Identification of peptide ligands for target RNA structures derived from the HIV-1 packaging signal psi by screening phage-displayed peptide libraries.
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Amino Acid Sequence↗
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Isolation of a tripeptide from a random phage peptide library that inhibits P1,P4-diadenosine 5'-tetraphosphate binding to its receptor.
Extracellular P1,P4-diadenosine 5'-tetraphosphate (Ap4A) has been implicated as a modulator of cell stress. We have previously demonstrated specific receptors for Ap4A at the surface of cardiac myocytes (Walker et al., 1993a). In addition, we have isolated a monoclonal antibody (mAb TL4) that recognized the Ap4A receptor and inhibited binding of Ap4A to its receptor (Walker & Hilderman, 1993). As part of our effort to characterize the Ap4A receptor building domain, we screened a random phage peptide library with mAb TL4. After affinity purification of specifically bound phage, we isolated 38 individual phage clones. Twenty-eight of these clones bound mAb TL4 in ELISA and dot blot analyses. Twenty-two of the twenty-eight individual clones contained inserts with an RGS tripeptide sequence. Synthetic RGS peptide specifically inhibits the binding of mAb TL4 to its membrane receptor. Furthermore, the RGS peptide also inhibits [3H]Ap4A binding to its receptor. These data are consistent with the RGS peptide mimicking part of the mAb TL4 recognition site on the Ap4A receptor. The The RGS peptide may be used to help characterize the Ap4A receptor binding domain and to help determine the physiological significance of the interaction between Ap4A and its receptor.
Amino Acid Sequence↗
A novel matrix attachment region DNA binding motif identified using a random phage peptide library.
SATB1 is a nuclear matrix attachment DNA (MAR)-binding protein which is predominantly expressed in thymocytes. This protein binds to the minor groove specifically recognizing an unusual DNA context exhibited by a specific MAR region with strong base-unpairing propensity. A phage library displaying nonamer random peptides without any built-in structure was used to identify a MAR binding motif of SATB1. One predominant cyclic peptide C1 of CRQNWGLEGC selected by a MAR-affinity column showed 50% identity with a segment in SATB1 (amino acids 355-363). Replacement of the C1 similarity segment in SATB1 by a random amino acid sequence or its truncation resulted in more than 80% reduction in MAR binding. In contrast, replacement of the same SATB1 segment with the C1 peptide restored full MAR binding activity and specificity as the wild-type protein. Single amino acid mutation of the conserved Arg or Glu residue to Ala greatly reduced MAR binding. Taken together our data show that a nine amino acid sequence in SATB1 represents a key MAR binding motif. Phage display may provide a general tool for rapid identification of DNA binding peptide motifs.
Amino Acid Sequence↗
Use of peptides and peptide libraries as T-cell stimulants in flow cytometric studies.
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CD4-Positive T-Lymphocytes↗
Silica-precipitating peptides isolated from a combinatorial phage display peptide library.
Many biological organisms contain specialized structures composed of inorganic materials. Cellular processes in vivo facilitate the organized assembly of mineral building blocks into complex structures. The structural hierarchy and complexity across a range of length scales are providing new ideas and concepts for materials chemistry. Proteins that direct biomineralization can be used to control the production of nanostructured materials and facilitate the fabrication of new structures. Here, we demonstrate that some of the silica-binding peptides isolated from a combinatorial phage peptide display library can be used in precipitating silica from a solution of silicic acid. The results described in this report demonstrate that peptides displayed by phages act as templates in inorganic material synthesis and provide a means of understanding how some of the biological systems may be carrying out materials chemistry in vivo.
Biomimetic Materials↗
In vitro panning of a targeting peptide to hepatocarcinoma from a phage display peptide library.
Phage display technology has been used as a powerful tool in the discovery of ligands specific to receptor(s) on the surface of a cancer cell and could also impact clinical issues including functional diagnosis and cell-specific drug delivery. After three rounds of in vitro panning and two rounds of reverse absorption, a group of phages capable of addressing BEL-7402 enormously were obtained for further analysis. Through a cell-based ELISA, immunofluorescence, FACS, and in vivo binding study, WP05 (sequence TACHQHVRMVRP) was demonstrated to be the most effective peptide in targeting four kinds of liver cancer cell lines (BEL-7402, BEL-7404, SMMC-7721, and HepG2), but not the normal liver cell line HL-7702. In conclusion, the peptide WP05 which was screened by in vitro phage display technology was proved to be a targeting peptide to several common hepatocellular carcinoma cell lines.
