The Enzyme Function Initiative (EFI) will develop a robust sequence/structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic/physiological functions of unknown enzymes discovered in genome projects, a crucial limitation in genomic biology. The EFI will accomplish this goal by integrating bioinformatics, structural biology, and computation with enzymology, genetics, and metabolomics. The EFI will establish five Scientific Cores for: 1) directing target selection as well as devising strategies for functional assignment based on sequence relationships and genome context;2) expression and purification of targets;3) experimental determination of structures of targets;4) computational determination of structures of targets (homology modeling) and, also, in silico docking of ligand libraries to direct experimental assignment of in vitro functions by focused library screening;and 5) microbiological and metabolomic characterization of the in vivo roles of the in vitro assigned functions. The functional predictions will be tested by five Bridging Projects that focus on the functionally diverse amidohydrolase (AH), enolase (EN), glutathione transferase (GST), haloalkanoic acid dehalogenase (HAD), and isoprenoid synthase (IS) superfamilies. These superfamilies were selected because functional assignment cannot be accomplished by transfer of prior annotations based only on sequence or structural similarity: the reactions within each superfamily share conserved partial reactions but the identities of the substrates/products are not conserved. The EFI will disseminate to the scientific community the intellectual, computational, and experimental tools, protocols, materials, and guidelines for determining in vitro and in vivo functions of unknown enzymes. In achieving this goal, the EFI will nucleate and enable a larger consortium of investigators working toward the goal of realizing the biomedical potential of the vast amount of sequence data provided by genome projects.
Assignment of function to the complete set of proteins encoded by genomes is a major challenge. However, when solved, their roles in molecular, cellular, and organismal functions will be known, and novel targets for specific small molecule intervention and new approaches for therapeutic design can be identified. The Enzyme Function Initiative will develop and implement an integrated sequence/structure-based strategy for predicting the substrate specificities of unknown enzymes discovered in genome projects, including classes of proteins with direct relevance to human health.
|Mashiyama, Susan T; Malabanan, M Merced; Akiva, Eyal et al. (2014) Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol 12:e1001843|
|Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E et al. (2014) The Structure-Function Linkage Database. Nucleic Acids Res 42:D521-30|
|Zheng, Heping; Hou, Jing; Zimmerman, Matthew D et al. (2014) The future of crystallography in drug discovery. Expert Opin Drug Discov 9:125-37|
|Wichelecki, Daniel J; Graff, Dylan C; Al-Obaidi, Nawar et al. (2014) Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily. Biochemistry 53:4087-9|
|Dong, Guang Qiang; Calhoun, Sara; Fan, Hao et al. (2014) Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 54:1687-99|
|Wichelecki, Daniel J; Vendiola, Jean Alyxa Ferolin; Jones, Amy M et al. (2014) Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate. Biochemistry 53:5692-9|
|Bouvier, Jason T; Groninger-Poe, Fiona P; Vetting, Matthew et al. (2014) Galactaro ?-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53:614-6|
|Wichelecki, Daniel J; Froese, D Sean; Kopec, Jolanta et al. (2014) Enzymatic and structural characterization of rTS? provides insights into the function of rTS?. Biochemistry 53:2732-8|
|Pandya, Chetanya; Dunaway-Mariano, Debra; Xia, Yu et al. (2014) Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily. Proteins 82:1896-906|
|Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W et al. (2014) Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5:e00933-13|
Showing the most recent 10 out of 49 publications