Specific metal ion binding sites in unstructured regions of proteins

Integrative chemoproteomics reveals anticancer mechanisms of silver(i) targeting the proteasome regulatory complex

Silver compounds have favorable properties as promising anticancer drug candidates, such as low side effects, anti-inflammatory properties, and high potential to overcome drug resistance. However, the exact mechanism by which Ag(i) confers anticancer activity remains unclear, which hinders further development of anticancer applications of silver compounds. Here, we combine thermal proteome profiling, cysteine profiling, and ubiquitome profiling to study the molecular mechanisms of silver(i) complexes supported by non-toxic thiourea (TU) ligands. Through the formation of AgTU complexes, TU ligands deliver Ag+ ions to cancer cells and tumour xenografts to elicit inhibitory potency. Our chemical proteomics studies show that AgTU acts on the ubiquitin-proteasome system (UPS) and disrupts protein homeostasis, which has been identified as a main anticancer mechanism. Specifically, Ag+ ions are released from AgTU in the cellular environment, directly target the 19S proteasome regulatory complex, and may oxidize its cysteine residues, thereby inhibiting proteasomal activity and accumulating ubiquitinated proteins. After AgTU treatment, proteasome subunits are massively ubiquitinated and aberrantly aggregated, leading to impaired protein homeostasis and paraptotic death of cancer cells. This work reveals the unique anticancer mechanism of Ag(i) targeting the 19S proteasome regulatory complex and opens up new avenues for optimizing silver-based anticancer efficacy.

Metal Binding of Alzheimer's Amyloid-β and Its Effect on Peptide Self-Assembly

Metal ions have been identified as key factors modulating the aggregation of amyloid-β peptide (Aβ) implicated in Alzheimer's disease (AD). The presence of elevated levels of metal ions in the amyloid plaques in AD patients supports the notion that the dysfunction of metal homeostasis is connected to the development of AD pathology. Here, recent findings from high- and low-resolution biophysical techniques are put into perspective, providing detailed insights into the molecular structures and dynamics of metal-bound Aβ complexes and the effect of metal ions on the Aβ aggregation process. In particular, the development of theoretical kinetic models deducing different microscopic nucleation events from the macroscopic aggregation behavior has enabled deciphering of the effect of metal ions on specific nucleation processes. In addition to these macroscopic measurements of bulk aggregation to quantify microscopic rates, recent NMR studies have revealed details about the structures and dynamics of metal-Aβ complexes, thereby linking structural events to bulk aggregation. Interestingly, transition-metal ions, such as copper, zinc, and silver ions, form a compact complex with the N-terminal part of monomeric Aβ, respectively, where the metal-bound "folded" state is in dynamic equilibrium with an "unfolded" state. The rates and thermodynamic features of these exchange dynamics have been determined by using NMR relaxation dispersion experiments. Additionally, the application of specifically tailored paramagnetic NMR experiments on the Cu(II)-Aβ complex has been fruitful in obtaining structural constraints within the blind sphere of conventional NMR experiments. This enables the determination of molecular structures of the "folded" Cu(II)-coordinated N-terminal region of Aβ. Furthermore, the discussed transition-metal ions modulate Aβ self-assembly in a concentration-dependent manner, where low metal ion concentrations inhibit Aβ fibril formation, while at high metal ion concentrations other processes occur, resulting in amorphous aggregate formation. Remarkably, the metal-Aβ interaction predominately reduces one specific nucleation step, the fibril-end elongation, whereas primary and surface-catalyzed secondary nucleation mechanisms are less affected. Specific inhibition of fibril-end elongation theoretically predicts an enhanced generation of Aβ oligomers, which is an interesting contribution to understanding metal-Aβ-associated neurotoxic effects. Taken together, the metal binding process creates a metal-bound Aβ complex, which is seemingly inert to aggregation. This process hence efficiently reduces the aggregation-prone peptide pool, which on the macroscopic level is reflected as slower aggregation kinetics. Thus, the specific binding of metals to the Aβ monomer can be linked to the macroscopic inhibitory effect on Aβ bulk aggregation, providing a molecular understanding of the Aβ aggregation mechanism in the presence of metal ions, where the metal ion can be seen as a minimalist agent against Aβ self-assembly. These insights can help to target Aβ aggregation in vivo, where metal ions are key factors modulating the Aβ self-assembly and Aβ-associated neurotoxicity.

