By Frank J. Dixon (Eds.)
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Computer graphics model by E. Getzoff, A. Feinstein, and J. 7. Crystal packing for the Fab Kol. , 1980), the antigen combining site shows direct interactions with neighboring molecules in the crystal. In this cross-section of the crystal lattice, the a-carbon backbones are color coded to show the location of the framework and CDR residues for the light chains (lavender framework bonds and green CDRs) and the heavy chains (light blue framework bonds and red CDRs). Crystal packing places the CDRs from o n e 9 a b against the C, and C,,1 of the next.
Residues from least reactive positions cluster into a cylindrical core within the most tightly packed portion of the protein, extending through the molecule to include residues at two surface regions. , 1986). V. Defining the Mechanisms of Antigenic Recognition A. IDENTIFICATION OF CRITICAL RESIDUES Chemical interactions are described in terms of reaction mechanisms. Thus, the modern interpretation of molecular interactions details electron and/or bond movements and conformational rearrangements in terms of the specific stereochemistry of the molecular species involved.
Areas of average reactivity occur in every helix and connecting or terminal loop region of MHr secondary structure. 7. Sites Mapped by Peptides Cluster into Conformational Epitopes In general, peptide mapping identifies sequential epitopes (which are primarily portions of assembled epitopes) where antibody binding to peptide homologs is competitively inhibited by native protein. However, where peptide mapping results are examined in terms of the three-dimensional topography of the MHr atomic structure, these sequential epitopes cluster into groups of superassemblies that may represent assembled, conformational epitopes.