Metal Ion Binding Sites Research Articles

The Structure of Cyclic Neuropeptide Somatostatin and Octapeptide Octreotide in the Presence of Copper Ions: Insights from Transition Metal Ion FRET and Native Ion Mobility-Mass Spectrometry.

The conformation and function of somatostatin (SST), a cyclic neuropeptide, was recently found to be altered in the presence of Cu(II) ions, which leads to self-aggregation and loss of biological function as a neurotransmitter. However, the impact of Cu(II) ions on the structure and function of SST is not fully understood. In this work, transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) were utilized to study the structures of well-defined gas-phase ions of SST and of a smaller analogue, octreotide (OCT). The tmFRET results suggest two binding sites of Cu(II) ions in both native-like SST and OCT ions, either in close proximity to the disulfide bond or complexed by two aromatic residues, consistent with results obtained from collision-induced dissociation (CID). The former binding site was reported to initiate aggregation of SST, while the latter binding site could directly affect the essential motif for receptor binding and therefore impair the biological function of SST and OCT when bound to SST receptors. Our results demonstrate that tmFRET is capable of locating transition metal ion binding sites in neuropeptides. Furthermore, multiple distance constraints (tmFRET) and global shape (IM-MS) provide additional structural insights of SST and OCT ions upon metal binding, which is related to the self-aggregation mechanisms and overall biological functions.

Structural dynamics and mechanistic action guided engineering of lipolytic enzymes.

Lipases have been established as important biocatalysts in several industrial applications, owing to their diverse substrate specificity. The availability of data on three-dimensional crystal structures for various lipases offers an opportunity for modulating their structural and functional aspects to design and engineer better versions of lipases. With the aim of investigating the structural components governing the extremophilic behavior of lipases, structural analysis of microbial lipases was performed using advanced bioinformatics and molecular dynamics simulation approaches. In sequences and functionally distinct alkaliphilic and thermophilic lipases were investigated for their functional properties to understand the distinguishing features of their structures. The alkaliphilic lipase from Bacillus subtilis (LipA) showed conformational changes in the loop region Ala132-Met137, subsequently, the active site residue His156 shows two conformations, toward the active site nucleophilic residues Ser77 and away from the Ser77. Interestingly, the active site of LipA is more solvent-exposed and can be correlated with the adoption of an open conformation which might extend and expose the active site region to solvents during the catalysis process. Furthermore, the MD simulation of thermophilic lipase from marine Streptomyces (MAS1) revealed the role of N- and C-terminal regions with disulfide bridges and identified a metal ion binding site that facilitates the enzyme stability. The novel thermo-alkaliphilic lipase can be designed to integrate the stability features of MAS1 into the alkaliphilic LipA. These structural-level intrinsic characteristics can be used for lipase engineering to amend the lipase activity and stability as per the requirements of the industrial processes.

Investigating Native Metal Ion Binding Sites in Mammalian Histidine-Rich Glycoprotein.

Mammalian histidine-rich glycoprotein (HRG) is a highly versatile and abundant blood plasma glycoprotein with a diverse range of ligands that is involved in regulating many essential biological processes, including coagulation, cell adhesion, and angiogenesis. Despite its biomedical importance, structural information on the multi-domain protein is sparse, not least due to intrinsically disordered regions that elude high-resolution structural characterization. Binding of divalent metal ions, particularly ZnII, to multiple sites within the HRG protein is of critical functional importance and exerts a regulatory role. However, characterization of the ZnII binding sites of HRG is a challenge; their number and composition as well as their affinities and stoichiometries of binding are currently not fully understood. In this study, we explored modern electron paramagnetic resonance (EPR) spectroscopy methods supported by protein secondary and tertiary structure prediction to assemble a holistic picture of native HRG and its interaction with metal ions. To the best of our knowledge, this is the first time that this suite of EPR techniques has been applied to count and characterize endogenous metal ion binding sites in a native mammalian protein of unknown structure.

Ion-Induced Polysaccharide Gelation: Peculiarities of Alginate Egg-Box Association with Different Divalent Cations.

