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At least 109 records · Page 6Linked to original sources
PubMed2006

Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.

Methodology is described here for the efficient parallel synthesis and cyclization of linear peptide libraries using intramolecular S-alkylation chemistry in combination with Multipin solid phase peptide synthesis (Multipin SPPS). The effective use of this methodology was demonstrated with the synthesis of a 72-member combinatorial library of cyclic thioether peptide derivatives of the conserved four-residue structural motif DD/EXK found in the active sites of the five crystallographically defined orthodox type II restriction endonucleases, EcoRV, EcoRI, PvuII, BamHI and BglI.

Alkylation↗
PubMed1995

Identification of a peptide inhibitor against glycosomal phosphoglycerate kinase of Trypanosoma brucei by a synthetic peptide library approach.

A synthetic peptide library, composed of 2.5 million L-amino acid pentapeptides anchored on polystyrene beads was prepared with each bead bearing a single pentapeptide sequence. This library was screened for interaction with glycosomal phosphoglycerate kinase (gPGK) of Trypanosoma brucei labelled with fluorescein or with biotin. Affinity beads that bound the enzyme were selected with a pipette or with streptavidin coated magnetic beads. The beads that bound to the enzyme were individually subjected to Edman microsequence analysis to determine the sequence of the corresponding peptide ligands. The corresponding peptide-sequences were synthesised as free peptide acids and evaluated for enzyme activity inhibition. The pentapeptide NWMMF was able to selectively inhibit gPGK with an IC50 of approximately 80 microM.

Affinity Labels↗
PubMedDate not supplied

Simultaneous synthesis of peptide libraries on single resin and continuous cellulose membrane supports: examples for the identification of protein, metal and DNA binding peptide mixtures.

Peptide libraries were simultaneously synthesized on single supports by double coupling 0.8 equivalents of an equimolar acylating amino acid mixture consisting of 19 amino acids (cysteine omitted) at randomized sites, thus compensating for the different coupling rates of the amino acids. Peptide epitope mixtures, as well as very complex mixtures such as a completely randomized hexapeptide, were prepared and analyzed by HPLC and amino acid analysis. The results obtained indicate that this method can be applied to the synthesis of peptide libraries. Parts of a simultaneously synthesized solution phase combinatorial library XXB1B2XX were successfully used for the detection of the linear epitope HFND of transforming growth factor-alpha (TGF alpha) recognized by the monoclonal antibody Tab2. Furthermore, novel combinatorial peptide libraries XXB1B2XX were prepared on continuous cellulose membrane supports, also allowing the identification of TGF alpha epitope sequences. In addition, peptide mixtures that bound to a double-stranded DNA (15mer) and silver were identified. These preliminary results indicate that cellulose-bound combinatorial peptide libraries can be used for the rapid and inexpensive screening of millions of peptides to identify single molecules that bind any given ligand such as proteins, nucleic acids and metals.

Amino Acid Sequence↗
PubMed1995

A conformationally homogeneous combinatorial peptide library.

In search for a rational way to convert the information encoded in peptide structures into peptidomimetics, major progress could be made by coupling the power of selection methods, now enormously increased in number as a result of the development of combinatorial peptide libraries, with the rational design of structure-inducing templates for the selectable sequences. The availability of libraries of peptides with predetermined structure would enable selection-driven peptidomimetic design, whereby a conformational model for the peptide pharmacophore would be directly derived from the screening, allowing the design of a suitable non-peptidic scaffold to replace the peptide backbone. We describe here the first example of a conformationally homogeneous combinatorial peptide library, which yields ligands with the expected structure upon selection. The library was built by randomising five positions in the alpha-helical portion of a 26 amino acid Cys2His2 consensus "zinc-finger" motif. Since in zinc-fingers metal coordination and folding are coupled, in our library metal-dependent binding represents a built-in control against the selection of structurally undefined sequences. The alpha-helical library was produced as both fusion with the pVIII protein of filamentous phage and soluble peptides by chemical synthesis, the latter enabling the expansion of the selectable repertoire by the inclusion of non-coded amino acids. The two libraries were independently screened with the same receptor (a monoclonal IgA reactive against the lipopolysaccharide of the human pathogen Shigella flexneri), yielding a very similar consensus. In particular, the peptides defined by both methods showed very strong, zinc-dependent binding to the IgA. The geometrical arrangement of the side-chains of the selected peptide pharmacophore was shown by circular dichroism, Co(II)-complex absorption and high-resolution NMR to be structurally invariant with respect to the parent zinc-finger.

Amino Acid Sequence↗
PubMed1995

Purification of synthetic peptide libraries by affinity chromatography using the avidin-biotin system.

