Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis
Abstract Background Carnivorous plants possess diverse sets of enzymes with novel functionalities applicable to biotechnology, proteomics, and bioanalytical research. Chitinases constitute an important class of such enzymes, with future applications including human-safe antifungal agents and pesticides. Here, we compare chitinases from the genome of the carnivorous plant Drosera capensis to those from related carnivorous plants and model organisms. Methods Using comparative modeling, in silico maturation, and molecular dynamics simulation, we produce models of the mature enzymes in aqueous solution. We utilize network analytic techniques to identify similarities and differences in chitinase topology. Results Here, we report molecular models and functional predictions from protein structure networks for eleven new chitinases from D. capensis , including a novel class IV chitinase with two active domains. This architecture has previously been observed in microorganisms but not in plants. We use a combination of comparative and de novo structure prediction followed by molecular dynamics simulation to produce models of the mature forms of these proteins in aqueous solution. Protein structure network analysis of these and other plant chitinases reveal characteristic features of the two major chitinase families. General significance This work demonstrates how computational techniques can facilitate quickly moving from raw sequence data to refined structural models and comparative analysis, and to select promising candidates for subsequent biochemical characterization. This capability is increasingly important given the large and growing body of data from high-throughput genome sequencing, which makes experimental characterization of every target impractical. Highlights We report eleven new chitinases from the carnivorous plant Drosera capensis . A novel two domain class IV chitinase similar to those found in microbes was found. Protein structure prediction and comparison to other carnivorous plant chitinases reveals commonalities. Sequence and structural motifs are conserved among carnivorous plant chitinases. Protein structure networks reveal structural differences and predict functionality. Graphical Abstract [DISPLAY OMISSION]
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