Structural aspects of polysaccharide hydrogels based on sodium alginate and divalent cations Ba2+, Ca2+, Sr2+, Cu2+, Zn2+, Ni2+ and Mn2+ was studied using data on hydrogel elemental composition and combinatorial analysis of the primary structure of alginate chains. It was shown that the elemental composition of hydrogels in the form of freezing dried microspheres gives information on the structure of junction zones in the polysaccharide hydrogel network, the degree of filling of egg-box cells by cations, the type and magnitude of the interaction of cations with alginate chains, the most preferred types of alginate egg-box cells for cation binding and the nature of alginate dimers binding in junction zones. It was ascertained that metal-alginate complexes have more complicated organization than was previously desired. It was revealed that in metal-alginate hydrogels, the number of cations of various metals per C12 block may be less than the limiting theoretical value equal to 1 for completely filled cells. In the case of alkaline earth metals and zinc, this number is equal to 0.3 for calcium, 0.6 for barium and zinc and 0.65-0.7 for strontium. We have determined that in the presence of transition metals copper, nickel and manganese, a structure similar to an egg-box is formed with completely filled cells. It was determined that in nickel-alginate and copper-alginate microspheres, the cross-linking of alginate chains and formation of ordered egg-box structures with completely filled cells are carried out by hydrated metal complexes with complicated composition. It was found that an additional characteristic of complex formation with manganese cations is the partial destruction of alginate chains. It has been established that the existence of unequal binding sites of metal ions with alginate chains can lead to the appearance of ordered secondary structures due to the physical sorption of metal ions and their compounds from the environment. It was shown that hydrogels based on calcium alginate are most promising for absorbent engineering in environmental and other modern technologies.

Identification of metal ion-binding sites in RNA structures using deep learning method.

Metal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA structures, it becomes possible to identify the metal ion-binding sites in RNA structures through in-silico methods. Here, we propose an approach called Metal3DRNA to identify the binding sites of the most common metal ions (Mg2+, Na+ and K+) in RNA structures by using a three-dimensional convolutional neural network model. The negative samples, screened out based on the analysis for binding surroundings of metal ions, are more like positive ones than the randomly selected ones, which are beneficial to a powerful predictor construction. The microenvironments of the spatial distributions of C, O, N and P atoms around a sample are extracted as features. Metal3DRNA shows a promising prediction power, generally surpassing the state-of-the-art methods FEATURE and MetalionRNA. Finally, utilizing the visualization method, we inspect the contributions of nucleotide atoms to the classification in several cases, which provides a visualization that helps to comprehend the model. The method will be helpful for RNA structure prediction and dynamics simulation study. Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/Metal3DRNA.

Mechanics of divalent ion sensitivity of the manganese-sensing riboswitch measured by combined high-resolution optical tweezers and single-molecule fluorescence.

Riboswitches are structured non-coding RNA typically found in the 5′ untranslated regions of bacterial mRNAs. They modulate gene expression through the binding of specific ligands that induce changes in the riboswitch structure, most often at the level of transcription and translation. The Mn2+-sensing yybP-ykoY RNA motif is one of the most widespread riboswitches across bacteria, including human and plant pathogens. It contains two divalent metal ion binding sites: one is specific for Mn2+ whereas the other is nonspecific for a divalent metal ion, including Mg2+. Previous crystal structures have shown that Mn2+ binds in between the two distal helical legs of a four-way junction and induces a large “docking” conformational change. It is unclear how competition between Mn2+ and Mg2+ for the two binding sites and the associated RNA conformational changes give rise to Mn2+ detection function and sensitivity. Therefore, we explored the global structural dynamics of the L. lactis Mn2+-sensing riboswitch in the presence of competing divalent cations using high-resolution optical tweezers simultaneous with confocal Förster resonance energy transfer (FRET) spectroscopy. Initial non-equilibrium force ramp measurements revealed force-dependent docking distribution, suggesting a highly selective docked state at suboptimal Mn2+ ion concentration. Follow-up high-resolution equilibrium fixed-force measurements directly measured docking and undocking rate constants versus force to determine docking and undocking mechanics, including transition states and pathways, at varying Mn2+ vs Mg2+ concentrations. Simultaneous FRET measurements confirmed specific conformational transitions. Docking and undocking were symmetric processes with nearly equal force sensitivity and a transition state located nearly midway between the docked and undocked states. Mn2+ sensitivity appears to optimize at a concentration where further increasing Mn2+ competes with Mg2+ ions for the non-specific divalent metal ion binding site.

