Redundancy-aware learning of protein structure-function relationships

D. H. Bryant, “Redundancy-aware learning of protein structure-function relationships,” PhD thesis, Rice University, Department of Computer Science, Houston, Texas, 2012.


The protein kinases are a large family of enzymes that play a fundamental role in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug compounds with high specificity among the kinases has proven difficult. However, computational approaches to comparing the 3-dimensional geometry and physicochemical properties of key binding site residues, referred to here as substructures, have been shown to be informative of inhibitor selectivity. This thesis intro- duces two fundamental approaches for the comparative analysis of substructure similarity and demonstrates the importance of each method on a variety of large protein structure datasets for multiple biological applications. The Family-wise Alignment of SubStructural Templates Framework (The FASST Frame- work) provides an unsupervised learning approach for identifying substructure clusterings. The substructure clusterings identified by FASST allow for the automatic evaluation of sub- structure variability, the identification of distinct structural conformations and the selec- tion of anomalous outlier structures within large structure datasets. These clusterings are shown to be capable of identifying biologically meaningful structure trends among a di- verse number of protein families. The FASST Live visualization and analysis platform provides multiple comparative analysis pipelines and allows the user to interactively explorethe substructure clusterings computed by The FASST Framework. The Combinatorial Clustering Of Residue Position Subsets (CCORPS) method provides a supervised learning approach for identifying structural features that are correlated with a given set of annotation labels. The ability of CCORPS to identify structural features pre- dictive of functional divergence among families of homologous enzymes is demonstrated across 48 distinct protein families. The CCORPS method is further demonstrated to gen- eralize to the very difficult problem of predicting protein kinase inhibitor affinity. CCORPS is demonstrated to make perfect or near-perfect predictions for the binding ability of 12 of the 38 kinase inhibitors studied, while only having overall poor predictive ability for 1 of the 38 compounds. Additionally, CCORPS is shown to identify shared structural features across phylogenetically diverse groups of kinases that are correlated with binding affinity for particular inhibitors; such instances of structural similarity among phylogenetically di- verse kinases are also shown to not be rare among kinases. Finally, these function-specific structural features may serve as potential starting points for the development of highly spe- cific kinase inhibitors. Importantly, both The FASST Framework and CCORPS implement a redundancy-aware approach to dealing with structure overrepresentation that allows for the incorporation of all available structure data. As shown in this thesis, surprising structural variability exists even among structure datasets consisting of a single protein sequence. By incorporating the full variety of structural conformations within the analysis, the methods presented here provide a richer view of the variability of large protein structure datasets.

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