Coordination of Ni2+ and Cu2+ to metal ion binding domains of E. coli SlyD protein

Exploring divalent metal ion coordination. Unraveling binding modes in Staphylococcus aureus MntH fragments

Metal ion coordination is crucial in bacterial metabolism, while divalent metal ions serve as essential cofactors for various enzymes involved in cellular processes. Therefore, bacteria have developed sophisticated regulatory mechanisms to maintain metal homeostasis. These involve protein interactions for metal ion uptake, efflux, intracellular transport, and storage. Staphylococcus aureus, a member of the commensal flora, colonizes the anterior nares and skin harmlessly but can cause severe illness. MntH transporter is responsible for acquiring divalent metal ions necessary for metabolic functions and virulence. It is a 450-amino-acid protein analogous to Nramp1 (Natural Resistance-Associated Macrophage Protein 1) in mammals. Herein, the coordination modes of copper(II), iron(II), and zinc(II) ions with select fragments of the MntH were established employing potentiometry, mass spectrometry, and spectroscopic methods. Four model peptides, MNNKRHSTNE-NH2, Ac-KFDHRSS-NH2, Ac-IMPHNLYLHSSI-NH2, and Ac-YSRHNNEE-NH2, were chosen for their metal-binding capabilities and examined to determine their coordination properties and preferences. Our findings suggest that under physiological pH conditions, the N-terminal fragment of MntH demonstrates the highest thermodynamic stability with copper(II) and iron(II) ions. Furthermore, a comparison with other peptides from the S. aureus FeoB transporter indicates different binding affinities.

Microwave-Induced CuO Nanorods: A Comparative Approach between Curcumin, Quercetin, and Rutin to Study Their Antioxidant, Antimicrobial, and Anticancer Effects against Normal Skin Cells and Human Breast Cancer Cell Lines MCF-7 and T-47D

Herein, we explore the biological properties of curcumin, quercetin, and rutin by loading them onto porous CuO nanorods (NRs). The CuO NRs were synthesized using the microwave irradiation method through a chemical reaction between CuSO₄·5H₂O and NaOH in the presence of the anionic stabilizer sodium dodecyl sulfate. The shape and surface morphology of CuO NRs were examined with two microscopic techniques: high-resolution transmission electron microscopy (HR-TEM) and field emission scanning electron microscopy (FESEM). Their average diameter was measured by TEM to be 15 ± 2 nm. The porosity and interfacial area of the fabricated material were determined by Brunauer-Emmett-Teller analysis. After successful synthesis, CuO NRs were loaded with polyphenolic curcumin, quercetin, and rutin, with the loading efficiency of 57.8, 62.2, and 81.2%, respectively, which was confirmed by UV-visible and infra-red spectroscopy and finally with a thermal gravimetric technique. Their radical scavenging activity was measured with the 2,2-diphenyl-1-picrylhydrazyl radical and compared with the control (ascorbic acid). Further, good bactericidal effects were observed against both Gram-positive bacterial strains, including Staphylococcus aureus and Bacillus subtilis, and Gram-negative bacterial strains, including Salmonella typhi, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae. Excellent anticancer activity was observed against normal skin cells and breast cancer cells T-47D and MCF-7.

Metal specificity of the Ni(II) and Zn(II) binding sites of the N-terminal and G-domain of E. coli HypB

HypB is one of the chaperones required for proper nickel insertion into [NiFe]-hydrogenase. Escherichia coli HypB has two potential Ni(II) and Zn(II) binding sites-the N-terminal one and the so-called GTPase one. The metal-loaded HypB-SlyD metallochaperone complex activates nickel release from the N-terminal HypB site. In this work, we focus on the metal selectivity of the two HypB metal binding sites and show that (i) the N-terminal region binds Zn(II) and Ni(II) ions with higher affinity than the G-domain and (ii) the lower affinity G domain binds Zn(II) more effectively than Ni(II). In addition, the high affinity N-terminal domain, both in water and membrane mimicking SDS solution, has a larger affinity towards Zn(II) than Ni(II), while an opposite situation is observed at basic pH; at pH 7.4, the affinity of this region towards both metals is almost the same. The N-terminal HypB region is also more effective in Ni(II) binding than the previously studied SlyD metal binding regions. Considering that the nickel chaperone SlyD activates the release of nickel and blocks the release of zinc from the N-terminal high-affinity metal site of HypB, we may speculate that such pH-dependent metal affinity might modulate HypB interactions with SlyD, being dependent on both pH and the protein's metal status.

