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PubMed1991

The use of peptides to reconstruct conformational determinants; a brief review.

In many biological processes, defined regions of proteins are involved in selective recognition. These regions can often be mimicked with peptides and are the main targets for vaccine and drug development. The authors review the use of peptides, to define and ultimately mimic defined protein regions of interest. Especially the role of the Pepscan method is emphasized. This method has been proven to be a useful and fast tool in defining protein regions of interest. It is based on the simultaneously synthesis of multiple peptides coupled to solid supports. Hundreds of peptides can be produced and tested in a relatively short period of time. With the construction of random peptide libraries in recombinant DNA systems, it is now even possible to screen for peptidic determinants without the requirement of preliminary knowledge of primary structure. Having this information, the affinity of peptides can be further enhanced with the Pepscan approach. The power of this approach will be illustrated with results from studies on the development of synthetic vaccines and hormone analogues.

Biological Assay↗
PubMed1994

Recognition by human sera and immunogenicity of HBsAg mimotopes selected from an M13 phage display library.

We used two mouse monoclonal antibodies (mAb) specific for the human hepatitis B virus surface antigen (HBsAg) to screen a random peptide library of 15 amino-acid residues displayed as a fusion to protein III of filamentous phage M13. By a combination of affinity selection, immuno-screening and ELISA techniques, we selected peptides that are recognized by the anti-HBsAg mAb and show aa similarity with the natural antigen. The selected phage-displayed epitopes (phagotopes) behave as antigenic mimics of HBsAg. One phagotope is specifically recognized by human sera from HBsAg-immunized individuals, pointing to the possible use of phagotopes as markers to detect the presence of specific Ab in the serum. The same phagotope also elicits Ab directed against HBsAg in mice, indicating that mAb-selected phagotopes can also be immunogenic mimics of the natural antigen. These findings demonstrate that it is possible to identify disease-specific epitopes that can be used as diagnostic reagents and as leads for the development of acellular vaccines.

Animals↗
PubMed2005

Novel TLR4-antagonizing peptides inhibit LPS-induced release of inflammatory mediators by monocytes.

Toll-like receptor 4 (TLR4) has become a new target for combating Gram-negative bacterium-induced sepsis. In this study, we screened peptides that can interact with TLR4 from a random 16-peptide library using yeast two-hybrid system and performed functional identification for the obtained peptides. We got two positive clones out of 1.28x10(7) transformants. The peptides were sequenced and synthesized. Protein sequence comparison confirmed that the two peptides had no homologous proteins. The two peptides were found to significantly inhibit LPS-induced NF-kappaB activation in HEK-293 cells that were transfected with TLR4 cDNA, LPS-induced IkappaBalpha (IkappaB alpha) phosphorylation and NF-kappaB activation in monocytes, and release of IL-1, IL-6, and TNF-alpha by monocytes. We further confirmed that the No. 9 peptide could bind to TLR4 extracellular domain, but the No. 24 peptide could not, suggesting that two novel peptides were identified as the antagonists of TLR4, which significantly inhibited the effects of endotoxin in vitro. The No. 9 peptide may function through binding to TLR4 extracellular domain. Our findings suggest a promising countermeasure against Gram-negative bacterium-induced sepsis.

Cells, Cultured↗
PubMed2004

Comparative structural and energetic analysis of WW domain-peptide interactions.

WW domains are small globular protein interaction modules found in a wide spectrum of proteins. They recognize their target proteins by binding specifically to short linear peptide motifs that are often proline-rich. To infer the determinants of the ligand binding propensities of WW domains, we analyzed 42 WW domains. We built models of the 3D structures of the WW domains and their peptide complexes by comparative modeling supplemented with experimental data from peptide library screens. The models provide new insights into the orientation and position of the peptide in structures of WW domain-peptide complexes that have not yet been determined experimentally. From a protein interaction property similarity analysis (PIPSA) of the WW domain structures, we show that electrostatic potential is a distinguishing feature of WW domains and we propose a structure-based classification of WW domains that expands the existent ligand-based classification scheme. Application of the comparative molecular field analysis (CoMFA), GRID/GOLPE and comparative binding energy (COMBINE) analysis methods permitted the derivation of quantitative structure-activity relationships (QSARs) that aid in identifying the specificity-determining residues within WW domains and their ligand-recognition motifs. Using these QSARs, a new group-specific sequence feature of WW domains that target arginine-containing peptides was identified. Finally, the QSAR models were applied to the design of a peptide to bind with greater affinity than the known binding peptide sequences of the yRSP5-1 WW domain. The prediction was verified experimentally, providing validation of the QSAR models and demonstrating the possibility of rationally improving peptide affinity for WW domains. The QSAR models may also be applied to the prediction of the specificity of WW domains with uncharacterized ligand-binding properties.

