8536dch030649/10/0210:12 AM Page64mac46mac46:385REB ART II Generation of B-Cell and T-Cell Respons are hidden within the interior of a protein often consist of predominantly hydrophobic amino acids, and cannot fun tion as B-cell epitopes unless the protein is first denatured In the crystallized antigen-antibody complexes analyzed date, the interface between antibody and antigen shows nu- merous complementary protrusions and depressions(Figure I 3-5).Between 15 and 22 amino acids on the antigen contact the antibody by 75-120 hydrogen bonds as well as by i and hydrophobic interactions. B-cell epitopes can contain sequential or nonsequential amino acids. Epitopes may be composed of sequential con tiguous residues along the polypeptide chain or nonsequen tial residues from segments of the chain brought together by the folded conformation of an antigen. Most antibodies elicited by globular proteins bind to the protein only when it is in its native conformation Because denaturation of such antigens usually changes the structure of their epitopes, anti- bodies to the native protein do not bind to the denatured Five distinct sequential epitopes, each containing six eight contiguo acids, have been found in sperm whale myoglobin. Each of these epitopes is on the surface the molecule at bends between the a-helical regions( Figure 3-6a) Sperm whale myoglobin also contains several nonse- quential epitopes, or conformational determinants. The residues that constitute these epitopes are far apart in the mary amino acid sequence but close together in the tertiary structure of the molecule. Such epitopes depend on the FIGURE3-3(a)Model of interaction between hen egg-white lysozyme(HEL) and Fab fragment of anti-HEL antibody based on x HyHel-5 HyHel-10 ay diffraction analysis. HEL is shown in green, the Fab heavy chain in blue, and the Fab light chain in yellow. a glutamine residue lysozyme(red) fits into a pocket in the Fab fragment.(b)Representa- tion of HEL and the Fab fragment when pulled apart showing com- plementary surface features. (c) View of the interacting surfaces of the Fab fragment and HEL obtained by rotating each of the mole BV04 cules. The contacting residues are numbered and shown in red with the protruding glutamine(#14)in HEL now shown in white. / From A. G. Amit et al, 1986, Science 233: 747. J IGURE 3-4 Models of the variable domains of six Fab fragments ith their antigen-binding regions shown in purple. The op three an tibodies are specific for lysozyme, a large globular protein. The lower The B-cell epitopes on native proteins generally are com- three antibodies are specific for smaller molecules or very small seg posed of hydrophilic amino acids on the protein surface that are ments of macromolecules: McPC603 for phosphocholine; BVO4 for a topographically accessible to membrane-bound or free anti- small segment of a single- stranded DNA molecule; and 17/9 for a body. A B-cell epitope must be accessible in order to be able to peptide from hemagglutinin, an envelope protein of influenza virus bind to an antibody; in general, protruding regions on the In general, the binding sites for small molecules are deep pockets, urface of the protein are the most likely to be recognized as whereas binding sites for large proteins are flatter, more undulating epitopes, and these regions are usually composed of predom- surfaces.(From I. A. Wilson and R. L. Stanfield, 1993, Curr. Opin inantly hydrophilic amino acids. Amino acid sequences that Struc. Biol. 3: 113The B-cell epitopes on native proteins generally are com￾posed of hydrophilic amino acids on the protein surface that are topographically accessible to membrane-bound or free anti￾body.A B-cell epitope must be accessible in order to be able to bind to an antibody; in general, protruding regions on the surface of the protein are the most likely to be recognized as epitopes, and these regions are usually composed of predom￾inantly hydrophilic amino acids. Amino acid sequences that are hidden within the interior of a protein often consist of predominantly hydrophobic amino acids, and cannot func￾tion as B-cell epitopes unless the protein is first denatured. In the crystallized antigen-antibody complexes analyzed to date, the interface between antibody and antigen shows nu￾merous complementary protrusions and depressions (Figure 3-5). Between 15 and 22 amino acids on the antigen contact the antibody by 75–120 hydrogen bonds as well as by ionic and hydrophobic interactions. B-cell epitopes can contain sequential or nonsequential amino acids. Epitopes may be composed of sequential con￾tiguous residues along the polypeptide chain or nonsequen￾tial residues from segments of the chain brought together by the folded conformation of an antigen. Most antibodies elicited by globular proteins bind to the protein only when it is in its native conformation. Because denaturation of such antigens usually changes the structure of their epitopes, anti￾bodies to the native protein do not bind to the denatured protein. Five distinct sequential epitopes, each containing six to eight contiguous amino acids, have been found in sperm whale myoglobin. Each of these epitopes is on the surface of the molecule at bends between the -helical regions (Figure 3-6a). Sperm whale myoglobin also contains several nonse￾quential epitopes, or conformational determinants. The residues that constitute these epitopes are far apart in the pri￾mary amino acid sequence but close together in the tertiary structure of the molecule. Such epitopes depend on the 64 PART II Generation of B-Cell and T-Cell Responses (a) (b) (c) FIGURE 3-3 (a) Model of interaction between hen egg-white lysozyme (HEL) and Fab fragment of anti-HEL antibody based on x￾ray diffraction analysis. HEL is shown in green, the Fab heavy chain in blue, and the Fab light chain in yellow. A glutamine residue of lysozyme (red) fits into a pocket in the Fab fragment. (b) Representa￾tion of HEL and the Fab fragment when pulled apart showing com￾plementary surface features. (c) View of the interacting surfaces of the Fab fragment and HEL obtained by rotating each of the mole￾cules. The contacting residues are numbered and shown in red with the protruding glutamine (#14) in HEL now shown in white. [From A. G. Amit et al., 1986, Science 233: 7 47.] FIGURE 3-4 Models of the variable domains of six Fab fragments with their antigen-binding regions shown in purple. The top three an￾tibodies are specific for lysozyme, a large globular protein. The lower three antibodies are specific for smaller molecules or very small seg￾ments of macromolecules: McPC603 for phosphocholine; BV04 for a small segment of a single-stranded DNA molecule; and 17/9 for a peptide from hemagglutinin, an envelope protein of influenza virus. In general, the binding sites for small molecules are deep pockets, whereas binding sites for large proteins are flatter, more undulating surfaces. [From I. A. Wilson and R. L. Stanfield, 1993, Curr. Opin. Struc. Biol. 3:113.] HyHel-5 HyHel-10 D1/3 McPC603 BV04 17/9 8536d_ch03_064 9/10/02 10:12 AM Page 64 mac46 mac46:385_REB: