Designing hydrolytic zinc metalloenzymes

In Silico Analysis of Protein-Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe

Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on proposing the first prediction of PPI by comparison of the interologues between humans and yeasts, as well as the molecular docking and dynamics of the M28 domain of Ermp1 with possible target proteins. As results, 45 proteins are proposed that could interact with the metalloprotease. Most of these proteins are related to the transport of Ca2+ and the metabolism of amino acids and proteins. Docking and molecular dynamics suggest that the M28 domain of Ermp1 could hydrolyze leucine and methionine residues of Amk2, Ypt5 and Pex12. These results could support future experimental investigations of other Fxna peptidases, such as human ERMP1.

Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase

Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.

Design of Functional Globular β-Sheet Miniproteins

The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.

Relationship of Thermostability and Binding Affinity in Metal-binding WW-Domain Minireceptors

The design of metallo-miniproteins advances our understanding of the structural and functional roles of metals in proteins. We recently designed a metal-binding WW domain, WW-CA-Nle, which displays three histidine residues on its surface for coordination of divalent metals Ni(II), Zn(II) and Cu(II). However, WW-CA-Nle is a molten globule in the apo state and thus showed only moderate binding affinities with Kd values in the μM regime. In this report, we hypothesize that improved thermal stability of the apo state of the metal binding WW-domain scaffold should lead to improved preorganization of the metal-binding site and consequently to higher metal-binding affinities. By redesigning WW-CA-Nle, we obtained WW-CA variants, WW-CA-min and WW-CA-ANG, which were fully folded in the apo states and displayed moderate to excellent thermostabilities in the apo and holo states. We were able to show that the improved thermal stabilities led to improved metal binding, which was reflected in Kd values that were at least one order of magnitude lower compared to WW-CA-Nle. EPR spectroscopy and ITC measurements revealed a better defined and predisposed metal binding site in WW-CA-ANG.

Study of Serum Copper and Zinc Levels and Serum Cu/Zn Ratio among Polish Women with Endometrial Cancer

BACKGROUND

Micronutrients are important components for the homeostasis of the human body. The studies available in the literature of the subject on their impact on the risk of population diseases, including malignant neoplasms, are ambiguous. In this paper, the relationship between Cu and Zn serum levels and the occurrence of endometrial cancer have been analyzed.

METHODS

306 patients (153 test group and 153 control group) matched for age were analyzed for Cu and Zn levels. Microelements levels were determined for sera collected during the hospitalization of patients by means of an inductively coupled plasma mass spectrometry. In addition, the Cu/Zn ratio in the population included in the study was analyzed. Univariable and multivariable analyzes were used to examine the relationship between the factors under study and the incidence of endometrial cancer.

RESULTS

Lower levels of elements were observed in the study group compared with the control group (Cu: 959.39 μg/L vs. 1176.42 μg/L, p < 0.001; Zn: 707.05 μg/L vs. 901.67 μg/L, p < 0.001). A statistically significant relationship with the occurrence of endometrial cancer was observed for Cu and Zn. The patients with the lowest Cu level had a significantly higher occurrence of endometrial cancer compared with reference tertile (OR 8.54; p < 0.001). Similarly, compared with the reference tertile, the patients with the lowest Zn levels had a significantly greater incidence of endometrial cancer (OR 15.0; p < 0.001).

CONCLUSION

The results of the study suggest an association of endometrial cancer occurrence with lower Cu and Zn serum levels.

Catalytic Mechanism of Collagen Hydrolysis by Zinc(II)-Dependent Matrix Metalloproteinase-1

Human matrix metalloproteinase-1 (MMP-1) is a zinc(II)-dependent enzyme that catalyzes collagenolysis. Despite the availability of extensive experimental data, the mechanism of MMP-1-catalyzed collagenolysis remains poorly understood due to the lack of experimental structure of a catalytically productive enzyme-substrate complex of MMP-1. In this study, we apply molecular dynamics and combined quantum mechanics/molecular mechanics to reveal the reaction mechanism of MMP-1 based on a computationally modeled structure of the catalytically competent complex of MMP-1 that contains a large triple-helical peptide substrate. Our proposed mechanism involves the participation of an auxiliary (second) water molecule (wat2) in addition to the zinc(II)-coordinated water (wat1). The reaction initiates through a proton transfer to Glu219, followed by a nucleophilic attack by a zinc(II)-coordinated hydroxide anion nucleophile at the carbonyl carbon of the scissile bond, leading to the formation of a tetrahedral intermediate (IM2). The process continues with a hydrogen-bond rearrangement to facilitate proton transfer from wat2 to the amide nitrogen of the scissile bond and, finally, C-N bond cleavage. The calculations indicate that the rate-determining step is the water-mediated nucleophilic attack with an activation energy barrier of 22.3 kcal/mol. Furthermore, the calculations show that the hydrogen-bond rearrangement/proton-transfer step can proceed in a consecutive or concerted manner, depending on the conformation of the tetrahedral intermediate, with the consecutive mechanism being energetically preferable. Overall, the study reveals the crucial role of a second water molecule and the dynamics for effective MMP-1-catalyzed collagenolysis.