Amino Acid Sequence↗
PubMed2003

Selection of peptides with affinity for the N-terminal domain of GATA-1: Identification of a potential interacting protein.

As most transcription factors, GATA-1 activities are mediated by interactions with multiple proteins. Those identified so far associate with the zinc-finger domain and/or surrounding sequences. In contrast, no proteins interacting with the N-terminal domain have been identified although several evidences suggest its involvement in the control of hematopoiesis. In an attempt to identify proteins that interact with the N-terminal transactivation domain of GATA-1, a random phage peptide library was screened with recombinant GATA-1 protein and the sequence of a selected peptide was used for database protein sequence retrieval. We selected a set of peptides sharing the core sequence phi-B((2-3))-nu((2-4)) (where phi, B, and nu represent hydrophobic, basic, and neutral residues, respectively). Using the sequence of the most represented peptide (pep5) as query, we retrieved the HIV accessory protein Nef. We show that Nef binds GATA-1 and GATA-3 in vitro in virtue of its sequence homology with pep5.

Amino Acid Sequence↗
PubMed1995

Catalytic specificity of protein-tyrosine kinases is critical for selective signalling.

How do distinct protein-tyrosine kinases activate specific down-stream events? Src-homology-2 (SH2) domains on tyrosine kinases or targets of tyrosine kinases recognize phosphotyrosine in a specific sequence context and thereby provide some specificity. The role of the catalytic site of tyrosine kinases in determining target specificity has not been fully investigated. Here we use a degenerate peptide library to show that each of nine tyrosine kinases investigated has a unique optimal peptide substrate. We find that the cytosolic tyrosine kinases preferentially phosphorylate peptides recognized by their own SH2 domains or closely related SH2 domains (group I; ref. 3), whereas receptor tyrosine kinases preferentially phosphorylate peptides recognized by subsets of group III SH2 domains. The importance of these findings for human disease is underscored by our observation that a point mutation in the RET receptor-type tyrosine kinase, which causes multiple endocrine neoplasia type 2B, results in a shift in peptide substrate specificity.

Amino Acid Sequence↗
PubMed2003

Identification of critical residues of an immunodominant region of Echinococcus granulosus antigen B.

Immune evasion strategies often shape the immunogenicity of parasite components. We recently found that the N-terminal extension of the major subunit of Echinococcus granulosus antigen B (AgB), the causative agent of hydatid disease, concentrates the immunoreactive B cell epitopes of the native molecule. The nature of this immunodominance was analyzed using four monoclonal antibodies (mAbs) defining overlapping epitopes in this region of the AgB molecule. The minimal epitope requirements of these mAbs were determined using phage display peptide libraries. The consensus sequences isolated with the mAbs, and alanine replacement analysis with synthetic peptides mapped the relevant molecular contacts within a short stretch corresponding to residues 17-24 of the AgB major subunit. Substitution of two critical residues within this stretch produced a dramatic loss of antigenicity, as determined by using patient sera. The circular dichroism spectra of the antigen, together with the distribution of the contact residues, suggest that this region adopts an amphipathic alpha-helix structure that clusters the contact residues on its polar side. To provide further insight in the interpretation of the structure activity relationships for this immunoreactive region of E. granulosus AgB, we developed a model for the N-terminal extension of the AgB major subunit, which helps to rationalize our data.

Amino Acid Sequence↗
PubMed2002

Yeast assays for G-protein-coupled receptors.

