CDR-FR Peptides

The non-immunogenic antigen binder has emerged as an important component in the research of cell recognition and targeting with the high degree of specificity inherited from prototypical antibody (Hoogenboom 2005; Holliger and Hudson 2005; Hu et al. 1996; Olafsen et al. 2004; Shahied et al. 2004). However, the optimal binding interfaces of the antigen binders remained to be defined though various entities had been proposed (Hoogenboom 2005; Holliger and Hudson 2005; Hu et al. 1996; Olafsen et al. 2004; Shahied et al. 2004; Cortez-Retamozo et al. 2002; Genst et al. 2004). In a classic antibody, antigen recognition is accomplished with the multiple noncovalent forces, which are synergistically produced by three complementarity determining regions (CDRs) of V_H and other three CDRs of V_L domains (Laune et al. 1997; Aburatani et al. 2002; Ewert et al. 2003; Borg et al. 2005; Hunt et al. 2005; Rothlisberger et al. 2005). The synergic interactions of V_H and V_L domains, inevitably, comprise a substantial component of the multiple noncovalent forces. However, the contribution of such synergic interactions to antigen recognition by an antibody has not yet been thoroughly investigated (Hu et al. 1996; Olafsen et al. 2004; Shahied et al. 2004; Ewert et al. 2003; Borg et al. 2005). On the other hand, the energetic studies of CDRs in the lymphocyte receptor had indicated that in the variable domains each CDR loop may play different hierarchical roles for antigen recognition (Borg et al. 2005). Therefore, the “cross-reactivity” of CDRs in V_H and V_L domains should not be neglected in the composition of non-immunogenic antigen binder. To accommodate the “cross-reactivity” between the structural elements of heavy and light variable domains, we assumed that one V_H CDR and one V_L CDR sequentially linked with a framework region (FR) that linked CDRs would consist of a 28-residue antigen binder as a rational non-immunogenic antigen-binding interface model with the minimized structural form (Laune et al. 1997; Aburatani et al. 2002; Ewert et al. 2003).