The dynamics of zinc sites in proteins: electronic basis for coordination sphere expansion at structural sites

Resolving the zinc binding capacity of honey bee vitellogenin and locating its putative binding sites

The protein vitellogenin (Vg) plays a central role in lipid transportation in most egg-laying animals. High Vg levels correlate with stress resistance and lifespan potential in honey bees (Apis mellifera). Vg is the primary circulating zinc-carrying protein in honey bees. Zinc is an essential metal ion in numerous biological processes, including the function and structure of many proteins. Measurements of Zn²⁺ suggest a variable number of ions per Vg molecule in different animal species, but the molecular implications of zinc-binding by this protein are not well-understood. We used inductively coupled plasma mass spectrometry to determine that, on average, each honey bee Vg molecule binds 3 Zn²⁺ -ions. Our full-length protein structure and sequence analysis revealed seven potential zinc-binding sites. These are located in the β-barrel and α-helical subdomains of the N-terminal domain, the lipid binding site, and the cysteine-rich C-terminal region of unknown function. Interestingly, two potential zinc-binding sites in the β-barrel can support a proposed role for this structure in DNA-binding. Overall, our findings suggest that honey bee Vg bind zinc at several functional regions, indicating that Zn²⁺ -ions are important for many of the activities of this protein. In addition to being potentially relevant for other egg-laying species, these insights provide a platform for studies of metal ions in bee health, which is of global interest due to recent declines in pollinator numbers.

Fabrication of a Reusable Carbon Dot/Gold Nanoparticle/Metal-Organic Framework Film for Fluorescence Detection of Lead Ions in Water

Solid-state sensing platforms are desirable for the development of reusable sensors to promote public health measures such as testing for drinking water contamination. A bioinspired metal-organic framework (MOF)-based material has been developed by imitating metal-protein interactions in biological systems to attain high sensitivity and selectivity to Pb²⁺ through fluorescence sensing. A zirconium terephthalate-type framework (also known as NH₂-UiO-66) was modified with both gold nanoparticles and thiol-functionalized carbon dots to give HS-C/Au(x)/UiO-66 composites with different Au content (x) and were subsequently adapted into films that show extraordinary sensitivity to Pb²⁺. The HS-C/Au(1.4)/UiO-66 film that consists of 1.4 wt % Au shows a quenching response with the limit of detection of 80 parts per trillion and sustained performance for five cycles. Moreover, the fluorescence response of the HS-C/Au(x)/UiO-66 film to Pb²⁺ can be reversed from emission quenching to enrichment of fluorescence by increasing the Au content. The performance of the HS-C/Au(x)/UiO-66 film as a solid-state sensor demonstrates its potential for application in reusable sensing devices to ensure public safety from Pb²⁺ contamination in drinking water.

Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins

Zinc metalloproteins are ubiquitous, with protein zinc centers of structural and functional importance, involved in interactions with ligands and substrates and often of pharmacological interest. Biomolecular simulations are increasingly prominent in investigations of protein structure, dynamics, ligand interactions, and catalysis, but zinc poses a particular challenge, in part because of its versatile, flexible coordination. A computational workflow generating reliable models of ligand complexes of biological zinc centers would find broad application. Here, we evaluate the ability of alternative treatments, using (nonbonded) molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) at semiempirical (DFTB3) and density functional theory (DFT) levels of theory, to describe the zinc centers of ligand complexes of six metalloenzyme systems differing in coordination geometries, zinc stoichiometries (mono- and dinuclear), and the nature of interacting groups (specifically the presence of zinc-sulfur interactions). MM molecular dynamics (MD) simulations can overfavor octahedral geometries, introducing additional water molecules to the zinc coordination shell, but this can be rectified by subsequent semiempirical (DFTB3) QM/MM MD simulations. B3LYP/MM geometry optimization further improved the accuracy of the description of coordination distances, with the overall effectiveness of the approach depending upon factors, including the presence of zinc-sulfur interactions that are less well described by semiempirical methods. We describe a workflow comprising QM/MM MD using DFTB3 followed by QM/MM geometry optimization using DFT (e.g., B3LYP) that well describes our set of zinc metalloenzyme complexes and is likely to be suitable for creating accurate models of zinc protein complexes when structural information is more limited.