The specific interaction between biotin and avidin was exploited in the affinity purification of solid-phase synthesized peptide libraries. During peptide library synthesis, by means of the single-resin method in which coupling on variable positions is carried out using an equimolar mixture of amino acids, biotin was used to cap the unreacted amino groups remaining after coupling of the equimolar amino acid mixture. The following synthesis and deprotection procedures were performed as usual in tert,-butyloxycarbonyl chemistry. The purification of the peptide mixture containing N-biotinylated sequences was performed by affinity chromatography on an avidin-agarose column. The unwanted terminated sequences were retained in the avidin column while the purified peptide mixture was eluted as indicated by reverse-phase HPLC and MS analysis monitoring. The avidin column was regenerated and the biotinylated sequences were released under reversible denaturing conditions. The usefulness of biotinylation for peptide library purification is demonstrated here for the first time for a peptide mixture containing by-products that cannot be separated from the mixture by classical HPLC purification. This purification technique could be applied to all syntheses, presenting difficult reacting steps.

Amino Acid Sequence↗
PubMed2006

[Isolation of a novel peptide that binds to BLyS from a 12-mer phage display peptide library].

A 12-mer phage display peptide library was screened for specific binders against B lymphocyte stimulator (BLyS). After 3 rounds of panning, positive phage clones were enriched. ELISAs were used to identify positive phages, and the DNA encoding the positive peptide (RHKIQLRQNIIT) was cloned and expressed as a GST fusion protein in E. coli. After purification, the identity of the fusion protein was confirmed through its specific binding to BLyS by ELISA. We have obtained a peptide that can bind to BLyS and probably act as an antagonistic peptide against the natural BLyS receptor.

B-Cell Activating Factor↗
PubMed2002

Affinity purification of fibrinogen using a ligand from a peptide library.

An affinity resin containing the peptide ligand Phe-Leu-Leu-Val-Pro-Leu (FLLVPL) has been developed for the purification of fibrinogen. The ligand was identified by screening a solid-phase combinatorial peptide library using an immunostaining technique. The specific binding of fibrinogen to the ligand has been characterized by isothermal calorimetry and adsorption isotherms and is dominated by both hydrophobic interactions and ionic interactions with the N-terminal free amino group. The effective association constant of fibrinogen was substantially higher when the peptide was immobilized on the resin than in solution; moreover, it increased with increasing peptide density, suggesting a cooperative binding effect. A low ionic strength buffer at pH 4 was used successfully to elute adsorbed fibrinogen from the column with high purity, retention of factor XIII crosslinking activity, and minimal, if any, loss of biological function. This general approach to ligand selection and characterization can be used to develop peptide ligands for the affinity purification of diverse proteins on a large scale.

Adsorption↗
PubMed2000

[Mimic epitope recognized by monoclonal antibody MG7 against gastric cancer through screening phage displayed random peptide library].

OBJECTIVE: To get mimic peptide epitopes that could be recognized by a monoclonal antibody against gastric cancer named MG7 from random peptide library displayed by phage, and to provide useful information for further study of the interaction between antigen and antibody. METHODS: Through affinity enrichment and immunoscreening of two phage-displayed non-apeptide libraries constructed in pVIII with MG7 MAb separately, several positive phages were obtained. Fluorescence labeling and dot blot were carried out for further identification of their binding activities. Then, some of the positive phages were sequenced and their corresponding peptide sequence was deduced according to their DNA sequence. Finally, HLA binding prediction software was applied for HLA binding analysis. RESULTS: Based on several rounds of screening and binding activity detection, we got twelve and thirty positive phage clones respectively from two libraries. Through DNA sequencing, peptide deducing and sequence aligning analysis of the positive phages, some preserved epitope information such as PLX(0 - 2)S, SAVR, XRMX and YARN were obtained. The prediction using HLA binding analysis software showed that most of the sequenced peptide had the potentiality to bind with HLA molecules. CONCLUSION: PLX(0 - 2)S, SAVR, XRMX and YARN may be some of the motifs which could be recognized by monoclonal antibody MG7.

Antibodies, Monoclonal↗
PubMed2003

[Screening of TNF-alpha mimotopes from c7c phage display peptide library].

AIM: To acquire oligo-peptides mimicking TNF-alpha epitopes. METHODS: The TNF-alpha mimotopes were screened from c7c phage display peptide library by using neutralizing mAb J1D9 against TNF-alpha, and positive clones were identified by sandwich ELISA. RESULTS: 9 out of 20 phage clones were identified as positive clones which can bind to mAb J1D9. The deduced amino acid sequence analysis showed three different sequences: c-RRPAQSG-c, c-NKHNRKI-c and c-RGMSRKI-c. CONCLUSION: All of the three peptides obtained can mimic the epitopes of TNF-alpha and bind to mAb J1D9.