Transition Metal Complexes as Antimalarial Agents: A Review

In antimalarial drug development research, overcoming drug resistance has been a major challenge for researchers. Nowadays, several drugs like chloroquine, mefloquine, sulfadoxine, and artemisinin are used to treat malaria. But increment in drug resistance has pushed researchers to find novel drugs to tackle drug resistance problems. The idea of using transition metal complexes with pharmacophores as ligands/ligand pendants to show enhanced antimalarial activity with a novel mechanism of action has gained significant attention recently. The advantages of metal complexes include tunable chemical/physical properties, redox activity, avoiding resistance factors, etc. Several recent reports have successfully demonstrated that the metal complexation of known organic antimalarial drugs can overcome drug resistance by showing enhanced activities than the parent drugs. This review has discussed the fruitful research works done in the past few years falling into this criterion. Based on transition metal series (3d, 4d, or 5d), the antimalarial metal complexes have been divided into three broad categories (3d, 4d, or 5d metal-based), and their activities have been compared with the similar control complexes as well as the parent drugs. Furthermore, we have also commented on the potential issues and their possible solution for translating these metal-based antimalarial complexes into the clinic.

The Potential for the Use of Edible Insects in the Production of Protein Supplements for Athletes

Several types of proteins are used in athletes' supplementation; nevertheless, given the problem of protein deficiency in the world and the growing need for ecological sources of protein, it is very interesting to study the quality of alternative protein sources, such as insect protein. This study investigated the nutritional value, micronutrient content, amino acid profile, and chemical score of banded cricket protein quality in the form of flour, defatted flour, and a protein preparation, as well as popular commercial protein supplements. In addition, in vitro digestion was performed, and the antiradical activity of the hydrolysates was compared. Generally, the defatted cricket flour was the most similar to commercial supplements regarding nutritional value because it contained 73.68% protein. Furthermore, the defatted flour was abundant in essential minerals, such as iron (4.59 mg/100 g d.w.), zinc (19.01 mg/100 g d.w.), and magnesium (89.74 mg/100 g d.w.). However, the protein preparation had an amino acid profile more similar to that of commercial supplements (total content of 694 mg/g protein). The highest antiradical activity against ABTS·+ was noted for the defatted flour (0.901 mM TE/100 g) and against DPPH· for the cricket flour (2.179 mM TE/100 g). Therefore, cricket can be considered an organic protein source for the production of valuable protein supplements.

Molecular insights into LINC complex architecture through the crystal structure of a luminal trimeric coiled-coil domain of SUN1

The LINC complex, consisting of interacting SUN and KASH proteins, mechanically couples nuclear contents to the cytoskeleton. In meiosis, the LINC complex transmits microtubule-generated forces to chromosome ends, driving the rapid chromosome movements that are necessary for synapsis and crossing over. In somatic cells, it defines nuclear shape and positioning, and has a number of specialised roles, including hearing. Here, we report the X-ray crystal structure of a coiled-coiled domain of SUN1's luminal region, providing an architectural foundation for how SUN1 traverses the nuclear lumen, from the inner nuclear membrane to its interaction with KASH proteins at the outer nuclear membrane. In combination with light and X-ray scattering, molecular dynamics and structure-directed modelling, we present a model of SUN1's entire luminal region. This model highlights inherent flexibility between structured domains, and raises the possibility that domain-swap interactions may establish a LINC complex network for the coordinated transmission of cytoskeletal forces.

Roles of Cysteine Proteases in Biology and Pathogenesis of Parasites

Cysteine proteases, also known as thiol proteases, are a class of nucleophilic proteolytic enzymes containing cysteine residues in the enzymatic domain. These proteases generally play a pivotal role in many biological reactions, such as catabolic functions and protein processing, in all living organisms. They specifically take part in many important biological processes, especially in the absorption of nutrients, invasion, virulence, and immune evasion of parasitic organisms from unicellular protozoa to multicellular helminths. They can also be used as parasite diagnostic antigens and targets for gene modification and chemotherapy, as well as vaccine candidates, due to their species and even life-cycle stage specificity. This article highlights current knowledge on parasitic cysteine protease types, biological functions, and their applications in immunodiagnosis and chemotherapy.

Human papillomavirus infection, cervical cancer and the less explored role of trace elements

Cervical cancer is an aggressive type of cancer affecting women worldwide. Many affected individuals rely on smear tests for the diagnosis, surgery, chemotherapy, or radiation for their treatment. However, due to a broad set of undesired results and side-effects associated with the existing protocols, the search for better diagnostic and therapeutic interventions is a never-ending pursuit. In the purview, the bio-concentration of trace elements (copper, selenium, zinc, iron, arsenic, manganese, and cadmium) is seen to fluctuate during the occurrence of cervical cancer and its progression from pre-cancerous to metastatic nature. Thus, during the occurrence of cervical cancer, the detection of trace elements and their supplementation will prove to be highly advantageous in developing diagnostic tools and therapeutics, respectively. This review provides a detailed overview of cervical cancer, its encouragement by human papillomavirus infections, the mechanism of pathology, and resistance. Majorly, the review emphasizes the less explored role of trace elements, their contribution to the growth and inhibition of cervical cancer. Numerous clinical trials have been listed, thereby providing a comprehensive reference to the exploration of trace elements in the management of cervical cancer.

Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones

The de novo design of functional proteins requires specification of tertiary structure and incorporation of molecular binding sites. Here, we develop an inside-out design strategy in the molecular modeling program Rosetta that begins with amino acid side chains from one or two α-helices making well-defined contacts with a ligand. A full-sized protein is then built around the ligand by adding additional helices that promote the formation of a protein core and allow additional contacts with the ligand. The protocol was tested by designing 12 zinc-binding proteins, each with 4-5 helices. Four of the designs were folded and bound to zinc with equilibrium dissociation constants varying between 95 nM and 1.1 μM. The design with the tightest affinity for zinc, N12, adopts a unique conformation in the folded state as assessed with nuclear magnetic resonance (NMR) and the design model closely matches (backbone root-mean-square deviation (RMSD) < 1 Å) an AlphaFold model of the sequence. Retrospective analysis with AlphaFold suggests that the sequences of many of the failed designs did not encode the desired tertiary packing.

An Engineered β-Hairpin Peptide Forming Thermostable Complexes with ZnII , NiII , and CuII through a His3 Site

The three-dimensional structure of a peptide, which determines its function, can denature at elevated temperatures, in the presence of chaotropic reagents, or in organic solvents. These factors limit the applicability of peptides. Herein, we present an engineered β-hairpin peptide containing a His₃ site that forms complexes with Zn^II , Ni^II , and Cu^II . Circular dichroism spectroscopy shows that the peptide-metal complexes exhibit melting temperatures up to 80 °C and remain folded in 6 M guanidine hydrochloride as well as in organic solvents. Intrinsic fluorescence titration experiments were used to determine the dissociation constants of metal binding in the nano- to sub-nanomolar range. The coordination geometry of the peptide-Cu^II complex was studied by EPR spectroscopy, and a distorted square planar coordination geometry with weak interactions to axial ligands was revealed. Due to their impressive stability, the presented peptide-metal complexes open up interesting fields of application, such as the development of a new class of peptide-metal catalysts for stereoselective organic synthesis or the directed design of extremophilic β-sheet peptides.

Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1

Metalloproteinase-1 (MMP-1) catalyzed collagen degradation is essential for a wide variety of normal physiological processes, while at the same time contributing to several diseases in humans. Therefore, a comprehensive understanding of this process is of great importance. Although crystallographic and spectroscopic studies provided fundamental information about the structure and function of MMP-1, the precise mechanism of collagen degradation especially considering the complex and flexible structure of the substrate, remains poorly understood. In addition, how the protein environment dynamically reorganizes at the atomic scale into a catalytically active state capable of collagen hydrolysis remains unknown. In this study, we applied experimentally-guided multiscale molecular modeling methods including classical molecular dynamics (MD), well-tempered (WT) classical metadynamics (MetD), combined quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM MetD simulations to explore and characterize the early catalytic events of MMP-1 collagenolysis. Importantly the study provided a complete atomic and dynamic description of the transition from the open to the closed form of the MMP-1•THP complex. Notably, the formation of catalytically active Michaelis complex competent for collagen cleavage was characterized. The study identified the changes in the coordination state of the catalytic zinc(II) associated with the conformational transformation and the formation of catalytically productive ES complex. Our results confirm the essential role of the MMP-1 catalytic domain's α-helices (hA, hB and hC) and the linker region in the transition to the catalytically competent ES complex. Overall, the results provide unique mechanistic insight into the conformational transformations and associated changes in the coordination state of the catalytic zinc(II) that would be important for the design of effective MMP-1 inhibitors.

Antimicrobial Agents Based on Metal Complexes: Present Situation and Future Prospects

The rise in antimicrobial resistance is a cause of serious concern since the ages. Therefore, a dire need to explore new antimicrobial entities that can combat against the increasing threat of antibiotic resistance is realized. Studies have shown that the activity of the strongest antibiotics has reduced drastically against many microbes such as microfungi and bacteria (Gram-positive and Gram-negative). A ray of hope, however, was witnessed in early 1940s with the development of new drug discovery and use of metal complexes as antibiotics. Many new metal-based drugs were developed from the metal complexes which are potentially active against a number of ailments such as cancer, malaria, and neurodegenerative diseases. Therefore, this review is an attempt to describe the present scenario and future development of metal complexes as antibiotics against wide array of microbes.

