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At least 145 records · Page 8Linked to original sources
PubMed1997

Modified phage peptide libraries as a tool to study specificity of phosphorylation and recognition of tyrosine containing peptides.

Tyrosine phosphorylation and protein recognition, mediated by phosphotyrosine containing peptides, play an important role in determining the specific response of a cell, when stimulated by external signals. We have used peptide repertoires displayed by filamentous phage as a tool to study the substrate specificity of the protein tyrosine kinase (PTK) p55(fyn) (Fyn). Peptide libraries were incubated for a short time in the presence of Fyn and phages displaying efficiently phosphorylated peptides were selected by panning over anti-phosphotyrosine antibodies. The characterization of the peptides enriched after three phosphorylation/selection rounds allowed us to define a canonical substrate sequence for the kinase Fyn, E-(phi/T)YGx phi, where phi represents any hydrophobic residue. A peptide conforming to this sequence is a better substrate than a second peptide designed to be in accord with the consensus sequence recognised by the Fyn SH2 domain. When the library phosphorylation reaction is carried out in saturation conditions, practically all the tyrosine containing peptides are phosphorylated, irrespective of their context. These "fully modified" peptide libraries are a valuable tool to study the specificity of phosphotyrosine mediated protein recognition. We have used this new tool to identify a family of peptides that bind the PTB domain of the adapter protein Shc. Comparison of the peptide sequences permits us to confirm the essential role of N at position -3, while P often found at position -2 in natural targets is not absolutely required. Furthermore, our approach permits us to reveal an "extended" consensus indicating that residues that do not seem to influence binding in natural peptides can make productive contacts, at least in linear peptides.

Consensus Sequence↗
PubMed2004

[Screening anti-adhesion polypeptides from phage peptide library].

AIM: To screen the active peptides which can suppress adhesion of monocytes to endothelial cells(ECs) from a random peptide phage library. METHODS: The ECs injured by oxidized low density lipoprotein (ox-LDL) 100 mg/L was used as target cells and polypeptides specifically binding to the injured ECs were isolated from the phage-displayed peptide library. The positive clones were characterized by ELISA, and the amino acid sequences of the peptides were deduced by DNA sequencing. Cell counting was used to evaluate the adhesion rate between ECs and monocytes. RESULTS: Six positive clones specifically binding to injured EC were isolated. Four of them contained a repeated sequence of leucine-leucine. Among the four clones, two had an identical sequence, which could reduce the adhesion rate of monocytes to ECs by 17%. CONCLUSION: One peptide which can suppress adhesion of monocytes to ECs is isolated from a random peptide phage library.

Amino Acid Sequence↗
PubMed2002

[Application of laser capture microdissection in screening phage-display peptide library from osteosarcoma tissues].

OBJECTIVE: To establish a novel approach by using laser capture microdissection (LCM) for phage-display peptide library screening and direct recovery of the peptides specifically bound to the cells from fresh human tissue. METHODS: Fresh human osteosarcoma (OS) tissue specimens obtained from biopsy were incubated in phage peptide library solution, followed by shaking at 4 degrees celsius and subsequent preparation of frozen sections. Immunohistochemistry was employed to examine the infiltration of the phage in the tissues. After modification to improve the viability of the phage during the operation, LCM was used to isolate the targeted tumor cells that specifically bound the phage peptides. The phage was then recovered by transfecting the host bacteria, and the specificity of the selected phage was assessed by calculating the recovered phage transfection unit on different tissue sections. RESULTS: Enough phages that specifically bound to tumor cells were recovered from the sections. After three rounds of screening, the eluted phage showed up to 16-fold selectivity for OS tissue. CONCLUSION: Application of LCM makes it possible to screen phage display peptide library directly from fresh human tissue. Specific cell-binding peptides can be selected directly from fresh human tumor cells in their native tissue environment at the single cell level.

Animals↗
PubMedDate not supplied

Evaluation of peptide libraries: an iterative strategy to analyze the reactivity of peptide mixtures with antibodies.

