The precise and entire antigenic structure of lysozyme: implications of surface-simulation synthesis and the molecular features of protein antigenic sites

SUPERFICIAL--surface mapping of proteins via structure-based peptide library design

Background

The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being prevailant. Conventional mapping techniques with arrays of synthetic peptides have limitations with regard to the location of discontinuous or non-linear binding sites of proteins.

Results

We present a structure-based approach to the design of peptide libraries that mimic the whole surface or a particular region of a protein. Neighbouring sequence segments are linked by short spacers to conserve local conformation. To this end, we have developed SUPERFICIAL, a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions.

Conclusion

Based on 3D structures, SUPERFICIAL may help to negotiate some of the existing limitations, since binding sites consisting of several linear pieces can now be detected.

Antigenic structures of proteins. Their determination has revealed important aspects of immune recognition and generated strategies for synthetic mimicking of protein binding sites

Studies in this laboratory have resulted in the delineation and synthetic verification of several complete protein antigenic structures that are recognized by antibodies. More recently, for the first time, the full profiles of the sites that are recognized by T cells have been localized and confirmed by synthesis for two proteins, myoglobin and lysozyme. These have thus far constituted the only complete antigenic structures to be determined. The availability of these antigenic structures has enabled us to investigate in detail the molecular and cellular parameters responsible for immune recognition, responses to, and control and regulation of these responses to protein antigens at the molecular and submolecular levels. Moreover, these investigations have afforded general strategies for the synthetic mimicking of not only antigenic sites, but also protein binding sites involved in other biological activities.

The major B and T cell determinant on pigeon cytochrome c in B10.a mice

The specificities of B10.A B and T cells responding to pigeon cytochrome c have been examined. Proliferating T cells recognize glutamine 100 and lysine 104 and can be stimulated in vitro by either native cytochrome c molecules or certain of their CNBr-cleavage fragments. In contrast only molecules with the native cytochrome c conformation were found to interact with B10.A antipigeon cytochrome c antibodies. Antibodies appear to recognize a determinant or determinants which overlaps with that which elicits the T cell proliferative response.

Reverse turns in peptides and proteins

The evidence that reverse turns frequently occur as structural components of proteins, as well as of linear and cyclic peptides, is overwhelming. This review summarizes and examines critically the experimental evidence derived from physical methods such as 1H and 13C nuclear magnetic resonance spectroscopy, spin-lattice relaxation time, circular dichroism, IR spectroscopy, and X-ray crystallography. Secondly, theoretical evidence obtained from energy calculations, which rely on empirical energy functions, and correlative methods, which rely on algorithms based on the frequency of occurrence of amino acids, is evaluated. In particular, those theoretical studies for which complementary physical studies have been completed are emphasized. Finally, examples of structure-function relationships involving reverse turns and their biological recognition are demonstrated.