Complementarity determining regions CDR

FIGURE 18.10 Cloning natural V regions. FR Framework CDR Complementarity determining region. 

Abbreviations used in table MC - Monte Carlo aa - amino acid vdW - van der Waals potential Ig - immunoglobulin or antibody CDR - complementarity-determining regions in antibodies RMS -root-mean-square deviation r-dependent dielectric - distance-dependent dielectric constant e - dielectric constant MD - molecular dynamics simulation self-loops - prediction of loops performed by removing loops from template structure and predicting their conformation with template sequence bbdep - backbone-dependent rotamer library SCMF - self-consistent mean field PDB - Protein Data Bank Jones-Thirup distances - interatomic distances of 3 Ca atoms on either side of loop to be modeled. 

The differences in sequence within the variable region produce a practically unlimited number of possible three-dimensional arrangements for the amino acid side chains to form the complementarity-determining region (CDR), which actually binds to the antigen. 

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