CH vs. HC-Promiscuous Metal Sponges in Antimicrobial Peptides and Metallophores

Histidine and cysteine residues, with their imidazole and thiol moieties that deprotonate at approximately physiological pH values, are primary binding sites for Zn(II), Ni(II) and Fe(II) ions and are thus ubiquitous both in peptidic metallophores and in antimicrobial peptides that may use nutritional immunity as a way to limit pathogenicity during infection. We focus on metal complex solution equilibria of model sequences encompassing Cys-His and His-Cys motifs, showing that the position of histidine and cysteine residues in the sequence has a crucial impact on its coordination properties. CH and HC motifs occur as many as 411 times in the antimicrobial peptide database, while similar CC and HH regions are found 348 and 94 times, respectively. Complex stabilities increase in the series Fe(II) < Ni(II) < Zn(II), with Zn(II) complexes dominating at physiological pH, and Ni(II) ones-above pH 9. The stabilities of Zn(II) complexes with Ac-ACHA-NH₂ and Ac-AHCA-NH₂ are comparable, and a similar tendency is observed for Fe(II), while in the case of Ni(II), the order of Cys and His does matter-complexes in which the metal is anchored on the third Cys (Ac-AHCA-NH₂) are thermodynamically stronger than those where Cys is in position two (Ac-ACHA-NH₂) at basic pH, at which point amides start to take part in the binding. Cysteine residues are much better Zn(II)-anchoring sites than histidines; Zn(II) clearly prefers the Cys-Cys type of ligands to Cys-His and His-Cys ones. In the case of His- and Cys-containing peptides, non-binding residues may have an impact on the stability of Ni(II) complexes, most likely protecting the central Ni(II) atom from interacting with solvent molecules.

New insight into scale inhibition during tea brewing: Ca2+/Mg2+ complexing and alkalinity consumption

Scale not only affects the taste and color of water, but also increases the risks of osteoporosis and cardiovascular diseases associated with drinking it. As a popular beverage, tea is rich many substances that have considerable potential for scale inhibition, including protein, tea polyphenols and organic acids. In this study, the effect of tea brewing on scale formation was explored. It was found that the proteins, catechins and organic acids in tea leaves could be released when the green tea was brewed in water with sufficient hardness and alkalinity. The tea-released protein was able to provide carboxyl groups to chelate with calcium ions (Ca²⁺), preventing the Ca²⁺ from reacting with the carbonate ions (CO₃^2-). The B rings of catechins were another important structure in the complexation of Ca²⁺ and magnesium ions (Mg²⁺). The carboxyl and hydroxyl groups on the organic acids was able to form five-membered chelating rings with Ca²⁺ and Mg²⁺, resulting in a significant decrease in Ca²⁺ from 100.0 to 60.0 mg/L. Additionally, the hydrogen ions (H⁺) provided by the organic acids consumed and decreased the alkalinity of the water from 250.0 to 131.4 mg/L, leading to a remarkable reduction in pH from 8.93 to 7.73. It further prevented the bicarbonate (HCO₃^-) from producing CO₃^2- when the water was heated. The reaction of the tea constituents with the hardness and alkalinity inhibited the formation of scale, leading to a significant decrease in turbidity from 10.6 to 1.4 NTU. Overall, this study provides information to help build towards an understanding of the scale inhibition properties of tea and the prospects of tea for anti-scaling in industrial applications.

Progress in the Development of Biosensors Based on Peptide-Copper Coordination Interaction

Copper ions, as the active centers of natural enzymes, play an important role in many physiological processes. Copper ion-based catalysts which mimic the activity of enzymes have been widely used in the field of industrial catalysis and sensing devices. As an important class of small biological molecules, peptides have the advantages of easy synthesis, excellent biocompatibility, low toxicity, and good water solubility. The peptide-copper complexes exhibit the characteristics of low molecular weight, high tenability, and unique catalytic and photophysical properties. Biosensors with peptide-copper complexes as the signal probes have promising application prospects in environmental monitoring and biomedical analysis and diagnosis. In this review, we discussed the design and application of fluorescent, colorimetric and electrochemical biosensors based on the peptide-copper coordination interaction.

