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At least 127 records · Page 7Linked to original sources

Characterization of a novel NCAM ligand with a stimulatory effect on neurite outgrowth identified by screening a combinatorial peptide library.

The neural cell adhesion molecule, NCAM, plays a key role in neural development and plasticity mediating cell adhesion and signal transduction. By screening a combinatorial library of synthetic peptides with NCAM purified from postnatal day 10 rat brains, we identified a nonapeptide, termed NCAM binding peptide 10 (NBP10) and showed by nuclear magnetic resonance analysis that it bound the NCAM IgI module of NCAM. NBP10 modulated cell aggregation as well as neurite outgrowth induced specifically by homophilic NCAM binding. Moreover, both monomeric and multimeric forms of NBP10 stimulated neurite outgrowth from primary hippocampal neurons. The neurite outgrowth response to NBP10 was inhibited by a number of compounds previously shown to inhibit neurite outgrowth induced by homophilic NCAM binding, including voltage-dependent calcium channel antagonists, suggesting that NBP10 induced neurite outgrowth by activating a signal transduction pathway similar to that activated by NCAM itself. Moreover, an inhibitor of intracellular calcium mobilization, TMB-8, prevented NBP10-induced neurite outgrowth suggesting that NCAM-dependent neurite outgrowth also requires mobilization of calcium from intracellular calcium stores in addition to calcium influx from extracellular sources. By single-cell calcium imaging we further demonstrated that NBP10 was capable of inducing an increase in intracellular calcium in PC12E2 cells. Thus, the NBP10 peptide is a new tool for the study of molecular mechanisms underlying NCAM-dependent signal transduction and neurite outgrowth, and could prove to be a useful modulator of regenerative processes in the peripheral and central nervous system.

Animals↗

Development of an antagonist of molluscan neuropeptide APGWamide with a peptide library.

Fifty-seven kinds of APGWamide-related peptides and a peptide library consisting of 38 peptide mixtures, each of which contained 19 kinds of APGWamide-related peptides, were synthesized with a multipeptide synthesizer, and their APGWamide-agonistic or -antagonistic effects were examined on the anterior byssus retractor muscle of the bivalve Mytilus edulis and the crop of the land snail Euhadra congenita. The peptide mixtures having agonistic or antagonistic effects were subjected to HPLC purification to isolate the active peptides using the muscles as bioassay systems. Many peptides having agonistic or antagonistic effects were obtained. Of the antagonists, APGWGNamide, isolated from the peptide mixture of APGWGXamide, was the most potent. At 10(-4) M, APGWGNamide almost completely blocked the actions of 10(-6) M APGWamide on the anterior byssus retractor muscle of M. edulis and the crop of E. congenita.

Animals↗

Peptide libraries for T cell epitope screening and characterization.

Screening with synthetic peptide libraries is the fastest and most efficient method for locating helper T cell (Th) and cytotoxic T cell (Tc) epitopes in proteins of known sequence. Epitope detection and analysis can be performed on clones, lines or freshly isolated ex-vivo T cells. Novel approaches to peptide library design ensure that the peptides are presented in a format which is optimized for Th or Tc epitope detection and analysis. The major histocompatibility complex (MHC) binding motif can be determined by binding or functional assays using analogs of the minimal active sequence.

Combinatorial Chemistry Techniques↗

[Screening of mimic epitopes of Trichinella spiralis antigen from phage 12-mer peptide library].

OBJECTIVE: To screen special mimic epitopes of Trichinella spiralis antigen from peptide library for exploring new diagnostic antigens. METHODS: Ts-IgG purified from serum of trichinosis patients was used to screen the phage 12-mer peptide library for 5 rounds. 24 clones were picked out randomly to detect the immunoactivity. The sensitivity and specificity of the 6 clones (T1 - T6) whose A values were higher than others were tested by ELISA. RESULTS: The sensitivity of the clones T1 - T6 was the same with larval antigen of Trichinella spiralis (TsA) (positive rate: 100%, P > 0.05), and there was no difference in specificity between T1 - T6 and TsA (negative rate: 0 - 40%, P > 0.05); T3 and T6 did not react with sera from patients of paragonimiasis, showing higher specificity than TsA (P < 0.05); T6 did not react with sera from patients of schistosomiasis, also showing higher specificity than TsA (P < 0.05). CONCLUSION: The mimic antigenic epitopes of Trichinella spiralis have been successfully obtained by screening phage 12-mer peptide library.

