Bivalent Metal Ions Research Articles

DFT Study on the His-Tag Binding Affinity of Metal Ions in Modeled Hexacationic Metal Complexes.

Histidine oligomers (His-tags) are commonly used as affinity tags in recombinant protein purification to enable in vitro experimental studies, including biochemical and biophysical assays and structure determination. His-tags enable protein purification by specifically and efficiently coordinating bivalent metal ions present in the purification resins, such as Cu2+, Zn2+, and Ni2+. Although His-tags, combined with Ni2+-based resins, are widely used due to their biophysical properties and commercial availability, the structure and nature of the metal cation coordination have remained unclear. In this study, the chemical structure of metal-coordinating His-tags was modeled to elucidate the metal preferences for better binding and to determine the structural changes that occur upon metal coordination. 6His-tag is a string of 6 histidine residues usually coordinated to bivalent metal ions (M2+), such as Ni2+, Zn2+, and Cu2+, through the nitrogen atoms of the imidazole rings. The metals complete their octahedral coordination shell with the lone pair of electrons of the oxygen atoms of the resin to which they are attached to. The resin was modeled as an oxalaldehyde group with the closed formula of (OCH)4. The geometry optimizations were carried out using the DFT method at the B3LYP/6-31g (d, p) level and in implicit water using the IEFPCM solvent model. The impact of Ni2+, Zn2+, and Cu2+ metals on the resin binding ability of 6His-tags was tested by adding amino acids to the N-terminus of metal-coordinated hexahistidine chains. The activity of the metals as electron donors or acceptors to the coordination bonds that they form was estimated by calculating the NBO energies. The complexation enthalpies of metal-bearing resin with hexahistidine, naked or having an amino acid tail, were calculated. Our results showed that Ni2+ has the highest affinity for the recombinant 6His-tag.

Ammonium vanadate doped by transition bivalent metal ions for high-performance zinc-ion batteries

Vanadium-based materials are considered as promising cathode materials in aqueous zinc-ion (Zn2+) batteries (AZIBs) because of their abundant valence states and adjustable ion diffusion channels. However, the slow kinetics of the Zn2+ intercalation and the instability of the layered structure during long cycle are the bottlenecks restricting their further development. In this paper, the transition bivalent manganese ions (Mn2+) are introduced into ammonium vanadate (NH4V4O10) to partly replace the NH4+ ions to prepare a high-performance AZIB cathode. After doping transition bivalent Mn2+, the interlayer spacing of NH4V4O10 is enlarged, providing a broadened channel for the diffusion of Zn2+ accordingly. The results reveal that the electrode with the optimal doping quantity has a very high discharge capacity (539.4 mAh/g at 0.2 A/g) and excellent cyclic stability (85.3 % retention of the initial capacity after 3000 cycles at 5 A/g). A highly competitive energy density of 378 Wh kg−1 at 362 W kg−1 is delivered by the corresponding AZIB. Moreover, this method is a general and effective strategy for developing high-performance AZIB cathode materials, as demonstrated by the consistent crystal structure and stable cycling properties for NH4V4O10 doped with other transition bivalent metal cations.

Bivalent metal ion co-doped methylammonium lead tribromide perovskite nanocrystal scintillator for X-ray imaging

Perovskite scintillators with low cost, easy preparation, environmental stability, and high-resolution have become candidates for X-ray imaging applications. Here, based on the calculation results of surface formation energy (Ef) and vacancy defect energy (Evac), a series of co-doped perovskite nanocrystals (NCs) with photoluminescence high quantum yield (PLQY) and fast luminescence decay time had been prepared by doping several bivalent metal ions into the B-site of methylammonium lead tribromide (MAPbBr3). In addition, the scintillator with flexibility was prepared using poly(vinylidene fluoride-hexafluoropropylene) (PVDF-HFP) as the carrier, showing excellent stability and scintillation performance, with a light yield of 21,200 photons/MeV, imaging resolution reached 11.7 lp/mm, and low detection limits of 462 nGyair s−1. Finally, we demonstrated the scintillator characteristic with high-quality imaging results and excellent tolerance under high dose rate X-ray (25 mGy s−1). Therefore, the combination of co-doped nanocrystals with excellent optical properties and PVDF-HFP further paves the way for the development of a scintillator.

