Multiple pathways of vanadate reduction and denitrification mediated by denitrifying bacterium Acidovorax sp. strain BoFeN1.

Contamination of aquifers by a combination of vanadate [V(V)] and nitrate (NO3-) is widespread nowadays. Although bioremediation of V(V)- and nitrate-contaminated environments is possible, only a limited number of functional species have been identified to date. The present study demonstrates the effectiveness of V(V) reduction and denitrification by a denitrifying bacterium Acidovorax sp. strain BoFeN1. The V(V) removal efficiency was 76.5 ± 5.41 % during 120 h incubation, with complete removal of NO3- within 48 h. Inhibitor experiments confirmed the involvement of electron transport substances and denitrifying enzymes in the bioreduction of V(V) and NO3-. Cyt c and riboflavin were important for extracellular V(V) reduction, with quinone and EPS more significant for NO3- removal. Intracellular reductive compounds including glutathione and NADH directly reduce V(V) and NO3-. Reverse transcription quantitative PCR confirmed the important roles of nirK and napA genes in regulating V(V) reduction and denitrification. Bioaugmentation by strain BoFeN1 increased V(V) and NO3- removal efficiency by 55.3 % ± 2.78 % and 42.1 % ± 1.04 % for samples from a contaminated aquifer. This study proposes new microbial resources for the bioremediation of V(V) and NO3-contaminated aquifers, and contributes to our understanding of coupled vanadium, nitrogen, and carbon biogeochemical processes.

Physiological temperature drives TRPM4 ligand recognition and gating.

Temperature profoundly affects macromolecular function, particularly in proteins with temperature sensitivity1,2. However, its impact is often overlooked in biophysical studies that are typically performed at non-physiological temperatures, potentially leading to inaccurate mechanistic and pharmacological insights. Here we demonstrate temperature-dependent changes in the structure and function of TRPM4, a temperature-sensitive Ca2+-activated ion channel3-7. By studying TRPM4 prepared at physiological temperature using single-particle cryo-electron microscopy, we identified a 'warm' conformation that is distinct from those observed at lower temperatures. This conformation is driven by a temperature-dependent Ca2+-binding site in the intracellular domain, and is essential for TRPM4 function in physiological contexts. We demonstrated that ligands, exemplified by decavanadate (a positive modulator)8 and ATP (an inhibitor)9, bind to different locations of TRPM4 at physiological temperatures than at lower temperatures10,11, and that these sites have bona fide functional relevance. We elucidated the TRPM4 gating mechanism by capturing structural snapshots of its different functional states at physiological temperatures, revealing the channel opening that is not observed at lower temperatures. Our study provides an example of temperature-dependent ligand recognition and modulation of an ion channel, underscoring the importance of studying macromolecules at physiological temperatures. It also provides a potential molecular framework for deciphering how thermosensitive TRPM channels perceive temperature changes.

Mitochondria-targeted cerium vanadate nanozyme suppressed hypoxia-ischemia injury in neonatal mice via intranasal administration.

Oxidative stress is a major obstacle for neurological functional recovery after hypoxia-ischemia (HI) brain damage. Nanozymes with robust anti-oxidative stress properties offer a therapeutic option for HI injury. However, insufficiency of nanozyme accumulation in the HI brain by noninvasive administration hinders their application. Herein, we reported a cerium vanadate (CeVO4) nanozyme to realize a noninvasive therapy for HI brain in neonatal mice by targeting brain neuron mitochondria. CeVO4 nanozyme with superoxide dismutase activity mainly co-located with neuronal mitochondria 1 h after administration. Pre- and post-HI administrations of CeVO4 nanozyme were able to attenuate acute brain injury, by inhibiting caspase-3 activation, microglia activation, and proinflammation cytokine production in the lesioned cortex 2 d after HI injury. Moreover, CeVO4 nanozyme administration led to short- and long-term functional recovery following HI insult without any potential toxicities in peripheral organs of mice even after prolonged delivery for 4 weeks. These beneficial effects of CeVO4 nanozyme were associated with suppressed oxidative stress and up-regulated nuclear factor erythroid-2-related factor 2 (Nrf2) expression. Finally, we found that Nrf2 inhibition with ML385 abolished the protective effects of CeVO4 nanozyme on HI injury. Collectively, this strategy may provide an applicative perspective for CeVO4 nanozyme therapy in HI brain damage via noninvasive delivery.

Topical vanadate improves tensile strength and alters collagen organisation of excisional wounds in a mouse model.