Peptide libraries corresponding to a presumed mixture of 50,625 tetrapeptides or 16,777,216 hexapeptides were each prepared in a single assembly by standard solid-phase peptide synthesis. By enzyme-linked immunosorbent assay, the tetrapeptide library was shown to inhibit the binding of an antiserum to FMRF amide with an FLRF capture antigen; the hexapeptide library was shown to inhibit the binding of a monoclonal antibody to a 28 amino acid peptide with the corresponding peptide capture antigen. An iterative strategy of variation was used to determine for each position in the tetra- or hexapeptides which amino acid contributed the most to activity. As a result we were able to logically select out of the tetrapeptide library the sequence FLRF and to select out of the hexapeptide library a sequence that differed from the apparent probable epitope but was twice as active. A single amino acid substitution in the logically derived sequence gave a peptide that was 35 times as active as the hexapeptide sequence in the original 28 amino acid peptide.

Amino Acid Sequence↗
PubMed2003

Construction of a protein-detection system using a loop peptide library with a fluorescence label.

Construction of a novel protein-detection system was carried out using a designed peptide library with fluorescent labels based on loop structures. As a basic model study, detection of alpha-amylase using fluorescent-labeled peptides derived from an active loop of tendamistat was examined. The detection methods for proteins with immobilized peptides as well as peptides in solution have been successfully established. Based on these results, a loop peptide library that has various turn sequences grafted on a stable loop structure has been constructed. Various proteins with recognition patterns corresponding, for instance, to "protein fingerprints" could be detected using an immobilized peptide library. The present results suggest that the system can be applied to the development of a peptide microarray that behaves as a protein chip.

Amino Acid Sequence↗
PubMed2002

A synthetic peptide with estrogen-like activity derived from a phage-display peptide library.

We describe a novel approach to develop peptides with estrogen like activity using a monoclonal antibody specific to estradiol (mAb E2-15) for the affinity selection of phage displayed peptides from a combinatorial peptide library. Based on the sequences of the selected phage, we synthesized a 15-mer linear peptide LPALDPTKRWFFETK which was derivatized to a 23 mer cyclic peptide CAELPALDPTKRWFFETKPPPPC. Both peptides displayed estrogen-like activity according to the following criteria:(i) in inhibiting the binding of [3H]estradiol to mAb E2-15 and to estrogen receptor (ER)alpha; (ii) in inducing transcriptional activity in MCF7 human breast cancer cells transfected with an estrogen receptor element luciferase construct and (iii) in causing an increase in creatine kinase specific activity in rat tissues in vivo. This approach can be employed to design peptide mimetic for other hormones as well.

Animals↗
PubMed1993

Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli.

I describe a technique for screening peptide libraries of over 10(9) independent clones for substrates of peptide-modifying enzymes. The peptides, linked to their genetic material by the lac repressor, are exposed to the enzyme and then screened by affinity purification on a receptor specific for the modified product. The enzyme characterized, E. coli biotin holoenzyme synthetase, normally adds biotin to a specific lysine residue in complex protein domains. The 13 residue substrate identified by this library screening approach is much smaller than the 75 amino acid required sequence of the natural substrate, and can function at either end of a fusion protein. The sequence is quite distinct at some positions from that region of the natural substrates, presumably because the peptides have to mimic the folded structure formed by the natural substrate. This technique should be useful for mapping the substrate specificity of a variety of peptide-modifying enzymes. In addition, small peptide substrates that are enzymatically biotinylated at a single site should be useful for a variety of purposes in labeling, purification, detection, and immobilization of proteins.

Amino Acid Sequence↗
PubMed1997

Limitations of the coupling of amino acid mixtures for the preparation of equimolar peptide libraries.

The standard method of peptide library synthesis involves coupling steps in which a single amino acid is reacted with a mixture of resin-bound amino acids. The more recently described positional scanning strategy (in which each position in the peptide sequence is occupied in turn by a single residue) is different since it involves the coupling of mixtures of amino acids to mixtures of resin-bound amino acids. In the present study, we analyze the compounds produced under these conditions measuring coupling rates and amounts of formed products, using mainly UV, HPLC, LC/MS and MS/MS techniques. Our data do not permit to conclude that the resulting libraries are complete. Indeed, our analytical data indicate that a large part of the di-, tri- and tetrapeptides synthesized with this method are not present in the final mixture. Although chemical compensation (in which poor coupling kinetics is compensated by a larger excess of the incoming amino acid) has been thought to counterbalance these biases, our experiments show that the compensation method does not take into account the crucial influence of the resin-bound amino acid and that even the dipeptide libraries obtained in this way are far from completeness. The present work provides strong evidence that the coupling of mixtures of amino acids to resin-bound residues, which is required by the positional scanning strategy, results in incomplete and/or non-equimolar libraries. It also clearly confirms that coupling rates in solid-phase peptide synthesis are dependent on the nature of both the incoming and the immobilized amino acid.