A structure-function analysis of chlorophyllase reveals a mechanism for activity regulation dependent on disulfide bonds

Chlorophyll pigments are used by photosynthetic organisms to facilitate light capture and mediate the conversion of sunlight into chemical energy. Due to the indispensable nature of this pigment and its propensity to form reactive oxygen species, organisms heavily invest in its biosynthesis, recycling, and degradation. One key enzyme implicated in these processes is chlorophyllase, an α/β hydrolase that hydrolyzes the phytol tail of chlorophyll pigments to produce chlorophyllide molecules. This enzyme was discovered a century ago, but despite its importance to diverse photosynthetic organisms, there are still many missing biochemical details regarding how chlorophyllase functions. Here, we present the 4.46-Å resolution crystal structure of chlorophyllase from Triticum aestivum. This structure reveals the dimeric architecture of chlorophyllase, the arrangement of catalytic residues, an unexpected divalent metal ion-binding site, and a substrate-binding site that can accommodate a diverse range of pigments. Further, this structure exhibits the existence of both intermolecular and intramolecular disulfide bonds. We investigated the importance of these architectural features using enzyme kinetics, mass spectrometry, and thermal shift assays. Through this work, we demonstrated that the oxidation state of the Cys residues is imperative to the activity and stability of chlorophyllase, illuminating a biochemical trigger for responding to environmental stress. Additional bioinformatics analysis of the chlorophyllase enzyme family reveals widespread conservation of key catalytic residues and the identified "redox switch" among other plant chlorophyllase homologs, thus revealing key details regarding the structure-function relationships in chlorophyllase.

Effect of Brassinosteroids on the Ion-Exchange Properties of the Cell Walls of Barley Roots and Shoots under the Action of Heavy Metals

The effect of polymetallic contamination and concomitant treatment with brassinosteroids (homocastasterone or homobrassinolide) on barley plants and on the ion-exchange capacity of cell walls isolated from shoots and roots was studied. Under the influence of polymetals, a decrease in the dry mass of roots, water content, and the proportion of the cell wall in them was observed, but the addition of homocastasterone to the medium led to the restoration of these parameters almost to the control level. In the aerial part of plants, the influence of both polymetals and brassinosteroids on these parameters was weakly expressed. In the presence of homocastasterone, the content of demethylated carboxyl groups of polygalacturonic acid increased in the pectins of the cell walls of roots and leaves, which are the main binding sites for heavy metal ions in the apoplast. Thus, it can be assumed that treatment with brassinosteroids (homocastasterone) leads to a change in the composition and ion-exchange properties of the cell wall, which makes it possible to reduce the toxic effect of polymetals due to their immobilization in the apoplast.

Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus.

Enzyme-catalyzed reaction cascades play an increasingly important role for the sustainable manufacture of diverse chemicals from renewable feedstocks. For instance, dehydratases from the ilvD/EDD superfamily have been embedded into a cascade to convert glucose via pyruvate to isobutanol, a platform chemical for the production of aviation fuels and other valuable materials. These dehydratases depend on the presence of both a Fe-S cluster and a divalent metal ion for their function. However, they also represent the rate-limiting step in the cascade. Here, catalytic parameters and the crystal structure of the dehydratase from Paralcaligenes ureilyticus (PuDHT, both in presence of Mg2+ and Mn2+ ) were investigated. Rate measurements demonstrate that the presence of stoichiometric concentrations Mn2+ promotes higher activity than Mg2+ , but at high concentrations the former inhibits the activity of PuDHT. Molecular dynamics simulations identify the position of a second binding site for the divalent metal ion. Only binding of Mn2+ (not Mg2+ ) to this site affects the ligand environment of the catalytically essential divalent metal binding site, thus providing insight into an inhibitory mechanism of Mn2+ at higher concentrations. Furthermore, in silico docking identified residues that play a role in determining substrate binding and selectivity. The combined data inform engineering approaches to design an optimal dehydratase for the cascade.

