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Structural consensus among antibodies defines the antigen binding site.

Kunik V, Peters B, Ofran Y - PLoS Comput. Biol. (2012)

Bottom Line: Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically.Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding.These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.

View Article: PubMed Central - PubMed

Affiliation: The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel.

ABSTRACT
The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that ~20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.

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Structure-based identification of ABRs.(A) Using the non-redundant set of all Ab-Ag complexes in the PDB, (B) we created a multiple structure alignment of the Abs. Residues that are in contact with the Ag were identified by searching for structurally aligned positions that systematically create contacts with the Ag (black and grey solid circles) and disregarded positions that contact the Ag only sporadically (open shapes). (C) The contacting positions were mapped to the sequence representation of the multiple structure alignment (bold letters). The stretches of amino acids in which at least 10% of the Abs are in contact with the Ag were defined as ABRs (white rectangle).
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pcbi-1002388-g001: Structure-based identification of ABRs.(A) Using the non-redundant set of all Ab-Ag complexes in the PDB, (B) we created a multiple structure alignment of the Abs. Residues that are in contact with the Ag were identified by searching for structurally aligned positions that systematically create contacts with the Ag (black and grey solid circles) and disregarded positions that contact the Ag only sporadically (open shapes). (C) The contacting positions were mapped to the sequence representation of the multiple structure alignment (bold letters). The stretches of amino acids in which at least 10% of the Abs are in contact with the Ag were defined as ABRs (white rectangle).

Mentions: The outline of our structure-based ABRs identification method is delineated in Figure 1. Briefly, the algorithm structurally aligns all known Abs and marks the residues that contact the Ag in each of them. We have shown [19], [20] that in this multiple structure alignment there is a consensus among Abs that some structurally aligned positions contact the Ag. These positions form six sequence stretches along the Ab sequence that roughly correspond to the six CDRs. Beyond the edges of these stretches there were no structurally aligned positions in which more than 10% of the Abs contact the Ag. Thus, we defined the boundaries of the ABRs based on these stretches and marked the ABRs in all the Abs in our dataset.


Structural consensus among antibodies defines the antigen binding site.

Kunik V, Peters B, Ofran Y - PLoS Comput. Biol. (2012)

Structure-based identification of ABRs.(A) Using the non-redundant set of all Ab-Ag complexes in the PDB, (B) we created a multiple structure alignment of the Abs. Residues that are in contact with the Ag were identified by searching for structurally aligned positions that systematically create contacts with the Ag (black and grey solid circles) and disregarded positions that contact the Ag only sporadically (open shapes). (C) The contacting positions were mapped to the sequence representation of the multiple structure alignment (bold letters). The stretches of amino acids in which at least 10% of the Abs are in contact with the Ag were defined as ABRs (white rectangle).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3285572&req=5

pcbi-1002388-g001: Structure-based identification of ABRs.(A) Using the non-redundant set of all Ab-Ag complexes in the PDB, (B) we created a multiple structure alignment of the Abs. Residues that are in contact with the Ag were identified by searching for structurally aligned positions that systematically create contacts with the Ag (black and grey solid circles) and disregarded positions that contact the Ag only sporadically (open shapes). (C) The contacting positions were mapped to the sequence representation of the multiple structure alignment (bold letters). The stretches of amino acids in which at least 10% of the Abs are in contact with the Ag were defined as ABRs (white rectangle).
Mentions: The outline of our structure-based ABRs identification method is delineated in Figure 1. Briefly, the algorithm structurally aligns all known Abs and marks the residues that contact the Ag in each of them. We have shown [19], [20] that in this multiple structure alignment there is a consensus among Abs that some structurally aligned positions contact the Ag. These positions form six sequence stretches along the Ab sequence that roughly correspond to the six CDRs. Beyond the edges of these stretches there were no structurally aligned positions in which more than 10% of the Abs contact the Ag. Thus, we defined the boundaries of the ABRs based on these stretches and marked the ABRs in all the Abs in our dataset.

Bottom Line: Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically.Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding.These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.

View Article: PubMed Central - PubMed

Affiliation: The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel.

ABSTRACT
The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that ~20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.

Show MeSH
Related in: MedlinePlus