Wound dehiscence, oftentimes a result of the poor tensile strength of early healing wounds, is a significant threat to the post-operative patient, potentially causing life-threatening complications. Vanadate, a protein tyrosine phosphatase inhibitor, has been shown to alter the organisation of deposited collagen in healing wounds and significantly improve the tensile strength of incisional wounds in rats. In this study, we sought to explore the effects of locally administered vanadate on tensile strength and collagen organisation in both the early and remodelling phases of excisional wound healing in a murine model. Wild-type mice underwent stented excisional wounding on their dorsal skin and were divided equally into three treatment conditions: vanadate injection, saline injection control and an untreated control. Tensile strength testing, in vivo suction Cutometer analysis, gross wound measurements and histologic analysis were performed during healing, immediately upon wound closure, and after 4 weeks of remodelling. We found that vanadate treatment significantly increased the tensile strength of wounds and their stiffness relative to control wounds, both immediately upon healing and into the remodelling phase. Histologic analysis revealed that these biomechanical changes were likely the result of increased collagen deposition and an altered collagen organisation composed of thicker and distinctly organised collagen bundles. Given the risk that dehiscence poses to all operative patients, vanadate presents an interesting therapeutic avenue to improve the strength of post-operative wounds and unstable chronic wounds to reduce the risk of dehiscence.

Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.

Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.

Inhibition of Plasma Membrane Calcium Pump Influences Intracellular Calcium Signaling Pathways in Breast Cancer.

The plasma membrane calcium pump (PMCA) is an important transporter that maintains intracellular calcium concentration ([Ca2+]i). It allows the calcium (Ca2+) from inside the cell to go out of the cell through the plasma membrane. For this, it cooperates with the proteins in the cell. The aim of this study is to demonstrate the effect of PMCA on intracellular calcium signaling in breast cancer cells. In this study, PMCA was inhibited by orthovanadate (OV), and changes in Calmodulin (CaM), Calcineurin (CaN) and cMyc proteins were demonstrated. Intracellular calcium accumulation was measured when PMCA was inhibited in MDA-MB-231 cells. At the same time, it was observed that the cell movement decreased with time. Over time, CaN and CaM were slightly suppressed, and cMyc protein was not expressed. As a result, when PMCA protein is targeted correctly in breast cancer cells, it has an indirect effect on cancer-promoting proteins.

p38-dependent c-Jun degradation contributes to reduced PGE2 production in sodium orthovanadate-treated macrophages.

In particular, the phenomenon of c-Jun degradation within the inflammatory response has not yet been fully analyzed. In order to verify this, we investigated LPS-stimulated murine macrophages pre-treated with sodium orthovanadate (SO) in order to uncover the regulatory mechanisms of the MAPKs which regulate c-Jun degradation within the inflammatory response. Through our study, we found that SO suppressed the production of prostaglandin E2 (PGE2) and the expression of COX-2 in LPS-stimulated RAW264.7 cells. Additionally, SO decreased total c-Jun levels, without altering the amount of mRNA, although the phospho-levels of p38, ERK, and JNK were strongly enhanced. Through the usage of selective MAPK inhibitors, and knockdown and overexpression strategies, p38 was revealed to be a major MAPK which regulates c-Jun degradation. Further analysis indicates that the phosphorylation of p38 is a determinant for c-Jun degradation, and is sufficient to induce ubiquitination-dependent c-Jun degradation, recovered through MG132 treatment. Therefore, our results suggest that the hyperphosphorylation of p38 by SO contributes to c-Jun degradation, which is linked to the suppression of PGE2 secretion in inflammatory responses; and thus, finding drugs to increase p38 activity could be a novel strategy for the development of anti-inflammatory drugs. [BMB Reports 2022; 55(8): 389-394].

Modification of plasma membrane H+-ATPase in Masson pine (Pinus massoniana Lamb.) seedling roots adapting to acid deposition.