Digestion and absorption characteristics of iron-chelating silver carp scale collagen peptide and insights into their chelation mechanism

Iron deficiency is widespread throughout the world, supplementing sufficient iron or improving the bioavailability of iron is the fundamental strategy to solve the problem of iron scarcity. Herein, we explored a new form of iron supplement, iron chelates of silver carp scales (SCSCP-Fe) were prepared from collagen peptide of silver carp scales (SCSCP) and FeCl2·4H2O, the effects of external environment and simulated gastrointestinal digestive environment on the stability of SCSCP-Fe and the structural changes of peptide iron chelates during digestion were investigated. The results of in vitro iron absorption promotion showed that the iron bioavailability of SCSCP-Fe was higher than that of FeSO4. Two potential high iron chelating peptides DTSGGYDEY (DY) and LQGSNEIEIR (LR) were screened and synthesized from the SCSCP sequence by molecular dynamics and LC-MS/MS techniques. The FTIR results displayed that the binding sites of DY and LR for Fe2+ were the carboxyl group, the amino group, and the nitrogen atom on the amide group on the peptide. ITC results indicated that the chelation reactions of DY and LR with Fe2+ were mainly dominated by electrostatic interactions, forming chelates in stoichiometric ratios of 1:2 and 1:1, respectively. Both DY and LR had a certain ability to promote iron absorption. The transport of DY-Fe chelate may be a combination of the three pathways: PepT1 vector pathway, cell bypass, and endocytosis, while LR-Fe chelate was dominated by bivalent metal ion transporters. This study is expected to provide theoretical reference and technical support for the high-value utilization of silver carp scales and the development of novel iron supplements.

Functional characterization of a novel flavin reductase from a deep-sea sediment metagenomic library and its application for indirubin production.

Microbial synthesis is a desirable approach to produce indirubin but suffers from low synthetic efficiency. Insufficient supply of reduced flavins is one major factor limiting synthetic efficiency. To address this, a novel flavin reductase, MoxB, was discovered through screening of the metagenomic library. MoxB showed a strong preference for NADH over NADPH as the electron source for FMN/FAD reduction and exhibited the highest activity at pH 8.0 and 30°C. It displayed remarkable thermostability by maintaining 80% of full activity after incubation at 60°C for 1 h. Furthermore, MoxB showed great organic solvent tolerance and its activity could be significantly increased by bivalent metal ions. In addition, heterologous expression of the moxB gene in the indirubin-producing E. coli significantly improved indirubin production up to 15.12-fold. This discovery expands the understanding of flavin reductases and provides a promising catalytic tool for microbial indirubin production.IMPORTANCEMuch effort has been exerted to produce indirubin using engineered Escherichia coli, but high-level production has not been achieved so far. Insufficient supply of reduced flavins is one key factor limiting the catalytic efficiency. However, the flavin reductases involved in indirubin biosynthesis have not been hitherto reported. Discovery of the novel flavin reductase MoxB provides a useful tool for enhancing indirubin production by E. coli. Overexpression of MoxB in indirubin-producing E. coli increased indirubin production by 15.12-fold in comparison to the control strain. Our results document the function of flavin reductase that reduces flavins during indirubin biosynthesis and provide an important foundation for using the flavin reductases to improve indirubin production by engineered microorganisms.

A pyocin-like T6SS effector mediates bacterial competition in Yersinia pseudotuberculosis.

