From Protein Structure to Function with Bioinformatics.pdf

8 3D Motifs 2018.3.2 Motif Discovery8.3.2.1 LiteraturePerhaps the most reliable but least automatable approach to motif discovery is tomine the published literature for experimental evidence on which residues areimportant for the function of a protein. For 3D motifs, the focus is more on residuesthat provide a specific binding or catalytic capability rather than stabilizing thestructure, although it is not always possible to separate these aspects of function.The Catalytic Site Atlas (CSA) (Table 8.1) contains several hundred familiesof enzymes, each comprised of a structure with catalytic residue annotations fromthe literature and a set of related sequences (Porter et al. 2004). Representativestructural templates (3D motifs) based on side chain functional atoms or onalpha- and beta-carbons are available for a subset of the families (Torrance et al.2005). These can be searched with a structure of interest or downloaded (Table8.1). Searching is performed with the program JESS (Barker and Thornton 2003);chemically similar residue types such as aspartate and glutamate are allowed tomatch. Statistical significance is evaluated with a formula that incorporates thenumber of residues in a motif, the number of points per residue, residue abundances,and parameters determined empirically by treating the RMSD distributionsas exponents of power functions (Stark et al. 2003). This formula estimatesbackground RMSD distributions a priori so it is not necessary to compare eachmotif to a random or reference set of structures.8.3.2.2 Undirected MiningUndirected mining refers to finding common patterns in an unbiased set of structures,where “unbiased” means not chosen based on any common feature or function.In practice, there are too many possible combinations of amino acids instructures to consider them all, and the search space must be restricted.Russell performed all-by-all pairwise comparisons among a representative set ofstructures (Russell 1998). The search space was limited with distance constraintsand by disregarding nonpolar residues, disulphide-bonded cysteines, and residuesnot well conserved in sequence alignments. To detect cases of convergent evolution,matches between proteins of the same fold were ignored. The process identifiedseveral metal-binding sites and active site patterns, including the catalytic triad.The program TRILOGY also disregards residues that are not well conserved insequence alignments (Bradley et al. 2002). Patterns are required to occur in at leastthree different SCOP superfamilies. Triplets of potentially matching residues, includingconservative substitutions, are identified and merged into larger patterns. However,TRILOGY is designed to identify sequence-structure patterns, not simply 3D motifs;residue patterns must be similar in sequence spacing and order as well as in 3D.