Connecting the protein structure universe by using sparse recurring fragments.
The quest to order and classify protein structures has lead to various classification schemes, focusing mostly on hierarchical relationships between structural domains. At the coarsest classification level, such schemes typically identify hundreds of types of fundamental units called folds. As a result, we picture protein structure space as a collection of isolated fold islands. It is obvious, however, that many protein folds share structural and functional commonalities. Locating those commonalities is important for our understanding of protein structure, function, and evolution. Here, we present an alternative view of the protein fold space, based on an interfold similarity measure that is related to the frequency of fragments shared between folds. In this view, protein structures form a complicated, crossconnected network with very interesting topology. We show that interfold similarity based on sequence/structure fragments correlates well with similarities of functions between protein populations in different folds.
Friedberg
Iddo
I
Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, California 92037, USA. idoerg@burnham.org
Godzik
Adam
A
D019151:Peptide Library; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification*; D040681:Structural Homology, Protein
D019151:Peptide Library; D011506:Proteins