Absence Of Zn Research Articles

Significance of Zn2+ in RyR1 for Structural Integrity and Ligand Binding: Insight from Molecular Dynamics.

Ryanodine receptor type 1 (RyR1) is a Ca2+-release channel central to skeletal muscle excitation-contraction (EC) coupling. RyR1's cryo-EM structures reveal a zinc-finger motif positioned within the cytoplasmic C-terminal domain (CTD). Yet, owing to limitations in cryo-EM resolution, RyR1 structures lack precision in detailing the metal coordination structure, prompting the need for an accurate model. In this study, we employed molecular dynamics (MD) simulations and the density functional theory (DFT) method to refine the binding characteristics of Zn2+ in the zinc-finger site of the RyR1 channel. Our findings also highlight substantial conformational changes in simulations conducted in the absence of Zn2+. Notably, we observed a loss of contact at the interface between protein domains proximal to the zinc-finger site, indicating a crucial role of Zn2+ in maintaining structural integrity and interdomain interactions within RyR1. Furthermore, this study provides valuable insights into the modulation of ATP, Ca2+, and caffeine binding, shedding light on the intricate relationship between Zn2+ coordination and the dynamic behavior of RyR1. Our integrative approach combining MD simulations and DFT calculations enhances our understanding of the molecular mechanisms governing ligand binding in RyR1.

Molecular basis for the increased activity of ZMS-2 serine protease in the presence of metal ions and hydrogen peroxide

Serine proteases are important enzymes widely used in commercial products and industry. Recently, we identified a new serine protease from the desert bacterium Bacillus subtilis ZMS-2 that showed enhanced activity in the presence of Zn2+, Ag+, or H2O2. However, the molecular basis underlying this interesting property is unknown. Here, we report comparative studies between the ZMS-2 protease and its homolog, subtilisin E (SubE), from B. subtilis ATCC 6051. In the absence of Zn2+, Ag+, or H2O2, both enzymes showed the same level of proteolytic activity, but in the presence of Zn2+, Ag+, or H2O2, ZMS-2 displayed increased activity by 22%, 8%, and 14%, whereas SubE showed decreased activity by 16%, 12%, and 9%, respectively. In silico studies showed that both proteins have almost identical amino acid sequences and folding structures, except for two amino acids located in the protruding loops of the proteins. ZMS-2 contains Ser236 and Ser268, whereas SubE contains Thr236 and Thr268. Replacing Ser236 or Ser268 in ZMS-2 with threonine resulted in variants whose activities were not enhanced by Zn2+ or Ag+. However, this single mutation did not affect the enhancement by H2O2. This finding may be used as a basis for engineering better proteases for industrial uses.

Fused double oxazolidine vs Imine ligands and Zn-complexes formation: Experimental and theoretical calculations

The condensation reaction between minodiols and carboxaldehydes offers the possibility to obtain either 1-aza-3,7-dioxabicycle[3.3.0]octane (namely here as fused double oxazolidine) or imine compounds. Till now, only limited information is available regarding the factors influencing this behavior. Thus, the present work explored the substituent effect on the reactivity of aminodiols with pyridine carboxaldehydes both in the presence and absence of Zn (II). Without the presence of the metal, the condensation reactions favor the production of fused double oxazolidine derivatives, with identification of both cis and trans isomers in relation to the pyridyl moieties. Notably, the presence of a methyl substituent favors the trans isomers owing to the steric hindrance effect, while a hydrogen substituent favors the cis isomers. Conversely, in the presence of ZnCl2, the main product is the imine-metal complex when the substituent is a methyl group. However, in the presence of a hydrogen substituent, both the imine-metal and the fused double oxazolidine-metal complexes were produced as a mixture in similar proportions. These experimental results are supported by theoretical calculations.

Dynamic Copper Site Redispersion through Atom Trapping in Zeolite Defects.

