Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 Å resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 Å resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.crystallography ͉ DNA complex ͉ nickel ͉ transcription factor ͉ metalloregulator M etal ions are essential nutrients for all cells, but their intracellular concentrations and distribution must be tightly regulated to avoid toxicity. Nickel ions are particularly important to the physiology of microorganisms such as the model prokaryote Escherichia coli and the human gastric pathogen Helicobacter pylori. In these organisms, incorporation of nickel into enzymes such as [NiFe]-hydrogenase and urease is necessary for metabolic adaptation to changing environmental conditions (1). In E. coli, nickel is acquired via an ABC-type membrane transporter, NikABCDE (2). Transcription of the operon encoding this nickel importer, nikABCDE, is repressed in the presence of nickel by the transcription factor NikR (3, 4). NikR therefore serves as a cytoplasmic nickel sensor, stopping production of the nickel importer when intracellular levels of nickel are sufficient. In H. pylori, which requires the nickel enzyme urease to survive and colonize the acidic gastric mucus of the human stomach, NikR plays a more complex regulatory role. Transcriptome analysis of a deletion mutant and in vitro promoter-binding assays have revealed that H. pylori NikR (HpNikR) regulates transcription of not only the nickel importer and urease enzyme, but also other regulatory networks, some through repression of the gene encoding the ferric uptake regulator (Fur) protein (5-8).The NikR protein that has been characterized most extensively at the molecular level is the homolog from E. coli. E. coli NikR (EcNikR or NikR) is a homotetramer that binds one nickel(II) ion per subunit with picomolar affinity (9, 10). Stoichiometric nickel ions activate NikR to bind a 28-bp palindromic operator sequence (GTATGA-N 16 -TCATAC) within the promoter of nikABCDE with low-nanomolar affinity (9, 11). Recently, it was demonstrated that NikR can bind a variety of divalent transition metal ions with high affinity and that stoichiometric amounts of these other ions can activate N...

Multidrug resistance is a serious barrier to successful treatment of many human diseases, including cancer, wherein chemotherapeutics are exported from target cells by membrane-embedded pumps. The most prevalent of these pumps, the ATP-Binding Cassette transporter P-glycoprotein (P-gp), consists of two homologous halves each comprising one nucleotide-binding domain and six transmembrane helices. The transmembrane region encapsulates a hydrophobic cavity, accessed by portals in the membrane, that binds cytotoxic compounds as well as lipids and peptides. Here we use mass spectrometry (MS) to probe the intact P-gp small molecule-bound complex in a detergent micelle. Activation in the gas phase leads to formation of ions, largely devoid of detergent, yet retaining drug molecules as well as charged or zwitterionic lipids. Measuring the rates of lipid binding and calculating apparent K D values shows that up to six negatively charged diacylglycerides bind more favorably than zwitterionic lipids. Similar experiments confirm binding of cardiolipins and show that prior binding of the immunosuppressant and antifungal antibiotic cyclosporin A enhances subsequent binding of cardiolipin. Ion mobility MS reveals that P-gp exists in an equilibrium between different states, readily interconverted by ligand binding. Overall these MS results show how concerted small molecule binding leads to synergistic effects on binding affinities and conformations of a multidrug efflux pump.mass spectrometry from native state | real time substrate monitoring P -glycoprotein (P-gp) is an ATP-driven low-specificity efflux pump that plays an important role in the clearance of xenotoxins (1, 2). P-gp is also a member of the ATP-Binding Cassette (ABC) family of transporters and exports hydrophobic cytotoxic compounds as well as natural products, cyclic, and linear peptides (1, 3-5). Overexpression of P-gp in tumor cells impairs targeted drug delivery and is a major pitfall for chemotherapies. Small molecule substrates partition in the plasma membrane (6, 7), before binding in the internal hydrophobic cavity formed in the inward conformation of the pump (8). Export is then thought to proceed in an ATP-dependent way through conformational changes from the inward to the outward facing forms, evidenced by FRET spectroscopy (9). Recent highresolution structures of eukaryotic P-gp from mouse (8) and Caenorhabditis elegans (10) were obtained in inward conformations. Two prokaryotic homologs of P-gp [Sav1866 (11) and MsbA (12)] were captured crystallographically in outward-facing conformers, reflecting ATP-bound states, as well as two different inward states for MsbA. From these X-ray structures it is possible to build up a picture of P-gp, alternating between inward-and outward-facing conformations.Despite decades of careful biochemical studies (13), and recent insights from crystallography, many questions remain, however. Specifically it has not yet been possible to trap P-gp in an outwardfacing state or to show how substrate binding activates ATPase act...