To understand the regulation of roots plasma membrane H+-ATPase in Masson pine responding to acid deposition, the changes in biomass, plant morphology, intracellular H+, enzyme activity and H+-ATPase genes expression in Masson pine seedlings exposed to simulated acid rain (SAR, pH 5.6 and 4.6) with and without vanadate were studied. Simulated acid rain exposure for 60 days increased the intracellular H+ in pine roots whether added with 0.1 mM Na3VO4 or not. The growth of seedlings treated with SAR was maintained well, even the primary lateral root length, root dry weight and number of root tips in seedlings exposed to SAR at pH 4.6 were higher than that of the control (pH 6.6). However, the addition of vanadate resulted in severe growth inhibition and obvious decline in morphological parameters. Similarly, ATP hydrolytic activity and H+ transport activity of roots plasma membrane H+-ATPase, both were stimulated by SAR whereas they were inhibited by vanadate, and the highest activity stimulation was observed in pine roots subjected to SAR at pH 4.6. In addition, SAR also induced the expression of the investigated H+-ATPase subunits (atpB, atpE, atpF, atpH and atpI). Therefore, the roots plasma membrane H+-ATPase is instrumental in the growth of Masson pine seedlings adapting to acid rain by a manner of pumping more protons across the membrane through enhancing its activity, and which involves the upregulated gene expression of roots H+-ATPase subunits at transcriptional level.

Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5.

Pdr5, a member of the extensive ABC transporter superfamily, is representative of a clinically relevant subgroup involved in pleiotropic drug resistance. Pdr5 and its homologues drive drug efflux through uncoupled hydrolysis of nucleotides, enabling organisms such as baker's yeast and pathogenic fungi to survive in the presence of chemically diverse antifungal agents. Here, we present the molecular structure of Pdr5 solved with single particle cryo-EM, revealing details of an ATP-driven conformational cycle, which mechanically drives drug translocation through an amphipathic channel, and a clamping switch within a conserved linker loop that acts as a nucleotide sensor. One half of the transporter remains nearly invariant throughout the cycle, while its partner undergoes changes that are transmitted across inter-domain interfaces to support a peristaltic motion of the pumped molecule. The efflux model proposed here rationalises the pleiotropic impact of Pdr5 and opens new avenues for the development of effective antifungal compounds.

Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase.

The isonitrile moiety is found in marine sponges and some microbes, where it plays a role in processes such as virulence and metal acquisition. Until recently only one route was known for isonitrile biosynthesis, a condensation reaction that brings together a nitrogen atom of l-Trp/l-Tyr with a carbon atom from ribulose-5-phosphate. With the discovery of ScoE, a mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase from Streptomyces coeruleorubidus, a second route was identified. ScoE forms isonitrile from a glycine adduct, with both the nitrogen and carbon atoms coming from the same glycyl moiety. This reaction is part of the nonribosomal biosynthetic pathway of isonitrile lipopeptides. Here, we present structural, biochemical, and computational investigations of the mechanism of isonitrile formation by ScoE, an unprecedented reaction in the mononuclear Fe(II) α-ketoglutarate-dependent dioxygenase superfamily. The stoichiometry of this enzymatic reaction is measured, and multiple high-resolution (1.45-1.96 Å resolution) crystal structures of Fe(II)-bound ScoE are presented, providing insight into the binding of substrate, (R)-3-((carboxylmethyl)amino)butanoic acid (CABA), cosubstrate α-ketoglutarate, and an Fe(IV)=O mimic oxovanadium. Comparison to a previously published crystal structure of ScoE suggests that ScoE has an "inducible" α-ketoglutarate binding site, in which two residues arginine-157 and histidine-299 move by approximately 10 Å from the surface of the protein into the active site to create a transient α-ketoglutarate binding pocket. Together, data from structural analyses, site-directed mutagenesis, and computation provide insight into the mode of α-ketoglutarate binding, the mechanism of isonitrile formation, and how the structure of ScoE has been adapted to perform this unusual chemical reaction.

Polyoxometalates function as indirect activators of a G protein-coupled receptor.

The luteinizing hormone receptor (LHR), a G protein-coupled receptor (GPCRs), can initiate signaling in the presence of some vanadium-containing compounds as a result of vanadium compound interactions with the membrane lipids and/or the cell membrane lipid interface. The ability of LHR expressed in CHO cells to initiate signaling in the presence of highly charged and water-soluble polyoxovanadates (POV) including Na3[H3V10O28] (V10) and two mixed-valence heteropolyoxovanadates, K(NH4)4[H6V14O38(PO4)]·11H2O (V14) and [(CH3)4N]6[V15O36(Cl)] (V15), was investigated here. Interactions of the vanadium compounds with CHO cells decreased the packing of membrane lipids, drove aggregation of LHR and increased signal transduction by LHR. Cell responses were comparable to, or in the case of V14 and V15, greater than those seen for cells treated with human chorionic gonadotropin (hCG), a naturally-occurring LHR ligand produced in early pregnancy in humans. POV effects were observed for CHO cells where LHR was expressed at 10 000 or 32 000 LHR per cell but not when LHR was overexpressed with receptor numbers >100 000 LHR per cell. To determine which POV species were present in the cell medium during cell studies, the speciation of vanadate (V1), V10, V14 or V15 in cell medium was monitored using 51V NMR and EPR spectroscopies. We found that all the POVs initiated signaling, but V15 and V10 had the greatest effects on cell function, while V1 was significantly less active. However, because of the complex nature of vanadium compounds speciation, the effects on cell function may be due to vanadium species formed in the cell medium over time.

Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome.

Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.

Microbial vanadate and nitrate reductions coupled with anaerobic methane oxidation in groundwater.

Vanadate contaminant in groundwater receives increasing attentions, but little is known on its biogeochemical transformation with gaseous electron donors. This study investigated bio-reduction of vanadate coupled with anaerobic methane oxidation and its relationship with nitrate reduction. Results showed 95.8 ±â€¯3.1% of 1 mM vanadate was removed within 7 days using methane as the sole electron donor. Tetravalent vanadium compounds were the main reduction products, which precipitated naturally in groundwater environment. The introduction of nitrate inhibited vanadate reduction, though both were reduced in parallel. Accumulations of volatile fatty acids (VFAs) were observed from methane oxidation. Preliminary microbial community structure and metabolite analyses indicated that vanadate was likely reduced via Methylomonas coupled with methane oxidation or through synergistic relationships between methane oxidizing bacteria and heterotrophic vanadate reducers with VFAs served as the intermediates.

Conformation space of a heterodimeric ABC exporter under turnover conditions.

Cryo-electron microscopy (cryo-EM) has the capacity to capture molecular machines in action1-3. ATP-binding cassette (ABC) exporters are highly dynamic membrane proteins that extrude a wide range of substances from the cytosol4-6 and thereby contribute to essential cellular processes, adaptive immunity and multidrug resistance7,8. Despite their importance, the coupling of nucleotide binding, hydrolysis and release to the conformational dynamics of these proteins remains poorly resolved, especially for heterodimeric and/or asymmetric ABC exporters that are abundant in humans. Here we present eight high-resolution cryo-EM structures that delineate the full functional cycle of an asymmetric ABC exporter in a lipid environment. Cryo-EM analysis under active turnover conditions reveals distinct inward-facing (IF) conformations-one of them with a bound peptide substrate-and previously undescribed asymmetric post-hydrolysis states with dimerized nucleotide-binding domains and a closed extracellular gate. By decreasing the rate of ATP hydrolysis, we could capture an outward-facing (OF) open conformation-an otherwise transient state vulnerable to substrate re-entry. The ATP-bound pre-hydrolysis and vanadate-trapped states are conformationally equivalent; both comprise co-existing OF conformations with open and closed extracellular gates. By contrast, the post-hydrolysis states from the turnover experiment exhibit asymmetric ATP and ADP occlusion after phosphate release from the canonical site and display a progressive separation of the nucleotide-binding domains and unlocking of the intracellular gate. Our findings reveal that phosphate release, not ATP hydrolysis, triggers the return of the exporter to the IF conformation. By mapping the conformational landscape during active turnover, aided by mutational and chemical modulation of kinetic rates to trap the key intermediates, we resolved fundamental steps of the substrate translocation cycle of asymmetric ABC transporters.

Neuroprotective effects of a protein tyrosine phosphatase inhibitor against hippocampal excitotoxic injury.

Neuronal excitotoxicity is the neuronal cell death arising from prolonged exposure to glutamate and the associated excessive influx of ions into the cell. Sodium orthovanadate (Na3VO4,) competitively inhibits the protein tyrosine phosphatases that affect intracellular protein phosphorylation. No study has examined the role of protein tyrosine phosphatases in kainic acid (KA)-induced excitotoxic injury using sodium orthovanadate. Thus, the present study was conducted to determine the neuroprotective effects of sodium orthovanadate on KA-induced neuronal death in organotypic hippocampal slice culture. We also performed an in vivo electrophysiology study in Sprague-Dawley rats to observe the function of surviving cells after sodium orthovanadate treatment in KA-induced excitotoxicity. Rats were anaesthetized with sodium pentobarbital and KA was injected unilaterally in CA3 of the hippocampus by microinjection-cannula. Neuronal cell death, as assessed by propidium iodide uptake, was reduced by 10 and 25 µM sodium orthovanadate treatment (24 and 48 h) compared with the KA-only group. Sodium orthovanadate enhanced survival signals by increasing levels of phospho-Akt and superoxide dismutase. In addition, sodium orthovanadate treatment reduced calcineurin level for neuronal protection, which regulates activation of cellular calcium caused by KA-induced injury. In vivo results showed that sodium orthovanadate treatment elicited resistance to KA-induced behavior seizures and significantly reduced the duration of epileptiform discharges. In addition, sodium orthovanadate treatment (25 mM) significantly prevented the increase in power spectra induced by KA injection. These results suggest that sodium orthovanadate decreases the acute effects of KA, thereby inducing neuroprotective effects with reduced reactive oxygen species and cellular Ca2+. Thus, sodium orthovanadate may protect hippocampal neurons against excitotoxicity, and surviving neurons may function to reduce seizures.