Single-site copper-based catalysts have shown remarkable activity and selectivity for a variety of reactions. However, deactivation by sintering in high-temperature reducing environments remains a challenge and often limits their use due to irreversible structural changes to the catalyst. Here, we report zeolite-based copper catalysts in which copper oxide agglomerates formed after reaction can be repeatedly redispersed back to single sites using an oxidative treatment in air at 550 °C. Under different environments, single-site copper in Cu-Zn-Y/deAlBeta undergoes dynamic changes in structure and oxidation state that can be tuned to promote the formation of key active sites while minimizing deactivation through Cu sintering. For example, single-site Cu2+ reduces to Cu1+ after catalyst pretreatment (270 °C, 101 kPa H2) and further to Cu0 nanoparticles under reaction conditions (270-350 °C, 7 kPa EtOH, 94 kPa H2) or accelerated aging (400-450 °C, 101 kPa H2). After regeneration at 550 °C in air, agglomerated CuO was dispersed back to single sites in the presence and absence of Zn and Y, which was verified by imaging, in situ spectroscopy, and catalytic rate measurements. Ab initio molecular dynamics simulations show that solvation of CuO monomers by water facilitates their transport through the zeolite pore, and condensation of the CuO monomer with a fully protonated silanol nest entraps copper and reforms the single-site structure. The capability of silanol nests to trap and stabilize copper single sites under oxidizing conditions could extend the use of single-site copper catalysts to a wider variety of reactions and allows for a simple regeneration strategy for copper single-site catalysts.

Zn deficiency disrupts Cu and S homeostasis in Chlamydomonas resulting in over accumulation of Cu and Cysteine.

Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding "first responder" proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, γ-glutamylcysteine, and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ∼80-fold, corresponding to ∼2.8× 109 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.

A ThT Derivative as Zn2+ Sensor Based on DNA G-quadruplex.

In this report, we developed a sensing strategy based on ThT-E(a ThT derivative) and DNA G-quadruplex for the label-free detection of Zn2+. In the absence of Zn2+, there was a fluorescence enhancement of ThT-E by interaction with human telomere sequence. On the addition of Zn2+, Zn2+ induced a more compact antiparallel G-quadruplex to release ThT-E, resulting in fluorescence quenching. The detection limit was 0.6996μM, and the fluorescence intensity showed a good linear relationship with the concentration of Zn2+ in the range of 0-10μM. This sensing strategy which only needs to mix two kinds of materials has the characteristics of label-feel, simple operation, short response time, economical and efficient.

Zinc(II) complexation strategy for ultra-sensitive fluorimetric estimation of molnupiravir: Applications and greenness evaluation.

The endemicity of the pandemic coronavirus disease 2019 (COVID-19) infection proved to be transitional only. Spikes are forming again in 2023, and high expectations are returning for reinfections and viral mutations. Molnupiravir (MOL) has been approved as an oral antiviral drug for the treatment of the COVID-19 causative virion. Therefore, the development of an ultrasensitive, instantaneous, and cost-effective method for the quantification of MOL in real plasma samples and formulated dosage form are mandatory. The proposed approach is based on the synthesis of a MOL metal-chelation product. MOL as a ligand was chelated with 1.0 mM zinc(II) in an acetate buffer (pH 5.3). After illumination at 340 nm, the intensity of the MOL fluorescence measured at 386 nm was increased by about 10-fold. The linearity range was found to be from 60.0 to 800.0 ng mL-1 with limit of quantitation (LOQ) of 28.6 ng mL-1 . Two methods were utilized for measuring the greenness of the proposed method (Green Analytical Procedure Index [GAPI] and analytical greenness metric [AGREE] methods), with results equal to 0.8. The binding stoichiometry of MOL with the zinc(II) ion was found to be 2:1. All the experimental parameters were optimized and validated using International Conference on Harmonization (ICH) and United States Food and Drug Administration (US-FDA)recommendations. Furthermore, the fluorescent probes were successfully utilized in real human plasma with high percentages of recovery (95.6%-97.1%) without any matrix interferences. The mechanism of fluorescent complex formation was confirmed using 1 H NMR in the presence and absence of Zn(II). The method was further utilized for testing content uniformity of MOL in its marketed capsule dosage forms.