Bivalent copper ions presence triggers removal and homeostatic mechanisms in the metal-resistant microorganism Apiotrichum loubieri M12

Microorganisms, especially those habiting mining environments, are of great importance for the retention of toxic metals in the environment. This work aimed to isolate a copper removing-microorganism from sediments of an Acid Mine Drainage-affected environment and to study the cellular responses trigger by metal presence. Apiotrichum loubieri M12 was able to tolerate and remove Cu(II) from liquid culture media, reaching a 30–35% removal capacity when it was exposed to 40 μg mL−1 Cu(II) after 48 h. Analysis of the biomass exposed to the metal through SEM-EDS showed copper presence on the cell surface and variations in the proportion of other biomass constituent elements. Proteomics revealed that the presence of Cu(II) induces differential expression of intracellular proteins involved in a wide variety of metabolic processes. Interestingly, a specific response to the metal was detected in cell-free supernatants, in which copper binding proteins were identified. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The microorganism responds not only by adjusting intracellular protein expression, but also by adjusting expression of proteins in the extracellular space.

Metal Binding to Sodium Heparin Monitored by Quadrupolar NMR.

Heparins and heparan sulfate polysaccharides are negatively charged glycosaminoglycans and play important roles in cell-to-matrix and cell-to-cell signaling processes. Metal ion binding to heparins alters the conformation of heparins and influences their function. Various experimental techniques have been used to investigate metal ion-heparin interactions, frequently with inconsistent results. Exploiting the quadrupolar 23Na nucleus, we herein develop a 23Na NMR-based competition assay and monitor the binding of divalent Ca2+ and Mg2+ and trivalent Al3+ metal ions to sodium heparin and the consequent release of sodium ions from heparin. The 23Na spin relaxation rates and translational diffusion coefficients are utilized to quantify the metal ion-induced release of sodium ions from heparin. In the case of the Al3+ ion, the complementary approach of 27Al quadrupolar NMR is employed as a direct probe of ion binding to heparin. Our NMR results demonstrate at least two metal ion-binding sites with different affinities on heparin, potentially undergoing dynamic exchange. For the site with lower metal ion binding affinity, the order of Ca2+ > Mg2+ > Al3+ is obtained, in which even the weakly binding Al3+ ion is capable of displacing sodium ions from heparin. Overall, the multinuclear quadrupolar NMR approach employed here can monitor and quantify metal ion binding to heparin and capture different modes of metal ion-heparin binding.

Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning.

More than one-third of the proteins contain metal ions in the Protein Data Bank. Correct identification of metal ion-binding residues is important for understanding protein functions and designing novel drugs. Due to the small size and high versatility of metal ions, it remains challenging to computationally predict their binding sites from protein sequence. Existing sequence-based methods are of low accuracy due to the lack of structural information, and time-consuming owing to the usage of multi-sequence alignment. Here, we propose LMetalSite, an alignment-free sequence-based predictor for binding sites of the four most frequently seen metal ions in BioLiP (Zn2+, Ca2+, Mg2+ and Mn2+). LMetalSite leverages the pretrained language model to rapidly generate informative sequence representations and employs transformer to capture long-range dependencies. Multi-task learning is adopted to compensate for the scarcity of training data and capture the intrinsic similarities between different metal ions. LMetalSite was shown to surpass state-of-the-art structure-based methods by more than 19.7, 14.4, 36.8 and 12.6% in area under the precision recall on the four independent tests, respectively. Further analyses indicated that the self-attention modules are effective to learn the structural contexts of residues from protein sequence. We provide the data sets, source codes and trained models of LMetalSite at https://github.com/biomed-AI/LMetalSite.

