Calculating three‐dimensional changes in protein structure due to amino‐acid substitutions: The variable region of immunoglobulins

Abstract

A procedure (coupled perturbation procedure, CPP) is introduced as a specific method for calculating the detailed three-dimensional structure of a protein molecule which has a nummber of amino-acid substitutions relative to some previously determined “parent” protein structure. The accuracy of the procedure is tested by calculating the conformation of a region of the human immunoglobulin fragment Fab Kol based on the analogous region of the human immunoglobulin fragment Fab New. Both structures have previously been determined crystallographically. The calculated model is accurate to the extent that both of the sequence differences in the region are modeled correctly and that conformational changes in a number of nearby residues are correctly identified. CPP is shown to give better results than other commonly used modeling procedures when applied to the same problem.