Virulence regulation of Zn2+ uptake system znuABC on mesophilic Aeromonas salmonicida SRW-OG1.

Psychrophilic Aeromonas salmonicida could not grow above 25°C and therefore thought unable to infect mammals and humans. In our previous study, a mesophilic A. salmonicida SRW-OG1 was isolated from Epinephelus coioides with furunculosis. Through the analysis of preliminary RNA-seq, it was found that the Zn2+ uptake related genes znuA, znuB and znuC might be involved in the virulence regulation of A. salmonicida SRW-OG1. Therefore, the purpose of this study was to explore the effect of znuABC silencing on the virulence regulation of A. salmonicida SRW-OG1. The results showed that the growth of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains was severely restricted under the Fe2+ starvation, but surprisingly there was no significant difference under the Zn2+ restriction. In the absence of Zn2+ and Fe2+, the expression level of znuABC was significantly increased. The motility, biofilm formation, adhesion and hemolysis of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains were significantly reduced. We also detected the expression of znuABC under different growth periods, temperatures, pH, as well as Cu2+ and Pb2+ stresses. The results showed that znuABC was significantly up-regulated in the logarithmic phase and the decline phase of A. salmonicida. Interestingly, the trend of expression levels of the znuABC at 18, 28, and 37°C was reversed to another Zn2+ uptake related gene zupT. Taken together, these indicated that the znuABC was necessary for A. salmonicida SRW-OG1 pathogenicity and environmental adaptability, and was cross regulated by iron starvation, but it was not irreplaceable for A. salmonicida SRW-OG1 Zn2+ uptake in the host.

Diversity and expression analysis of ZIP transporters and associated metabolites under zinc and iron stress in Capsicum

The members of ZRT, IRT-like protein (ZIP) family are involved in the uptake and transportation of several metal ions. Here, we report a comprehensive identification of ZIP transporter genes from Capsicum annuum, C. chinense, and C. baccatum, and their expression analysis under Zn and Fe stress. Changes in root morphology and differential accumulation of several metabolites from sugars, amino acids, carboxylic acids, and fatty acids in root and leaf tissues of plants in the absence of Zn and Fe were observed. Further, metabolites such as L-aspartic acid, 2-ketoglutaric acids, β-L-fucopyranose, quininic acid, chlorogenic acid, and aucubin were significantly upregulated in root and leaf tissues under Zn/Fe deprived conditions. qRT-PCR analysis of 17 CaZIPs in different tissues revealed tissue-specific expression of CaZIP1-2, CaZIP4-8, CaZIP13, and CaZIP16-17 under normal conditions. However, the absence of Zn and Fe significantly induced the expression of CaZIP4-5, CaZIP7-9, and CaZIP14 genes in root and leaf tissues. Additionally, in the absence of Fe, upregulation of CaZIP4-5 and CaZIP8 and increased uptake of mineral elements Cu, Zn, Mg, P, and S were observed in roots, suggesting their potential role in metal-ion uptake in Capsicum. The identified genes provide the basis for future studies of mineral uptake and their biofortification to increase the nutritional values in Capsicum.

Inferring the transport stoichiometry of the proton/zinc transporter YiiP from microscale thermophoresis and simulations.

The transport stoichiometry of the Zn2+/H+ antiporter YiiP remains an open question. We used experimental microscale thermophoresis (MST) zinc binding data in combination with a microscopic thermodynamic model and constant pH simulation in order to infer the likely microstates of H+ and Zn2+ binding. The pH dependence of Zn2+ binding in different binding sites was measured with MST. For these sites, we constructed microscopic, thermodynamically consistent models based on the pKas of the binding residues and zinc binding affinities. Such a model relates the macroscopically measured MST binding curves to microscopic protonation states and zinc binding in a concentration and pH-dependent manner. We inferred microscopic model parameters from the experimental data with a Monte Carlo approach. We compared the MST-inferred microscopic parameters to results from atomistic constant pH MD simulations in the absence of Zn2+. For zinc binding site B on a solvent-exposed loop between transmembrane helices 2 and 3, MST and simulation data broadly agree with each other. For the transport site A in the transmembrane domain, the CpHMD simulations indicate that the binding site His residue is protonated before any Asp. Using the CpHMD results as a starting point for the MST inference approach, we find that the microstate distribution that best fits the experimental data indicates competitive binding between either one Zn2+ ion or two or three protons bound, with the one-proton state suppressed, possibly due to high cooperativity between the Asp and His residues. The microscopic model indicates a transport stoichiometry of 1:2, or possibly 1:3 at lower pH.