Amino Acid Sequence↗
Differential multisite phosphorylation of the trehalose-6-phosphate synthase gene family in Arabidopsis thaliana: a mass spectrometry-based process for multiparallel peptide library phosphorylation analysis.
Multisite protein phosphorylation plays a fundamental role in metabolic regulation. To detect and quantify in vitro kinase phosphorylation activities, we developed a highly selective LC-MS/MS-based method using high resolution multiple reaction monitoring on a triple quadrupole mass spectrometer. This method eliminates the need for stable isotope labeling and enables multiparallel kinase target assays. Using these assays, we made the first observation of in vitro phosphorylation of different trehalose-6-phosphate synthase (TPS) isozymes. TPSs possess putative Ca2+-independent, sucrose non-fermenting 1-related protein kinase 1 (SnRK1) phosphorylation sites. Sixteen synthetic peptides from six different Arabidopsis thaliana TPS isozymes containing the SnRK1 consensus recognition motif were phosphorylated simultaneously in vitro, and their phosphorylation dynamics were determined. We achieved absolute quantification of TPS peptide phosphorylation by tuning the mass spectrometer to the corresponding synthetic standard phosphopeptides. The selectivity of the mass spectrometer in the multiple reaction monitoring mode compensates for the low ionization efficiency of phosphopeptides in the presence of a complex matrix. Results are in close agreement with recent in vivo studies of TPS phosphorylation and regulation and reveal significant differences in the phosphorylation levels of different TPS members within the TPS gene family ranging over 3 orders of magnitude. Substituting EGTA for CaCl2 in the reaction mixture reduced the formation of some of the phospho-TPS peptides drastically, indicating that Ca2+-dependent kinases are active in the presence of Ca2+-independent SnRKs. This agrees with the proposed overlap of the consensus motifs of these kinases and enables delineation between Ca2+-independent and Ca2+-dependent phosphorylation. Results demonstrate that multiparallel kinase target assays are sensitive enough to provide evidence for differential multisite phosphorylation of homologous TPS proteins and their highly conserved putative phosphorylation sites.
Amino Acid Sequence↗
Cellular localization and antiproliferative effect of peptides discovered from a functional screen of a retrovirally delivered random peptide library.
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Alkyl and Aryl Transferases↗
Use of combinatorial peptide libraries for T-cell epitope mapping.
T lymphocytes play important roles not only in infectious diseases and autoimmunity, but also in immune responses against tumors. For many of these disorders, the relevant target antigens are not known. Designing effective methods that allow the search for T-cell epitopes is therefore an important goal in the areas of infectious diseases, oncology, vaccine development, and numerous other biomedical specialties. So far, the strategies used to examine T-cell recognition have been based largely on mapping T-cell epitopes with overlapping peptides from known proteins or with entire proteins, e.g., from a specific virus, bacterium, or human tissue. These approaches are tedious and have a number of limitations. It is, for example, almost impossible to isolate T cells that infiltrate an organ or infectious site and identify their specificity unless one already has a concept as to which antigens may be relevant. During recent years, a number of laboratories have developed less biased approaches that employ either the selection of putative T-cell epitopes based on the prediction of binding to certain major histocompatibilty complex (MHC) molecules and peptide or protein libraries that have been generated in expression systems, e.g. phage, or rely on combinatorial peptide chemistry. The latter technique has been refined by a number of laboratories including ours. Bead-bound or, preferably, positional scanning synthetic and soluble combinatorial peptide libraries allow the identification of T-cell epitopes within complex mixtures of proteins even for T cells that have been expanded from an organ infiltrate with a polyclonal stimulus. The practical steps that are involved in the latter method are described in this article.
Amino Acid Sequence↗
New inhibitors of Helicobacter pylori urease holoenzyme selected from phage-displayed peptide libraries.
