ArticleBiochemistry2015
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Article in Biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- Analytical Ultracentrifugation for Studying the Oligomeric State and Protein-Protein Interactions of Membrane Transporters.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Probing the core metabolism ofJournal of bacteriology · 2025Article
- The Corrinoid Model for Dissecting Microbial Community Interactions Across Scales.Annual review of microbiology · 2025Review
- Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition.PLoS pathogens · 2025Article
- A new class of binding-protein dependent solute transporter exemplified by the TAXI-GltS system from Bordetella pertussis.Communications biology · 2025Article
- Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering.Molecular biology and evolution · 2025Article
- Metabolic engineering for microbial production of sugar acids.BMC biotechnology · 2025Review
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Duplicate entries in the Protein Data Bank: how to detect and handle them.Acta crystallographica. Section D, Structural biology · 2025Article
- Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter.eLife · 2025Article
- Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.Microbiome · 2025Article
- Lipid Trafficking in Diverse Bacteria.Accounts of chemical research · 2025Review
- Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium.Advances in biochemical engineering/biotechnology · 2025Review
- On the function of TRAP substrate-binding proteins: the isethionate-specific binding protein IseP.The Biochemical journal · 2024Article
- Structure and selectivity of a glutamate-specific TAXI TRAP binding protein from Vibrio cholerae.The Journal of general physiology · 2024Article
- Allosteric substrate release by a sialic acid TRAP transporter substrate binding protein.Communications biology · 2024Article
- Enhancing catalytic efficiency of Bacillus subtilis laccase BsCotA through active site pocket design.Applied microbiology and biotechnology · 2024Article
- Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacteriummSystems · 2024Article
- Designing optimal experiments in metabolomics.Metabolomics : Official journal of the Metabolomic Society · 2024Review
13 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors.
Funding
Abstract
The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data.
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Registered trials
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