Yeast assays for G-protein-coupled receptors have many attractions due to their simplicity, low cost, and lack of endogenous receptors. Since the first report of functional coupling of the human beta 2 adrenergic receptor to the yeast pheromone-response pathway in 1990, the technology has developed to a point at which more than 30 heterologous GPCRs are now published to couple. Major breakthroughs have come from an understanding of receptor-G protein interactions, alongside advances in knowledge of the structure of heterotrimeric G proteins. Yeast screens have been used to identify ligands both from compound collections and through the autocrine expression of peptide libraries. Yeast genetics has also been applied to a functional analysis of GPCRs and peptide ligands. In this review we describe the historical development of yeast GPCR assay systems and their current applications.

Biochemistry↗
PubMed2006

Using annotated peptide mass spectrum libraries for protein identification.

A system for creating a library of tandem mass spectra annotated with corresponding peptide sequences was described. This system was based on the annotated spectra currently available in the Global Proteome Machine Database (GPMDB). The library spectra were created by averaging together spectra that were annotated with the same peptide sequence, sequence modifications, and parent ion charge. The library was constructed so that experimental peptide tandem mass spectra could be compared with those in the library, resulting in a peptide sequence identification based on scoring the similarity of the experimental spectrum with the contents of the library. A software implementation that performs this type of library search was constructed and successfully used to obtain sequence identifications. The annotated tandem mass spectrum libraries for the Homo sapiens, Mus musculus, and Saccharomyces cerevisiae proteomes and search software were made available for download and use by other groups.

Amino Acid Sequence↗
PubMedDate not supplied

High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads.

The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.

Combinatorial Chemistry Techniques↗
PubMed2003

Her-2/ neu altered peptide ligand-induced CTL responses: implications for peptides with increased HLA affinity and T-cell-receptor interaction.

In this study, we developed two Her-2/ neu-derived E75 altered peptide ligands (APLs) that demonstrate increased affinities for the HLA-A*0201 allele compared with wild-type E75 peptide. The APLs contain amino acids from E75(369-377), an immunodominant Her-2/ neu-derived peptide, and preferred primary and auxiliary HLA-A*0201 molecule anchor residues previously identified from combinatorial peptide library screening with the recombinant molecule. CTL lines were generated against wild-type E75 peptide (KIFGSLAFL) and APLs by multiple rounds of peptide stimulation of peripheral blood mononuclear cells (PBMCs) from HLA-A2+ antigen normal individuals. CTL lines raised on wild-type E75 peptide cross-reacted with APLs and similarly, CTL lines raised on APLs cross-reacted with wild-type E75 peptide, as measured by IFN-gamma ELISpot and target cell lysis assays. One of five individuals demonstrated specificity for APL 2 (FLFGSLAFL), whereas APL 5 (FLFESLAFL)-specific responses were observed from all five individuals tested. Molecular models of the E75, APL 2, and APL 5/HLA-A2 complexes indicated that the substitution of glycine with glutamic acid at position four of APL 5 resulted in the presentation of a large, negatively charged side chain that interacts with the outer edge of the HLA-A2 antigen alpha helix and is freely available to interact with cognate T-cell receptors. The results of this study further substantiate the concept that rational design of T-cell epitopes may lead to stronger peptide immunogens than natural, wild-type peptides.

Antigens, Neoplasm↗
PubMed2006

Gangliosides, Ab1 and Ab2 antibodies I. Towards a molecular dissection of an idiotype-anti-idiotype system.

This report is focused on the molecular basis for the interaction of a monoclonal antibody (mAb) and its anti-idiotypic mAb. P3 mAb (Ab1) recognizes N-glycolyl-gangliosides, and 1E10 mAb is one of its anti-idiotypic mAbs (Ab2). Chimeric versions of both antibodies retained their specificity. Charged residues in their H-CDRs, particularly H-CDR3, were considered to play a major role in their binding and immunogenic properties. P3 mAb has the unusual property of generating a strong antibody response in syngeneic mice, even when it is administered in saline. We selected phagotopes from a 12mer peptide library displayed on filamentous phage to characterize amino acid motifs recognized by these antibodies. The peptides were enriched in charged amino acids similar to those present in P3 and 1E10 mAb H-CDR3. We also report the construction of four mutants of the P3 antibody, where arginine residues in the heavy chain CDRs were substituted by serine residues, and the characterization of their interaction with 1E10 mAb and GM3(NeuGc) ganglioside, as well as their immunogenic properties in Balb/c mice. H-CDR1 R31 residue appears to have a central role in P3 mAb reactivity and antigenicity. H-CDR3 R100a residue seems to be more involved in the immunogenicity of the P3 idiotype.

