Visualization of structural similarity in proteins

Abstract

Two new methods for the visualization of structural similarity in proteins with known three-dimensional structures are presented. They are based on the degree of equivalence of α-carbon pairs in two proteins. The quantitative measure for residue equivalence is the comparison score generated using the sequence and structure alignment method of Taylor and Orengo, which is based on the comparison of interatomic distances (and other properties that can be defined on a residue basis). The first method uses information on corresponding α-carbon positions to display vectors joining these structurally equivalent residues. These vectors can be defined as target constraints, and their minimization “bends” the two proteins toward a common average structure. In the average structure the corresponding residues virtually superpose, while insertions and deletions become clearly visible. The second method uses the comparison scores to perform a weighted least-squares fit of the two structures. It is further used to color code the two structures according to the score value, i.e., their similarity, on a continuous scale from red to blue. Examples of the methods for the comparison of flavodoxin, chemotaxis Y protein and L-arabinose-binding protein are given.