Construction of a three-dimensional model of the polypeptide backbone of the variable region of kappa immunoglobulin light chains.

From (varphi,Psi) data for the middle amino acid, n, in the series of tripeptides (n - 1)(n)(n + 1) in six proteins whose three-dimensional structure is known from x-ray studies, (varphi,Psi) values for the residues 2-107 of kappa Bence Jones proteins and immunoglobulin light chains were computed. It was assumed that all residues except those in the hypervariable regions 24-34, 50-56, and 89-97, were involved essentially in three-dimensional structure, and hence, their (varphi,Psi) angles would mostly be those best satisfying all kappa tri- and constituent di-peptides that occur at those positions. A set of criteria for selecting and averaging (varphi,Psi) angles is given. In the hypervariable regions, which are presumed to be involved in site complementarity, the (varphi,Psi) angles were selected for a single Bence Jones protein Ag. The three-dimensional models, constructed from the computed (varphi,Psi) values by hand and by display computer were very similar, and residues 23 and 88 were sufficiently close for the disulfide bond to form.