Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Abstract

The annotation of protein function has not kept pace with the exponential growth of raw sequence and structure data. An emerging solution to this problem is to identify 3D motifs or templates in protein structures that are necessary and sufficient determinants of function. Here, we demonstrate the recurrent use of evolutionary trace information to construct such 3D templates for enzymes, search for them in other structures, and distinguish true from spurious matches. Serine protease templates built from evolutionarily important residues distinguish between proteases and other proteins nearly as well as the classic Ser-His-Asp catalytic triad. In 53 enzymes spanning 33 distinct functions, an automated pipeline identifies functionally related proteins with an average positive predictive power of 62%, including correct matches to proteins with the same function but with low sequence identity (the average identity for some templates is only 17%). Although these template building, searching, and match classification strategies are not yet optimized, their sequential implementation demonstrates a functional annotation pipeline which does not require experimental information, but only local molecular mimicry among a small number of evolutionarily important residues.

Figure 1.

Distribution of matches for serine protease motifs: (A) catalytic triad, (B) noncatalytic quartet, (C) negative control, (D) surface trace cluster. The vertical lines represent the points at which the p-value = 1% (solid green) and 5% (dashed purple). Structural template representations created using PyMOL (DeLano 2002).

Figure 2.

Distribution of matches for 53 enzymes in a single dimension, LRMSD (A), and two dimensions, LRMSD and evolutionary importance (B).