Animals↗

Investigating the substrate specificity of the HER2/Neu tyrosine kinase using peptide libraries.

The product of the HER2/Neu oncogene is a receptor tyrosine kinase that is amplified in 25-30% of human primary breast tumors. In this project, we have isolated the HER2/Neu kinase from Sf9 cells infected with a baculovirus expression vector. We probed the substrate specificity of the HER2/Neu kinase using two peptide libraries: (1) a soluble peptide library containing three degenerate positions N-terminal to tyrosine; and (2) a bead-supported combinatorial library possessing six degenerate positions at P-1, P-2, P-3, P+1, P+2, and P+3. We identified four novel substrate sequences for HER2/Neu from the two peptide libraries. We synthesized these peptides as individual sequences and measured steady-state kinetic properties for phosphorylation by HER2/Neu. One of the peptides, AAEEIYAARRG, is the best synthetic peptide substrate reported to date for HER2/Neu. All of the sequences bear a resemblance to sites of autophosphorylation on HER2/Neu and related epidermal growth factor (EGF) receptor family tyrosine kinases.

Amino Acid Sequence↗

Definition of the primary structure of hepatitis B virus (HBV) pre-S hepatocyte binding domain using random peptide libraries.

The pre-S-specific monoclonal antibody MA 18/7 has been shown to inhibit the binding of HBV to HepG2 cells and liver membranes. This antibody can thus be used to identify the critical residues of the pre-S region involved in the hepatocyte-binding domain. Using overlapping 7-mer peptides representing the pre-S region of HBV, the epitope recognized by MA 18/7 was shown to contain sequences from both the pre-S1 and pre-S2 regions, thus indicating that the hepatocyte-binding domain is conformationally dependent. To further characterize the primary structure of the hepatocyte-binding domain on the pre-S protein, a phage-displayed 15-mer peptide library and a 8-mer solid phase peptide library were used to analyze the fine specificity of the monoclonal antibody MA 18/7. Several mimotopes were identified with the phage-displayed peptide library, the majority of which possess a central motif with at least three identical residues present within the native pre-S1 sequence. No significant consensus sequences were found when these mimotopes were compared to the pre-S2 sequence. Mimotopes identified using the solid-phase peptide library also contained a similar motif. All phage mimotopes and a single mimotope from the solid-phase peptide library competed with recombinant HBsAg particles containing the pre-S1 region for binding to MA 18/7. Mouse antisera raised against four mimotopes from the phage display library reacted with HBsAg particles containing pre-S sequences. The data show that the structure of the pre-S molecule around the conserved DPAF motif in the pre-S region may have a functional role in binding HBV to cellular receptors, and that the central motif identified in mimotopes of this region may offer a novel strategy target for the improvement of existing hepatitis B vaccines which, at present, are mostly devoid of pre-S specificities.

Amino Acid Sequence↗

Selection of SARS-coronavirus-specific B cell epitopes by phage peptide library screening and evaluation of the immunological effect of epitope-based peptides on mice.

Antibodies to SARS-Coronavirus (SARS-CoV)-specific B cell epitopes might recognize the pathogen and interrupt its adherence to and penetration of host cells. Hence, these epitopes could be useful for diagnosis and as vaccine constituents. Using the phage-displayed peptide library screening method and purified Fab fragments of immunoglobulin G (IgG Fab) from normal human sera and convalescent sera from SARS-CoV-infected patients as targets, 11 B cell epitopes of SARS-CoV spike glycoprotein (S protein) and membrane protein (M protein) were screened. After a bioinformatics tool was used to analyze these epitopes, four epitope-based S protein dodecapeptides corresponding to the predominant epitopes were chosen for synthesis. Their antigenic specificities and immunogenicities were studied in vitro and in vivo. Flow cytometry and ELISPOT analysis of lymphocytes as well as a serologic analysis of antibody showed that these peptides could trigger a rapid, highly effective, and relatively safe immune response in BALB/c mice. These findings might aid development of SARS diagnostics and vaccines. Moreover, the role of S and M proteins as important surface antigens is confirmed.

