Angela Stufano

Peptidology: short amino acid modules in cell biology and immunology

Summary.Short amino acid motifs, either linear sequences or discontinuous amino acid groupings, can interact with specific protein domains, so exerting a central role in cell adhesion, signal transduction, hormone activity, regulation of transcript expression, enzyme activity, and antigen-antibody interaction. Here, we analyze the literature for such critical short amino acid motifs to determine the minimal peptide length involved in biologically important interactions. We report the pentapeptide unit as a common minimal amino acid sequence critically involved in peptide-protein interaction and immune recognition. The present survey may have implications in defining the dimensional module for peptide-based therapeutical approaches such as the development of novel antibiotics, enzyme inhibitors/activators, mimetic agonists/antagonists of neuropeptides, thrombolitic agents, specific anti-viral agents, etc. In such a therapeutical context, it is of considerable interest that low molecular weight peptides can easily cross biological barriers, are less susceptible to protease attacks, and can be administered at high concentrations. In addition, small peptides are a rational target for strategies aimed at antigen-specific immunotherapeutical intervention. As an example, specific short peptide fragments might be used to elicit antibodies capable of reacting with the full-length proteins containing the peptide fragment’s amino acid sequence, so abolishing the risk of cross-reactivity.

Massive peptide sharing between viral and human proteomes

Abstract Thirty viral proteomes were examined for amino acid sequence similarity to the human proteome, and, in parallel, a control of 30 sets of human proteins was analyzed for internal human overlapping. We find that all of the analyzed 30 viral proteomes, independently of their structural or pathogenic characteristics, present a high number of pentapeptide overlaps to the human proteome. Among the examined viruses, human T-lymphotropic virus 1, Rubella virus, and hepatitis C virus present the highest number of viral overlaps to the human proteome. The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus–host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs.

Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis.

Using the currently available proteome databases and based on the concept that a rare sequence is a potential epitope, epitopic sequences derived from Mycobacterium tuberculosis were examined for similarity score to the proteins of the host in which the epitopes were defined. We found that: (i) most of the bacterial linear determinants had peptide fragment(s) that were rarely found in the host proteins and (ii) the relationship between low similarity and epitope definition appears potentially applicable to T-cell determinants. The data confirmed the hypothesis that low-sequence similarity shapes or determines the epitope definition at the molecular level and provides a potential tool for designing new approaches to prevent, diagnose, and treat tuberculosis and other infectious diseases.

Proteome-guided search for influenza A B-cell epitopes.

The influenza A linear peptide epitopes recognized by murine antibodies, and currently cataloged at http://www.immuneepitope.org, were examined for the identity score to the host mouse proteome. It was found that almost all of the linear viral determinants are (or contain) regions formed by pentapeptide fragments with no or only very low similarity to the murine proteins. The present study adds to previous reports in suggesting a main role of amino acid sequence similarity in the modulation and definition of the B-cell epitope repertoire, inspiring innovative vaccine approaches able to avoid cross-reactive autoimmune collateral phenomena, and addressing future research in the study of immunity against the influenza A virus and infectious diseases in general.

Proteome-based epitopic peptide scanning along PSA.

The specific definition of the immunogenic peptide repertoire from tumor-associated-antigens (TAAs) is of crucial importance for designing effective immunotherapeutical treatments. Multiple mechanisms, at different levels and in complementary manners, contribute to the generation of immunogenic peptides. Using as an experimental model the prostate specific antigen (PSA) and a murine monoclonal antibody (MAb) raised against human PSA, the role of PSA peptide 1) similarity to the murine proteome, 2) affinity to H2-Ad/Ed molecules, and 3) proteasomal cleavage pattern were investigated. We report that the core of the interaction between the anti-PSA MAb ER-PR8 and the prostatic antigen is located in the pentapeptide motif PSA(27-31)GGWEC. The pentapeptide motif is characterized by having no sequence similarity to the murine proteome and a low number of potential proteolytic sites.

Sub-epitopic dissection of HCV E1315–328HRMAWDMMMNWSPT sequence by similarity analysis

Summary.Our labs are focused on identifying amino acid sequences having the ability to react specifically with the functional binding site of a complementary antibody. Our epitopic definition is based on the analysis of the similarity level of antigenic amino acid sequences to the host proteome. Here, the similarity profile to the human proteome of an HCV E1 immunodominant epitope, i.e. the HCV E1315–328HRMAWDMMMNWSPT sequence, led to i) characterizing the immunoreactive HCV E1 315–328 region as a sequence endowed with a low level of similarity to human proteins; ii) defining 2 contiguous immunodominant linear determinants respectively located at the NH2 and COOH terminus of the conserved viral antigenic sequence. This study supports the hypothesis that low sequence similarity to the host’s proteome modulates the pool of epitopic amino acid sequences in a viral antigen, and appears of potential value in defining immunogenic viral peptide sequences to be used in immunotherapeutic approaches for HCV treatment.