title: Accurate high-throughput structure mapping and prediction with transition metal ion FRET.
abstract: Mapping the landscape of a protein's conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein maltose binding protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells.
authors.affiliation: Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Xiaozhen
authors.initials: X
authors.lastname: Yu
authors.affiliation: Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Xiongwu
authors.initials: X
authors.lastname: Wu
authors.affiliation: Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Guillermo A
authors.initials: GA
authors.lastname: Bermejo
authors.affiliation: Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.affiliation: Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: justin.taraska@nih.gov.
authors.forename: Justin W
authors.initials: JW
authors.lastname: Taraska
mesh_terms: D019943:Amino Acid Substitution; D001059:Apoproteins / Q000737:chemistry / Q000235:genetics; D003300:Copper / Q000737:chemistry*; D005452:Fluoresceins / Q000737:chemistry; D005454:Fluorescence Polarization; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry; D058619:Maltose-Binding Proteins / Q000737:chemistry / Q000235:genetics; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009532:Nickel / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013194:Staining and Labeling
chemical_list: D001059:Apoproteins; D005452:Fluoresceins; D005456:Fluorescent Dyes; D058619:Maltose-Binding Proteins; C037041:fluorescein 5-maleimide; D003300:Copper; D009532:Nickel