Sodium ion interactions with aqueous glucose: Insights from quantum mechanics, molecular dynamics, and experiment

In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a- and B-glucose

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex

ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is “transmitted” to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK2E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the “EAA motif” (especially in the “coupling helices” region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the “coupling helices”

Distinct extracytoplasmic siderophore binding proteins recognize ferrioxamines and ferricoelichelin in streptomyces coelicolor A3(2)

Under iron limitation, the Gram-positive bacterium Streptomyces coelicolor A3(2) excretes three siderophores of the hydroxamate type: desferrioxamine B, desferrioxamine E, and coelichelin. These sequester iron from insoluble ferric hydroxides, and the resulting ferric complexes are believed to be transported into the cell via siderophore-binding proteins (SBPs) associated with ATP-binding cassette (ABC) transporters. Previous studies indicated that some of the genes in the desferrioxamine (des) and coelichelin (cch) biosynthetic clusters encode ABC transporter components required for efficient uptake of ferrioxamine E and ferricoelichelin, respectively, and a third ABC transporter gene cluster (cdt), not associated with siderophore biosynthesis genes, was implicated in the import of ferrioxamine B. In this study, the putative SBPs associated with these three gene clusters, DesE, CchF, and CdtB, were recombinantly overproduced in Escherichia coli and purified to homogeneity, and their binding affinity for cognate siderophores and noncognate siderophores was examined using fluorescence and circular dichroism spectroscopy. DesE was found to bind all of the ferric-tris-hydroxamates tested except ferricoelichelin, while CchF was found to bind only ferricoelichelin efficiently, providing further evidence that the cch cluster is a complete siderophore biosynthesis export uptake gene cluster. The picture was more complicated for CdtB, because it was found to be unstable in solution but was found to bind both ferrioxamine B and ferricoelichelin with high affinity. This was surprising because the cch cluster was previously reported to be necessary for efficient ferricoelichelin uptake. The remarkable specificity of the DesE and CchF proteins for different ferric-tris-hydroxamates raises intriguing questions about the molecular basis of their substrate specificity