Evaluation of nutrients in bread: a systematic review

Background

A balanced and optimized amount of nutrients in bread, which is the main food in many countries, is necessary to maintain human health. Considering the importance of nutritional values of bread in the food basket of Iranian households, the purpose of this study was to determine the nutrients and their concentrations in breads consumed in Iran.

Methods

This systematic review study was performed to determine the types of nutrients in breads consumed in Iran by searching reputable international databases including Scopus and Google scholar, PubMed, Science direct, ISI (Web of Science). Data were collected according to inclusion and exclusion criteria and by searching for relevant keywords, emphasizing the types of nutrients in breads consumed in Iran. Qualitative data were collected using the standard PRISMA checklist (preferential reporting items for systematic reviews and meta-analysis). After verifying the quality of the articles, the information was entered into a checklist such as the name of the first author and year of publication of the research, type of study, number of samples, type of nutrition, type of bread and amount of nutrition measured.

Results

After reviewing the information and quality of articles, 10 articles were qualified for systematic review. The review of the articles showed that different breads were experimented, including: Sangak, Barbari, Taftoon, Lavash, French and local bread. The highest number of experimented bread samples was Sangak. Examination of the articles showed that 6 nutrients were experimented in different breads such as Fe, K, Mg, Ca, Cu and Zn. The highest number of experimented in breads was related to the amount of Zn (13 times) and Cu (10 times), respectively. The results of quality assessment of articles showed that most of the studies were of good quality. The results of articles on the amount of nutrients measured in different breads showed that only in two articles the amount of nutrients was reported to be desirable. In most articles, the amount of nutrients in breads was reported to be lower or higher than standard.

Conclusion

The results of this study showed that the concentration of nutrients in most articles was undesirable. It is suggested that optimal methods of enrichment of breads and flours be done with interdisciplinary cooperation between food hygiene, environmental health, nutrition, farmers and bakers. It is recommended that food hygiene and environmental health researchers investigate other nutrients (including phosphorus, selenium, manganese, boron and molybdenum) in breads and other staple foods used by people to constructive and practical measures to increase public health.

Assessment of Serum Zinc and Selenium Levels in Children with COVID-19

Objective Zinc and selenium levels are being investigated with increasing frequency in adult patients with coronavirus disease 2019 (COVID-19). However, levels of zinc and selenium in children with COVID-19 have not been adequately studied to date.

Methods This prospective, observational study was conducted on 146 pediatric patients diagnosed with COVID-19 and 49 healthy controls between 2020 and 2021. Normal serum zinc reference values were 0.60 to 1.20 µg/mL for children 0 to 10 years old and 0.66 to 1.10 µg/mL for children ≥11 years old. The normal range for serum selenium concentration was considered between 70 and 150 µg/L. Deficiencies were defined for values below the reference range.

Results Zinc and selenium levels were significantly lower in the COVID-19 (+) group compared with the controls (zinc: 0.7 ± 0.2 vs 0.9 ± 0.2 µg/mL, p < 0.001; selenium: 57.1 ± 9.1 vs 66.5 ± 11.4 µg/L, p < 0.01, respectively). Also, zinc and selenium levels were found to be statistically significantly lower in the hospitalized group compared with the outpatient group (zinc: 0.6 ± 0.2 vs 0.8 ± 0.2 µg/mL, p < 0.001; selenium: 52.1 ± 9.6 vs 58.8 ± 8.3 µg/L, p < 0.001). In the receiver operating characteristic curve analysis, selenium levels with a cutoff value of 55.50 µg/L, with 75% sensitivity and 70% specificity, and zinc levels with a cutoff value of 0.7 µg/mL, with 56% sensitivity and 53% specificity, predicted hospitalization.

Conclusion Our data showed that serum zinc and selenium levels were significantly lower in patients with COVID-19 compared with healthy control group. Also, zinc and selenium levels were found to be lower in the hospitalized group compared with the outpatient COVID-19 group.

Viscosity increase/gelation of therapeutic IgG monoclonal antibodies induced by Zn2+: one possible root cause of clogging of staked-in-needle prefilled syringes

We investigated the elution of zinc ions (Zn²⁺) from the elastomer of rigid needle shields (RNS) attached to staked-in-needle prefilled syringes (SIN-PFS) and the physicochemical impacts of Zn²⁺ on therapeutic IgG monoclonal antibody (mAb) solutions. The elution of metal ions from typical RNS elastomer under realistic buffer and storage conditions was investigated by inductively coupled plasma-mass spectrometry. Among the metal ions examined, only Zn²⁺ was detected. The elution of Zn²⁺ from RNS elastomer was found to be buffer-dependent. We investigated the influence of Zn²⁺ on the viscosity of seven mAb solutions at 180 mg/mL. The effect of Zn²⁺ clearly depended on antibody type. Drastic increases in viscosity or gelation were observed in four out of the seven mAbs. Dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) showed the effect of Zn²⁺ on mAb viscosity was explained by the colloidal destabilization of mAb solutions. Thus, Zn²⁺ leaching from RNS elastomer may possibly increase viscosity or cause gelation, and consequently cause possible needle clogging during long-term storage. DLS and SAXS can predict reactivity of mAbs to Zn²⁺, and require only small amounts of samples. This makes it possible to predict compatibility with RNS elastomer and evaluate needle clogging risk in SIN-PFSs in the early stages of mAb development.

