The 3 dimensional structure of a compound can influence immunogenicity. Peptides used in a particular vaccine immunogen are often chosen such that they generate an antibody response to the location site of that peptide in the context of the full lenght native protein. Thus, in order to generate antibodies that bind to such chosen locations, the peptide in the immunogen must assume substantially the same shape as it would exist if it was confined by the flanking regions of the full lenght native protein. However, merely conjugating a linear peptide sequence, by conventional chemistry, to a carrier protein rarely ahceives this goal. This is because such an immunogen presents the linear peptide with too much confromational freedom, such thtat the peptide may adopt a loose structure that either is not well recognised by the immune system, or may be entirely different to the conformation adopted by the peptide in the context of the flanking regions of the full lenght native protein. In order to ovecome this conformational freedom problem, it is known to design peptides in a constrained manner, by chemical interactions between distinct amino acid risdues, such that the peptide is held in a curved structure which closely resembles the curve in which the peptide would be held by the flanking sequences in the full lenght native protein (US 5,939,383). To do this it is most common to incorporate two cysteine residues in the peptide sequence between which the desired intramolecular disulphide bridge forms. The cyclised peptide thsu formed is commonly conjugated to a protein carrier to form an immunogen by one of several chemistry methods such as by theio-ether linkages (US 2004/0030106 begin_of_the_skype_highlighting 
0030106 FREE end_of_the_skype_highlighting).
The following are important structural motifs.
(a) Geta-harpin loop structure which often occurs between tow antiparallel beta strands are often relatively easily accessible. As a result, immune reponse are often directed against epitopes present in the beta hairpin sequences.
(b) Cystine-knot (Cys-knot) superfamily. These members have an unusual arrangement of 6 cysteins linked to form a “cystine-knot” conformation with distorted beta-hairpin loops above the knot and a single beta hairpin loop below the knot. The active forms of these proteins are dimers, either homo- or heterodimers. Many members of the Cys-knot family are growth factors.