Comparative Toxicity of Interferon Beta-1a Impurities of Heavy Metal Ions

Background and Objectives: Providing a proper quality control of drugs is essential for efficient treatment of various diseases minimizing the possible side effects of pharmaceutical active substances and potential impurities. Recent in vitro and in vivo studies have shown that certain heavy metalloids and metals interfere with protein folding of nascent proteins in cells and their biological function can be altered. It is unknown whether the drug impurities including heavy metals may affect the tertiary protein structure. Materials and Methods: ReciGen and Rebif are pharmaceutical interferon beta-1a (IFNβ-1a) contained in preparations that are used for parenteral administration. Heavy metal impurities of these samples have been studied by gel electrophoresis, Fourier-transform infrared spectroscopy (FTIR) and inductively coupled plasma mass spectrometry analysis (ICP MS). The concentration of heavy metals including mercury, arsenic, nickel, chromium, iron, and aluminum did not exceed permitted levels established by International Council for Harmonisation guideline for elemental impurities. Results: The ICP MS analysis revealed the presence of heavy metals, moreover zeta potential was significantly different for IFNβ-1a, which can be an indirect indication of the difference in composition of ReciGen and Rebif samples, respectively. FTIR analysis revealed very similar amide I and II bonds at 1654 and 1560 cm−1 attributed to the peptide absorption peaks of IFNβ-1a in Rebif and ReciGen. Conclusions: It was hypothesized that the IFNβ-1a complex binds heavy metals affecting the tertiary protein structure and may lead to some side effects of drug administration. Further testing of IFNβ-1a bioequivalence for parenteral application is necessary.

The effect of side chains on the complex formation processes of N-terminally free hexapeptides containing C-terminal cysteinyl functions

Ratio of isomers of 1 to 1 nickel-ligand complexes formed in equimolar systems at pH 11 (left) and pH 7 (right) showing the influence of an internal coordinating side chain.

Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules

The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.

A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding

Helicobacter pylori (H. pylori) secretes the chaperone and serine protease high temperature requirement A (HtrA) that cleaves gastric epithelial cell surface proteins to disrupt the epithelial integrity and barrier function. First inhibitory lead structures have demonstrated the essential role of HtrA in H. pylori physiology and pathogenesis. Comprehensive drug discovery techniques allowing high-throughput screening are now required to develop effective compounds. Here, we designed a novel fluorescence resonance energy transfer (FRET) peptide derived from a gel-based label-free proteomic approach (direct in-gel profiling of protease specificity) as a valuable substrate for H. pylori HtrA. Since serine proteases are often sensitive to metal ions, we investigated the influence of different divalent ions on the activity of HtrA. We identified Zn⁺⁺ and Cu⁺⁺ ions as inhibitors of H. pylori HtrA activity, as monitored by in vitro cleavage experiments using casein or E-cadherin as substrates and in the FRET peptide assay. Putative binding sites for Zn⁺⁺ and Cu⁺⁺ were then analyzed in thermal shift and microscale thermophoresis assays. The findings of this study will contribute to the development of novel metal ion-dependent protease inhibitors, which might help to fight bacterial infections.

