Families and the structural relatedness among globular proteins

Protein structures come in families. Are families "closely knit" or "loosely knit" entities? We describe a measure of relatedness among polymer conformations. Based on weighted distance maps, this measure differs from existing measures mainly in two respects: (1) it is computationally fast, and (2) it can compare any two proteins, regardless of their relative chain lengths or degree of similarity. It does not require finding relative alignments. The measure is used here to determine the dissimilarities between all 12,403 possible pairs of 158 diverse protein structures from the Brookhaven Protein Data Bank (PDB). Combined with minimal spanning trees and hierarchical clustering methods, this measure is used to define structural families. It is also useful for rapidly searching a dataset of protein structures for specific substructural motifs. By using an analogy to distributions of Euclidean distances, we find that protein families are not tightly knit entities.