Zn-Enhanced Asp-Rich Antimicrobial Peptides: N-Terminal Coordination by Zn(II) and Cu(II), Which Distinguishes Cu(II) Binding to Different Peptides

The antimicrobial activity of surfactant-associated anionic peptides (SAAPs), which are isolated from the ovine pulmonary surfactant and are selective against the ovine pathogen Mannheimia haemolytica, is strongly enhanced in the presence of Zn(II) ions. Both calorimetry and ITC measurements show that the unique Asp-only peptide SAAP3 (DDDDDDD) and its analogs SAAP2 (GDDDDDD) and SAAP6 (GADDDDD) have a similar micromolar affinity for Zn(II), which binds to the N-terminal amine and Asp carboxylates in a net entropically-driven process. All three peptides also bind Cu(II) with a net entropically-driven process but with higher affinity than they bind Zn(II) and coordination that involves the N-terminal amine and deprotonated amides as the pH increases. The parent SAAP3 binds Cu(II) with the highest affinity; however, as shown with potentiometry and absorption, CD and EPR spectroscopy, Asp residues in the first and/or second positions distinguish Cu(II) binding to SAAP3 and SAAP2 from their binding to SAAP6, decreasing the Cu(II) Lewis acidity and suppressing its square planar amide coordination by two pH units. We also show that these metal ions do not stabilize a membrane disrupting ability nor do they induce the antimicrobial activity of these peptides against a panel of human pathogens.

Biophysical approaches for the study of metal-protein interactions

Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.

HENRYK - An endless source of metal coordination surprises

The basic knowledge about biological inorganic chemistry, thermodynamics and metal binding sites of metalloproteins is crucial for the understanding of their metal binding-structure-function relationship. Metal-peptide complexes are useful and commonly used models of metal-enzyme active sites, among which copper and zinc models are one of the most extensively studied. HENRYK is a peptide sequence present in numerous proteins, and serves as a potentially tempting binding site for Cu²⁺ and Zn²⁺. Maybe more importantly, HENRYK also happens to be the first name of our group leader. The results of this work, which, at the first glance, might seem to be a 'chemical scrabble', went far beyond our expectations and surprised us with a novel, uncommon behavior of a Cu²⁺ complex with a peptide with a histidine in position one. At low pH, the binding is a typical histamine-like coordination, but with the increase of pH, the imidazole nitrogen is moved to the axial position and replaced with an amide; at basic pH, the binding mode is a {NH₂, 3N^-} one in the equatorial plane. It is important to note, that no dimeric species are formed in between. Such binding is thermodynamically much more stable than a simple complex with histamine, and quite comparable to complexes with several possible imidazole anchoring sites.

Copper and nickel bind via two distinct kinetic mechanisms to a CsoR metalloregulator

The intricate interplay between polypeptide and metal ion binding underscores many of life's fundamental processes. Metalloregulators recognise and bind cognate metal ions during cellular metal stress, evoking a transcriptional response so as to maintain metal ion homeostasis. Members of the copper sensitive operon repressor (CsoR) family of metalloregulators bind to their operator DNA in the absence of a bound metal ion, but on binding Cu(I) an allosteric conformational switch is induced that causes dissociation of the bound DNA. Other divalent metal ions are capable of binding to CsoR members but do not induce the allosteric response observed with Cu(I). The thermodynamics of Cu(I) binding has been studied in this family of metalloregulators, but the binding kinetics and mechanism of Cu(I) or a non-cognate metal ion is unknown. In the present study we have used stopped-flow absorbance kinetics and site-directed variants of the CsoR from Streptomyces lividans to monitor binding of Cu(I) and non-cognate Ni(II). The variants have been designed to individually replace known metal ion binding ligands and also to test the role of a histidine residue (His103) close, but not considered part of the Cu(I) first coordination sphere. Cu(I)/Ni(II) ion displacement studies have also been investigated. The kinetic data are most consistent with the existence of two distinct mechanisms that account for Cu(I) and Ni(II) ion binding to this CsoR. In particular Ni(II) has two binding sites; one that has identical amino acid coordination as the Cu(I) binding site and the second involving His103, a residue determined here not to be involved in the mechanism of Cu(I) binding.