Urease is an important virulence factor for Helicobacter pylori and is critical for bacterial colonization of the human gastric mucosa. Specific inhibition of urease activity has been proposed as a possible strategy to fight this bacteria which infects billions of individual throughout the world and can lead to severe pathological conditions in a limited number of cases. We have selected peptides which specifically bind and inhibit H. pylori urease from libraries of random peptides displayed on filamentous phage in the context of pIII coat protein. Screening of a highly diverse 25-mer combinatorial library and two newly constructed random 6-mer peptide libraries on solid phase H. pylori urease holoenzyme allowed the identification of two peptides, 24-mer TFLPQPRCSALLRYLSEDGVIVPS and 6-mer YDFYWW that can bind and inhibit the activity of urease purified from H. pylori. These two peptides were chemically synthesized and their inhibition constants (Ki) were found to be 47 microM for the 24-mer and 30 microM for the 6-mer peptide. Both peptides specifically inhibited the activity of H. pylori urease but not that of Bacillus pasteurii.
Amino Acid Sequence↗
Characterization of combinatorial peptide libraries by electrospray ionization Fourier transform mass spectrometry.
The advantages of Fourier transform mass spectrometry (FTMS) are precision high mass accuracy measurements and the capability of high resolution, multistage mass spectrometry together with a number of other advanced features. These powerful facilities can be used to rapidly screen complex mixtures without the necessity of chromatographic separations. The example shown here illustrates the use of the high resolving power and accurate mass capabilities of FTMS for the rapid, direct analysis of a complex mixture, which had been ionized by direct infusion electrospray ionization.
Electrochemistry↗
Anti-Galectin-3 IgG autoantibodies in patients with Crohn's disease characterized by means of phage display peptide libraries.
Galectin-3, a member of beta-galactoside-binding lectins, is expressed and secreted by a variety of cell types including human intestinal epithelial cells. The presence of anti-galectin-3 antibody in the sera of patients was analyzed by immunoblotting using recombinant human galectin-3. A substantially higher percentage of sera from Crohn's disease patients contained anti-galectin-3 IgG autoantibodies than from patients with ulcerative colitis, primary biliary cirrhosis, or autoimmune hepatitis and of apparently healthy control volunteers. In Crohn's disease patients the titer of autoantibodies was high and interestingly correlated negatively with disease activity. To characterize and generate artificial epitopes (mimotopes), the anti-galectin-3 monoclonal antibodies A3A12 and B2C10 were used for biopannings of phage display nonapeptide libraries. These mimotopes interfered with the binding of autoantibodies to recombinant and native intestinal epithelial galectin-3. Our data may suggest that galectin-3 mimotopes could be used for the induction of IgG with desired specificity to regulate immune responses in Crohn's disease patients.
Amino Acid Sequence↗
Identification of receptor ligands with phage display peptide libraries.
With the development and maturation of the technology of displaying peptides on bacteriophage, it has become possible to isolate peptide ligands to various targets. In the phage display strategy, up to 10(9) peptides of different permutations are expressed on the surface of filamentous phage. Thus, peptides capable of binding target molecules in vitro and even target tissues in vivo can be identified. In recent years, a series of libraries that display degenerate peptides of different lengths have been constructed, and specific ligands to cell surface receptors, such as integrins, have been isolated. In the in vivo biopanning, peptides targeting distinct organs or tumors have been rescued after intravenous administration of phage libraries into mice. In one application, the isolated peptide ligands have been used to direct a cytotoxic drug to tumor vasculature in mice. Further applications in radioimaging and radiotherapy are being investigated.
Animals↗
Identification of the peptides that inhibit the stimulation of thyrotropin receptor by Graves' immunoglobulin G from peptide libraries.
Graves' disease is characterized by the overproduction of thyroid hormones due to the persistent stimulation of TSH receptor by autoantibodies. To determine the epitopes recognized by the autoantibodies, an enzyme-linked immunosorbent assay was developed that uses the human TSH receptor extracellular domain attached to plastic wells. The total IgG from some of the Graves' patients interacted with the bound TSH receptor (TSHR) at a significantly higher level than that in normal individuals. The IgG preparation that showed the highest binding activity was used for the identification of peptide sequences that prevent binding of Graves' IgG to TSHR from positional scanning synthetic peptide combinatorial libraries. A hexapeptide mixture, X1X2FDDA (X1 is a mixture of E, M, and Y; X2 is a mixture of E, H, and T), was found to be effective for inhibiting the binding of Graves' IgG to the TSHR. Further fractionation of X1X2FDDA showed that the following three sequences were highly effective: EEFDDA, ETFDDA, and EHFDDA. The second position of the three peptides did not appear to be important. The peptides also inhibited the cAMP synthesis induced by IgG of four of eight patients with Graves' disease tested. The synthesis of cAMP by TSH was also inhibited by the peptides to some extent. The peptide sequences most likely mimic a part of the conformational epitopes recognized by at least one class of Graves' IgG.