A comparative study on the nickel binding ability of peptides containing separate cysteinyl residues

Nickel(ii) complexes of peptides CSSACS-NH2, ACSSACS-NH2, SSCSSACS-NH2 and GACAAH-NH2 have been studied by potentiometric and various spectroscopic (UV-vis, CD, NMR, and ESI-MS) techniques. All peptides have high nickel(ii) binding ability in the form of square planar complexes and the stability order of the peptides is: CSSACS-NH2 > ACSSACS-NH2 > SSCSSACS-NH2 ∼ GACAAH-NH2. The different metal binding affinities of these peptides are related to the differences in the speciation and in the binding modes of the major species. An almost exclusive formation of bis(ligand) complexes via an (NH2,S-) 5-membered chelate from the amino terminus is characteristic of CSSACS-NH2. The (NH2,N-,S-) tridentate chelate is the major coordination mode of ACSSACS-NH2 but the distant cysteine can also contribute to metal binding. The higher nickel(ii) binding ability of AC[combining low line]SSAC[combining low line]S-NH2 relative to the peptides containing an N-terminal XY-Cys motif may have important biological consequences. For example, the occurrence of the (NH2,N-,S-,S-) donor set is a common feature of both the ACSSACS-NH2 ligand and the nickel(ii) binding loop of the NiSOD enzyme (HC[combining low line]DLPC[combining low line]G…..,). In the case of SSCSSACS-NH2 and GACAAH-NH2 the amino terminus of one peptide can completely saturate the coordination sphere of the nickel(ii) ion via the formation of the (NH2,N-,N-,S-) binding mode. This rules out the formation of bis(ligand) complexes and any contribution of the distant cysteine or histidine to nickel(ii) binding in the 1 : 1 complexes. On the other hand the distant cysteine of SSCSSACS-NH2 and histidine of GACAAH-NH2 can behave as independent metal binding sites for the formation of dinuclear complexes in the presence of excess metal ions.

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.

Strong Uranium(VI) Binding onto Bovine Milk Proteins, Selected Protein Sequences, and Model Peptides

Hexavalent uranium is ubiquitous in the environment. In view of the chemical and radiochemical toxicity of uranium(VI), a good knowledge of its possible interactions in the environment is crucial. The aim of this work was to identify typical binding and sorption characteristics of uranium(VI) with both the pure bovine milk protein β-casein and diverse related protein mixtures (caseins, whey proteins). For comparison, selected model peptides representing the amino acid sequence 13-16 of β-casein and dephosphorylated β-casein were also studied. Complexation studies using potentiometric titration and time-resolved laser-induced fluorescence spectroscopy revealed that the phosphoryl-containing proteins form uranium(VI) complexes of higher stability than the structure-analog phosphoryl-free proteins. That is in agreement with the sorption experiments showing a significantly higher affinity of caseins toward uranium(VI) in comparison to whey proteins. On the other hand, the total sorption capacity of caseins is lower than that of whey proteins. The discussed binding behavior of milk proteins to uranium(VI) might open up interesting perspectives for sustainable techniques of uranium(VI) removal from aqueous solutions. This was further demonstrated by batch experiments on the removal of uranium(VI) from mineral water samples.

Molecularly engineered metal-based bioactive soft materials - Neuroactive magnesium ion/polymer hybrids

The development of bioactive soft materials that can guide cell behavior and have biomimetic mechanical properties is an active and challenging topic in regenerative medicine. A common strategy to create a bioactive soft material is the integration of biomacromolecules with polymers. However, limited by their complex structures and sensitivity to temperature and chemicals, it is relatively difficult to maintain the bioactivity of biomacromolecules during their preparation, storage, and application. Here, a new kind of bioactive soft material based on the molecular integration of metal ions and polymers is designed and exemplified by a hybrid of magnesium ion (Mg²⁺) and poly(glycerol-sebacate-maleate) (PGSM-Mg). Mg²⁺ was firmly incorporated into PGSM molecules through a complexation interaction as evidenced by X-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared spectroscopy (FTIR). The PGSM matrix provided the soft nature and facile processing of the hybrid, which could serve as an injectable material and be fabricated into elastic porous three-dimensional (3D) scaffolds. The Mg²⁺ immobilized in the PGSM chain conferred neuroactivity to the resultant hybrid. PGSM-Mg exhibited adequate biodegradability and a sustained release of Mg²⁺. PGSM-Mg 3D scaffolds promoted the adhesion and proliferation of Schwann cells (SCs) more effectively than poly(lactic-co-glycolic acid) (PLGA) scaffolds. Furthermore, SCs on PGSM-Mg scaffolds expressed significantly more neural specific genes than those on PLGA, PGS, and PGSM, including nerve growth factor (NGF) and neurotrophic factor-3 (NTF3). All these results indicated that Mg²⁺ immobilized through molecular integration could efficiently regulate the bioactivity of polymers. In view of the wide availability, diverse bioactivity, and high stability of metal ions, the strategy of molecular coupling of metal ions and polymers is expected to be a new general approach to construct bioactive soft materials. STATEMENT OF SIGNIFICANCE: Bioactive soft materials are designed on the basis of the molecular integration of metal ions and polymers. Immobilized metal ions offer a new way to endow bioactivity to polymers. Different from biomolecules such as proteins and genes, metal ions are quite stable and can resist harsh processing conditions. Further, the polymeric matrix provides the soft nature and facile processing of the hybrid. Different from stiff metal-containing inorganic materials, the hybrid is a biomimetic soft material and can be readily processed just like its polymer precursor under mild conditions. In view of the diversity of metal ions and polymers, this strategy is expected to be a new powerful and general approach to construct bioactive soft materials for a wide range of biomedical applications.