Insights into the Responding Modes of Highly Potent Gadolinium-Based Magnetic Resonance Imaging Probes Sensitive to Zinc Ions.

Zn ions (Zn2+) play an important biological role in many diseases; hence, an imaging method for monitoring the Zn2+ distribution in tissues could provide important clinical insights. Recently, we reported a potent Zn-sensitive probe based on the Gd-DO3A (DO3A = 1,4,7,10-tetraazacyclododecane-1,4,7-tricarboxylic acid), modified tyrosine. and di(2-picolyl)amine chelator for this metal cation, which generates an outstanding magnetic resonance imaging (MRI) response. Here we further explored the origin of this unprecedented response and expanded the choice of potential MRI probes by preparing the free acid version of the initial MRI sensor. We report a detailed investigation of the 1H NMR dispersion, 17O NMR, and isothermal titration calorimetry properties of these two MRI probes upon interaction with Zn2+. The performed experiments confirm selective interaction of the MRI probes and target metal cation, which causes substantial changes in the coordination sphere of the paramagnetic center. It also evidenced some aggregation, which enhances the relaxivity response. Interestingly, conversion of the methyl ester to the free carboxylic acid of the tyrosine moiety changes the nature of the aggregates and leads to a smaller relaxivity response. The probes interact with human serum albumin (HSA) in the absence of Zn2+, which leads to a possible modification of the coordination sphere of Gd3+ or a substantial change in the exchange rate of second-sphere water molecules. In the presence of Zn2+, the interaction with HSA is very weak, demonstrating the importance of the Zn2+ coordination sphere in the behavior of these systems.

H2, B−H, and Si−H Bond Activation and Facile Protonolysis Driven by Pt‐Base Metal Cooperation

We report a series of heterobimetallic Pt/Zn and Pt/Ca complexes to study the effect of proximity of a dicationic base metal on the organometallic Pt species. Varying degrees of Pt∙∙∙Zn and Zn interaction with the bridging Me group are achieved, showcasing snapshots of a hypothetical process of retrotransmetalation from Pt to Zn. In contrast, only weak interactions were observed for Ca with a Pt-bound Me group. Activation of H 2 , B-H and Si-H bonds leads to the formation of hydride-bridged Pt-H-Zn complexes, which is not observed in the absence of Zn, pointing out the importance of metal-metal cooperation. Reactivity of PtMe 2 /M 2+ with terminal acetylene, water and methanol is also studied, leading to facile protonation of one of the Me group at the Pt center only when Zn is present. This study sheds light at various ways in which the presence of a 2+ metal cation significantly affects the reactivity of a common organoplatinum complex.

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. Invitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

Mechanisms of inhibition and activation of extrasynaptic \u03b1\u03b2 GABAA receptors

