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By Frank J. Dixon (Eds.)

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Variable. In much of immunology, experiments involve complex systems containing many different variables, which can be difficult to define and impossible to eliminate. , 1987) was initiated on the immune response to MHr. , 1987). , 1972). The MHr protein fold consists of an antiparallel bundle of four a-helices (named A, B, C, and D in sequence order) that surround a two-iron center a t the active site, an N-terminal loop region, and shorter loops between the helices and a t the Cterminus. , 1987a).

The ratio of main-chain to side-chain surface area is similar for positions with most and average reactivity and lower for the least reactive positions. In the folded protein, the side-chain surface exposure can also be measured as a percentage of the total surface exposure of the same sidechain conformation in the absence of the other protein residues. 9. Superassemblies of MHr sequential epitopes. Three categories of immunological reactivity (red, most reactive; yellow, average; blue, least reactive) are mapped by color coding onto the solvent-exposed molecular surface of MHr, shown i n front and back views.

A. Padlan, E. W. Silverton, S. Sheriff, G. H. Cohen, S. Smith-Gill, and D. R. Davies) from X-ray diffraction studies of these antibodies in antibody-lysozyme complexes (H. M. Geysen and S. J. Smith-Gill, unpublished results). Although preliminary, the peptide mapping results identified the unpublished HyHELlO site and correctly suggested the involvement of Trp and Arg in the complex. , 1982). In principle, the characterization of critical residues, originally studied by peptide mapping and comprehensive single-residue substitution in peptides (see Sections IV and V), can be done in the context of the native protein fold, using cloning and site-directed mutation methods.

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