[Structural, dynamic and interaction studies of proteins: the example of immunology]

The three-dimensional structure of a protein or of one of its functional domains cannot be predicted simply from the amino-acid sequence. It has to be determined either in the crystal, generally by X-ray diffraction, or in solution by high resolution NMR, or it can be modelled by comparison with a highly homologous protein. It cannot be represented simply by an average set of atomic coordinates. The dynamics of the molecule is part of its definition. The relative role of the structure and of the local and segmental mobility will be illustrated for recognition processes, mainly in immunological reactions. A unique conformational domain, member of the immunoglobulin superfamily, recognises differently its partners for an antigen-antibody reaction or for a cell adhesion process involving immunological determinants such as CD2 or CD4. Similar structural domains can be observed for completely different amino acid sequences, with the same type of dynamical properties, e.g. in neocarzinostatin. Restrained mobility of CDR loops and water molecules participation at the interface can explain the rapid binding of the ligands in AG/AB reactions, but cellular adhesion involves more hydrophobic and rigid interactions. This difference can be related to evolutionary aspects. Recognition mechanisms in cellular immunology, e.g. that of an intracellular foreign viral protein by a T lymphocyte cell, involve rather different biochemical processes in the so-called "peptidic self" model including proteolysis and cell surface presentation of the resulting peptides by MHC Class I proteins. These complexes are then recognised by the T cell receptors. The binding site of the TCR alpha and beta chains are structurally related to the antigen binding site of immunoglobulins. The peptide is anchored at both C- and N-terminals and should possess a restrained mobility. Recognition is thus a similar structural and dynamical process as in AG/AB reactions but is more secure due to the larger number of epitopes for a single protein.