Amino Acid Sequence↗
PubMed2006

Rapid and efficient identification of epitopes/mimotopes from random peptide libraries.

Phage-displayed random peptide libraries are important tools in identifying novel epitopes/mimotopes that may lead to the determination of antigen specificity. In this approach, high-affinity phage peptides are enriched by affinity selection (panning) on a monoclonal antibody. To facilitate identification of all potential phage peptides specific for recombinant monoclonal antibodies (rAbs) previously generated from clonally expanded plasma cells from the cerebrospinal fluid of patients with multiple sclerosis (MS), we developed a high-throughput method to determine phage specificity. In contrast to the 8-9 days needed in the standard large-scale method of amplifying phage clones for ELISA, the high-throughput method takes only 1 day. ELISA using phage clones amplified directly in 96-well plates avoids large-scale phage purification and enables rapid identification of specific epitopes/mimotopes. This technique will expedite identification of MS-specific peptides that can be used to discover the corresponding protein antigens.

Amino Acid Sequence↗
PubMed1999

Identification of inhibitors of an 80 kDa protease from Trypanosoma cruzi through the screening of a combinatorial peptide library.

Two orthogonal peptide combinatorial libraries were screened to discover inhibitors of Tc80 protease, a novel target from Trypanosoma cruzi involved in host cell invasion. These libraries were composed of 15,625 structurally diversified tripeptides, partitioned in 125 mixtures. The screening led to a low micromolar inhibitor which was actually an HF cleavage by-product H-Ipe-D-Tic-D-Glu(S-paratolyl)-OH. IC50 values of several analogous molecules of this hit were determined and are discussed. For the best compounds, conformational analysis revealed a high degree of similarity in shape with a potent prolylendopeptidase inhibitor, SUAM-1221.

Animals↗
PubMed2005

[Utilizing tabacco genomic DNA to construct nearly random peptide libraries].

We developed a novel method for constructing nearly random peptide library. Genomic DNAs extracted from tissue or cells of large genome species were digested with frequent cutter to produce short DNA fragments. These short fragments can be considered nearly random. Nearly random peptide libraries can be constructed by cloning the short fragments into appropriate expression vectors and transformation into host cells. Genomic DNA from one species can be digested with different restriction enzymes and ligated to different reading frames to produce several different libraries. In this study, we digested tobacco genomic DNA with two enzymes and cloned into three different reading frames to make totally six nearly random peptide libraries.

DNA, Plant↗
PubMedDate not supplied

Screening and identification of linear B-cell epitopes and entry-blocking peptide of severe acute respiratory syndrome (SARS)-associated coronavirus using synthetic overlapping peptide library.

A 10-mer overlapping peptide library has been synthesized for screening and identification of linear B-cell epitopes of severe acute respiratory syndrome associated coronavirus (SARS-CoV), which spanned the major structural proteins of SARS-CoV. One hundred and eleven candidate peptides were positive according to the result of PEPscan, which were assembled into 22 longer peptides. Five of these peptides showed high cross-immunoreactivities (approximately 66.7 to 90.5%) to SARS convalescent patients' sera from the severest epidemic regions of the China mainland. Most interestingly, S(471-503), a peptide located at the receptor binding domain (RBD) of SARS-CoV, could specifically block the binding between the RBD and angiotensin-converting enzyme 2, resulting in the inhibition of SARS-CoV entrance into host cells in vitro. The study demonstrated that S(471-503) peptide was a potential immunoantigen for the development of peptide-based vaccine or a candidate for further drug evaluation against the SARS-CoV virus-cell fusion.

Amino Acid Sequence↗
PubMed2005

Computational design of combinatorial peptide library for modulating protein-protein interactions.

Screening phage-displayed combinatorial peptide library is an effective approach for discovery of peptide modulators for protein-protein interactions. However, as peptide length increases, the chance of finding active peptides in a finite size library diminishes. To increase the likelihood of finding peptides that bind to a protein, we develop statistical potential for computational construction of biased combinatorial antibody-like peptide libraries. Based on the alpha shapes of antibody-antigen complexes, we developed an empirical pair potential for antigen-antibody interactions that depends on local packing. We validate this potential and show that it can successfully discriminate the native interface peptides from a simulated library of 10,000 random peptides for 34 antigen-antibody complexes. In addition, we show that it can successfully recognize the native binding surface patch among all possible surface patches taken from either the antibody or the antigen for seven antibody-antigen protein complexes contained in the CAPRI (Critical Assessment of Predicted Interactions) dataset. We then develop a Weighted Amino Acid Residue sequence Generator (WAARG) for design of biased peptide library. When compared with a random peptide library, WAARG libraries contain more native-like binding peptides at a significantly smaller size. Our method can be used to construct peptide library for screening of antibody variants with improved specificity and affinity to a target antigen. It can also be used for screening of antibody-like antagonist peptides modulating other protein-protein interactions.