Animals↗
PubMed2002

Investigations of cyclophilin interactions with oligopeptides containing proline by affinity capillary electrophoresis.

Affinity capillary electrophoresis using mobility-shift analysis was utilized to characterize the binding of peptide ligands to cyclophilins, which are members of the enzyme family of peptidyl-prolyl cis/trans isomerases. Peptides derived from the human immunodeficiency virus capsid protein p24 exhibited different affinities to the isoenzymes cyclophilin18 and cyclophilin20. For the interaction of the peptide hormone bradykinin with cyclophilin18, a dissociation constant of 1.4 +/- 0.1 mM was determined. Finally, the affinity of cyclophilin20 to peptides from a cellulose-bound peptide library scanning the sequence of Drosophila melanogaster protein cappuccino was investigated. The affinities of selected peptides to cyclophilin20 and a green fluorescent fusion protein with cyclophilin20 were compared.

Amino Acid Sequence↗
PubMed1997

Concept and early development of solid-phase peptide synthesis.

There are several reasons for the success of the solid-phase approach to peptide synthesis. The first is the ease of the procedure, the acceleration of the overall process, and the ability to achieve good yields of purified products. The second was the unanticipated discovery of many new biologically active peptides and the expanded need for synthetic peptides to help solve problems in virtually all disciplines of biology. In many cases, the solid-phase technique has been the method of choice. This approach, of course, does not replace the classic solution synthesis methods, but rather supplements them. The choice of techniques depends on the objectives of the synthesis. When carefully worked out, the solution methods can give high yields of highly purified products in large quantities. Many superb syntheses of active peptides have been achieved in this way. The solid-phase method has also yielded many large active peptides. It is particularly useful when large numbers of analogs, in relatively small quantities, are required as in structure-function studies on hormones, growth factors, antibiotics, and other biologically active peptides or for determining the antigenic epitopes of proteins. In addition, it has on occasion been scaled up for production of kilogram quantities. One of the unique uses of solid-phase synthesis has been the synthesis of peptide libraries. Most of the work on this new field in which thousands or millions of peptides are prepared simultaneously has been by solid-phase methods. This new technique is proving to be of great practical importance in rapid drug discovery of peptide, peptide mimetic, and nonpeptide compounds. Developments in screening methods now allow the examination of large numbers of compounds, and active products with structures unpredictable from natural product sequences are being found in this way. The properties of the solid-phase system, the changes in the chemistry, and the applications of the technique to biological problems are discussed in detail in subsequent articles of this volume.

Biochemistry↗
PubMed1997

High-affinity binding of the Drosophila Numb phosphotyrosine-binding domain to peptides containing a Gly-Pro-(p)Tyr motif.

The phosphotyrosine-binding (PTB) domain is a recently identified protein module that has been characterized as binding to phosphopeptides containing an NPXpY motif (X = any amino acid). We describe here a novel peptide sequence recognized by the PTB domain from Drosophila Numb (dNumb), a protein involved in cell fate determination and asymmetric cell division during the development of the Drosophila nervous system. Using a Tyr-oriented peptide library to screen for ligands, the dNumb PTB domain was found to bind selectively to peptides containing a YIGPYphi motif (phi represents a hydrophobic residue). A synthetic peptide containing this sequence bound specifically to the isolated dNumb PTB domain in solution with a dissociation constant (Kd) of 5.78 +/- 0.74 microM. Interestingly, the affinity of this peptide for the dNumb PTB domain was increased (Kd = 1.41 +/- 0.10 microM) when the second tyrosine in the sequence was phosphorylated. Amino acid substitution studies of the phosphopeptide demonstrated that a core motif of sequence GP(p)Y is required for high-affinity binding to the dNumb PTB domain. Nuclear magnetic resonance experiments performed on isotopically labeled protein complexed with either Tyr- or pTyr-containing peptides suggest that the same set of amino acids in the dNumb PTB domain is involved in binding both phosphorylated and nonphosphorylated forms of the peptide. The in vitro selectivity of the dNumb PTB domain is therefore markedly different from those of the Shc and IRS-1 PTB domains, in that it interacts preferentially with a GP(p)Y motif, rather than NPXpY, and does not absolutely require ligand phosphorylation for binding. Our results suggest that the PTB domain is a versatile protein module, capable of exhibiting varied binding specificities.