Amino Acid Sequence↗

Peptide length preferences for rat and mouse MHC class I molecules using random peptide libraries.

MHC class I molecules bind short peptides for presentation to CD8+ T cells. The determination of the three-dimensional structure of various MHC class I complexes has revealed that both ends of the peptide binding site are composed of polar residues conserved among all human and murine MHC class I sequences, which act to lock the ends of the peptide into the groove. In the rat, however, differences in these important residues occur, suggesting the possibility that certain rat MHC class I molecules may be able to bind and present longer peptides. Here we have studied the peptide length preferences of two rat MHC class Ia molecules expressed in the TAP2-deficient mouse cell line RMA-S: RT1-A1c, which carries unusual key residues at both ends of the groove, and RT1.Aa which carries the canonical residues. Temperature-dependent peptide stabilization assays were performed using synthetic random peptide libraries of different lengths (7-15 amino acids) and successful stabilization was determined by FACS analysis. Results for two naturally expressed mouse MHC class I molecules revealed different length preferences (H2-Kb, 8-13-mer and H2-Db, 9-15-mer peptides). The rat MHC class Ia molecule, RT1-Aa, revealed a preference for 9-15-mer peptides, whereas RT1-A1c showed a more stringent preference for 9-12-mer peptides, thereby ruling out the hypothesis that unusual residues in rat MHC molecules allow binding of longer peptides.

Animals↗

Screening of tumor necrosis factor-alpha-binding peptides by phage display peptide library.

OBJECTIVE: To identify and characterize tumor necrosis factor (TNF)-alpha-binding peptides from c7c phage display peptide library, in an attempt to find short peptides that can be used as antagonist of TNF-alpha. METHODS: The TNF-alpha-binding peptides were screened from c7c phage display peptide library by using rhTNF-alpha as target protein and identified by sandwich ELISA. RESULTS: After 3 rounds of screening, 11 of 23 phage clones were identified as positive clones which can bind to rhTNF-alpha. The amino acid sequence in two of these 11 clones is c-ALWHWWH-c, and that in the others is c-(T/S)WLHWWA-c. CONCLUSION: These phage display peptides are TNFalpha-binding peptides.

Humans↗

Identification of the peptides that inhibit the function of human monoclonal thyroid-stimulating antibodies from phage-displayed peptide library.

Autoantibodies against TSH receptor (TSHR) are known to be involved in the occurrence of Graves' disease. It is obvious that mapping of epitopes of the autoantibodies found in the patients with Graves' disease is an important step in elucidating possible mechanism of generation of the autoantibodies against TSHR as well as in developing effective diagnostic and therapeutic approaches for Graves' disease. In this report we have identified the peptide sequences that bind to two human monoclonal thyroid-stimulating antibodies (mTSAbs; B6B7 and 101-2) from a disulfide-constrained phage-displayed peptide library. The peptides selected by three rounds of biopanning showed half-maximal inhibitory activities for cAMP synthesis induced by mTSAbs at about 0.1 micromol/L. SPWTLGA and TQWNMQH selected for B6B7 and 101-2, respectively, show specificity for their respective antibodies. This means that different clones of mTSAbs may have different epitopes for TSHR. The IgG of the patient from whom B6B7 was derived binds with specificity to the respective immobilized peptide in an enzyme-linked immunosorbant assay format, and its cAMP generation was also inhibited by selected peptide. It may be possible that the epitopes of TSAbs identified from the phage-displayed peptide library could be used for the classification of different clones of TSAbs present in patients with Graves' disease and for development of drugs to treat Graves' disease.

Amino Acid Sequence↗

Chemically derived peptide libraries: a new resin and methodology for lead identification.