Synergistic effect of copper and low temperature over Listeria monocytogenes

The capacity to grow at low temperatures has allowed Listeria monocytogenes to become one of the primary food pathogens to date, representing a major public health problem worldwide. Several works have described the homeostatic response of L. monocytogenes under different copper (Cu) treatments growing at mild temperature (30 °C). The aims of this report were to evaluate if changes in the external concentration of Cu affected viability and Cu homeostasis of L. monocytogenes growing at low temperature. Ours results showed that L. monocytogenes growing at 8 °C had a reduced viability relative to 30 °C when exposed to Cu treatments. This decrease was correlated with an increase in the internal concentration of Cu, probably linked to the transcriptional down-regulation of mechanisms involved in Cu homeostasis. This combined effect of Cu and low temperature showed a synergistic impact over the viability and homeostasis of L. monocytogenes, where low temperature exacerbated the toxic effect of Cu. These results can be useful in terms of the use of Cu as an antibacterial agent.

African Viper Poly-His Tag Peptide Fragment Efficiently Binds Metal Ions and Is Folded into an α-Helical Structure

Snake venoms are complex mixtures of toxic and often spectacularly biologically active components. Some African vipers contain polyhistidine and polyglycine peptides, which play a crucial role in the interaction with metal ions during the inhibition of snake metalloproteases. Polyhistidine peptide fragments, known as poly-His tags, play many important functions, e.g., in metal ion transport in bacterial chaperon proteins. In this paper, we report a detailed characterization of Cu(2+), Ni(2+), and Zn(2+) complexes with the EDDHHHHHHHHHG peptide fragment (pHG) derived from the venom of the rough scale bush viper (Atheris squamigera). In order to determine the thermodynamic properties, stoichiometry, binding sites, and structures of the metal-pHG complexes, we used a combination of experimental techniques (potentiometric titrations, electrospray ionization mass spectrometry, UV-vis spectroscopy, circular dichroism spectroscopy, and electron paramagnetic resonance spectroscopy) and extensive computational tools (molecular dynamics simulations and density functional theory calculations). The results showed that pHG has a high affinity toward metal ions. The numerous histidine residues located along this sequence are efficient metal ion chelators with high affinities toward Cu(2+), Ni(2+), and Zn(2+) ions. The formation of an α-helical structure induced by metal ion coordination and the occurrence of polymorphic binding states were observed. It is proposed that metal ions can "move along" the poly-His tag, which serves as a metal ion transport pathway. The coordination of Cu(2+), Ni(2+), and Zn(2+) ions to the histidine tag is very effective in comparison with other histidine-rich peptides. The stabilities of the metal-pHG complexes increase in the order Zn(2+) < Ni(2+)≪ Cu(2+).

Ni²⁺ chemistry in pathogens--a possible target for eradication

The survival of all urease and/or hydrogenase containing pathogens depends on the proper homeostasis of nickel. In the scope of this perspectives paper, details of Ni(2+) metabolism of Helicobacter pylori, a widespread stomach-ulcer causing bacterium, are described. Nickel binding proteins and thermodynamics of such metal complexes are discussed in detail and special focus is given to potential nickel binding sequences in this metal's chaperones and regulators. A list of potential Ni(2+) binding sites in various pathogens is presented, which points out numerous examples of nickel interactions that still need to be understood.

Insight into the coordination and the binding sites of Cu(2+) by the histidyl-6-tag using experimental and computational tools

His-tags are specific sequences containing six to nine subsequent histydyl residues, and they are used for purification of recombinant proteins by use of IMAC chromatography. Such polyhistydyl tags, often used in molecular biology, can be also found in nature. Proteins containing histidine-rich domains play a critical role in many life functions in both prokaryote and eukaryote organisms. Binding mode and the thermodynamic properties of the system depend on the specific metal ion and the histidine sequence. Despite the wide application of the His-tag for purification of proteins, little is known about the properties of metal-binding to such tag domains. This inspired us to undertake detailed studies on the coordination of Cu(2+) ion to hexa-His-tag. Experiments were performed using the potentiometric, UV-visible, CD, and EPR techniques. In addition, molecular dynamics (MD) simulations and density functional theory (DFT) calculations were applied. The experimental studies have shown that the Cu(2+) ion binds most likely to two imidazoles and one, two, or three amide nitrogens, depending on the pH. The structures and stabilities of the complexes for the Cu(2+)-Ac-(His)6-NH2 system using experimental and computational tools were established. Polymorphic binding states are suggested, with a possibility of the formation of α-helix structure induced by metal ion coordination. Metal ion is bound to various pairs of imidazole moieties derived from the tag with different efficiencies. The coordination sphere around the metal ion is completed by molecules of water. Finally, the Cu(2+) binding by Ac-(His)6-NH2 is much more efficient compared to other multihistidine protein domains.