Structural basis of lipopolysaccharide extraction by the LptB2FGC complex.

In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide from the inner to the outer membrane. The ATP-binding cassette transporter LptB2FG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptB2FG-LptC complex (LptB2FGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptB2FG and LptB2FGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptB2FGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptB2FG, which represents a previously unknown regulatory mechanism for ATP-binding cassette transporters. Our results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptB2FG in the inner membrane and Lpt protein interactions in the periplasm.

Effects of vanadate on the mycelium of edible fungus Coprinus comatus.

Vanadate is proposed to play a pivotal role in application of edible fungus Coprinus comatus for medical purposes. In this study the concentration of extracellular vanadate acceptable for the submerged cultivation of C. comatus mycelium was established. The mycelium could grow, and overcome vanadate toxic effects, up to the concentration of 3.3 mM. Moreover, in this condition, at the end of the exponential phase of growth, biomass yield was almost identical to that in the control. 31P NMR spectroscopy showed that addition of 10 mM vanadate to the mycelium in the exponential phase of growth provoked instantaneous increase of a sugar phosphates level which could be related to changes in activities of glycolytic enzymes. Exposure to higher vanadate concentration was toxic for the cell. 51V NMR measurements revealed that monomer of vanadate is present in the cytoplasm causing the metabolic changes. C. comatus has also capacity for vanadate reduction, as shown by EPR measurements, but vanadyl uptake is significantly less comparing to vanadate.

Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.

Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.

X-ray Diffraction and Density Functional Theory Provide Insight into Vanadate Binding to Homohexameric Bromoperoxidase II and the Mechanism of Bromide Oxidation.

X-ray diffraction of native bromoperoxidase II (EC 1.11.1.18) from the brown alga Ascophyllum nodosum reveals at a resolution of 2.26 Å details of orthovanadate binding and homohexameric protein organization. Three dimers interwoven in contact regions and tightened by hydrogen-bond-clamped guanidinium stacks along with regularly aligned water molecules form the basic structure of the enyzme. Intra- and intermolecular disulfide bridges further stabilize the enzyme preventing altogether the protein from denaturing up to a temperature of 90 °C, as evident from dynamic light scattering and the on-gel ortho-dianisidine assay. Every monomer binds one equivalent of orthovanadate in a cavity formed from side chains of three histidines, two arginines, one lysine, serine, and tryptophan. Protein binding occurs primarily through hydrogen bridges and superimposed by Coulomb attraction according to thermochemical model on density functional level of theory (B3LYP/6-311++G**). The strongest attractor is the arginine side chain mimic N-methylguanidinium, enhancing in positive cooperative manner hydrogen bridges toward weaker acceptors, such as residues from lysine and serine. Activating hydrogen peroxide occurs in the thermochemical model by side-on binding in orthovanadium peroxoic acid, oxidizing bromide with virtually no activation energy to hydrogen bonded hypobromous acid.

The effect of drug binding on specific sites in transmembrane helices 4 and 6 of the ABC exporter MsbA studied by DNP-enhanced solid-state NMR.

MsbA, a homodimeric ABC exporter, translocates its native substrate lipid A as well as a range of smaller, amphiphilic substrates across the membrane. Magic angle sample spinning (MAS) NMR, in combination with dynamic nuclear polarization (DNP) for signal enhancement, has been used to probe two specific sites in transmembrane helices 4 and 6 of full length MsbA embedded in lipid bilayers. Significant chemical shift changes in both sites were observed in the vanadate-trapped state compared to apo state MsbA. The reduced spectral line width indicates a more confined conformational space upon trapping. In the presence of substrates Hoechst 33342 and daunorubicin, further chemical shift changes and line shape alterations mainly in TM6 in the vanadate trapped state were detected. These data illustrate the conformational response of MsbA towards the presence of drugs during the catalytic cycle. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.