Nearest-neighbour analysis of myoglobin antigenic sites. Nearest-neighbour residues whose replacement can alter the environment of binding-site residue(s) and thus change their characteristics and binding capability

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Abstract
By using the known antigenic structure of sperm-whale myoglobin previously determined in this laboratory and the X-ray coordinates for the myoglobin molecule, the nearest-atom distances were calculated between each of the residues of the antigenic sites and all the other amino acids of the myoglobin molecule. These calculations have enabled the identification of the neareast-neighbor residues to each of the residues in the 5 antigenic sites, and which thus describe the immediate molecular environment of the sites. The influences of chemical changes or replacements in these environmental residues on the binding capacity of an antigenic site, when considered together with replacements directly in the antigenic sites, are expected to account for the major effects and will be extremely useful in explaining the cross-reactions of myoglobins from various species. The analysis has limitations due to the qualitative estmates of the effects, the influences of substitutions at once-removed or even at more distant locations (especially when they are cumulative) and finally the influences of any conformational re-adjustments when these occur as a result of the replacement(s).

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