Type A GABA (γ-aminobutyric acid) receptors represent a diverse population in the mammalian brain, forming pentamers from combinations of α-, β-, γ-, δ-, ε-, ρ-, θ- and π-subunits1. αβ, α4βδ, α6βδ and α5βγ receptors favour extrasynaptic localization, and mediate an essential persistent (tonic) inhibitory conductance in many regions of the mammalian brain1,2. Mutations of these receptors in humans are linked to epilepsy and insomnia3,4. Altered extrasynaptic receptor function is implicated in insomnia, stroke and Angelman and Fragile X syndromes1,5, and drugs targeting these receptors are used to treat postpartum depression6. Tonic GABAergic responses are moderated to avoid excessive suppression of neuronal communication, and can exhibit high sensitivity to Zn2+ blockade, in contrast to synapse-preferring α1βγ, α2βγ and α3βγ receptor responses5,7–12. Here, to resolve these distinctive features, we determined structures of the predominantly extrasynaptic αβ GABAA receptor class. An inhibited state bound by both the lethal paralysing agent α-cobratoxin13 and Zn2+ was used in comparisons with GABA–Zn2+ and GABA-bound structures. Zn2+ nullifies the GABA response by non-competitively plugging the extracellular end of the pore to block chloride conductance. In the absence of Zn2+, the GABA signalling response initially follows the canonical route until it reaches the pore. In contrast to synaptic GABAA receptors, expansion of the midway pore activation gate is limited and it remains closed, reflecting the intrinsic low efficacy that characterizes the extrasynaptic receptor. Overall, this study explains distinct traits adopted by αβ receptors that adapt them to a role in tonic signalling.

Interaction Effects of Nitrogen Rates and Forms Combined With and Without Zinc Supply on Plant Growth and Nutrient Uptake in Maize Seedlings.

Previous studies have shown that zinc (Zn) accumulation in shoot and grain increased as applied nitrogen (N) rate increased only when Zn supply was not limiting, suggesting a synergistic effect of N on plant Zn accumulation. However, little information is available about the effects of different mineral N sources combined with the presence or absence of Zn on the growth of both shoot and root and nutrient uptake. Maize plants were grown under sand-cultured conditions at three N forms as follows: NO3– nutrition alone, mixture of NO3–/NH4+ with molar ratio of 1:1 (recorded as mixed-N), and NH4+ nutrition alone including zero N supply as the control. These treatments were applied together without or with Zn supply. Results showed that N forms, Zn supply, and their interactions exerted a significant effect on the growth of maize seedlings. Under Zn-sufficient conditions, the dry weight (DW) of shoot, root, and whole plant tended to increase in the order of NH4+ < NO3– < mixed-N nutrition. Compared with NH4+ nutrition alone, mixed-N supply resulted in a 27.4 and 28.1% increase in leaf photosynthetic rate and stomatal conductance, which further resulted in 35.7 and 33.5% of increase in shoot carbon (C) accumulation and shoot DW, respectively. Furthermore, mixed-N supply resulted in a 19.7% of higher shoot C/N ratio vs. NH4+ nutrition alone, which means a higher shoot biomass accumulation, because of a significant positive correlation between shoot C/N ratio and shoot DW (R2 = 0.682***). Additionally, mixed-N supply promoted the greatest root DW, total root length, and total root surface area and synchronously improved the root absorption capacity of N, iron, copper, manganese, magnesium, and calcium. However, the above nutrient uptake and the growth of maize seedlings supplied with NH4+ were superior to either NO3– or mixed-N nutrition under Zn-deficient conditions. These results suggested that combined applications of mixed-N nutrition and Zn fertilizer can maximize plant growth. This information may be useful for enabling integrated N management of Zn-deficient and Zn-sufficient soils and increasing plant and grain production in the future.

Isotherm and selectivity study of Ni(II) removal using natural and acid-activated nanobentonites.

In this research, natural bentonite and its acid-activated forms were employed as adsorbents for the adsorption of Ni2+ ions from wastewater. Natural bentonite was activated with 2 M sulfuric acid, 4.5 h and 95 °C (the best acid-activated sample with the highest adsorption capacity) and the other 6 M sulfuric acid, 7.5 h and 95 °C (the worst acid-activated sample with the lowest adsorption capacity). The adsorption of Ni2+ was studied through experiments including equilibrium contact time and selectivity. The equilibrium contact time for bentonite was obtained at 180 min. The Ni2+ separation process along with Zn2+ selectivity studies was considered through adsorption experiments. The results showed that there was a maximum amount of Ni2+ adsorption in the absence of Zn2+ for all samples. The results showed the best fit is obtained with the pseudo-second-order kinetic model. Working out different bentonite types to determine the best kinetic models, we explored the Langmuir and Florry-Huggins models provided a good fit with experimental data for acid-activated bentonites and the best results from linear forms of the adsorption isotherm models for fitting the experimental data of natural bentonite are obtained for Langmuir, Temkin and Freundlich models.

Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding

We designed peptides that formed helix bundle structures upon binding of the metal-ions to His residues to form a stable hydrophobic core, in order to analyze the effects of Ala, Val, Ile, and Leu residues, located in the hydrophobic core, together with His, on the conformational changes in respective peptides designated as HA, HV, HI, and HL, respectively. Circular dichroism measurements showed that HV and HI changed from random coil to helix bundle structures upon Zn2+ binding, similar to that observed for HA, while HL existed in the helix bundle structure even in the absence of Zn2+. Electron spin resonance measurements showed that Cu2+ coordination of HI and HL was quite different from that of HA and HV, indicating that HA and HV fluctuated to a greater extent in the solution, despite that their apparent α-helical contents being similar to those of HI and HL. This was also supported by the results obtained from the analyses of thermal stabilities. The change in the structural fluctuation for each peptide upon Zn2+ binding was evaluated based on binding thermodynamics using isothermal titration calorimetry. The structural flexibility in the metal-ion-bound state was found to be in the order HA > HV > HI, and that in the metal-ion-unbound state was found to be greater for HI than that for HL.

MOF derived non-noble metal catalysts to control the distribution of furfural selective hydrogenation products

Furfural, as one of the most important and attractive platform molecules, could produce high-value chemicals through selective hydrogenation, which had attracted wide attention in recent years. Hereon, a ZnCo bimetal ZIF (ZnCo-ZIF-US) was quickly and efficiently prepared by an ultrasonic-assisted method, and a series of nitrogen-doped carbon-coated bimetallic composites ([email protected]T, T refers to the calcination temperature) were prepared by a one-step calcination technique from ZnCo-ZIF-US and their structures were characterized in detail by PXRD, SEM, TEM, and XPS etc. The obtained [email protected] showed higher catalytic performance in the selective hydrogenation of furfural to furfuryl alcohol than the derivatives of ZnCo bimetal ZIF prepared without ultrasonic-assisted. Surprisingly, the results showed the presence or absence of Zn in the catalysts could regulate the hydrogenation products of furfural to produce furfuryl alcohol or tetrahydrofurfuryl alcohol. In addition, the catalyst could be recycled with almost no significant change in catalytic performance and its microstructure was still well maintained. This work provides an ingenious strategy for the selective regulation of biomass products.

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.

YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

Transition metal cation inhibition of Mycobacterium tuberculosis esterase RV0045C.

Mycobacterium tuberculosis virulence is highly metal-dependent with metal availability modulating the shift from the dormant to active states of M. tuberculosis infection. Rv0045c from M. tuberculosis is a proposed metabolic serine hydrolase whose folded stability is dependent on divalent metal concentration. Herein, we measured the divalent metal inhibition profile of the enzymatic activity of Rv0045c and found specific divalent transition metal cations (Cu2+ ≥ Zn2+ > Ni2+ > Co2+ ) strongly inhibited its enzymatic activity. The metal cations bind allosterically, largely affecting values for kcat rather than KM . Removal of the artificial N-terminal 6xHis-tag did not change the metal-dependent inhibition, indicating that the allosteric inhibition site is native to Rv0045c. To isolate the site of this allosteric regulation in Rv0045c, the structures of Rv0045c were determined at 1.8Å and 2.0Å resolution in the presence and absence of Zn2+ with each structure containing a previously unresolved dynamic loop spanning the binding pocket. Through the combination of structural analysis with and without zinc and targeted mutagenesis, this metal-dependent inhibition was traced to multiple chelating residues (H202A/E204A) on a flexible loop, suggesting dynamic allosteric regulation of Rv0045c by divalent metals. Although serine hydrolases like Rv0045c are a large and diverse enzyme superfamily, this is the first structural confirmation of allosteric regulation of their enzymatic activity by divalent metals.