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Abstract

The present disclosure includes a method for locating functionally relevant atoms in protein structures, and a representation of spatial arrangements of these atoms allowing for flexible description of active sites in proteins. The search method can be based on comparison of local structure features of proteins that share a common biochemical function. Generally, the method does not depend on overall similarity of structures and sequences of compared proteins, or on previous knowledge about functionally relevant residues. The compared protein structures can be condensed to a graph representation, with atoms as nodes and distances as edge labels. Protein graphs can then be compared to extract all possible Common Structural Cliques. These cliques can be merged to create structural templates: graphs that describe structural analogies between compared proteins. Structures of serine endopeptidases were compared in pairs using the presented algorithm with different geometrical parameters. Additionally, a structural template was extracted from the structures of aminotransferases, two different proteins that catalyze the same type of chemical reaction. Presented results show that the method works efficiently even in the case of large protein systems, and allows for extraction of common structural features from proteins catalyzing a particular chemical reaction, but that evolved from different ancestors by convergent evolution.

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First Claim