We have developed a new resin for peptide synthesis that can be used to synthesize and evaluate directly combinatorial peptide libraries for binding target proteins. Fidelity of the peptide synthesis using this hydrophilic resin is comparable to polystyrene-based resins. Peptide libraries synthesized on this resin were probed by a two color PEptide Library Immunostaining Chromatographic ANalysis (PELICAN) technique for sequences binding the serine protease Factor IX zymogen. This PELICAN technique readily distinguishes between beads interacting with the reagents for target detection (blue beads) from those beads specific for the target protein itself (red beads). Validation of the PELICAN technique, as well as purification of Factor IX from plasma, is demonstrated utilizing this resin.

Chromatography, Affinity↗

Investigation of the 'switch-epitope' concept with random peptide libraries displayed as thioredoxin loop fusions.

The 'FLITRX' random peptide library, consisting of dodecamer loop peptides displayed on a thioredoxin-flagellin scaffold on Escherichia coli, was used to select peptide sequences with affinity for a monoclonal antibody. These peptides were further screened for pH- and metal-sensitive antibody binding. Several zinc-sensitive peptides were identified, termed 'switch epitopes'. A soluble, monomeric thioredoxin loop ('Trxloop') insertion analog of a FLITRX switch epitope was constructed and its antibody binding properties were characterized by Western blots. Zinc-dependent antibody recognition was maintained in the Trxloop protein although the apparent antibody affinity was lower. This Trxloop protein bound to an immobilized metal affinity chromatography matrix, similar to a 'histidine-patch' thioredoxin variant, and was reversibly precipitated by 1 mM Zn(2+) or Cu(2+) ions. Residues important for zinc and antibody binding were determined by site-directed mutagenesis. The Trxloop antibody affinity was increased by saturation mutagenesis. Biotinylated Trxloop ('Biotrxloop') variants of the original and improved affinity Trxloop proteins were constructed and characterized by surface plasmon resonance measurements. Increased antibody affinity was partially due to a slower antibody desorption rate, although the relative adsorption rates were dependent on the amount of immobilized Biotrxloop protein, indicating an influence of avidity on the apparent affinity.

Amino Acid Sequence↗

Screening of combinatorial peptide libraries: identification of ligands for affinity purification of proteins using a radiological approach.

Peptides deduced from peptide libraries may serve as affinity ligands for protein purification. Identification of a ligand that binds the protein of interest depends highly on the screening method used. One approach which offers simple and direct detection involves screening a solid-phase peptide library against a radiolabeled target protein. We have developed a radiological screening method, using 14C as a radioactive label, that offers high resolution and sensitivity. Less than 100 DPM/bead are detectable after a one-day exposure using autoradiography. The validity of the technique was illustrated by screening a solid-phase hexameric-peptide library spiked with YNFEVL-beads against 14C-labeled ribonuclease S-protein. For this particular system, the amount of protein bound to a single bead was estimated to be in the femtomolar range with a peptide:protein ratio of 500:1. Finally, a portion of the library was screened against 14C-labeled fibrinogen. Three peptides deduced from the library, WQEHYN, WQETYQ, and YENYGY, purified fibrinogen from a mixture with albumin.

Autoradiography↗

Analysis of the resveratrol-binding protein using phage-displayed random peptide library.

Resveratrol, a plant polyphenol, is found in significant amounts in the skin of grapes and in some traditional herbs. It is reported to exert different biological activities, such as inhibiting lipid peroxidation, scavenging free radicals, inhibiting platelet aggregation, and anticancer activity. In order to screen the resveratrol-binding proteins, we synthesized biotinylated resveratrol, purified by liquid chromatography and immobilized it into streptavidin-coated microplate wells. 3-(4,5-Demethylthiazol-)-2,5-diphenyl tetrazolium bromide assay showed little change in the anticancer activity of biotinylated resveratrol in vitro. A random library of phage-displayed peptides was screened for binding to immobilized resveratrol to isolate resveratrol-binding proteins. Several peptides were found to bind to resveratrol specifically, which was proven by enzyme-linked immunosorbent assay. Through amino acid sequence analysis of the selected peptides and human proteins using the BLAST program, the results showed that resveratrol has an affinity for various proteins such as breast cancer-associated antigen, breast cancer resistance protein, death-associated transcription factor, and human cyclin-dependent kinase. These results demonstrate that our study provides a feasible method for the study of binding proteins of natural compounds using a phage-displayed random peptide library.