Amino Acids↗
PubMed2003

Identification of mimotopes by screening of a bacterially displayed random peptide library and its use in eliciting an immune response to native HBV-preS.

Bacterially-displayed peptide libraries have been widely used as an alternative to phage-displayed peptide libraries in screening epitopes or mimotopes of antibodies. Using a protective monoclonal antibody (mAb) 3B9 against hepatitis B virus (HBV) preS protein as target, mimotopes were successfully screened from a FliTrx random peptide library. To monitor the enrichment ratios of each round and to isolate higher affinity clones from the library, a modified procedure was performed in which the titer of eluted bacteria from an antibody-coated well (P value) was compared with that from a non-coated well (N value). After sufficient enrichment of the library, bacterial colonies were randomly picked and identified further by the monoclonal bacterial P/N value assay and Western blotting analysis. Immunization of mice with the selected bacterially-displayed mimotopes, including the enriched populations without clone identification, elicited strong specific immune responses against the recombinant preS protein. The present study provides a potentially rapid and effective strategy for the development of engineered live bacterial vaccines without the need for information about the aetiological agents or their antigens.

Animals↗
PubMed1994

Use of synthetic peptide libraries and phosphopeptide-selective mass spectrometry to probe protein kinase substrate specificity.

To search for peptides which serve as substrates for protein kinases, an approach based on peptide libraries has been developed. These peptide libraries are chemically synthesized by a modified "divide-couple-recombine" strategy. After reaction with the kinase of interest, the most highly phosphorylated substrate (selected from the library) is identified using on-line liquid chromatography-electrospray mass spectrometry (LC-ESMS). Negative ion LC-ESMS with stepped collision energy is used to identify phosphorylated peptides in the enzyme reactions. As predicted, the cAMP-dependent protein kinase is shown to preferentially phosphorylate Kemptide (Leu-Arg-Arg-Ala-Ser-Leu-Gly) in a library consisting of 19 variants of Kemptide substituted at position 2. Additional experiments have been carried out on the nonreceptor tyrosine kinase v-Abl using a peptide library based on the v-Src autophosphorylation site (Arg-Arg-Leu-Ile-Glu-Asp-Ala-Glu-Tyr-Ala-Ala-Arg-Gly). These results indicate that Ile is the optimal residue at the position N-terminal to tyrosine. Individual peptides containing the Glu-Asp-Ala-Ile-Tyr motif have Vmax/Km values 6-fold higher than the peptide based on the autophosphorylation site itself, confirming the results of the library experiments. This motif has been identified in several tyrosine kinases at a position in the sequence not previously reported to serve as a phosphorylation or autophosphorylation site.

Amino Acid Sequence↗
PubMed1999

Identification of peptide superagonists for a self-K-ras-reactive CD4+ T cell clone using combinatorial peptide libraries and mass spectrometry.

The proliferative responses of a human CD4+ T cell clone 29.15.2, reactive with a self-K-ras-derived peptide (3EYKLVVVGAGGVGKSALT20), were tested using a set of X9 combinatorial peptide libraries containing the flanking residues (EYKLVXXXXXXXXXSALT, where X indicates random amino acids). Certain peptide libraries, such as EYKLVXXXXXX M XXSALT and EYKLVXXXXXXX H XSALT, stimulated a marked proliferation of 29.15.2. However, no combinations of substitutions tested, such as EYKLVXXXXXX MH XSALT, exhibited additive effects. We subsequently synthesized peptides with degenerate sequences (a mixture of 480 species), where each position is composed of the wild-type (wt) residue or of amino acids that induced the proliferation of 29.15.2, in positional scanning. Interestingly, one fraction of degenerate peptides, separated by reverse-phase HPLC, stimulated much higher proliferation than did the wt; in addition, the retention time of this fraction was distinct from that of the wt. Mass spectrometry analysis of this fraction and flanking fractions identified five peptide species that exhibit strong signals in a manner that parallels the antigenic activity. Finally, 17 candidate peptide sequences were deduced from mass spectrometry and hydrophobicity scoring results, of which two peptides (EYKLVVVGAGG ML KSALT and EYKLVVVGAGG MI KSALT) did induce 52- and 61-fold stronger proliferation, respectively, compared with the wt. These findings indicate that: 1) synthetic peptides that carry "the best" residue substitution at each position of combinatorial peptide libraries do not always exhibit superagonism, and 2) such a drawback can be overcome with the use of mass spectrometry. This approach provides new perspectives for the accurate and efficient identification of peptide superagonists.

