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Protein function depends on the structure of a protein in the cell, and many significant changes in protein sequence are known which preserve 3D structure (eg circular permutations or fusion of interacting monomers). We discuss algorithms for detecting such rearrangements, and provide a framework for interpreting them in the context of evolution with the goal of explaining the emergence of novel protein folds.
This poster was created for ISMB 2012.
The nature of protein fold space is hotly debated. Do the protein folds observed in nature fall into clean, discrete clusters, or is fold space more accurately modeled as a vast continuum, of which only a small sample of proteins has yet been observed? Previous efforts to answer this question have focused on geometric spaces (PCA, multidimensional scaling, locally linear embedding) or network models (conformational space networks) (Chodera, 2011). While such schemes may facilitate protein comparison and classification, the choice of a mathematical framework for fold space is arbitrary without a connection to concrete biological processes. To accurately capture the true relationships between protein folds, a model must consider the evolutionary history of those folds.
Here we present a high-level model of protein evolution, which focuses on mutations that preserve the global 3D structure of proteins. We hypothesize that the combination of subtle local changes (e.g. PTMs) and large, but structure-preserving, rearrangements (e.g. duplications) can account for both the continuity of intermediate structures within protein folds and the evolution of seemingly novel folds. Our model categorizes known biological mutation processes, such as DNA replication errors and crossover errors, and places them in a simple theoretical framework.
To test this model, we present evidence from the analysis of a recent systematic comparison of all protein domains from the Protein Data Bank (PDB). We also show that the model is consistent with existing evolutionary models for gene duplication, circular permuted proteins, and proteins with internal symmetry. Future work will focus on explicitly determining evolutionary events relating distantly homologous folds.