Within the realm of Gram-negative bacteria, bacteriocins are secreted almost everywhere, and the most representative are colicin and pyocin, which are secreted by Escherichia coli and Pseudomonas aeruginosa, respectively. Signal peptides at the amino terminus of bacteriocins or ABC transporters can secrete bacteriocins, which then enter bacteria through cell membrane receptors and exert toxicity. In general, the bactericidal spectrum is usually narrow, killing only the kin or closely related species. Our previous research indicates that YPK_0952 is an effector of the third Type VI secretion system (T6SS-3) in Yersinia pseudotuberculosis. Next, we sought to determine its identity and characterize its toxicity. We found that YPK_0952 (a pyocin-like effector) can achieve intra-species and inter-species competitive advantages through both contact-dependent and contact-independent mechanisms mediated by the T6SS-3 while enhancing the intestinal colonization capacity of Y. pseudotuberculosis. We further identified YPK_0952 as a DNase dependent on Mg2+, Ni2+, Mn2+, and Co2+ bivalent metal ions, and the homologous immune protein YPK_0953 can inhibit its activity. In summary, YPK_0952 exerts toxicity by degrading nucleic acids from competing cells, and YPK_0953 prevents self-attack in Y. pseudotuberculosis.IMPORTANCEBacteriocins secreted by Gram-negative bacteria generally enter cells through specific interactions on the cell surface, resulting in a narrow bactericidal spectrum. First, we identified a new pyocin-like effector protein, YPK_0952, in the third Type VI secretion system (T6SS-3) of Yersinia pseudotuberculosis. YPK_0952 is secreted by T6SS-3 and can exert DNase activity through contact-dependent and contact-independent entry into nearby cells of the same and other species (e.g., Escherichia coli) to help Y. pseudotuberculosis to exert a competitive advantage and promote intestinal colonization. This discovery lays the foundation for an in-depth study of the different effector protein types within the T6SS and their complexity in competing interactions. At the same time, this study provides a new development for the toolbox of toxin/immune pairs for studying Gram-negative bacteriocin translocation.

Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion.

The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.

Molecular mechanism of dissolvable metal nanoparticles-enhanced CO2 fixation by algae: Metal-chlorophyll synthesis

Algae-driven photosynthetic CO2 fixation is a promising strategy to mitigate global climate changes and energy crises. Yet, the presence of metal nanoparticles (NPs), particularly dissolvable NPs, in aquatic ecosystems introduces new complexities due to their tendency to release metal ions that may perturb metabolic processes related to algal CO2 fixation. This study selected six representative metal NPs (Fe3O4, ZnO, CuO, NiO, MgO, and Ag) to investigate their impacts on CO2 fixation by algae (Chlorella vulgaris). We discovered an intriguing phenomenon that bivalent metal ions released from the metal NPs, especially from ZnO NPs, substituted Mg2+ within the porphyrin ring. This interaction led to 81.8% and 76.1% increases in Zinc-chlorophyll and Magnesium-chlorophyll contents within algal cells at 0.01 mM ZnO NPs, respectively. Integrating metabolomics and transcriptomics analyses revealed that ZnO NPs mainly promoted the photosynthesis-antenna protein pathway, porphyrin and chlorophyll metabolism, and carbon fixation pathway, thereby mitigating the adverse effects of Zn2+ substitution in light harvesting and energy transfer for CO2 fixation. Ultimately, the genes encoding Rubisco large subunit (rbcL) responsible for CO2 fixation were upregulated to 2.60-fold, resulting in a 76.3% increase in carbon fixation capacity. Similar upregulations of rbcL expression (1.13-fold) and carbon fixation capacity (76.1%) were observed in algal cells even at 0.001 mM ZnO NPs, accompanied by valuable lipid accumulation. This study offers novel insights into the molecular mechanism underlying NPs on CO2 fixation by algae and potentially introduces strategies for global carbon sequestration.

Ternary Schiff base metal (II) complexes with N,N,N′,N′-Tetramethylethylenediamine: Influence of secondary chelates on antimicrobial, scavenging activity, DNA interaction and cytotoxicity

A series of complexes involving bivalent metal ions such as cobalt, nickel, copper, and zinc were synthesized using Schiff bases derived from l-tyrosine and salicylaldehyde. Utilizing both analytical and spectroscopic methods, the compounds underwent analysis. In terms of their potential biological effects, the antioxidant properties of the samples were gauged by their ability to scavenge DPPH radicals. Notably, all the compounds demonstrated enhanced activity in this aspect, with the exception of the ligand. To investigate their impact on DNA, the compounds' capability to cleave DNA was assessed via gel electrophoresis. Remarkably, the compounds effectively induced the cleavage of supercoiled plasmid DNA. Moreover, the interaction between calf thymus DNA and the metal-imine chelates were examined. The Cu(II) complex had a significant interaction, as evidenced by its binding constant of (3.46 ± 0.02 x 105 M−1).