An attempt to elucidate the role of iron and zinc ions in development of Alzheimer's and Parkinson's diseases

Neurodegenerative disorders are among the most studied issues both in medicine and pharmacy. Despite long and extensive research, there is no effective treatment prescribed for such diseases, including Alzheimer's or Parkinson's. Available data exposes their multi-faceted character that requires a complex and multidirectional approach to treatment. In this case, the most important challenge is to understand the neurodegenerative mechanisms, which should permit the development of more elaborate and effective therapies. In the submitted review, iron and zinc are discussed as important and perfectly possible neurodegenerative factors behind Alzheimer's and Parkinson's diseases. It is commonly known that these elements are present in living organisms and are essential for the proper operation of the body. Still, their influence is positive only when their proper balance is maintained. Otherwise, when any imbalance occurs, this can eventuate in numerous disturbances, among them oxidative stress, accumulation of amyloid β and the formation of neurofibrillary tangles, let alone the increase in α-synuclein concentration. At the same time, available research data reveals certain discrepancies in approaching metal ions as either impassive, helpful, or negative factors influencing the development of neurodegenerative changes. This review outlines selected neurodegenerative disorders, highlights the role of iron and zinc in the human body and discusses cases of their imbalance leading to neurodegenerative changes as shown in vitro and in vivo studies as well as through relevant mechanisms.

Synergistic effects of metal-induced aggregation of human serum albumin

Exposure to cobalt (Co), chromium (Cr), and nickel (Ni) occurs often via skin contact and from different dental and orthopedic implants. The metal ions bind to proteins, which may induce structural changes and aggregation, with different medical consequences. We investigated human serum albumin (HSA) aggregation in the presence of Co^II, Cr^III, and/or Ni^II ions and/or their nanoparticle precipitates by using scattering, spectroscopic, and imaging techniques, at simulated physiological conditions (phosphate buffered saline - PBS, pH 7.3) using metal salts that did not affect the pH, and at HSA:metal molar ratios of up to 1:8. Co ions formed some solid nanoparticles in PBS at the investigated conditions, as determined by nanoparticle tracking analysis, but the Cr^III anions and Ni^II ions remained fully soluble. It was found that all metal ions induced HSA aggregation, and this effect was significantly enhanced when a mixture of all three metal ions was present instead of any single type of ion. Thus, the metal ions induce aggregation synergistically. HSA aggregates formed linear structures on a mica surface in the presence of Cr^III ions. A clear tendency of aggregation and linearly aligned aggregates was seen in the presence of all three metal ions. Spectroscopic investigations indicated that the majority of the HSA molecules maintained their alpha helical secondary structure and conformation. This study highlights the importance of synergistic effects of metal ions and/or their precipitates on protein aggregation, which are highly relevant for implant materials and common exposures to metals.

Binding of Divalent Metal Ions with Deprotonated Peptides: Do Gas-Phase Anions Parallel the Condensed Phase?

