T cell epitope analysis with peptides simultaneously synthesized on cellulose membranes: fine mapping of two DQ dependent epitopes

PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions?

In a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to the target interaction. Here, we investigate the results of 14 new PEPscan experiments for protein complexes of known 3D structures. We show that for almost all complexes, PEPscan is able to identify candidate IPs that are located at the protein-protein interface. The information it provides about the binding site seems, however, too ambiguous to be exploited in a simple manner to assist the modeling of protein complexes. Moreover, these candidates are associated with false positives. For these, we suggest they could correspond to non-specific binders, which leaves room for further optimization of the PEPscan protocol. Another unexpected advance comes from the observation of the applicability of PEPscan for polysaccharides and labeled peptides, suggesting that PEPscan could become a large spectrum approach to investigate protein-binder interactions, the binder not necessarily being a protein.

Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment

PEPscan is an old approach that has recently gained renewed interest for the identification of interfering peptides (IPs), i.e., peptides able to interfere with protein-protein interactions (PPIs). Its principle is to slice a protein sequence as a series of short overlapping peptides that are synthesized on a peptide array and tested for their ability to bind a partner, with positive spots corresponding to candidate IPs. PEPscan has been applied with a rather large success in various contexts, but the structural determinants underlying this success remain obscure. Here, we analyze the results of 14 PEPscan experiments, and confront the in vitro results with the available structural information. PEPscan identifies candidate IPs in limited numbers that in all cases correspond to solvent-accessible regions of the structures, their location at the protein-protein interface remaining to be further demonstrated. A strong point of PEPscan seems to be its ability to identify specific IPs. IPs identified from the same protein differ depending on the target PPI, and correspond to patches not frequently involved in the interactions seen in the 3D structures available. Overall, PEPscan seems to provide a cheap and rapid manner to identify candidate IPs, that also comes with room for improvement.

Automated Solid-Phase Peptide Synthesis

The development of solid-phase peptide synthesis by Bruce Merrifield paved the way for a synthesis carried out by machines. Automated peptide synthesis is a fast and convenient way of synthesizing many peptides simultaneously. This chapter tries to give a general guidance for the development of synthesis protocols for the peptide synthesizer. It also provides some suggestions for the modification of the synthesized peptides. Additionally, many examples of possible challenges during and after the synthesis are given in order to support the reader in finding the best synthesis strategy. Numerous references are given to many of the described matters.

Interfering peptides targeting protein-protein interactions: the next generation of drugs?

Protein-protein interactions (PPIs) are well recognized as promising therapeutic targets. Consequently, interfering peptides (IPs) - natural or synthetic peptides capable of interfering with PPIs - are receiving increasing attention. Given their physicochemical characteristics, IPs seem better suited than small molecules to interfere with the large surfaces implicated in PPIs. Progress on peptide administration, stability, biodelivery and safety are also encouraging the interest in peptide drug development. The concept of IPs has been validated for several PPIs, generating great expectations for their therapeutic potential. Here, we describe approaches and methods useful for IPs identification and in silico, physicochemical and biological-based strategies for their design and optimization. Selected promising in-vivo-validated examples are described and advantages, limitations and potential of IPs as therapeutic tools are discussed.

Correlations between steric/thermochemical parameters and O-/N-acylation reactions of cellulose

N(α)-t-Butyloxycarbonyl (Boc)-amino acids (Xaa = Gly, Ala, or β-Ala) were reacted with the cellulose hydroxyl groups (O-acylation) using N,N'-carbonyl diimidazole. The degrees of substitution toward the total hydroxyl groups (DS%(/OH)s) were 38% for O-(Boc-Gly)-Cellulose, 29% for O-(Boc-Ala)-Cellulose and 53% for O-(Boc-β-Ala)-Cellulose. The one-by-one N-acylation between the O-(Xaa)-Celluloses and Boc-Ala-Gly using a water-soluble carbodiimide yielded the conjugates N-(Boc-Ala-Gly)-Xaa-Celluloses with DS%(/NH2) values of 25% (Xaa = Gly), 35% (Ala), and 48% (β-Ala), respectively. The results were well correlated with ΔG and ΔEstrain profiles, which were predicted by semi-empirical thermochemical parameter calculation coupled with conformer search (R(2)>0.90). N-acylation of the O-(β-Ala)-Cellulose using various length of oligo-peptides, Boc-(Ala-Gly)n and Boc-(Gly-Ala)n (where, n = 0.5, 1.0, 1.5, 2.0, 3.0), suggested that the DS%(/NH2) was dependent on the structural features of the symmetric anhydrides as the N-acylating agents, including conformer populations and their transition energy.