Amino Acid Sequence↗
Using peptide libraries to identify optimal cleavage motifs for proteolytic enzymes.
Proteases and peptidases are involved in a vast array of fundamental cellular processes, including cell growth, survival, motility, death, and differentiation, and can be important players in multicellular systems such as angiogenesis, inflammation, and immunity. Though long considered to be essentially digestive enzymes that mediate complete degradation of their substrates, many proteases are now known to be highly site specific. Knowledge of the cleavage site motif for a protease or peptidase can be useful in the design of substrates and inhibitors for the enzyme, and can also provide insight into its biological function through the identification and characterization of its protein substrates. Here, we describe in detail methodology that allows for the rapid and general determination of optimal recognition sequences for proteolytic enzymes.
Acetylation↗
Binding epitope of somatostatin defined by phage-displayed peptide libraries.
We have developed a versatile phagemid system to display peptides on the surface of M13 bacteriophage at a copy number which approaches monovalency. In this system, a phagemid encodes a peptide fused to the amino-terminus of the second domain (dII) of the minor coat protein pIII under control of the inducible lac promoter. The fusion protein is displayed in combination with several copies of wild-type pIII on the surface of phage. Two diverse random octapeptide libraries, one linear and one which contained flanking cysteines capable of forming disulfide bridges, were were generated using an in vitro mutagenesis approach and affinity selected on an anti-somatostatin mAb. Peptides with high affinity for the mAb were enriched only from the cyclic library and the tetrapeptide, FWKT, was identified by consensus as the binding epitope. The selected peptides exhibited not only the primary amino acid sequence but also shared structural features with somatostatin. One peptide, CRFWKTWC, also exhibited nanomolar affinities for the five known somatostatin receptor subtypes. This system can easily be adapted to display individual peptides or a wide range of custom peptide libraries.
Amino Acid Sequence↗
Small peptide libraries: combinatorial split-mix synthesis followed by combinatorial amino acid analysis of selected variants.
Peptides from small combinatorial libraries, covalently attached to polymeric TentaGel beads, can be directly sequenced using amino acid analysis. For libraries with restricted diversity, generated by the split-mix synthesis method, the amino acids on a selected single bead identified by pre-column derivatization with o-phthaldialdehyde (OPA) correlate directly with the sequence of a given peptide. This is shown on a tripeptide (343 different compounds) and a tetrapeptide (4096 different compounds) library. This method allows for rapid peptide sequence determination without relying on complex encoding strategies.
Amino Acid Sequence↗
Fine mapping of monoclonal antibody epitopes on human von Willebrand factor using a recombinant peptide library.
A recombinant human von Willebrand factor (vWF) cDNA fragment library was constructed in lambda gt11 for the localization of anti-vWF monoclonal antibody epitopes. Twelve of 21 monoclonal antibodies screened identified epitopes expressed in lambda gt11 as beta-galactosidase fusion proteins. By sequence analysis, these antigenic determinants were localized to segments ranging from 17 to 105 amino acids in length. Four epitopes apparently shared by more than one antibody were identified, suggesting the presence of immuno-dominant epitopes within vWF. Monoclonal antibody C3, which blocks factor VIII (FVIII) binding to vWF, bound to the same epitope previously identified by a second monoclonal antibody which also blocks this function, suggesting that this region may be at or near the vWF/FVIII binding domain. Three antibodies recognize the same region within the vWF A2 repeat. Mutations near this region appear to be responsible for Type IIA von Willebrand's disease. The co-localization of these antibodies suggests that this domain might be exposed on the surface of vWF, consistent with its apparent increased sensitivity to plasma proteases.
Antibodies, Monoclonal↗