Amino Acid Sequence↗
PubMed1998

Identification of an allosteric binding site on the transcription factor p53 using a phage-displayed peptide library.

Monoclonal antibody PAb1620 recognizes a conformational epitope on the transcription factor p53 and, upon binding, allosterically inhibits p53 binding to DNA. A highly diverse (1.5 x 10(10) members) phage-displayed library of peptides containing 40 random amino acids was used to identify the PAb1620 binding site on p53. Panning this library against PAb1620 resulted in three unique peptides which have statistically significant sequence identities with p53 sufficient to identify the binding site as being composed of amino acids 106-113 and 146-156. Based on these results, we propose a mechanism by which PAb1620 can allosterically inhibit p53 binding to DNA through an indirect interaction between the antibody binding site and the L1 loop (amino acids 112-124) of p53, which is a component of the DNA binding region.

Allosteric Regulation↗
PubMed1998

Identification of troponin C antagonists from a phage-displayed random peptide library.

Affinity purification of a phage-displayed library, expressing random peptide 12-mers at the N terminus of protein III, has identified 10 distinct novel sequences which bind troponin C specifically. The troponin C-selected peptides yield a consensus binding sequence of (V/L)(D/E)XLKXXLXXLA. Sequence comparison revealed as much as a 62.5% similarity between phiT5, the peptide sequence of the phage clone with the highest level of binding to troponin C, and the N-terminal region of troponin I isoforms. Biotinylated peptides corresponding to library-derived sequences and similar sequences from various isoforms of troponin I were synthesized shown to bind troponin C specifically. Alkaline phosphatase fusion proteins of two of the phage clone sequences bound troponin C specifically, and were specifically competed by both library-derived and native troponin I peptides. Measurement of equilibrium dissociation constants of the peptides by surface plasmon resonance yielded dissociation constants for troponin C as low as 0.43 microM for pT5; in contrast, dissociation constants for calmodulin were greater than 6 microM for all peptides studied. Nondenaturing polyacrylamide gel electrophoresis demonstrated that pT5 formed a stable complex with troponin C in the presence of calcium. We also found that the pT5 peptide inhibited the maximal calcium-activated tension of rabbit psoas muscle fibers.

Amino Acid Sequence↗
PubMed1996

Phage Peptide Libraries

Filamentous phage particles have been central in the construction of libraries displaying vast numbers of random peptides. These random peptides can be antigenically presented as fusions to coat proteins III and VIII of the phage. The isolation of ligate-reactive phage from an immense background of nonspecific phage is achieved by the biopanning process. Enrichment of reactive phage relative to unreactive phage occurs with alternate rounds of affinity selection to the desired molecular target and amplification of the specifically bound phage. This allows the isolation of rare binding species contained in the phage peptide libraries. Each phage particle contains the information in its genome pertaining to the type of random peptide insert displayed. Hence, the identification of binding motifs displayed on ligate-reactive phage is revealed by sequencing the relevant insert site in the phage genome. Phage peptide libraries have been used to isolate ligands to an array of protein ligates. The libraries have proved particularly effective in defining the binding sites of monoclonal antibodies and to some extent polyclonal sera. The analysis of the peptide insert sequences of a number of different clones of antibody binding phage can reveal a great deal about the nature and restriction of the amino acid residues critical for the antibody-antigen interaction.

Journal Article↗
PubMed1998

Efficient generation of major histocompatibility complex class I-peptide complexes using synthetic peptide libraries.