A Highly Selective MOF-Based Probe for Turn-On Luminescent Detection of Al3+, Cr3+, and Fe3+ in Solution and Test Paper Strips through Absorbance Caused Enhancement Mechanism.

Trivalent metal ions (Cr3+, Al3+, and Fe3+) constitute a major section of the environmental pollutants, and their excess accumulation has a detrimental effect on health, so their detection in trace quantity has been a hot topic of research. A highly scalable 3D porous Zn-based luminescent metal-organic framework (MOF) has been synthesized by exploiting the mixed ligand synthesis concept. The strategic selection of an aromatic π-conjugated organic linker and N-rich spacer containing the azine functionality as metal ion binding sites immobilized across the pore spaces, have made this MOF an ideal turn-on sensor for Al3+, Cr3+, and Fe3+ ions with very high sensitivity, selectivity, and recyclability. An in-depth study revealed absorbance caused enhancement mechanism (ACE) responsible for such turn-on phenomena. In order to make the detection process straightforward, convenient, portable, and economically viable, we have fabricated MOF test paper strips (the MOF could be simply immobilized onto the paper strips) for naked eye visual detection under UV light, which, thus, manifests its potential as a real-time smart sensor for these trivalent ions.

Temoneira-1 β-lactamase is not a metalloenzyme, but its native metal ion binding sites allow for purification by immobilized metal ion affinity chromatography

β-lactamases protect bacteria from β-lactam antibiotics. Temoneira (TEM) is a class A serine β-lactamase and its coding sequence is designed into DNA vectors, such as pET-21a (+), to provide antibiotic resistance. TEM-1 β-lactamase was overexpressed efficiently from this vector upon inducing protein expression by IPTG in BL21(DE3) cells. Immobilized metal ion affinity chromatography (IMAC) was used based on the three native putative metal ion binding sites of TEM-1 β-lactamase, each consisting of a pair of histidine sidechains. Elution was achieved at low concentrations of imidazole (∼15–200 mM). Two steps of IMAC and a subsequent anion exchange purification produced highly pure TEM-1 β-lactamase with a yield of 1.9 mg/g of wet bacterial pellet weight. Mass spectrometry revealed that the mature form of β-lactamase (without the signal sequence) was obtained. The secondary structure composition, calculated from the circular dichroism spectrum, showed that the target protein was folded similar to the published crystal structure. Ni(II) binding to the enzyme was also investigated. Increasing amounts of Ni(II) ions had only a small effect on the protein structure. Mass spectrometry detected up to three bound metal ions at 10:1 Ni(II):protein molar ratio, but the major peak was assigned to the monometallated β-lactamase indicating the presence of a paramount metal ion binding site formed by the H151/H156 pair.

Interactions of Heavy Metals on Enzymes in Carbohydrate Metabolism: In silico study on glucokinase and pyruvate kinase

Cadmium (Cd2+) and mercury (Hg2+) are heavy metals, which can cause chronic inflammation, oxidative stress, obesity, hyperglycemia, and diabetes. Exposure to heavy metals cadmium and mercury can interfere with glycolysis metabolic functions through the inactivation of two key enzymes: glucokinase (GK) and pyruvate kinase (PyK). However, pathomechanism is unknown. Based on the background, this research was conducted. Enzyme structures were obtained from the RCSB Protein Data Bank (http://www.rcsb.org) with the following codes, GK (GDP ID: 3IDH) and PyK (GDP ID: 4IP7). The interaction between Cd and Hg with this enzyme was used via the MIB site: Metal Ion Binding site prediction and docking server (http://bioinfo.cmu.edu.tw/MIB/). Next, the target protein's interaction between metal ions and amino acids was visualized on UCSF Chimera 1.15. Based on the research results, the metal ion bond of mercury was more reactive than cadmium based on the number of amino acid residues bound. The bond was stronger based on a lower distance with PyK and GK enzymes. Therefore, mercury and cadmium metal ions were considered to inhibit the glycolysis process by causing the inactivation of the two enzymes.