Natural Selection on the Influenza Virus Genome

Influenza viruses are the etiological agents of influenza. Although vaccines and drugs are available for the prophylaxis and treatment of influenza virus infections, the generation of escape mutants has been reported. To develop vaccines and drugs that are less susceptible to the generation of escape mutants, it is important to understand the evolutionary mechanisms of the viruses. Here natural selection operating on all the proteins encoded by the H3N2 human influenza A virus genome was inferred by comparing the numbers of synonymous (d(S) [D(S)]) and nonsynonymous (d(N) [D(N)]) substitutions per site. Natural selection was also inferred for the groups of functional amino acid sites involved in B-cell epitopes (BCEs), T-cell epitopes (TCEs), drug resistance, and growth in eggs. The entire region of PB1-F2 was positively selected, and positive selection also appeared to operate on BCEs, TCEs, and growth in eggs. The frequency of escape mutant generation appeared to be positively correlated with the d(N)/d(S) (D(N)/D(S)) values for the targets of vaccines and drugs, suggesting that the amino acid sites under strong functional constraint are suitable targets. In particular, TCEs may represent candidate targets because the d(N)/d(S) (D(N)/D(S)) values were small and negative selection was inferred for many of them.

Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides

Since its invention the SPOT-synthesis methodology has become one of the most efficient strategies for the miniaturized assembly of large numbers of peptides. The combination of a facile synthetic method with high throughput solid- and solution-phase screening assays qualifies the SPOT-technique as a valuable tool in biomedical research. Recent developments such as the introduction of novel polymeric surfaces, new linker and cleavage strategies as well as automated robot systems extended the scope of practical chemical reactions that can be accommodated as well as the numbers of compounds obtainable by this technique. Thus, highly complex spatially addressed compound arrays have become accessible. Together with the introduction of novel screening assays, the method is excellently suited to elucidate recognition events on the molecular level.

Applications of peptide arrays prepared by the SPOT-technology

The growing range of applications for peptide arrays synthesized on coherent membranes by the SPOT-synthesis method proves they have emerged as a powerful proteomics technique to study molecular recognition events and identify biologically active peptides. Several developments, such as the introduction of novel polymeric surfaces, linkers, synthesis/cleavage strategies and detection methods, are facilitating an increasing spectrum of accessible compounds and applications in biological or pharmaceutical research.

In situ stimulation of a T helper cell hybridoma with a cellulose-bound peptide antigen

Many enzyme-linked immunosorbent assays take advantage of immobilized antigens for the identification of antibody binding sites. Generally, the analysis of cellulose membrane-bound B-cell epitopes is currently considered of high utility. We adapted this methodology for the stimulation of a T helper cell hybridoma with known specificity. Forty overlapping peptides corresponding to the entire rabies virus nucleoprotein were synthesized in duplicates on a single sheet of 90x130 mm size amino-modified paper. The efficacy of the peptide assembly was monitored by color staining of the unreacted amino groups. After completion of the synthesis, the side-chain protecting groups were removed, and the membrane was thoroughly cleaned of all organic and inorganic contaminants. The membrane was cut into pieces, and a standard lymphokine release assay was performed directly from the paper-bound antigens. From all the 40 peptide spots only peptide 31D stimulated the proliferation of the 9C5.D8-H T-cell hybridoma, known to react to this peptide. By using this protocol, as little as 0.4 microgram (approximately 200 pmole) of peptide could be detected. According to mass spectrometry the T-cell stimulation proceeded as a true solid-phase assay. The peptide neither leached from the membrane nor was cleaved by the medium-splenocyte mixture. Additionally, tryptic digestion of the cellulose membrane released the expected peptide fragments.

Spot synthesis: observations and optimizations

Positionally addressable syntheses of peptides on continuous cellulose membranes (spot synthesis) have often been reported in detail, but important questions dealing with synthesis quality, reproducibility and subsequent binding assays have largely been under-emphasized. In this report we have investigated some of these problems. The most important results were: (i) the signal intensity of ligate binding to cellulose-bound peptides and the affinity of the corresponding soluble peptides show good correlation, illustrated by three different ligate binding assays; (ii) reducing peptide density on the cellulose avoids the 'ring spot' effect, i.e. where less binding is observed in the spot-center compared to the rim. We recommend a peptide density of 10 nmol/cm2 as a reasonable starting point for further optimization; (iii) statistical analysis of binding assay reproducibility with more than 15000 peptides resulted in a mean standard signal deviation of 0.18; and (iv) optimization of side-chain deprotection revealed that a 30-min pretreatment of the cellulose with 90% trifluoroacetic acid followed by the standard deprotection protocol resulted in higher purity of the synthesized products.