Bioactive Compounds and Therapeutics from Fish: Revisiting Their Suitability in Functional Foods to Enhance Human Wellbeing

Global public awareness about fish-based diet and its health/nutritional benefits is on the rise. Fish nutritional profile projects promising bioactive and other compounds with innumerable health benefits for human wellbeing. As various reported researches involving fish/marine-derived molecules reveal promising attributes, and as the position of fish-based nutrients as nutraceuticals continue to strengthen, health challenges still confront communities worldwide, from cardiovascular disease, diabetes, and obesity to hypertension. Thus, further understanding of fish-based nutrient impact as functional foods remains crucial given the diverse prevailing compositional/nutraceutical merits. In this review, therefore, we provide important information regarding bioactive compounds and therapeutics obtained from fish, specific to the context of their suitability in functional foods to enhance human health. This contribution is hereby constructed as follows: (a) fish nutraceutical/therapeutic components, (b) constituents of fish-based nutrients and their suitability in functional foods, (c) fish antioxidant/bioactive compounds to help alleviate health conditions, (d) common human ailments alleviated by fish-based nutrients, and (e) role of fish in mental health and immune system. As increased fish consumption should be encouraged, the potential of the quality proteins, omega-3 fatty acids, and other compounds inherent in fish should steadily be harnessed.

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.

Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses

In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.

Onion Peel Waste Mediated-Green Synthesis of Zinc Oxide Nanoparticles and Their Phytotoxicity on Mung Bean and Wheat Plant Growth

Nanoparticles and nanomaterials have gained a huge amount of attention in the last decade due to their unique and remarkable properties. Metallic nanoparticles like zinc oxide nanoparticles (ZnONPs) have been used very widely as plant nutrients and in wastewater treatment. Here, ZnONPs were synthesized by using onion peel and characterized by various sophisticated instruments like Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and field emission scanning electron microscopes (FESEM). FTIR confirmed ZnONPs synthesis due to the formation of the band in the region of 400-800 cm^-1, while FESEM confirmed the spherical shape of the particles whose size varies in the range of 20-80 nm. FTIR revealed several bands from 1000-1800 cm^-1 which indicates the capping by the organic molecules on the ZnONPs, which came from onion peel. It also has carbonyl and hydroxyl groups, due to the organic molecules present in the Allium cepa peel waste. The average hydrodynamic size of ZnONPs was 500 nm as confirmed by DLS. The synthesized ZnONPs were then used as a plant nutrient where their effect was evaluated on the growth of Vigna radiate (mung bean) and Triticum aestivum (wheat seeds). The results revealed that the germination and seedling of mung and wheat seeds with ZnONPs were grown better than the control seed. However, seeds of mung and wheat with ZnONPs at median concentration exposure showed an enhancement in percent germination, root, and shoot length in comparison to control. Thus, the effect of ZnONPs has been proved as a nano-based nutrient source for agricultural purposes.

Regulation of zinc-dependent enzymes by metal carrier proteins

Zn²⁺ ions are essential in many physiological processes, including enzyme catalysis, protein structural stabilization, and the regulation of many proteins. The affinities of proteins for Zn²⁺ ions span several orders of magnitude, with catalytic Zn²⁺ ions generally held more tightly than structural or regulatory ones. Metal carrier proteins, most of which are not specific for Zn²⁺, bind these ions with a broad range of affinities that overlap those of catalytic, structural, and regulatory Zn²⁺ ions and are thought to be responsible for distributing the metal through most cells, tissues, and fluid compartments. While little is known about how many proteins obtain or release these ions, there is now considerable experimental evidence suggesting that metal carrier proteins may be responsible for transferring metals to and from some Zn²⁺-dependent proteins, thus serving as a major regulatory factor for them. In this review, the biological roles of Zn²⁺ and structures of Zn²⁺ binding sites are examined, and experimental evidence demonstrating the direct participation of metal carrier proteins in enzyme regulation is discussed. Mechanisms of metal ion transfer are also offered, and the potential physiological significance of this phenomenon is explored.

Switchable Zinc(II)-Responsive Globular β-Sheet Peptide

The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His₃-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pK_a of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.