NikR from Escherichia coli is a nickel-responsive transcription factor that regulates the expression of a nickel ion transporter. Metal analysis reveals that NikR can bind a variety of divalent transition metals, including Ni(II), Cu(II), Zn(II), Co(II), and Cd(II). The selectivity of metal binding to NikR was investigated by using electronic absorption spectroscopy and small-molecule competitors. The relative affinities, Mn(II) < Co(II) < Ni(II) < Cu(II) > or = Zn(II), follow the Irving-Williams series of metal-complex stabilities. Similar metal affinities were measured for the isolated metal-binding domain of NikR. To determine if any of these metal ions confer a differential effect on NikR, the stability of the metal-bound complexes was examined. In both thermal and chemical denaturation experiments, nickel binding stabilizes the protein more than any of the other metals tested. Thermal denaturation experiments indicate that metal dissociation occurs after loss of secondary structure, but there was no evidence for metal binding to unfolded protein following reversible chemical denaturation. These experiments demonstrate that, although several different metals can bind to NikR, nickel exerts a selective allosteric effect. The implications of these experiments on the in vivo role of NikR as a nickel metalloregulator are discussed.

BackgroundCurrent wound assessment practices are lacking on several measures. For example, the most common method for measuring wound size is using a ruler, which has been demonstrated to be crude and inaccurate. An increase in periwound temperature is a classic sign of infection but skin temperature is not always measured during wound assessments. To address this, we have developed a smartphone application that enables non-contact wound surface area and temperature measurements. Here we evaluate the inter-rater reliability and accuracy of this novel point-of-care wound assessment tool.Methods and findingsThe wounds of 87 patients were measured using the Swift Wound app and a ruler. The skin surface temperature of 37 patients was also measured using an infrared FLIR™ camera integrated with the Swift Wound app and using the clinically accepted reference thermometer Exergen DermaTemp 1001. Accuracy measurements were determined by assessing differences in surface area measurements of 15 plastic wounds between a digital planimeter of known accuracy and the Swift Wound app. To evaluate the impact of training on the reproducibility of the Swift Wound app measurements, three novice raters with no wound care training, measured the length, width and area of 12 plastic model wounds using the app. High inter-rater reliabilities (ICC = 0.97–1.00) and high accuracies were obtained using the Swift Wound app across raters of different levels of training in wound care. The ruler method also yielded reliable wound measurements (ICC = 0.92–0.97), albeit lower than that of the Swift Wound app. Furthermore, there was no statistical difference between the temperature differences measured using the infrared camera and the clinically tested reference thermometer.ConclusionsThe Swift Wound app provides highly reliable and accurate wound measurements. The FLIR™ infrared camera integrated into the Swift Wound app provides skin temperature readings equivalent to the clinically tested reference thermometer. Thus, the Swift Wound app has the advantage of being a non-contact, easy-to-use wound measurement tool that allows clinicians to image, measure, and track wound size and temperature from one visit to the next. In addition, this tool may also be used by patients and their caregivers for home monitoring.

In the presence of excess nickel, Escherichia coli NikR regulates cellular nickel uptake by suppressing the transcription of the nik operon, which encodes the nickel uptake transporter, NikABCDE. Previously published in vitro studies have shown that NikR is capable of binding a range of divalent transition metal ions in addition to Ni2+, including Co2+, Cu2+, Zn2+, and Cd2+. To understand how the high-affinity nickel binding site of NikR is able to accommodate these other metal ions, and to improve our understanding of NikR's mechanism of binding to DNA, we have determined structures of the metal-binding domain (MBD) of NikR in the apo form and in complex with Cu2+ and Zn2+ ions and compared them with the previously published structures with Ni2+. We observe that Cu2+ ions bind in a manner very similar to that of Ni2+, with a square planar geometry but with longer bond lengths. Crystals grown in the presence of Zn2+ reveal a protein structure similar to that of apo MBD with a disordered alpha3 helix, but with two electron density peaks near the Ni2+ binding site corresponding to two Zn2+ ions. These structural findings along with biochemical data on NikR support a hypothesis that ordering of the alpha3 helix is important for repressor activation.