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At least 649 records · Page 36Linked to original sources
PubMed2006

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This set of peptides is regarded as mimicking the genuine epitope of the antibody's interacting antigen and can be used to define it. Here we present PepSurf, an algorithm for mapping a set of affinity-selected peptides onto the solved structure of the antigen. The problem of epitope mapping is converted into the task of aligning a set of query peptides to a graph representing the surface of the antigen. The best match of each peptide is found by aligning it against virtually all possible paths in the graph. Following a clustering step, which combines the most significant matches, a predicted epitope is inferred. We show that PepSurf accurately predicts the epitope in four cases for which the epitope is known from a solved antibody-antigen co-crystal complex. We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs.

Algorithms↗
PubMed2000

A novel approach for the identification of unique tumor vasculature binding peptides using an E. coli peptide display library.

BACKGROUND: Tumor neovascularization is necessary for continued tumor growth and metastasis. During the process of endothelial cell (EC) recruitment and tumor infiltration, specific molecular markers unique for this interaction are expressed on the EC surface. Targeting these molecular markers would, in effect, allow for specific tumor targeting. Tripeptide sequence motifs have previously been reported that will bind to angiogenic tumor ECs. These sequences were identified from in vivo phage peptide display libraries. The purpose of this study was to use a more simplified bacterial peptide display library in an in vitro system to seek out peptide motifs with unique binding to tumor microvasculature. METHODS: FliTrx is a bacterial peptide display library containing the entire repertoire of possible random dodecapeptides expressed on the flagella tip of E. coli. Two EC populations were used for the screening process, Matrigel invading cells (MAGIC) and tumor-derived endothelial cells (TDEC). MAGIC are obtained from ECs that infiltrate a subcutaneous fibroblast growth factor-containing Matrigel deposit, and TDEC are ECs selectively obtained from tumor vasculature. FliTrx cells were incubated with MAGIC at 4 degrees C to remove any potential clones displaying peptides that will bind to nonspecific EC surface targets. The non-binding cells were then incubated with TDEC, allowing for clones displaying potential binding peptides to bind tumor specific targets on TDECs. The bacterial population was then expanded and this "panning" process was carried out a total of five times. Peptide insert sequences from 100 bacterial colonies were analyzed for potential repetitive peptide motifs. RESULTS: Recurring peptide sequences were detected that were 3-mers (13 sequences) and 4-mers (4 sequences). Of the 3-mers, four repeated 3 times, whereas none of the 4-mers repeated more than twice. All of the repeated sequences were basic in charge, and arginine was the most commonly seen amino acid. A tripeptide basic-basic-nonpolar amino acid arrangement was the most prevalent charge sequence in all repetitive motifs (17 repeat sequences). Two test peptides showed TDEC binding specificity, and both conformed to the basic-basic-nonpolar motif. CONCLUSIONS: We report peptide sequences derived from panning an in vitro system designed to detect tumor-EC specific markers. These putative motifs may serve as molecular determinants for a novel therapeutic modality aimed at specifically targeting tumors through tumor angiogenic vessels.

3T3 Cells↗
PubMed2002

Identification of novel hexapeptides bioactive against phytopathogenic fungi through screening of a synthetic peptide combinatorial library.