The use of synthetic random peptide libraries is a powerful technology for the study of many aspects of antigen presentation and peptide selection by major histocompatibility complex (MHC) molecules. Here we have used them in conjunction with a recombinant system to determine the peptide binding motifs of three classical class I MHC molecules of the laboratory rat: RT1-Aa, RT1-Au, and RT1-A1c. Described is a method for producing large amounts of soluble class I heavy and light chains in bacteria. Refolding RT1-Aa heavy chain (HC) with rat beta2-microglobulin (beta2m) in the presence of a specific peptide and the subsequent purification of the complex yielded conformationally correct material. This was assessed by gel chromatography, SDS-polyacrylamide gel electrophoresis, isoelectric focussing gel electrophoresis, enzyme-linked immunosorbent assay, and fluorescence-activated cell sorter analysis employing a previously unreported method utilizing a His-Tag affinity silica. By refolding RT1-Aa HC and rat beta2m around a random nonapeptide library and subjecting the resulting complex to acid elution of the bound peptides and pool sequencing, the peptide binding motif for this MHC class I molecule was determined. Results corresponded well with those previously determined from naturally bound peptides and in addition gave a clear and unambiguous signal for the C-terminal anchor residue. This method was then applied to determine the previously undescribed binding motifs for RT1-Au and RT1-A1c. For both molecules, the whole motif was confirmed from naturally bound peptides. We propose this method as an alternative way to obtain the whole class I MHC peptide motif, particularly when a specific antibody is unavailable and/or natural expression of the class I molecule of interest is low.

Animals↗
PubMed2000

A peptide library approach identifies a specific inhibitor for the ZAP-70 protein tyrosine kinase.

We utilized a novel peptide library approach to identify specific inhibitors of ZAP-70, a protein Tyr kinase involved in T cell activation. By screening more than 6 billion peptides oriented by a common Tyr residue for their ability to bind to ZAP-70, we determined a consensus optimal peptide. A Phe-for-Tyr substituted version of the peptide inhibited ZAP-70 protein Tyr kinase activity by competing with protein substrates (K(I) of 2 microM). The related protein Tyr kinases, Lck and Syk, were not significantly inhibited by the peptide. When introduced into intact T cells, the peptide blocked signaling downstream of ZAP-70, including ZAP-70-dependent gene induction, without affecting upstream Tyr phosphorylation. Thus, screening Tyr-oriented peptide libraries can identify selective peptide inhibitors of protein Tyr kinases.

Amino Acid Sequence↗
PubMed2006

Importin beta: a novel autoantigen in human autoimmunity identified by screening random peptide libraries on phage.

By screening random peptide libraries (RPLs) with sera of Type 1 diabetes (T1D) patients, we previously identified 5 disease-specific 'mimotopes' displayed on phages (phagotopes). We already characterised 1 phagotope (CH1p), as an epitope of human osteopontin, an autoantigen expressed within the somatostatin cells of human islets. In this paper, we report the characterization of the second phagotope, 195Dyn, by immunohistochemistry, Western Blotting and screening of a human islet cDNA library using rabbit anti-195Dyn antibodies. The 195Dyn mimotope was detected in human islets. The screening of a lambdagt11 cDNA library from human islets has identified a clone, which corresponded to human importin beta. ELISA detected autoantibodies against this protein in sera of around 60% of TD1 patients and in 30% of patients affected by other autoimmune diseases. In summary, RPLs technology proved again successful in identifying another novel autoantigen (importin beta), whose significance in the autoimmune process remains to be fully elucidated.

Animals↗
PubMed2001

Screening An alpha-glucosidase Inhibitor from A Phage-displayed Peptide Library.

A phage-displayed peptide library was biopanned with Aspergillus niger glucoamylase. Three specifically binding phage clones (GB-1, GB-2 and GB-3) were identified after three cycles of screening and amplification. All three peptides contained a disulfide bridge, and the impairment of disulfide bond greatly lowered the binding activity. One peptide, cyclic KCHFEECLAY, representing the N-terminal 10 amino acid residues from GB-1, competitively inhibited A. niger glucoamylase (K(I) 0.2 mmol/L) as well as rat intestinal alpha-glucosidase (KI 1.4 mmol/L).

Journal Article↗