Structural basis for the function of anti-idiotypic antibody in immune memory

Abstract

We had earlier proposed a hypothesis to explain the mechanism of perpetuation of immunological memory based on the operation of idiotypic network in the complete absence of antigen. Experimental evidences were provided for memory maintenance through anti-idiotypic antibody (Ab(2)) carrying the internal image of the antigen. In the present work, we describe a structural basis for such memory perpetuation by molecular modeling and structural analysis studies. A three-dimensional model of Ab(2) was generated and the structure of the antigenic site on the hemagglutinin protein H of Rinderpest virus was modeled using the structural template of hemagglutinin protein of Measles virus. Our results show that a large portion of heavy chain containing the CDR regions of Ab(2) resembles the domain of the hemagglutinin housing the epitope regions. The similarity demonstrates that an internal image of the H antigen is formed in Ab(2), which provides a structural basis for functional mimicry demonstrated earlier. This work brings out the importance of the structural similarity between a domain of hemagglutinin protein to that of its corresponding Ab(2). It provides evidence that Ab(2) is indeed capable of functioning as surrogate antigen and provides support to earlier proposed relay hypothesis which has provided a mechanism for the maintenance of immunological memory.

Fig. 1

(A) Alignment of sequences of several morbillivirus H proteins (see Section 2). Histograms indicate the level of similarity between the conserved regions. (B) 3D model of β-propeller domain of Rinderpest virus H viewed along the quasi-six fold axis (top view). Secondary structure elements in the ribbon diagram are colored blue to red from the N to the C terminus. The epitope recognized by the Ab₁ (A527-L556) is shown in violet color. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 1

(A) Alignment of sequences of several morbillivirus H proteins (see Section 2). Histograms indicate the level of similarity between the conserved regions. (B) 3D model of β-propeller domain of Rinderpest virus H viewed along the quasi-six fold axis (top view). Secondary structure elements in the ribbon diagram are colored blue to red from the N to the C terminus. The epitope recognized by the Ab₁ (A527-L556) is shown in violet color. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 2

(A) Schematic representation of immunoglobulin template structures chosen to build the model of variable regions of heavy and light chains of the Ab₂ D9D8; the three templates (32C2: activity suppressing Fab fragment to cytochrome p450 aromatase; 1IFH: anti-peptide Fab 17/9 and three different Fab–peptide complexes specific to influenza hemagglutinin; 1BLN: anti-p-glycoprotein Fab mrk-16) used were chosen based the structural alignment as mentioned in Section 2. The sequence similarity of D9D8 V_H and V_L with each chain and the angles between the heavy and light chains are shown. (B) Interface residues in 32C2 and the corresponding residues in D9D8: 32C2 was chosen as a template to construct the D9D8–Fv fragment comprising V_H and V_L, since the V_H–V_L interface residues were more conserved between D9D8 and 32C2. The conserved residues between both have been displayed. The number in subscript denotes the position of the amino acid residues.

Fig. 3

(A) Molecular model of D9D8: Fv region is shown in grey color, while the pink colored loops depict the V_H CDRs and the cyan colored regions represent the V_L CDRs. (B) Superposition of Ab₂ heavy chain (yellow) with a segment of hemagglutinin protein (Blue). Red colored regions depict the 551–554 aa region of hemagglutinin epitope and green colored region depict the 51–54 aa region of Ab₂ heavy chain. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 4

A schematic representation of different homologous regions between epitope on H protein and V_H and V_L of Ab₂: regions of sequence similarity are colored (Vani et al., 2007a). T cell epitopes as predicted by several MHC-peptide binding prediction algorithms (Vani et al., 2007c) are shown. B cell epitopes were analyzed by antigenicity plot. The antigenicity index was more than +1 for all the marked regions, as computed with a Jameson–Wolf plot (Jameson and Wolf, 1988). It is significant that the region of structural equivalence also matches with these regions.