Amino Acid Sequence↗
PubMed2001

Substrate specificity of the integral membrane protease OmpT determined by spatially addressed peptide libraries.

Escherichia coli outer membrane protease T (OmpT) is an endopeptidase that specifically cleaves between two consecutive basic residues. In this study we have investigated the substrate specificity of OmpT using spatially addressed SPOT peptide libraries. The peptide acetyl-Dap(dnp)-Ala-Arg/Arg-Ala-Lys(Abz)-Gly was synthesized directly onto cellulose membrane. The peptide contained the aminobenzoyl (Abz) fluorophore, which was internally quenched by the dinitrophenyl (dnp) moiety. Treatment of the SPOT membrane with the small, water-soluble protease trypsin resulted in highly fluorescent peptide SPOTs. However, no peptide cleavage was observed after incubation with detergent-solubilized OmpT, a macromolecular complex with an estimated molecular mass of 180 kDa. This problem could be solved by the introduction of a long, polar polyoxyethylene glycol linker between the membrane support and the peptide. Peptide libraries for the P(2), P(1), P(1)', and P(2)' positions in the substrate were screened with OmpT, and peptides of positive SPOTs were resynthesized and subjected to kinetic measurements in solution. The best substrate Abz-Ala-Lys-Lys-Ala-Dap(dnp)-Gly had a turnover number k(cat) of 40 s(-)(1), which is 12-fold higher than the starting substrate. Peptides containing an acidic residue at P(2) or P(2)' were not substrates for OmpT, suggesting that long-range electrostatic interactions are important for the formation of the enzyme-substrate complex. OmpT was highly selective toward L-amino acids at P(1) but was less so at P(1)' where a peptide with D-Arg at P(1)' was a competitive inhibitor (K(i) of 19 microM). An affinity chromatography resin based on these findings was developed, which allowed for the one-step purification of OmpT from a bacterial lysate. The implications of the determined consensus substrate sequence (Arg/Lys)/(Arg/Lys)-Ala for the proposed biological function of OmpT in defense against antimicrobial peptides are discussed.

Bacterial Outer Membrane Proteins↗
PubMed2005

Tagged polymerase chain reaction subtractive hybridization for the enrichment of phage display random peptide libraries.

Affinity selection of phage display peptide libraries is routinely used for isolating peptides capable of binding a range of molecules, including antibodies and receptors. This process is most successful when the selecting molecule is relatively pure, for example, a monoclonal antibody. However, isolation of peptides able to bind to target molecules present in a complex mixture is more difficult because the affinity selection process isolates peptides capable of binding to all molecules present in the mixture. Here we describe the development of a tagged polymerase chain reaction (PCR) subtractive hybridization method that is universally applicable for the targeted isolation of peptides able to bind to unique molecules within a complex mixture. We also describe a discriminatory limiting dilution PCR method that can be used to optimize hybridization conditions.

Bacteriophages↗
PubMed2005

Screening for PreS specific binding ligands with a phage displayed peptides library.

AIM: To construct a random peptide phage display library and search for peptides that specifically bind to the PreS region of hepatitis B virus (HBV). METHODS: A phage display vector, pFuse8, based on the gene 8 product (pVIII) of M13 phage was made and used to construct a random peptide library. E.coli derived thioredoxin-PreS was purified with Thio-bond beads, and exploited as the bait protein for library screening. Five rounds of bio-panning were performed. The PreS-binding specificities of enriched phages were characterized with phage ELISA assay. RESULTS: A phage display vector was successfully constructed as demonstrated to present a pVIII fused HBV PreS1 epitope on the phage surface with a high efficiency. A cysteine confined random peptide library was constructed containing independent clones exceeding 5+/-10(8) clone forming unit (CFU). A pool of phages showing a PreS-binding specificity was obtained after the screening against thio-PreS with an enrichment of approximately 400 times. Five phages with high PreS-binding specificities were selected and characterized. Sequences of the peptides displayed on these phages were determined. CONCLUSION: A phage library has been constructed, with random peptides displaying as pVIII-fusion proteins. Specific PreS-binding peptides have been obtained, which may be useful for developing antivirals against HBV infection.

Amino Acid Sequence↗