BackgroundTransporter proteins are one of an organism’s primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. The functional annotation of most transporters is currently limited to general classification into families. The development of capabilities to map ligands with specific transporters would improve our knowledge of the function of these proteins, improve the annotation of related genomes, and facilitate predictions for their role in cellular responses to environmental changes.ResultsTo improve the utility of the functional annotation for ABC transporters, we expressed and purified the set of solute binding proteins from Rhodopseudomonas palustris and characterized their ligand-binding specificity. Our approach utilized ligand libraries consisting of environmental and cellular metabolic compounds, and fluorescence thermal shift based high throughput ligand binding screens. This process resulted in the identification of specific binding ligands for approximately 64% of the purified and screened proteins. The collection of binding ligands is representative of common functionalities associated with many bacterial organisms as well as specific capabilities linked to the ecological niche occupied by R. palustris.ConclusionThe functional screen identified specific ligands that bound to ABC transporter periplasmic binding subunits from R. palustris. These assignments provide unique insight for the metabolic capabilities of this organism and are consistent with the ecological niche of strain isolation. This functional insight can be used to improve the annotation of related organisms and provides a route to evaluate the evolution of this important and diverse group of transporter proteins.

Background: Aromatic binding proteins in R. palustris transport lignin degradation products and have the potential for bioremediation. Results: The proteins bind aromatic compounds with high affinity and have dynamic elongated structures. Conclusion: Ligand binding induces local changes of residues that stabilize the compounds through hydrophobic interactions. Significance: The results provide thermodynamic and structural insights into solute-binding proteins for lignin degradation products.

The structure of the binding site of the stereoselective anti-D-amino acid antibody 67.36 was modeled utilizing web antibody modeling (WAM) and SWISS-MODEL. Although docking experiments performed with an aromatic amino acid as model ligand were unsuccessful with the WAM structure, ligand binding was achieved with the SWISS-MODEL structure. Incorporation of side-chain flexibility within the binding site resulted in a protein structure that stereoselectively binds to the D-enantiomer of the model ligand. In addition to four hydrogen bonds that are formed between amino acid residues in the binding site and the ligand, a number of hydrophobic interactions are involved in the formation of the antibody-ligand complex. The aromatic side chain of the ligand interacts with a tryptophan and a tyrosine residue in the binding site through pi-pi stacking. Fluorescence spectroscopic investigations also suggest the presence of tryptophan residues in the binding site, as ligand binding causes an enhancement of the antibody's intrinsic fluorescence at an emission wavelength of 350 nm. Based on the modeled antibody structure, the L-enantiomer of the model ligand cannot access the binding site due to steric hindrance. Additional docking experiments performed with D-phenylalanine and D-norvaline showed that these ligands are bound to the antibody in a way analogous to the D-enantiomer of the model ligand.

Key indicatorsSingle-crystal X-ray study T = 100 K Mean (C-C) = 0.002 Å R factor = 0.030 wR factor = 0.079 Data-to-parameter ratio = 22.2 For details of how these key indicators were automatically derived from the article, see

Key indicatorsSingle-crystal X-ray study T = 173 K Mean (C-C) = 0.003 Å R factor = 0.047 wR factor = 0.147 Data-to-parameter ratio = 20.0 For details of how these key indicators were automatically derived from the article, seeThe molecule of the title compound, C 22 H 29 NOS, is nonplanar, with a dihedral angle of 32.06 (9) between the two aromatic rings. organic papers Acta Cryst. (2006). E62, o3354-o3355 Hamaker and Corgliano C 22 H 29 NOS o3355