Over-expression of the BnVIT-L2 gene improves the lateral root development and biofortification under iron stress

The vacuolar iron transporter (VIT) family is responsible for absorbing and storing iron ions in vacuoles. Here, the BnVIT-L2 gene from Brassica napus has been cloned for the first time and was found to be expressed in multiple tissues and organs, induced by iron stress. The BnVIT-L2 protein is located in vacuolar membranes and has the ability to bind both iron and other bivalent metal ions. Over-expression of the BnVIT-L2 gene increased lateral root number and main root length, as well as chlorophyll and iron content in transgenic Arabidopsis plants (BnVIT-L2/At) exposed to iron stress, compared to wild type Col-0. Furthermore, over-expression of this gene improved the adaptability of transgenic B. napus plants (BnVIT-L2-OE) under iron stress. The regulation of plant tolerance under iron stress by BnVIT-L2 gene may involve in the signal of reactive oxygen species (ROS), as suggested by Ribosome profiling sequencing (Ribo-seq). This study provides a reference for investigating plant growth and biofortification under iron stress through the BnVIT-L2 gene.

Effect of Lipid Corona on Phenylalanine-Functionalized Gold Nanoparticles to Develop Stable and Corona-Free Systems.

Conventional gold nanoparticles (Au NPs) have many limitations, such as aggregation and subsequent precipitation in the medium of high ionic strength and protein molecules. Furthermore, when exposed to biological fluids, nanoparticles form a protein corona, which controls different biological processes such as the circulation lifetime, drug release profile, biodistribution, and in vivo cellular distribution. These limitations reduce the functionality of Au NPs in targeted delivery, bioimaging, gene delivery, drug delivery, and other biomedical applications. To circumvent these problems, there are numerous attempts to design corona-free and stable nanoparticles. Here, we report for the first time that lipid corona (coating of lipid) formation on phenylalanine-functionalized Au NPs (AuPhe NPs) imparts excellent stability against the high ionic strength of bivalent metal ions, amino acids, and proteins of different charges as compared to bare nanoparticles. Moreover, this work is focused on the ability of lipid corona formation on AuPhe NPs to prevent protein adsorption in the presence of cell culture medium (CCM), oppositely charged protein (e.g., histone 3), and human serum albumin (HSA). The results demonstrate that the lipid corona successfully protects the AuPhe NPs from protein adsorption, leading to the development of corona-free character. This unique achievement has profound implications for enhancing the biomedical utility and safety of these nanoparticles.

Quantification of Macrophage Cellular Ferrous Iron (Fe2+) Content Using a Highly Specific Fluorescent Probe in a Plate Reader.

Macrophages are at the center of innate immunity and iron metabolism. In the case of an infection, macrophages adapt their cellular iron metabolism to deprive iron from invading bacteria to combat intracellular bacterial proliferation. A concise evaluation of the cellular iron content upon an infection with bacterial pathogens and diverse cellular stimuli is necessary to identify underlying mechanisms concerning iron homeostasis in macrophages. For the characterization of cellular iron levels during infection, we established an in vitro infection model where the murine macrophage cell line J774A.1 is infected with Salmonella enterica serovar Typhimurium (S.tm), the mouse counterpart to S. enterica serovar Typhi, under normal and iron-overload conditions using ferric chloride (FeCl3) treatment. To evaluate the effect of infection and iron stimulation on cellular iron levels, the macrophages are stained with FerroOrange. This fluorescent probe specifically detects Fe2+ ions and its fluorescence can be quantified photometrically in a plate reader. Importantly, FerroOrange fluorescence does not increase with chelated iron or other bivalent metal ions. In this protocol, we present a simple and reliable method to quantify cellular Fe2+ levels in cultured macrophages by applying a highly specific fluorescence probe (FerroOrange) in a TECAN Spark microplate reader. Compared to already established techniques, our protocol allows assessing cellular iron levels in innate immune cells without the use of radioactive iron isotopes or extensive sample preparation, exposing the cells to stress. Key features • Easy quantification of Fe2+ in cultured macrophages with a fluorescent probe. • Analysis of iron in living cells without the need for fixation. • Performed on a plate reader capable of 540 nm excitation and 585 nm emission by trained employees for handling biosafety level 2 bacteria.