Probing the molecular basis for signal transduction through the Zinc-Activated Channel (ZAC)

The molecular basis for the signal transduction through the classical Cys-loop receptors (CLRs) has been delineated in great detail. The Zinc-Activated Channel (ZAC) constitutes a so far poorly elucidated fifth branch of the CLR superfamily, and in this study we explore the molecular mechanisms underlying ZAC signaling in Xenopus oocytes by two-electrode voltage clamp electrophysiology. In studies of chimeric receptors fusing either the extracellular domain (ECD) or the transmembrane/intracellular domain (TMD-ICD) of ZAC with the complementary domains of 5-HT₃A serotonin or α₁ glycine receptors, serotonin and Zn²⁺/H⁺ evoked robust concentration-dependent currents in 5-HT₃A/ZAC- and ZAC/α₁-Gly-expressing oocytes, respectively, suggesting that Zn²⁺ and protons activate ZAC predominantly through its ECD. The molecular basis for Zn²⁺-mediated ZAC signaling was probed further by introduction of mutations of His, Cys, Glu and Asp residues in this domain, but as none of the mutants tested displayed substantially impaired Zn²⁺ functionality compared to wild-type ZAC, the location of the putative Zn²⁺ binding site(s) in the ECD was not identified. Finally, the functional importance of Leu²⁴⁶ (Leu9') in the transmembrane M2 α-helix of ZAC was investigated by Ala, Val, Ile and Thr substitutions. In concordance with findings for this highly conserved residue in classical CLRs, the ZAC^L9'X mutants exhibited left-shifted agonist concentration-response relationships, markedly higher degrees of spontaneous activity and slower desensitization kinetics compared to wild-type ZAC. In conclusion, while ZAC is an atypical CLR in terms of its (identified) agonists and channel characteristics, its signal transduction seems to undergo similar conformational transitions as those in the classical CLR.

Molecular insights into the interaction of angiotensin I-converting enzyme (ACE) inhibitors and HEXXH motif

Nutraceuticals and functional foods garner a lot of attention as potential alternative therapies for treatment of (pre)hypertension. Food-derived proteins release large variety of bioactive peptides which are similar in structure to peptide sequences acting in the organism and therefore can modulate their physiological functions. Val-Pro-Pro (VPP) is a milk-derived tripeptide with assumed mild inhibitory activity against angiotensin-converting enzyme (ACE). Computational (DFT) methods are applied on simplified models of Zn2+-HEXXH binding motif without/with bound inhibitors in order to assess the ability of two pharmaceutical drugs (Captopril and Lisinopril) and Val-Pro-Pro to coordinate with Zn2+-HEXXH binding motif of ACE. Both drugs have significant affinity towards the active site, while the Val-Pro-Pro tripeptide has weaker affinity. The obtained results shed light on the thermodynamic aspects of the inhibitors coordination to the Zn2+-HEXXH binding motif of ACE.

Dietary and Physiological Effects of Zinc on the Immune System

Evidence for the importance of zinc for all immune cells and for mounting an efficient and balanced immune response to various environmental stressors has been accumulating in recent years. This article describes the role of zinc in fundamental biological processes and summarizes our current knowledge of zinc's effect on hematopoiesis, including differentiation into immune cell subtypes. In addition, the important role of zinc during activation and function of immune cells is detailed and associated with the specific immune responses to bacteria, parasites, and viruses. The association of zinc with autoimmune reactions and cancers as diseases with increased or decreased immune responses is also discussed. This article provides a broad overview of the manifold roles that zinc, or its deficiency, plays in physiology and during various diseases. Consequently, we discuss why zinc supplementation should be considered, especially for people at risk of deficiency. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

Biochemical Studies in Perfundates and Homogenates of Isolated Porcine Kidneys after Flushing with Zinc or Zinc-Prolactin Modified Preservation Solution Using a Static Cold Storage Technique

Zinc is an effective anti-inflammatory and antioxidant trace element. The aim of this study was to analyse the protective effect of zinc and zinc–prolactin systems as additives of preservation solutions in the prevention of nephron damage caused during ischemia. The study used a model for storing isolated porcine kidneys in Biolasol^®. The solution was modified with the addition of Zn at a dose of 1 µg/L and Zn: 1 µg/L with prolactin (PRL): 0.1 µg/L. After 2 h and 48 h of storage, the levels of alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, sodium, potassium, creatinine and total protein were determined. Zinc added to the Biolasol^® composition at a dose of 1 µg/L showed minor effectiveness in the protection of nephrons. In turn, Zn²⁺ added to Biolasol + PRL (PRL: 0.1 µg/L) acted as a prolactin inhibitor. We do not recommend the addition of Zn(II) (1 µg/L) and Zn(II) (1 µg/L) + PRL (0.1 µg/L) to the Biolasol solution.