Animals↗
PubMed2001

Monovalent fusion proteins of IgE mimotopes are safe for therapy of type I allergy.

By screening phage display random peptide libraries with purified immunoglobulin E (IgE) from birch pollen-allergic patients, we previously defined peptides mimicking natural IgE epitopes (mimotopes) of the major birch pollen allergen Bet v 1. The present study aimed to define a monovalent carrier for the IgE mimotopes to induce protective antibodies directed to the IgE epitopes, suitable for mimotope-specific therapy. We expressed the selected mimotopes as fusion proteins together with streptococcal albumin binding protein (ABP). The fusion proteins were recognized specifically by anti-Bet v 1 human IgE, which demonstrated that the mimotopes fused to ABP resemble the natural IgE epitope. Bet v 1-specific IgG was induced by immunization of BALB/c mice with fusion proteins. These IgG antibodies could inhibit IgE binding to Bet v 1. Skin testing of Bet v 1 allergic mice showed that the ABP mimotope constructs did not elicit type I skin reactions, although they possess IgE binding structures. Our data suggest that IgE mimotopes are safe for epitope-specific immunotherapy of sensitized individuals, when presented in a monovalent form. Therefore, ABP-fused mimotopes are promising candidates for a new type of immunotherapy based on the precise induction of blocking antibodies.

Allergens↗
PubMed2006

High-throughput and facile assay of antimicrobial peptides using pH-controlled fluorescence resonance energy transfer.

Amphipathic antimicrobial peptides can destroy bacteria cells by inducing membrane permeabilization, forming one strategy for innate defense by various organisms. However, although the antimicrobial peptides are considered a promising alternative for use against multidrug-resistant bacteria, large-scale screening of potential candidate antimicrobial peptides will require a simple, rapid assay for antimicrobial activity. Here, we describe a novel fluorescence resonance energy transfer (FRET)-based assay system for antimicrobial peptides which takes advantage of pH-related changes in FRET efficiency due to the instability of enhanced yellow fluorescent protein versus the stability of enhanced cyan fluorescent protein in a reduced-pH environment. We successfully showed that quantification of antimicrobial activity is possible through a difference of FRET efficiency between ECFP-EYFP fusion molecules released from disrupted Escherichia coli in an extracellular environment (pH 6) and those retained in an intracellular environment (pH approximately 7). Thus, we herein suggest a new simple, effective, and efficient pH-controlled FRET-based antimicrobial peptide screening method applicable to high-throughput screening of candidate peptide libraries.

Animals↗
PubMed1994

Discovery and structure-function analysis of alpha-melanocyte-stimulating hormone antagonists.

Structure-function relationships of alpha-melanocyte-stimulating hormone (alpha-MSH, alpha-melanotropin) were investigated and novel alpha-MSH receptor antagonists were identified. Based on the alpha-MSH-[5-13] peptide sequence, a multi-use peptide library consisting of 31,360 structurally different candidates was generated, and approximately 40% of the peptides were individually screened for their ability to block receptor function. This led to the identification of antagonists with a range of potencies and revealed structural requirements necessary for receptor inactivation. The most potent antagonist Met-Pro-D-Phe-Arg-D-Trp-Phe-Lys-Pro-Val-NH2 has an IC50 value of 11 +/- 7 nM. Analysis revealed that D-Trp5 and Phe6 were crucial to its antagonistic properties which could be potentiated by D-Phe3. This study demonstrates that residues in positions 5-6, 7-9, and 10 of the alpha-MSH sequence constitute crucial determinants for potent antagonist activity.

Amino Acid Sequence↗