The purpose of the present study was to improve the antifungal activity against selected phytopathogenic fungi of the previously identified hexapeptide PAF19. We describe some properties of a set of novel synthetic hexapeptides whose D-amino acid sequences were obtained through screening of a synthetic peptide combinatorial library in a positional scanning format. As a result of the screening, 12 putative bioactive peptides were identified, synthesized, and assayed. The peptides PAF26 (Ac-rkkwfw-NH(2)), PAF32 (Ac-rkwhfw-NH(2)), and PAF34 (Ac-rkwlfw-NH(2)) showed stronger activity than PAF19 against isolates of Penicillium digitatum, Penicillium italicum, and Botrytis cinerea. PAF26 and PAF32, but not PAF34, were also active against Fusarium oxysporum. Penicillium expansum was less susceptible to all four PAF peptides, and only PAF34 showed weak activity against it. Assays were also conducted on nontarget organisms, and PAF26 and PAF32 showed much-reduced toxicity to Escherichia coli and Saccharomyces cerevisiae, demonstrating selectivity towards certain filamentous fungi. Thus, the data showed distinct activity profiles for peptides differentiated by just one or two residue substitutions. Our conclusion from this observation is that a specificity factor is involved in the activity of these short peptides. Furthermore, PAF26 and PAF32 displayed activities against P. digitatum, P. italicum, and B. cinerea similar to that of the hemolytic 26-amino acid melittin, but they did not show the high toxicity of melittin towards bacteria and yeasts. The four peptides acted additively, with no synergistic interactions among them, and PAF26 was shown to have improved activity over PAF19 in in vivo orange fruit decay experiments.

Antifungal Agents↗
PubMed2006

Protease specificity determination by using cellular libraries of peptide substrates (CLiPS).

We report a general combinatorial approach to identify optimal substrates of a given protease by using quantitative kinetic screening of cellular libraries of peptide substrates (CLiPS). A whole-cell protease activity assay was developed by displaying fluorescent reporter substrates on the surface of Escherichia coli as N-terminal fusions. This approach enabled generation of substrate libraries of arbitrary amino acid composition and length that are self-renewing. Substrate hydrolysis by a target protease was measured quantitatively via changes in whole-cell fluorescence by using FACS. FACS enabled efficient screening to identify optimal substrates for a given protease and characterize their cleavage kinetics. The utility of CLiPS was demonstrated by determining the substrate specificity of two unrelated proteases, caspase-3 and enteropeptidase (or enterokinase). CLiPS unambiguously identified the caspase-3 consensus cleavage sequence DXVDG. Enteropeptidase was unexpectedly promiscuous, but exhibited a preference for substrates with the motif (D/E)RM, which were cleaved substantially faster than the canonical DDDDK recognition sequence, widely used for protein purification. CLiPS provides a straightforward and versatile approach to determine protease specificity and discover optimal substrates on the basis of cleavage kinetics.

Amino Acid Sequence↗
PubMed2005

Synthetic peptide arrays and peptide combinatorial libraries for the exploration of protein-ligand interactions and the design of protein inhibitors.

Synthetic peptides have a long tradition as molecular tools in biomedical research and drug discovery. The introduction of high-throughput synthesis and screening technologies for synthetic peptides, such as arrays and combinatorial libraries, enabled the large-scale and detailed exploration of protein-ligand interactions, as well as the discovery of novel biologically active peptides. This review summarizes currently available synthetic peptide array and library technologies, in particular mixture-based peptide libraries, which are illustrated by numerous applications in various fields of biomedical research.

Combinatorial Chemistry Techniques↗
PubMed1991

Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery.

Existing methods for the synthesis and screening of large numbers of peptides are limited by their inability to generate and screen the requisite number (millions) of individual peptides and/or their inability to generate unmodified free peptides in quantities able to interact in solution. We have circumvented these limitations by developing synthetic peptide combinatorial libraries composed of mixtures of free peptides in quantities which can be used directly in virtually all existing assay systems. The screening of these heterogeneous libraries, along with an iterative selection and synthesis process, permits the systematic identification of optimal peptide ligands. Starting with a library composed of more than 34 million hexa-peptides, we present here the precise identification of an antigenic determinant recognized by a monoclonal antibody as well as the straightforward development of new potent antimicrobial peptides.

Antibodies, Monoclonal↗
PubMed2000

Selection of an immunogenic peptide mimic of the capsular polysaccharide of Neisseria meningitidis serogroup A using a peptide display library.