Stability constants of ternary complexes β-lactam antibiotic drugs with bivalent transition metal(II) ions in the presence of aliphatic amino acids

Stability constants of ternary complexes β-lactam antibiotic drugs with bivalent transition metal(II) ions in the presence of aliphatic amino acids

Structural, magnetic, optical, and antibacterial properties of Mn1-xNixFe2O4 nanoparticles

Herein, we report the synthesis of Mn1-xNixFe2O4 (MNFO) nanoparticles (NPs) with lime peel and capsicum coating for different compositions (x = 0.0–0.4) by chemical co-precipitation method tested for antibacterial properties. The coated sample, Mn0.6Ni0.4Fe2O4 NPs has exhibited excellent antibacterial activity against gram positive and negative species compared to uncoated ones. Significantly, lime peel coated samples have exhibited more antibacterial effect as compared to capsaicin coated at x = 0.4. The crystallite size of the sample analysed via X-ray diffraction (XRD) is in nano regime, 7–10 nm. Results show considerably low strain for all samples except a peak value for composition at x = 0.1; which can be ascribed to the cation distribution and different ionic radii of the bivalent metal ions. Fourier transform infrared spectroscopy (FTIR) confirms presence of functional groups. The ultraviolet visible (UV–Vis) spectra reveal indirect band gap of 2–2.5 eV. The field emission scanning electron microscopy (FESEM) analysis shows nano cubical structure. The energy dispersive x-ray (EDX) spectroscopy confirms the presence of elements (Mn, Ni, Fe, and O) in the sample. The magnetic properties have investigated using vibrating sample magnetometer (VSM), shows saturation magnetization and remnant magnetization decreases with increasing Ni content. The low values of saturation magnetization and coercive force is indicative of formation of soft ferrite with super paramagnetic in nature.

Synergistic activation of P and orbital coupling effect for ultra-sensitive and selective electrochemical detection of Cd(II) over Fe-doped CoP

Despite significant advancements in the detection of cadmium (Cd(II)) based on nanomaterial adsorbability, limited research has been conducted on ultra-sensitive and selective detection mechanisms, resulting in a lack of guidance for designing efficient interface materials to detect Cd(II). Herein, reductive Fe doping on CoP facilitates an efficient Fe-Co-P electron transfer path, which renders P the electron-rich site and subsequently splits a new orbital peak that matches with that of Cd(II) for excellent electrochemical performance. The sensitivity of Cd(II) was remarkably up to 109.75 μA μM−1 on the Fe-CoP modified electrode with excellent stability and repeatability, surpassing previously reported findings. Meanwhile, the electrode exhibits exceptional selectivity towards Cd(II) ions compared to some bivalent heavy metal ions (HMIs). Moreover, X-ray absorption fine structure (XAFS) analysis reveals the interaction between P and Cd(II), which is further verified via density functional theory (DFT) calculation with the new hybrid peaks resulting from the splitting peak of P atoms coupled with the orbital energy level of Cd(II). Generally, doping engineering for specific active sites and regulation of orbital electrons not only provides valuable insights for the subsequent regulation of electronic configuration but also lays the foundation for customizing highly sensitive and selectivity sensors.

Biomass derived green carbon dots for sensing applications of effective detection of metallic contaminants in the environment

The rapid consumption of metals and unorganized disposal have led to unprecedented increases in heavy metal ion concentrations in the ecosystem, which disrupts environmental homeostasis and results in agricultural biodiversity loss. Mitigation and remediation plans for heavy metal pollution are largely dependent on the discovery of cost-effective, biocompatible, specific, and robust detectors because conventional methods involve sophisticated electronics and sample preparation procedures. Carbon dots (CDs) have gained significant importance in sensing applications related to environmental sustainability. Fluorescence sensor applications have been enhanced by their distinctive spectral properties and the potential for developing efficient photonic devices. With the recent development of biomass-functionalized carbon dots, a wide spectrum of multivalent and bivalent transition metal ions responsible for water quality degradation can be detected with high efficiency and minimal toxicity. This review explores the various methods of manufacturing carbon dots and the biochemical mechanisms involved in metal detection using green carbon dots for sensing applications involving Cu (II), Fe (III), Hg (II), and Cr (VI) ions in aqueous systems. A detailed discussion of practical challenges and future recommendations is presented to identify feasible design routes.