The specificity of interaction of Zn(2+), Ni(2+) and Cu(2+) ions with the histidine-rich domain of the TjZNT1 ZIP family transporter

The Zrt/Irt-like protein (ZIP) family contributes to the metal homeostasis by regulating the transport of divalent metal cations such as Fe(2+), Zn(2+), Mn(2+), Cd(2+) and sometimes even Cu(2+). Most ZIP members have a long variable loop between transmembrane domains (TMDs) III and IV; this region is predicted to be located in the cytoplasm and is postulated to be the metal ion binding site. In this study, we looked at the thermodynamic behavior and coordination chemistry of Zn(2+), Ni(2+) and Cu(2+) complexes with the histidine-rich domain, Ac-(185)RAHAAHHRHSH(195)-NH2 (HRD), from the yeast TjZNT1 protein, located between TMDs III and IV. The sequence is conserved also in higher species like Thlaspi japonicum. The stability of complexes increases in the series Ni(2+) < Zn(2+)≪ Cu(2+). The geometry of complexes is very different for each metal and in the case of Zn(2+) complexes, high specificity in binding is observed. Moreover, the stability of HRD-Cu(2+) complexes was compared with the five His residues containing peptide from Hpn protein (Helicobacter pylori). The results suggest a high ability of HRD in the binding of all three studied metals.

A minimalist chemical model of matrix metalloproteinases--can small peptides mimic the more rigid metal binding sites of proteins?

In order to mimic the active center of matrix metalloproteinases (MMPs), we synthesized a pentadecapeptide (Ac-KAHEFGHSLGLDHSK-NH2) corresponding to the catalytic zinc(II) binding site of human MMP-13. The multi-domain structural organization of MMPs fundamentally determines their metal binding affinity, catalytic activity and selectivity. Our potentiometric, UV-visible, CD, EPR, NMR, mass spectrometric and kinetic studies are aimed to explore the usefulness of such flexible peptides to mimic the more rigid metal binding sites of proteins, to examine the intrinsic metal binding properties of this naked sequence, as well as to contribute to the development of a minimalist, peptide-based chemical model of MMPs, including the catalytic properties. Since the multiimidazole environment is also characteristic for copper(II), and recently copper(II) containing variants of MMPs have been identified, we also studied the copper(II) complexes of the above peptide. Around pH 6-7 the peptide, similarly to MMPs, offers a {3Nim} coordination binding site for both zinc(II) and copper(II). In the case of copper(II), the formation of amide coordinated species at higher pH abolished the analogy with the copper(II) containing MMP variant. On the other hand, the zinc(II)-peptide system mimics some basic features of the MMP active sites: the main species around pH7 (ZnH2L) possesses a {3Nim,H2O} coordination environment, the deprotonation of the zinc-bound water takes place near the physiological pH, it forms relatively stable ternary complexes with hydroxamic acids, and the species ZnH2L(OH) and ZnH2L(OH)2 have notable hydrolytic activity between pH7 and 9.

Protein cohesion induced by metal ions observed with fluorescence correlation spectroscopy

Nine metal ions were evaluated in the point of denaturating action of proteins. When some metal ions were added to the diluted protein solutions, aggregates appear: stronger denaturation causes the appearance of the larger-size aggregate. The size of the aggregatates are determined by fluorescence correlation spectroscopy (FCS). Green fluorescent protein (ZsGreen) and PE(phycoerythrin)-conjugated human-antibody monoclonal protein were employed as the target protein, of which solution was diluted 100-500 times and mixed with metal ions. According to this process, the denaturation power of metal ions is in the order of Mn(2+)≈ Fe(2+)< Co(2+)< Ni(2+)< Tl(+)< Cd(2+)< Cu(+)< Cu(2+)< Pb(2+)for ZsGreen, and Tl(+)≈ Ni(2+)< Cd(2+)< Fe(2+)< Cr(3+)≪ Pb(2+)for PE-conjugated antibody protein. Pb(2+)exhibits the strongest power of denaturation. In the case of ZsGreen, the denaturation power of metal ions is on the order of the Irving-Williams series, which provide the coordination tendency against ligands possessing nitrogen and oxygen. The present method with FCS is effective to evaluate the denaturation power of metal ions against proteins.