New thiosemicarbazone-based Zinc(II) complexes. In vitro cytotoxicity competing with cisplatin on malignant melanoma A375 cells and its relation to neuraminidase inhibition

New thiosemicarbazone-based zinc(II) complexes were synthesized to study their cytotoxicity on A375 malignant melanoma cells. The complexes containing salicylidene (Zn1a), 3-methoxy-salicylidene (Zn1b) or 4-methoxy-salicylidene (Zn1c) moiety were characterized by analytical and spectroscopic methods. Anticancer potential of the complexes was determined by MTT test and HUVEC endothelial cells line was used to comprehend the effect on normal cells. Zn1b with an IC₅₀ of 13 μM was found to be highly cytotoxic against A375 cancer cells, more effective than cisplatin (IC₅₀: 37 μM). Zn1a and Zn1c did not have a negative effect on cell viability in the normal cells and gave the impression that they are more advantageous than cisplatin in this respect. Further, the ability of Zn1a-c to inhibit neuraminidase enzyme and its role in cytotoxicity was discussed. The test revealed that the Zn1b with 3-methoxy substituent exhibited higher inhibition activity against the neuraminidase than the Zn1a and Zn1c as analogical to the cytotoxicity results. In neuraminidase inhibition, IC₅₀ values of Zn1b and Zn1c were 14 and 66 μM, respectively. These concentrations were very close to the cytotoxicity concentrations for Zn1b and Zn1c. The findings may indicate the role of neuraminidase enzyme inhibition in cell death for Zn1b and Zn1c.

Benzimidazole–acid hydrazide Schiff–Mannich combo ligands enable nano–molar detection of Zn2+ via fluorescence turn–on mode from semi–aqueous medium, HuH–7 cells, and plants

Herein, we have synthesized two unsymmetrical and dipodal Schiff–Mannich combo ligands, benzoic acid (3–benzoimidazol–1–ylmethyl–2–hydroxy–5–methyl–benzylidene)–hydrazide (H2BBH) and the hydroxyl analogue, 2–hydroxy–benzoic acid (3–benzoimidazol–1–ylmethyl–2–hydroxy–5–methyl–benzylidene)–hydrazide (H3BSH) for selective detection of Zn2+ in semi–aqueous...

Identification of an optimal foldability criterion to design misfolding resistant protein

Proteins achieve their functional, active, and operative three dimensional native structures by overcoming the possibility of being trapped in non-native energy minima present in the energy landscape. The enormous and intricate interactions that play an important role in protein folding also determine the stability of the proteins. The large number of stabilizing/destabilizing interactions makes proteins to be only marginally stable as compared to the other competing structures. Therefore, there are some possibilities that they become trapped in the non-native conformations and thus get misfolded. These misfolded proteins lead to several debilitating diseases. This work performs a comparative study of some existing foldability criteria in the computational design of misfold resistant protein sequences based on self-consistent mean field theory. The foldability criteria selected for this study are E_f, Δ, and Φ that are commonly used in protein design procedures to determine the most efficient foldability criterion for the design of misfolding resistant proteins. The results suggest that the foldability criterion Δ is significantly better in designing a funnel energy landscape stabilizing the target state. The results also suggest that inclusion of negative design features is important for designing misfolding resistant proteins, but more information about the non-native conformations in terms of Φ leads to worse results compared to even simple positive design. The sequences designed using Δ show better resistance to misfolding in the Monte Carlo simulations performed in the study.

Metal Ion Interactions with mAbs: Part 2. Zinc-Mediated Aggregation of IgG1 Monoclonal Antibodies

PURPOSE

To evaluate the physical and chemical degradation of monoclonal antibodies in the presence of Zn²⁺.

METHODS

A full length IgG1 monoclonal antibody (mAb1) was formulated with various amounts of Zn²⁺. The resulting mixture was incubated for several weeks at room temperature and analyzed using a variety of biochemical techniques to look for various physical (e.g. aggregation) and chemical (e.g. fragmentation) degradation pathways.

RESULTS

mAb1 of the IgG1 subclass undergoes aggregation in the presence of Zn²⁺ in a concentration dependent manner. Up to hexamers were characterized using SEC-MALS. No fragmentation was noticed in the presence of Zn²⁺ as opposed to that found in our previous report when IgG1 mAbs were incubated in the presence of Cu²⁺ ions. Site directed mutagenesis indicated the involvement of Fc histidine (His 310) in Zn²⁺ mediated aggregation.

CONCLUSIONS

A novel metal ion mediated isodesmic aggregation mechanism was found in IgG1 class of monoclonal antibodies. Histidine residues in the Fc region were determined to be the binding site and implicated in Zn²⁺ mediated aggregation.