Novel azo metal chelates of 3-aminophthalhydrazide derivative: Structural investigation, evaluation of DNA cleavage, anticancer and molecular docking studies

Transition bivalent metal ion (Mn, Co, Ni, Cu, and Zn) complexes derived from an azo ligand (HLCU) having 1,3-diketone moiety with 3-aminophthalhydrazide were prepared and characterized by using elemental analyses, ultraviolet–visible, Fourier transform infrared, nuclear magnetic resonance (1H, 13C), electron spin resonance, molar conductivity and magnetic measurement studies. Molar conductivity value indicated the non-electrolytic nature of all complexes. The ligand coordinates with the metal ion as a tridentate pattern and the binding sites are carbonyl oxygen, hydrazo nitrogen and hydroxy oxygen of phthalhydrazide moiety. The fluorescence spectra of the compounds were recorded and the results revealed that ligand have higher emission intensity than metal complexes. The X-ray powder diffraction indicated that the ligand (HLCU) and nickel(II) complex have orthorhombic crystal lattices. The ligand and metal complexes were subjected to DNA cleavage activity on pUC18 plasmid DNA using the gel electrophoresis method. The cobalt(II) complex completely cleaved DNA and other compounds showing higher cleaving activity than the control. The antitumor activity of the compounds was screened using sulforhodamine B assay towards the breast cancer and leukaemia cancer cell lines. Manganese(II), cobalt(II) and nickel(II) complexes have more promising activity, and the IC50 value is < 10 μg/mL against the leukaemia carcinoma cell line, which is equally potent as the positive control (adriamycin). The molecular docking study was used to find the binding mode of ligand and complexes of cobalt(II) and nickel(II) towards the molecular target protein receptor. The binding affinity of these compounds is −9.8, −13.6 and −10.5 kcal/mol respectively. The cobalt(II) complex has a more effective binding nature than the ligand and nickel(II) complex. Drug-likeness character indicates moderate activity of HLCU, and [Co(HLCU)(H2O)3], [Ni(HLCU)H2O] complexes, in agreement with invitro results.

Synthesis of ternary metal complexes of bivalent metal ions with benzimidazole derivative and their antimicrobial studies

Synthesis of ternary metal complexes of bivalent metal ions with benzimidazole derivative and their antimicrobial studies

Conductometric, Spectrophotometric and Computational Investigation of Binary and Ternary Complexes of Co(II) and Cu(II) Bivalent Metal Ions with L-Valine Amino Acid and Paracetamol Drug

The conductivity and spectrophotometry techniques were employed to evaluate the binary and ternary complexes of the divalent metal ions Co(II) and Cu(II) with the physiologically relevant amino acid L-Valine (Val) and the analgesic paracetamol. The conductivity experiments were generated by direct conductivity equation from conductivity titration data, while the spectrophotometry experiments were performed using the continuous variations approach (Job's method). Both techniques were accomplished in an aqueous solution with a constant concentration of 0.004 M of divalent metal ions at (40.0 ± 0.1) °C. The binary complexes of Co(II) and Cu(II) have a 1:1 binding ratio of metal to paracetamol (M:para). However, the binary complexes of Co(II) and Cu(II) have metal: Val binding ratios of either 1:1 or 2:1. In addition, the Cu(II) binary complexes of both ligands have a higher stability constant than Co(II) binary complexes of paracetamol and Val ligands, which was in good agreement with the Rossotti-Willime order. The ternary complexes of Co(II) and Cu(II) have a 1:1:1 binding ratio of metal to paracetamol: L-valine, (M:para:Val). The stability constants were in order: The ternary metal complexes &amp;gt; The binary metal-L-Val complexes &amp;gt; The binary metal-para complexes. DFT (Density Functional Theory) simulations were used in order to gain a better understanding of the molecular interactions of Co(II) and Cu(II) divalent metal ions with L-Val and paracetamol. Calculations were made on the electronic structure, HOMOs and LUMOs, and molecular geometry of complexes and their corresponding ligands. The findings unequivocally demonstrate that the metal ion is bound to both the amide nitrogen in the paracetamol ligand and the oxygen atom of the carbonyl group. Moreover, the metal ion is bound to the nitrogen atom of the amine NH2 group and the oxygen atom of the hydroxyl group for the L-Val ligand.

Sensing preferences for prokaryotic solute binding protein families.

Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.