The presently available meningococcal vaccine is poorly immunogenic in infants and fails to induce long-lasting immunity in adults. Efforts to convert this TI-2 type vaccine into a T dependent vaccine are being actively pursued and include conjugate vaccine development. Alternatively, the meningococcal polysaccharide can be rendered into a T dependent antigen through the use of peptides which mimic the capsular polysaccharide complexed or conjugated to potent protein carrier molecules. We have previously developed an anti-idiotypic monoclonal antibody (mAb) based peptide mimic of meningococcal group C polysaccharide (MCPS). A direct approach to identification of peptide mimics of antigen is through the use of peptide display libraries. We have utilized a phage library and a mAb with specificity for meningococcal group A polysaccharide (MAPS) to screen for a peptide mimic of MAPS. Six different peptide motifs were selected with the use of the mAb. Thirty-eight of the 60 sequenced phage clones were represented by motif 1 and 2 which differed only in three amino acids at the carboxy terminus. Immunological assays were performed. Phage clones with motif 1 and 2 were capable of binding human hyperimmune sera and inhibiting the binding of human hyperimmune sera to nominal antigen. Immunization with motif 1 peptide complexed to proteosomes resulted in an anti-MAPS antibody response. Priming with the peptide proteosome complex induced an anamnestic response indicating the formation of immunological memory.

Amino Acid Sequence↗
PubMed1999

Identification of substrate sequences for membrane type-1 matrix metalloproteinase using bacteriophage peptide display library.

Membrane type-1 matrix metalloproteinase (MT1-MMP) has been reported to mediate the activation of progelatinase A (proMMP-2) which is associated with tumor invasion and metastasis, and also known to have an ability to digest extracellular matrix components. To clarify substrate specificity of MT1-MMP, we have searched for amino acid sequences cleaved by this protease using the hexamer substrate phage library consisting of a large number of randomized amino acids sequences. The consensus substrate sequences for MT1-MMP were deduced from the selected clones and appeared to be P-X-G/P-L at the P3-P1' sites. Peptide cleavage assay revealed that MT1-MMP preferentially digested a synthetic substrate containing Pro of the P1 position compared to that being substituted with Gly. Our results may have an important implication to identifying new target proteins for MT1-MMP and leading to the design of its selective inhibitors suitable for cancer chemotherapy.

Bacteriophages↗
PubMed1998

Selection of phage displayed peptides from a random 10-mer library recognising a peptide target.

BACKGROUND: Peptide display libraries are powerful tools in the search for detailed information about protein-protein interactions. Usual targets for isolation of phage displayed peptide ligands include antibodies, various receptors, other full size proteins or larger fragments thereof. Smaller protein fragments such as synthetic peptides have not been reported as targets for screening of peptide display libraries. OBJECTIVES: To investigate whether a protein target used for screening of a peptide display library could be scaled down to peptide size. As the peptide target we wanted to use a sequence derived from the cytosolic tail of MHC class II associated invariant chain containing a leucine class endosomal sorting signal, known to be recognised as an autonomous functional unit during targeting of class II complexes to antigen processing compartments. STUDY DESIGN: A screening procedure where a synthetic 15-mer invariant chain peptide was coupled to a methacrylate matrix of high binding capacity was developed, and three rounds of selection were performed from a random 10-mer fUSE5 display library. RESULTS: The peptide display library was successfully enriched for phage clones with affinity for the invariant chain peptide. Furthermore, the binding phage clones were able to distinguish between a functional and a mutated form of the target. These clones therefore displayed possible peptide mimetics of signal recognition sites in the cellular sorting machinery. CONCLUSION: The size of a protein target may be scaled down to peptide size and be recognised by a 10-mer peptide displayed on filamentous phage. This approach may particularly be useful when the peptide target contains a functional unit for recognition.

Amino Acid Sequence↗
PubMed1999

Selection of cell specific peptides in a rat carotid injury model using a random peptide-presenting bacterial library.