Selection of antibody probes to correlate protein sequence domains with their structural distribution

We propose a new approach that permits correlation of specific domains defined by their primary sequence with their location in the structure of complex macromolecular aggregates. It is based on the combination of well-established structural analysis methods that incorporate the use of overlapping peptides on cellulose membranes for the isolation and purification of specific antibodies from a polyclonal antiserum. Monospecific antibodies to the connector protein of bacteriophage phi29 were isolated from polyclonal antisera using a new development of the spotscan method. These antibodies can be purified in quantities that allow antigenicity testing in enzyme-linked immunosorbent assays, Western blotting and immunoprecipitations, demonstrating the specificity of this isolation procedure. This approach has allowed us to generate direct antibody probes for immunoelectron microscopy mapping of different connector protein domains in a low resolution three-dimensional epitope map.

An epitope delivery system for use with recombinant mycobacteria

We have developed a novel epitope delivery system based on the insertion of peptides within a permissive loop of a bacterial superoxide dismutase molecule. This system allowed high-level expression of heterologous peptides in two mycobacterial vaccine strains, Mycobacterium bovis bacille Calmette-Guérin (BCG) and Mycobacterium vaccae. The broader application of the system was analyzed by preparation of constructs containing peptide epitopes from a range of infectious agents and allergens. We report detailed characterization of the immunogenicity of one such construct, in which an epitope from the Der p1 house dust mite allergen was expressed in M. vaccae. The construct was able to stimulate T-cell hybridomas specific for Der p1, and it induced peptide-specific gamma interferon responses when used to immunize naive mice. This novel expression system demonstrates new possibilities for the use of mycobacteria as vaccine delivery vehicles.

KDEL motif interacts with a specific sequence in mammalian erd2 receptor

The ER retention of lumenal proteins is achieved by a process which involves binding of escaped proteins via the C-terminal KDEL-tags to a KDEL receptor (erd2 receptor) in a post-ER compartment and return of the protein-receptor complex back to the ER. The transmembrane topology of the human KDEL receptor, which is an integral membrane protein, has been proposed. We have synthesised sets of cellulose-bound overlapping peptides covering the complete se quence of the receptor to study the interaction of the erd2 receptor with lumenal ER proteins, CaBP1 and CaBP2. At the next stage, the proposed lumenal loops of the receptor were more closely mapped. A short sequence, essential for the protein binding to the most efficient binding site of the receptor, was identified as 22KIWK25, which is in accordance with one of the proposed structural models of the receptor. The binding was of high specificity and was almost completely inhibited by KDEL-containing soluble peptides. The phosphorylation state of CaBP1/CaBP2 did not affect their binding to the KDEL receptor.

Microscale epitope mapping by affinity capillary electrophoresis-mass spectrometry

Using beta-endorphin as a model system, a new microscale solution-based approach for linear epitope mapping based on affinity capillary electrophoresis-mass spectrometry (ACE-MS) is demonstrated. Tryptic peptides are separated in a neutral coated capillary and monitored by ultraviolet absorbance and electrospray mass spectrometry. Then, following injection of the peptide digest mixture, anti-beta-endorphin antibody is injected. The peptide, which binds to the antibody, is captured and disappears from its migration time. Following this subtraction-screening procedure, the binding of the individually synthesized or isolated immunoreactive peptide is examined by the ACE-MS procedure to confirm that the epitope resides on the peptide. A series of truncated peptides can then be made and the precise epitope determined by ACE-MS. The method utilizes low femtomole amounts of antibody and peptide digest per run and is rapid and easily automatable.

Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens

Identification of T-cell epitopes within a protein antigen is an important tool in vaccine design. The T-cell epitope prediction schemes often are exploited by workers but have proved unreliable in comparison with experimental techniques. We compared published T-cell epitope predictors against two databases of human and murine T-cell epitopes. Each predictor was assessed against random cyclic permutations of epitopes in order to determine significance. Predictor performance was expressed in terms of two parameters, specificity and sensitivity. Specificity is an expression of the quality of predictions, whereas sensitivity is an expression of the quantity of epitopes predicted. Against the human data set, the strip-of-hydrophobic helix algorithm [Stille et al., Molec. Immun. 24, 1021-1027 (1987)] was the only significant predictor (p < 0.05), whereas against murine data only, the Roth2 pattern [Rothbard and Taylor, EMBO J. 7, 93-100 (1988)] was significant (p < 0.05). Not only were the majority of algorithms no better than random against both data sets, against the murine data two schemes were significant (p < 0.05) anti-predictors. This report indicates which predictors are relevant statistically and is the first to describe anti-predictors which can themselves be useful in the identification of T-cell epitopes.