Zinc Biofortification in Food Crops Could Alleviate the Zinc Malnutrition in Human Health

Micronutrient malnutrition is a global health issue and needs immediate attention. Over two billion people across the globe suffer from micronutrient malnutrition. The widespread zinc (Zn) deficiency in soils, poor zinc intake by humans in their diet, low bioavailability, and health consequences has led the research community to think of an economic as well as sustainable strategy for the alleviation of zinc deficiency. Strategies like fortification and diet supplements, though effective, are not economical and most people in low-income countries cannot afford them, and they are the most vulnerable to Zn deficiency. In this regard, the biofortification of staple food crops with Zn has been considered a useful strategy. An agronomic biofortification approach that uses crop fertilization with Zn-based fertilizers at the appropriate time to ensure grain Zn enrichment has been found to be cost-effective, easy to practice, and efficient. Genetic biofortification, though time-consuming, is also highly effective. Moreover, a Zn-rich genotype once developed can also be used for many years without any recurring cost. Hence, both agronomic and genetic biofortification can be a very useful tool in alleviating Zn deficiency.

Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.

BODIPY-attached zinc(II) complexes of curcumin drug for visible light assisted photo-sensitization, cellular imaging and targeted PDT

Boron-dipyrromethene (BODIPY) based photosensitizers as porphyrinoids and curcumin as natural product possess exciting photophysical features suitable for theranostic applications, namely, imaging and photodynamic therapy (PDT). Limited aqueous solubility and insufficient physiological stability, however, reduce their efficacy significantly. We have designed a novel strategy to deliver these two unusable cytotoxins simultaneously in cancer cells and herein, report the synthesis, characterization and imaging-assisted photocytotoxicity of three zinc(II) complexes containing N³-donor dipicolylamine (dpa) ligands (L^1-3) and O,O-donor curcumin (Hcur) viz. [Zn(L¹)(cur)]Cl (1), [Zn(L²)(cur)]Cl (2) and [Zn(L³)(cur)]Cl (3), where L² and L³ have pendant fluorescent BODIPY and non-emissive di-iodo-BODIPY moieties. Metal chelation imparted remarkable biological stability (pH ∼7.4) to the respective ligands and induces significant aqueous solubility. These ternary complexes could act as replacements of the existing metalloporphyrin-based PDT photosensitizers as their visible-light photosensitizing ability is reinforced by the dual presence of blue light absorbing curcumin and green light harvesting BODIPY units. Complex 2 having emissive BODIPY unit L² and curcumin, showed mitochondria selective localization in HeLa, MCF-7 cancer cells and complex 3, the di-iodinated analogue of complex 2, exhibited type-I/II PDT activity via inducing apoptosis through mitochondrial membrane disruption in cancer cells while being significantly nontoxic in dark and to the healthy cells.

A de novo binuclear zinc enzyme with DNA cleavage activity

Metallohydrolases are broadly used throughout biology, often to catalyze the degradation of macromolecules such as DNA and proteins. Many of these enzymes function with zinc in their active site, and an important subset of these enzymes utilize a binuclear zinc active site. Mimics of these enzymes have been developed, some of which catalyze the digestion of DNA. However, the majority of the mimics that utilize zinc are small molecules, and most are mononuclear. Herein, we report DNA cleavage activity by the de novo designed Due Ferri single-chain (DFsc) protein containing a binuclear zinc active site. This binuclear zinc-protein complex is able to digest plasmid DNA at rates up to 50 ng/h, and these cleavage rates are affected by changes to amino acid residues near the zinc-binding site. These results indicate that the DFsc scaffold is a good model system to carry out careful structure-function relationship studies to understand key structural features that influence reactivity in natural binuclear zinc hydrolases, as it is the first report of a binuclear model system in a protein scaffold.

A combined experimental and theoretical rationalization of an unusual zinc(ii)-mediated conversion of 18-membered Schiff-base macrocycles to 18-membered imine–amine macrocycles with imidazolidine side rings: an investigation of their bio-relevant catalytic activities

Macrocyclic Zn(ii)-based Schiff base complexes exhibit significant phosphatase-like activity as well as high potential anticancer activity against breast cancer cells.

New Antimicrobial Strategies Based on Metal Complexes

Traditional organic antimicrobials mainly act on specific biochemical processes such as replication, transcription and translation. However, the emergence and wide spread of microbial resistance is a growing threat for human beings. Therefore, it is highly necessary to design strategies for the development of new drugs in order to target multiple cellular processes that should improve their efficiency against several microorganisms, including bacteria, viruses or fungi. The present review is focused on recent advances and findings of new antimicrobial strategies based on metal complexes. Recent studies indicate that some metal ions cause different types of damages to microbial cells as a result of membrane degradation, protein dysfunction and oxidative stress. These unique modes of action, combined with the wide range of three-dimensional geometries that metal complexes can adopt, make them suitable for the development of new antimicrobial drugs.

Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites

To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb₅₆₂ ) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb₅₆₂ surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)_3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2)₃ and (TriCyt3)₃ with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.