Cell specific peptides are possible candidates to enable targeted delivery of drugs and therapeutic genes in vivo. This study explores the utility of using a peptide-presenting bacterial library (pFliTrx) for the selection of new cell specific peptides, which bind to vascular cells of perfused tissues or organs. The balloon-injured rat carotid artery served as a model. Following perfusion of injured vascular segments with pFliTrx, 36 single clones could be identified. In radioligand binding studies, one of them, peptide P36, binds predominantly to perfused injured versus control vessel segments. It was additionally found that P36 binds with a 700-fold higher affinity in vitro to endothelial cells stimulated by treatment with LPS and TNF-alpha compared with unstimulated endothelial cells. The amino acid sequence of P36 reveals high homology to alpha(4)beta(1)-integrin, which mediates leukocyte migration from the vasculature at sites of inflammation via binding to cellular adhesion molecules, such as VCAM. In summary, this study demonstrates, that high specific peptides directed against injured vascular cells can be selected using a random peptide-presenting bacterial library.

Animals↗
PubMed2004

Selection and characterization of peptides specifically binding to HIV-1 psi (psi) RNA.

The packaging of HIV genomic RNA is mediated by a specific interaction between a nucleocapsid (NC) protein and packaging signal (psi, psi) RNA sequence. However, this interaction can be inhibited by the presence of peptides or proteins that specifically bind to the psi sequence. The 125-base-long psi RNA comprises a specific secondary structure that can be recognized by certain peptide sequences. Accordingly, the current study presents a method for selecting such peptides from a phage-displayed peptide library and characterization of resulting peptides in vitro. The RNA was covalently immobilized in a Covalink module using a carbodiimide condensation reaction at its 5'-end, leaving the proper secondary structure exposed and readily accessible. A phage display random peptide library was then screened against the RNA structure, and after five rounds of biopanning, enriched peptide sequences and conserved amino acid frames appeared. One of the enriched peptides was tested and shown to bind to psi RNA in a dose-dependent manner, plus it competed effectively with the NC protein as regards binding with the target RNA.

Gene Products, gag↗
PubMed2004

An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for PDZ domain binding studies.

SPOT synthesis permits parallel synthesis and screening of thousands of cellulose membrane-bound peptides to study protein-protein interactions in a proteomic context. Recognition of C-terminal residues is one of the most common binding features of PDZ domains. Unfortunately, most solid support-bound peptide libraries lack a free C terminus due to C-terminal fixation on the solid support. To overcome this restriction, we developed a robust methodology based on our previous strategy for generating peptides with authentic C termini. To validate this improved method, we screened a human peptide library of 6223 C termini with the syntrophin PDZ domain. Furthermore, using the same library, new peptide ligands derived from membrane proteins and receptors were found for the ERBIN PDZ domain. Finally, we identified the protein kinase breakpoint cluster region, which is known as a negative regulator of cell proliferation and oncogenic transformation, as an ERBIN ligand.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Probing biomolecular interactions of glutathione transferase M2-2 by using peptide phage display.

The interactions between biomolecules and human glutathione transferase M2-2 (GST M2-2) were probed by using 9- and 15-mer combinatorial peptide libraries displayed on phage. The peptide libraries were based on random DNA sequences fused to gIII, a gene that expresses a phage coat protein and thus causes the peptides to be displayed on the surface of phage particles. A peptide sequence was enriched through binding to GST M2-2, which indicated a successful selection. Binding studies with the peptide displayed on phage showed binding specificity. The sequence of the peptide had similarities to segments of proteins in the Swiss-Prot Database, to c-Jun N-terminal kinase (JNK), and to the protein Bcl3. JNK is linked to the regulation of the transcription factor AP-1. Use of cell-based assays of the transcriptional activity of AP-1 allowed a novel coactivation function of GST M2-2 to be demonstrated. Specificity in the activation was indicated by the lack of effect of GST A1-1. No coactivator function of GST M2-2 could be demonstrated in assays with Bcl3. These results suggest that GST M2-2 has biological roles in addition to catalysis of detoxication reactions, and demonstrate the potential of phage display in functional genomics research.

B-Cell Lymphoma 3 Protein↗
PubMed2004

Immunological factors that affect the in vivo fate of T7 phage in the mouse.