The process and mechanism for cesium and rubidium extraction with saponified 4-tert-butyl-2-(α-methylbenzyl) phenol

Cesium (Cs) and rubidium (Rb) separation from brine is an important and application-oriented topic. 4-tert-butyl-2-(α-methylbenzyl) phenol (t-BAMBP) has been used for Cs and Rb extraction. However, the traditional extraction technology is base and acid consumed. In the present work, an innovative process for Cs and Rb extraction with t-BAMBP is developed, which consists of saponification, extraction, scrubbing and stripping. Both infrared spectrum and electrostatic potential analysis indicate the hydrogen of phenolic hydroxyl is dissociated from t-BAMBP during saponification and the oxygen of phenolic hydroxyl is the binding site for alkali metal ions. Saponified organic phase shows an excellent extraction effect for Cs+ and Rb+. The extraction reaches equilibrium in 5 min, with 99.5% Cs+ and 46.7% Rb+ are loaded into the organic phase in the single-stage extraction. Slope method indicates the structure of the extraction complex is MOR·3ROH (M = Cs+, Rb+, K+), where the electrostatic attraction between M+ and the oxygen of phenolic hydroxyl is dominant, and the cation–π interaction has a significant effect also. The extraction complex of MOR·3ROH dissociates in the acid environment while scrubbing and stripping is completed. The Cs+ and Rb+ are separated from the mixture phase, the proton H bonds to the phenolic hydroxyl group, and the extractant is regenerated.

The Copper Chaperone Protein Gene GmATX1 Promotes Seed Vigor and Seedling Tolerance under Heavy Metal and High Temperature and Humidity Stresses in Transgenic Arabidopsis.

Abiotic stresses such as high temperature, high humidity, and heavy metals are important factors that affect seed development and quality, and restrict yield in soybean. The ATX1-type copper chaperones are an important type of proteins that are used for maintaining intracellular copper ion homeostasis. In our previous study, a copper chaperone protein GmATX1 was identified in developing seeds of soybean under high temperature and humidity (HTH) stresses. In this study, the GmATX1 gene was isolated, and multiple alignment analysis showed that its encoding protein shared high sequence identities with other plant orthologues of copper chaperone proteins containing the HMA domain, and a conserved metal ion-binding site, CXXC. A subcellular localization assay indicated that GmATX1 was localized in the cell membrane and nucleus. An expression analysis indicated that GmATX1 was involved in seed development, and in response to HTH and heavy metal stresses in soybean. GmATX1-silent soybean seedlings were found to be more severely damaged than the control under HTH stress. Moreover, the silencing of GmATX1 reduced antioxidase activity and reactive oxygen species (ROS) scavenging ability in the seedling leaves. The overexpression of GmATX1 in Arabidopsis improved seed vigor and seedling tolerance, and enhanced antioxidase activity and ROS scavenging ability under HTH and heavy metal stresses. Our results indicated that GmATX1 could promote seed vigor and seedling tolerance to HTH and heavy metal stresses in transgenic Arabidopsis, and this promotion could be achieved by enhancing the antioxidase activity and ROS scavenging ability.

Self-propelled nanomotors based on hierarchical metal-organic framework composites for the removal of heavy metal ions

