglobulin E anti-Der p 1 response.

BACKGROUND: More than 80% of individuals who are sensitive to the dust mite Dermatophagoides pteronyssinus produce immunoglobulin (Ig) E antibodies to Der p 1, the most significant domestic allergen. There is therefore considerable interest in elucidating the interaction between human IgE and Der p 1, as a basis for developing strategies for therapeutic intervention. OBJECTIVES: We have therefore sought to determine the Der p 1 epitope recognized by a mouse monoclonal anti-Der p 1 antibody (mAb 2C7) representative of a major component of the human IgE anti-Der p 1 response. METHODS: M13 15mer and T7 9mer bacteriophage-peptide display libraries were screened with mAb 2C7. Mimotope sequences were defined and compared with the native Der p 1 sequence and with those of three homologous molecules, namely chymopapain, papain and actinidin. The sequence of a candidate epitope was then located in the three-dimensional model of Der p 1 and the corresponding sequences in the homologous molecules were studied for accessibility in the three-dimensional structure. RESULTS: We have demonstrated that it is possible to isolate phage clones with peptide inserts specific for mAb 2C7. Examination of the sequences obtained and the location of the corresponding epitope within the three-dimensional model of Der p 1 has shown that mAb 2C7 recognizes a conformational epitope comprising the sequence Leu147-Gln160. The relevance of the identified epitope was established by showing that native Der p 1 can block the binding of specific phage clones to mAb 2C7. Similar sequences were identified within the three-dimensional structures of chymopapain, papain and actinidin, thereby providing a structure-based explanation for immunological cross-reactivity. CONCLUSION: The identification of the Der p 1 sequence Leu147-Gln160 as a potential epitope recognized by a major component of the human IgE anti-Der p 1 response may provide therapeutic opportunities for disrupting the interaction between IgE and this important allergen.

Amino Acid Sequence↗

Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic TCR and MHC peptide ligands.

The interaction of TCRs with MHC peptide ligands can be highly flexible, so that many different peptides are recognized by the same TCR in the context of a single restriction element. We provide a quantitative description of such interactions, which allows the identification of T cell epitopes and molecular mimics. The response of T cell clones to positional scanning synthetic combinatorial libraries is analyzed with a mathematical approach that is based on a model of independent contribution of individual amino acids to peptide Ag recognition. This biometric analysis compares the information derived from these libraries composed of trillions of decapeptides with all the millions of decapeptides contained in a protein database to rank and predict the most stimulatory peptides for a given T cell clone. We demonstrate the predictive power of the novel strategy and show that, together with gene expression profiling by cDNA microarrays, it leads to the identification of novel candidate autoantigens in the inflammatory autoimmune disease, multiple sclerosis.

Amino Acid Motifs↗