Phage display is a powerful method to study organ and tissue specific addresses. As part of our studies on the in vivo panning of tissue-homing peptide libraries, we examined the survival of T7 phage in the blood of C57BL/6J mice to estimate the half-life of T7 phage and the factors responsible for its inactivation. Amplified and purified T7 phage particles with or without random peptide library inserts were injected intravenously into the tail vein of wild-type (C57BL/6J) and immunocompromized (C57BL/6J) female mice. In wild-type mice, both the parent phage as well as phage carrying a peptide library were eliminated quickly from the blood, with only approximately 1% survival of detectable infectious phage after 60 min of injection. In SCID (C57BL/6J-Prkdc(scid)) mice, phage titers were stable over the same period of time with or without peptide library, suggesting a role for either B- or T cells or both in phage inactivation. The presumed role of B cell was indicated by demonstration of stable phage in the B-cell deficient mouse (C57BL/10-Igh-6(tm1Cgn)). In other immunocompromized mice, the phage titers were unstable, similar to that found in wild-type mice. In no case, was there a difference between phage with or without random peptide library. These data indicate that the presence of random C-X7-C peptides on the T7 phage coat protein does not affect the clearance of the phage in murine blood. Most likely, host immune factors play a role in the neutralization of T7 phage in blood by reacting with B-cell dependent immunoglobin.

Animals↗
PubMed2005

Combinatorial solid phase peptide synthesis and bioassays.

Solid phase peptide synthesis method, which was introduced by Merrifield in 1963, has spawned the concept of combinatorial chemistry. In this review, we summarize the present technologies of solid phase peptide synthesis (SPPS) that are related to combinatorial chemistry. The conventional methods of peptide library synthesis on polymer support are parallel synthesis, split and mix synthesis and reagent mixture synthesis. Combining surface chemistry with the recent technology of microelectronic semiconductor fabrication system, the peptide microarray synthesis methods on a planar solid support are developed, which leads to spatially addressable peptide library. There are two kinds of peptide microarray synthesis methodologies: pre-synthesized peptide immobilization onto a glass or membrane substrate and in situ peptide synthesis by a photolithography or the SPOT method. This review also discusses the application of peptide libraries for high-throughput bioassays, for example, peptide ligand screening for antibody or cell signaling, enzyme substrate and inhibitor screening as well as other applications.

Biological Assay↗
PubMed1998

Probing degeneracy in T-cell recognition using peptide combinatorial libraries.

Recent studies have demonstrated flexibility of the T-cell receptor (TCR) with respect to recognition of peptide bound to self major histocompatibility complex (MHC). With the introduction of peptide combinatorial libraries, it has become possible to dissect the extent of degeneracy in T-cell recognition. On the basis of these novel findings, Bernhard Hemmer and colleagues propose a conceptual framework for lymphocyte selection and survival and the occurrence of autoimmunity.

Humans↗
PubMed2005

Identification of the membrane-active regions of the severe acute respiratory syndrome coronavirus spike membrane glycoprotein using a 16/18-mer peptide scan: implications for the viral fusion mechanism.

We have identified the membrane-active regions of the severe acute respiratory syndrome coronavirus (SARS CoV) spike glycoprotein by determining the effect on model membrane integrity of a 16/18-mer SARS CoV spike glycoprotein peptide library. By monitoring the effect of this peptide library on membrane leakage in model membranes, we have identified three regions on the SARS CoV spike glycoprotein with membrane-interacting capabilities: region 1, located immediately upstream of heptad repeat 1 (HR1) and suggested to be the fusion peptide; region 2, located between HR1 and HR2, which would be analogous to the loop domain of human immunodeficiency virus type 1; and region 3, which would correspond to the pretransmembrane region. The identification of these membrane-active regions, which are capable of modifying the biophysical properties of phospholipid membranes, supports their direct role in SARS CoV-mediated membrane fusion, as well as facilitating the future development of SARS CoV entry inhibitors.

Amino Acid Sequence↗