Probing a Silent Metal: A Combined X-ray Absorption and Emission Spectroscopic Study of Biologically Relevant Zinc Complexes

As the second most common transition metal in the human body, zinc is of great interest to research but has few viable routes for its direct structural study in biological systems. Herein, Zn valence-to-core X-ray emission spectroscopy (VtC XES) and Zn K-edge X-ray absorption spectroscopy (XAS) are presented as a means to understand the local structure of zinc in biological systems through the application of these methods to a series of biologically relevant molecular model complexes. Taken together, the Zn K-edge XAS and VtC XES provide a means to establish the ligand identity, local geometry, and metal-ligand bond lengths. Experimental results are supported by correlation with density-functional-theory-based calculations. Combining these theoretical and experimental approaches will enable future applications to protein systems in a predictive manner.

Contributions of primary coordination ligands and importance of outer sphere interactions in UFsc, a de novo designed protein with high affinity for metal ions

Metalloproteins constitute nearly half of all proteins and catalyze some of the most complex chemical reactions. Recently, we reported a design of 4G-UFsc (Uno Ferro single chain), a single chain four-helical bundle with extraordinarily high (30 pM) affinity for zinc. We evaluated the contribution of different side chains to binding of Co(II), Ni(II), Zn(II) and Mn(II) using systematic mutagenesis of the amino acids that constitute the primary metal coordination and outer spheres. The binding affinity of proteins for metals was then measured using isothermal titration calorimetry. Our results show that both primary metal coordination environment and side chains in the outer sphere of UFsc are highly sensitive to even slight changes and can be adapted to binding different 3d metals, including hard-to-tightly bind metal ions such as Mn(II). The studies on the origins of tight metal binding will guide future metalloprotein design efforts.

DNA Cleavage by a De Novo Designed Protein-Titanium Complex

Titanium is one of the most abundant elements on Earth but is commonly thought to have no role in biology because of its propensity to hydrolyze. Nature stabilizes hard Lewis acidic metals from hydrolysis using a variety of mechanisms, providing inspiration for how titanium can be stabilized using biological ligands. The well-characterized Due Ferri single-chain (DFsc) de novo designed protein was developed to bind and stabilize iron and provides a binding site with hard Lewis basic residues able to bind two metal ions. We demonstrate that the DFsc scaffold stably binds 2 equiv of titanium and protects them from unwanted hydrolysis. The Ti⁴⁺-DFsc protein complex was tested for its ability to hydrolytically cleave DNA, where it was seen to linearize plasmid DNA in an overnight reaction. Ti⁴⁺-DFsc is thus the first example of a functional, soluble titanium-protein complex.

How the Local Environment of Functional Sites Regulates Protein Function

Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.

Structural and functional characterizations of the C-terminal domains of CzcD proteins

Zinc is a potent antimicrobial component of the innate immune response at the host-pathogen interface. Bacteria subvert or resist host zinc insults by metal efflux pathways that include cation diffusion facilitator (CDF) proteins. The structural and functional examination of this protein class has been limited, with only the structures of the zinc transporter YiiP proteins from E. coli and Shewanella oneidensis described to date. Here, we determine the metal binding properties, solution quaternary structures and three dimensional architectures of the C-terminal domains of the metal transporter CzcD proteins from Cupriavidus metallidurans, Pseudomonas aeruginosa and Thermotoga maritima. We reveal significant diversity in the metal-binding properties and structures of these proteins and discover a potential novel mechanism for metal-promoted dimerization for the Cupriavidus metallidurans and Pseudomonas aeruginosa proteins.

Dietary zinc and growth, carcass characteristics, immune responses, and serum biochemistry of broilers

Context Zinc (Zn) is an essential trace element, and plays an important role in growth, bone formation, feathering and appetite of broilers. Accurate supplementation of this mineral is the aim of the animal husbandry. Thus, it is crucial to optimise the Zn concentration in the diet of broilers. Aims The present study was performed to investigate the effects of dietary supplementation of Zn on the growth performance, carcass characteristics, immune responses and serum biochemistry of broilers. Methods A total of 180 1-day-old male broilers (Arbor Acres) were randomly allotted by bodyweight to one of five treatments with six replicates of six birds each. The birds were fed a Zn-unsupplemented corn–soybean meal basal diet (27.75 or 26.88 mg/kg Zn by analysis) or one of the four Zn-supplemented diets, which were the basal diet supplemented with 40, 80, 120, or 160 mg Zn /kg as Zn sulfate (reagent grade ZnSO4•7H2O), for 42 days. Key results No differences were detected on growth performance or carcass characteristics among treatment groups. However, the total protein concentration and albumin concentration tended (P = 0.09) to increase with an increasing concentration of dietary Zn. The antibody titer of Newcastle disease (ND), and alkaline phosphatase (ALP) in serum on Day 21 were significantly increased (P &lt; 0.05) as the Zn supplementation increased in broiler diets. Conclusions These results indicated that dietary Zn supplementation improves the serum antibody titer of ND and ALP activity of broilers, and 86 mg Zn/kg was appropriate for broilers when fed a corn–soybean meal diet in the early stage. Implications The present results have provided scientific basis for broiler production, and accurate supplementation of Zn would effectively improve the growth performance and reduce production costs.