Breast↗

Identification of antigenic sites on three hepatitis C virus proteins using phage-displayed peptide libraries.

A novel approach to screening phage-displayed peptide libraries has been used to identify hepatitis C virus (HCV) core, NS4 and NS5 sequences, which are antigenic in humans. Two random peptide libraries were used for screening using a mixture of HCV-positive sera or individual antibodies to core, NS3, NS4, and NS5 HCV proteins affinity-purified from this mixture. Sequencing of 56 selected phage clones resulted in 28 different peptide sequences and identification of seven antigenic regions, three in the core protein (19-26, 34-49, and 73-83), three in the NS4 (1681-1693, 1712-1718, and 1726-1736) and one in the NS5 protein (2251-2260). No NS3-specific peptides were identified. The immune response to core, NS4 and NS5 proteins includes a variety of linear determinants whereas epitopes on the investigated part of NS3 protein appear to be conformation-dependent.

Amino Acid Sequence↗

Screening of combinatorial Peptide libraries for nanocluster synthesis.

A significant challenge in bionanotechnology is the discovery of effective biological interfaces that allow inorganic nanoscale materials to mimic effectively their biological counterparts. Much like de novo design of proteins, the rational design of such interfaces is a daunting task. An alternative approach is to screen libraries of peptides, inspired by known biological examples of such hybrid protein-material interfaces, for peptide ligands capable of not only stabilizing a size-discrete population of nanoclusters, but providing the requisite biological compatibility. The protocol described in this chapter is an approach for the simultaneous screening of spatially addressable combinatorial libraries for the stabilization of a variety of metal sulfide, metal oxide, and zero-valent nanoclusters. Additionally, the screening process allows the researcher to characterize the resulting nanoclusters in terms of a variety of physical properties. Ultimately, an informatics structure-function analysis may be performed in order to elucidate specific properties of the ligand sets, which provides access to certain desired material characteristics.

Animals↗

[Study on the mimic epitopes screening program severe acute respiratory syndromes antigen with random phage peptide library].

OBJECTIVE: To screen the severe acute respiratory syndromes (SARS) mimotopes with random phage peptide library and to investigate their immunogenicity. METHODS: Using SARS sera as selective molecule, a 12 mer phage peptide library was biopanned and positive clones containing the mimic epitopes were selected. The immuno-characteriation of the epitopes were then investigated. RESULTS: 2 positive clones that having specific affinity to SARS sera were obtained. The DNA sequencing data showed no homology between the sequences of the deduced amino acid of the two mimic antigen peptides and the sequence of SARS. CONCLUSION: SARS mimotopes were obtained by phage peptide library screening. This method might provide a new approach for SARS therapy and vaccine development.

Animals↗

Utilization of oriented peptide libraries to identify substrate motifs selected by ATM.

The ataxia telangiectasia mutated (ATM) gene encodes a serine/threonine protein kinase that plays a critical role in genomic surveillance and development. Here, we use a peptide library approach to define the in vitro substrate specificity of ATM kinase activity. The peptide library analysis identified an optimal sequence with a central core motif of LSQE that is preferentially phosphorylated by ATM. The contributions of the amino acids surrounding serine in the LSQE motif were assessed by utilizing specific peptide libraries or individual peptide substrates. All amino acids comprising the LSQE sequence were critical for maximum peptide substrate suitability for ATM. The DNA-dependent protein kinase (DNA-PK), a Ser/Thr kinase related to ATM and important in DNA repair, was compared with ATM in terms of peptide substrate selectivity. DNA-PK was found to be unique in its preference of neighboring amino acids to the phosphorylated serine. Peptide library analyses defined a preferred amino acid motif for ATM that permits clear distinctions between ATM and DNA-PK kinase activity. Data base searches using the library-derived ATM sequence identified previously characterized substrates of ATM, as well as novel candidate substrate targets that may function downstream in ATM-directed signaling pathways.

Amino Acid Motifs↗