Our group aims to investigate the relationships between the amino acid sequence, three-dimensional structure and the corresponding function of the antibody molecules, as a model of molecular recognition.

Antibodies play a crucial role in adaptive immunity. They recognize non-self antigens and neutralize them and/or facilitate their elimination. These immune receptors thus evolved to bind any other molecule with exquisite specificity and high affinity. Such a feature has proven to be of great potential in molecular biology, clinical diagnostic research, therapeutic applications and proteomics.

As a result, a tremendous amount of antibody sequences and three-dimensional structures have been accumulated in the databases. Yet, we are unable to predict the specificity of a given antibody sequence. This has hampered our ability to design antibodies of predefined specificity and has limited our understanding of the origin and evolution of the antibody repertoire.

Studies we have conducted (Vargas-Madrazo et al., 1995; Lara-Ochoa et al., 1996) suggest that antibodies exhibit geometrical restrictions at the antigen-binding site that correlate with the type of antigen with which the antibody interacts. Such geometrical restrictions can be predicted using the information contained in the antibody sequence. Therefore, we have found a heuristic model to correlate patterns in the amino acid sequence of a given antibody with its specificity.

Currently, we are working on: (1) refinements of the model (Almagro, 2004), (2) analysis and comparison of antibody repertoires from different species (Almagro et al., 2006), and (3) design and validation of antibody repertoires biased toward the recognition of predefined antigens (Selected Presentations). It is expected that these repertoires increase the hit rate of obtaining specific antibodies. If so, our model should shed light on the origin and evolution of the antibody repertoire.

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