Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Abstract

Background: Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates -structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates.

Exploring the structure and function paradigm

“…Each hit is then compared to the query according to the sequence similarity of the local environment of the template. A recent extension of the Evolutionary Trace method for binding site prediction was to generate structural templates based on predicted functional residues [47]. SiteEngines [48] produces templates by comparing the physico-chemical properties of residues in binding site clefts.…”

Prediction and experimental validation of enzyme substrate specificity in protein structures

“…These results were equivalent and in some cases better than previously defined template (14,15,23,65) sequence- (29,30) or topology-(67, 76) based annotation methods. We then extended our testing to annotate previously uncharacterized proteins (14,25,26,46) to validate unique ETA predictions of function. Additionally, mutagenesis studies verified the essential role played by the noncatalytic residues that were selected to be in the 3D template.…”

“…In the case of the latter, these methods search between proteins for local structural similarities over a few signature residues that represent the telltale parts of a functional site, so-called "3D templates" (3,14,18,(22)(23)(24). The residue composition of 3D templates is critical, however, and derived from experiments (25) or from analyses of functional sites and determinants (14,15,26). The sensitivity and specificity of template-based annotations still needs to be established experimentally (27, 28), but retrospective controls suggest they often predict enzyme catalytic activity (14,16,17,29,30).…”

Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation

“…Ideally, they embody the key residues that are necessary and sufficient to determine function, and a classic example is the catalytic triad of serine proteases. When such templates can be matched in other (target) structures in terms of geometry and evolutionary importance, repeatedly and reversibly, 47,48,50 then such matches are likely to be relevant, rather than random, and to indicate that the query and the target have the same enzymatic activity and hence the same Enzyme Commission (EC) number.…”

“…As this involves just a small fraction of the known structural proteome, however, a second, high throughput test will be whether these improvements carry over to protein function predictions via ET Annotation (ETA). 47,48 In this approach, without any prior knowledge of functional or catalytic sites, ET guides the selection, in a query protein of unknown function, of a structural motif of (six) top-ranked, neighboring, surface residues that together define a 3D template. ETA then matches the 3D templates to previously annotated proteins across the PDB.…”