Structural and functional insights into nitrosoglutathione reductase from Chlamydomonas reinhardtii

Protein S-nitrosylation plays a fundamental role in cell signaling and nitrosoglutathione (GSNO) is considered as the main nitrosylating signaling molecule. Enzymatic systems controlling GSNO homeostasis are thus crucial to indirectly control the formation of protein S-nitrosothiols. GSNO reductase (GSNOR) is the key enzyme controlling GSNO levels by catalyzing its degradation in the presence of NADH. Here, we found that protein extracts from the microalga Chlamydomonas reinhardtii catabolize GSNO via two enzymatic systems having specific reliance on NADPH or NADH and different biochemical features. Scoring the Chlamydomonas genome for orthologs of known plant GSNORs, we found two genes encoding for putative and almost identical GSNOR isoenzymes. One of the two, here named CrGSNOR1, was heterologously expressed and purified. Its kinetic properties were determined and the three-dimensional structures of the apo-, NAD⁺- and NAD⁺/GSNO-forms were solved. These analyses revealed that CrGSNOR1 has a strict specificity towards GSNO and NADH, and a conserved folding with respect to other plant GSNORs. The catalytic zinc ion, however, showed an unexpected variability of the coordination environment. Furthermore, we evaluated the catalytic response of CrGSNOR1 to thermal denaturation, thiol-modifying agents and oxidative modifications as well as the reactivity and position of accessible cysteines. Despite being a cysteine-rich protein, CrGSNOR1 contains only two solvent-exposed/reactive cysteines. Oxidizing and nitrosylating treatments have null or limited effects on CrGSNOR1 activity and folding, highlighting a certain resistance of the algal enzyme to redox modifications. The molecular mechanisms and structural features underlying the response to thiol-based modifications are discussed.

•

Chlamydomonas protein extracts catalyze NAD(P)H-dependent GSNO degradation.

•

Chlamydomonas GSNOR1 is a zinc-containing protein strictly relying on GSNO and NADH.

•

The 3D-structure of CrGSNOR1 revealed a conserved folding with other plant GSNORs.

•

CrGSNOR1 contains only two solvent-exposed/reactive cysteines.

•

Oxidizing and nitrosylating treatments have limited effects on CrGSNOR1 activity.

Why Diorganyl Zinc Lewis Acidity Dramatically Increases with Narrowing C-Zn-C Bond Angle

The Lewis acidity of a metal center is influenced not only by the electronic properties of the bonded ligands but also by the bond angles, which we suggest to be important for zinc diorganyls. Molecular orbital correlation predicts that a narrower C-Zn-C bond angle of the R₂Zn fragment lowers its lowest unoccupied molecular orbital (LUMO) and increases its Lewis acidity, such that it binds added ligands more strongly. Computations on Me₂Zn(bipy) (bipy = 2,2'-bipyridine) yield that, for every 10° of C-Zn-C narrowing close to tetrahedral geometry, the Zn-N distance shortens by 0.027 Å (0.048 Å per 10° for the range 180-90°) and that the LUMO of the Me₂Zn fragment drops by 0.24 eV. A total of 10 dialkyl zinc complexes of bipy or 4,4'-di-tert-butyl-2,2'-bipyridine are crystallographically characterized here. Structure correlations (published and new data) confirm the link between the C-Zn-C angle and Zn-N distance. Principal component analysis provides a detailed picture of the correlated distortions. Relevance for zinc fingers/zinc enzymes is discussed.

High photoluminescent nitrogen and zinc doped carbon dots for sensing Fe3+ ions and temperature

High photoluminescent quantum yield carbon nanomaterials doped with heteroatoms are of profound attention in various fields like bio-imaging, chemical sensors and electronics. Among all heteroatoms, zinc is one of the low toxic significant elements and also involves in various electron-transfer processes. These properties are added advantages to utilize zinc as a dopant in CDs synthesis. In this investigation, our group reports a one-step microwave digestion method to synthesize nitrogen and Zinc doped carbon dots (N, Zn-CDs). The optical properties of N, Zn-CDs were investigated using UV-Vis and fluorescence spectrophotometry and also the N, Zn-CDs structural features were studied with other characterization tools like XPS, TEM, EDX, FTIR and XRD. N, Zn-CDs inherent the appreciable photoluminescent quantum yields about 63.28%. And the synthesized N, Zn-CDs utilized for detection of Fe³⁺ and temperature. The observed results are promising and exhibited the detection limit of 0.027 μM. Also, the proposed sensing system was successfully adopted for the detection of Fe³⁺ in the river and circulating water samples for the practical applications and satisfactory results are observed. The current synthesis methodology and sensing potential might open up a new prospect to develop potential applications in environmental monitoring.

Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays

This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC₅₀), binding affinity (K_i), and binding free energy (ΔG_ads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.

Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands

We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.

Unexpected Structure of a Helical N4 -Schiff-Base Zn(II) Complex and Its Demetallation: Experimental and Theoretical Studies

A new Zn-N₄ -Schiff base L=((±)-trans-N,N'-Bis(2-aminobenzylidene)-1,2-diaminocyclohexane) complex was synthesized and fully characterized, showing an unexpected self-assembled double-stranded helicate structure. The X-ray crystal analysis of the Zn₂ L₂ complex ((C₄₀ H₄₄ N₈ Zn₂ ,CH₂ Cl₂ , a=14.2375(3) Å, b=16.7976(4) Å, c=16.1613(4) Å, monoclinic, P2₁ /n, Z=4) shows a centrosymmetrical structure in which zinc atoms are in distorted tetrahedral environments, revealing an M- (R, R) left-handed helicity in its asymmetric unit. However, it was observed that this dinuclear complex is thermodynamically unstable in the presence of small water amounts and undergoes demetallation into free N4-Schiff base ligand and ZnO nanoparticles. This hydrolysis process was thoroughly identified and monitored through detailed ¹ H NMR, DOSY NMR analysis. The reaction mechanism of this demetallation event was elucidated by using the DFT method, involving an activation energy smaller than 13 kcal/mol. Besides, a theoretical mechanism of the demetallation process is given for the first time.

Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in human DPP III

Human dipeptidyl-peptidase III (h.DPP III) is a zinc-exopeptidase that hydrolyses dipeptides from the N-terminus of its substrates. Its mechanism of action was assumed to be similar to that of thermolysin, but was never thoroughly investigated. This study presents the first insight into the reaction mechanism of h.DPP III, determined on the model and real (hydrated enzyme with Leu-enkephalin bound in the active site) systems. The Glu451-assisted water addition on amide carbon atoms and nitrogen inversion (i.e. change of pyramidalization on the leaving nitrogen) are shown to be the rate-determining steps with the activation energies in a good agreement with the experimental results for the Leu-enkephalin hydrolysis. The energy barrier for nucleophilic attack is about 28 kJ mol^-1, while barriers for the N-inversion differ as a consequence of the number of hydrogen bonds that have to be changed, which is smaller in the model active site than in the solvated enzyme. Although precisely defined geometry of the enzyme binding site puts an additional restraint on the hydrogen bonding interactions, at the same time it stimulates the forward reaction towards the final hydrolytic product. Namely, different from the model, the N-inversion is in a concerted fashion followed by favourable hydrogen bonding with Glu451 that immediately "locks" the system into the configuration where reversion to the enzyme-substrate complex is hardly achievable. Therefore we propose that the functional significance of DPP III is dual: to lower the energy barrier of the peptide hydrolysis and to suppress the reverse reaction.

[(H2O)Zn(Imidazole)n]2+: the vital roles of coordination number and geometry in Zn–OH2 acidity and catalytic hydrolysis

The Zn(ii)–(Imidazole(ate))_n coordination motif occurs in numerous biochemical systems, including carbonic anhydrase and the matrix metalloproteinases (MMPs).

Validation and correction of Zn-CysxHisy complexes

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.

The biological inorganic chemistry of zinc ions

The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the “mobile” zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn²⁺ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn²⁺ differs from s-block cations such as Ca²⁺ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.

•

Zinc ions not bound to proteins have critical roles in cell biology.

•

Zinc has a unique coordination chemistry, poorly appreciated in the biosciences.

•

Its coordination chemistry is significantly different from that of calcium ions.

•

Specific conditions apply for buffering cellular zinc ions.

•

Investigations with zinc need to consider solution chemistry and metal buffering.

Zinc ion-doped carbon dots with strong yellow photoluminescence

Carbon dots doped with zinc ions and displaying strong yellow photoluminescence and a QY of 51.2% were produced, as were various applications of these carbon dots.

The influence of zinc(ii) on thioredoxin/glutathione disulfide exchange: QM/MM studies to explore how zinc(ii) accelerates exchange in higher dielectric environments

QM/MM calculations on thiolate disulfide exchange reveal that a polar, 4-centered, cyclic transition state is formed when Zn(ii) is present, helping to explain faster exchange rates in higher dielectric solvents for metal-assisted exchange.