The outstanding performance efficiency for the removal of heavy metal ions in solution is governed by various factors: (a) sufficient contact probability between heavy metal ions and the adsorbent, (b) convenient diffusion/accessibility of heavy metal ions to the surface and the interior of the adsorbent, and (c) abundant binding sites for heavy metal ions on the adsorbent. We designed an efficient MnFe2O4 @MIL-53 @UiO-66 @MnO2 adsorbent for Pb(II) and Cd(II) removal. The adsorbents were fabricated by merging self-propelled nanomotors, exploiting hierarchical structure, and using a metal-organic framework (MOF) composite to simultaneously meet the three requirements. The sufficient contact probability between Pb(II)/Cd(II) and MnFe2O4 @MIL-53 @UiO-66 @MnO2 was achieved via the self-propelled movement of MnFe2O4 @MIL-53 @UiO-66 @MnO2 which was induced by the catalytic decomposition of H2O2 by MnO2. The convenient diffusion/accessibility of Pb(II)/Cd(II) on the surface and interior of MnFe2O4 @MIL-53 @UiO-66 @MnO2 was achieved by exploiting the properties of the hierarchical structure of MnFe2O4 @MIL-53 @UiO-66 @MnO2. Abundant binding sites (-COOH) on MIL-53 and UiO-66 composites were present for the binding of the Pb(II)/Cd(II) ions to the adsorbent. The adsorption capacities of the nanomotor adsorbent for Pb(II) and Cd(II) were 1018 and 440.8 mg g–1 at 25 °C, respectively. Additionally, the complex formed of MnFe2O4 and MIL-53 endowed the adsorbent with easy-recyclable properties under the influence of an external magnet. The nanomotors exhibit satisfactory removal performances for Pb(II) and Cd(II).

Drying and rewetting induce changes in biofilm characteristics and the subsequent release of metal ions

Drying and rewetting can markedly influence the microbial structure and function of river biofilm communities and potentially result in the release of metal ions from biofilms containing metals. However, little information is available on the response of metal-enriched biofilms to drying and rewetting over time. In this study, natural biofilms were allowed to develop in four rotating annular bioreactors for 2–11 weeks, followed by drying for 5 days and rewetting for another 5 days. Subsequently, we assessed Zn, Cd, and As desorption from the biofilms and other related parameters (microbial community structure, biofilm morphology, enzyme activity, and surface components as well as characteristics). High-throughput sequencing of the 16 S rRNA gene and confocal laser scanning microscopy revealed that the biofilm architecture and bacterial communities were distinct in different growth phases and under drying and rewetting conditions (permutational multivariate analysis of variance; p = 0.001). Proteobacteria was the dominant bacterial phylum, accounting for 69.7–90.1% of the total content. Kinetic experiments revealed that the drying and rewetting process increased metal desorption from the biofilm matrix. The desorption of heavy metals was affected by the age of the biofilm, with the maximum amount of metal ions released from 2-week-old biofilms (one-way ANOVA, Zn: p < 0.001; Cd: p = 0.008; As: p < 0.001). The modifications in biofilm properties and decreased diversity of the bacterial community (paired t-test, p < 0.05) after drying and rewetting decreased the number of specific binding sites for metal ions. In addition, negatively charged arsenate and other anions in the liquid phase could compete with As ions for adsorption sites to promote the release of As(V) and/or reductive desorption of As(III). The results of this study and their interpretation are expected to help refine the behaviors of heavy metals in the aquatic environment.

IMPACT OF HEAVY METALS ON HEXOKINASE ISOFORMS: AN IN SILICO STUDY

Abstract: Coal mining activities in South Kalimantan produce waste that is very dangerous if not processed wisely. Coal waste produces heavy metals cadmium and mercury that can pollute the environment. Heavy metals that enter the human body will cause negative impacts in the field of health such as the disruption of the glycolysis process in humans. The purpose of this study was determine the interaction of heavy metals which is cadmium and mercury against hexokinase enzymes using hexokinase enzymes type I, II, III with PDB ID : 4F9O, 2NZT, 3HM8 taken from Protein Data Bank and using the molecular docking website MIB: Metal Ion Binding Site Prediction and Docking server. Docking results will be visualized using chimera app version 1.15. Molecular docking of the heavy metals cadmium and mercury can interact with all three types of hexokinase enzymes. Cadmium metal ions bind hydrophobicly to amino acid residues of hexokinase enzymes type I, II, and III, while mercury metal ions bind covalently coordinate with amino acid residues of hexokinase enzymes type I and III. Mercury metal ions bind more strongly than cadmium metal ions. Of the three types of hexokinase enzymes, mercury metal ions bind most strongly with hexokinase enzyme type II because mercury ions bind to the active site of the three amino acid residues of hexokinase enzymes type II.Keywords: Cadmium ; hexokinase enzyme ; mercury ; molecular docking