Chelation complexes of the histidine-containing tripeptides HisAlaAla, AlaHisAla, and AlaAlaHis with Ni(II) and Cu(II) having a −1 net charge are characterized in the gas phase by infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory calculations. We address the question of whether the gas-phase complexes carry over characteristics from the corresponding condensed-phase species. We focus particularly on three aspects of their structure: (i) square-planar chelation by the deprotonated amide nitrogens around the metal ion (low-spin for the Ni case), (ii) metal-ion coordination of the imidazole side chain nitrogen, and (iii) the exceptional preference for metal-ion chelation by peptides with His in the third position from the N-terminus, as in the amino terminal Cu and Ni (ATCUN) motif. We find that square-planar binding around the metal ion, involving bonds to both deprotonated backbone nitrogens, one of the carboxylate oxygens and the N-terminal nitrogen, is the dominant binding motif for all three isomers. In contrast to the condensed-phase behavior, the dominant mode of binding for all three isomers does not involve the imidazole side chain, which is instead placed outside the coordination zone. Only for the AlaAlaHis isomer, the imidazole-bound structure is also detected as a minority population, as identified from a distinctive short-wavelength IR absorption. The observation that this conformation exists only for AlaAlaHis correlates with condensed-phase behavior at neutral-to-basic pH, in the sense that the isomer with His in the third position is exceptionally disposed to metal ion chelation by four nitrogen atoms (4N) when compared with the other isomers. These results also emphasize the divergence between the conformational stabilities in the gas phase and in solution or crystalline environments: in the gas phase, direct metal binding of the imidazole is overall less favorable than the alternative of a remote imidazole that can act as an intramolecular H-bond donor enhancing the gas-phase stability.

Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein

Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.

Antimicrobial peptide–metal ion interactions – a potential way of activity enhancement

We discuss the potential correlation between the antimicrobial peptide–metal binding mode, structure, thermodynamics and mode of action.

Ni(II) interaction with a peptide model of the human TLR4 ectodomain

Ni(II) stimulates innate immunity via the direct binding to human Toll Like Receptor 4 (hTLR4), the bacterial lypopolysaccharide receptor. The binding is specific for humans and causes nickel contact allergy. The protein sequence analysis of hTLR4 revealed that the ectodomain, the region supposed to coordinate the metal ions, contains a histidine-rich motif that is not conserved among all organisms. To elucidate the role of each histidine residue on the protein-nickel binding, we examined the formation of Ni(II) complexes with the model peptide NH₂-FQHSNRKQMSERSVFRSRRNRIYRDISHTHTR-COO^-, which encompasses the sequence 429-460 of hTLR4. The amino acid sequence of the peptide has been modified by the substitution of some selected lipophilic residues (Leu and Phe) with hydrophilic residues (Arg), aiming at increasing the peptide hydro solubility of the protein fragment. Potentiometric, ultraviolet-visible (UV-vis), nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements demonstrate that the non-conserved histidines in the ectodomain cooperate in metal coordination and consequently enable the activation of the molecular mechanism of nickel hypersensitivity reaction.

Binding patterns of homo-peptides on bare magnetic nanoparticles: insights into environmental dependence

Magnetic nanoparticles (MNP) are intensively investigated for applications in nanomedicine, catalysis and biotechnology, where their interaction with peptides and proteins plays an important role. However, the characterisation of the interaction of individual amino acids with MNP remains challenging. Here, we classify the affinity of 20 amino acid homo-hexamers to unmodified iron oxide nanoparticles using peptide arrays in a variety of conditions as a basis to identify and rationally design selectively binding peptides. The choice of buffer system is shown to strongly influence the availability of peptide binding sites on the MNP surface. We find that under certain buffer conditions peptides of different charges can bind the MNP and that the relative strength of the interactions can be modulated by changing the buffer. We further present a model for the competition between the buffer and the MNP's electrostatically binding to the adsorption sites. Thereby, we demonstrate that the charge distribution on the surface can be used to correlate the binding of positively and negatively charged peptides to the MNP. This analysis enables us to engineer the binding of MNP on peptides and contribute to better understand the bio-nano interactions, a step towards the design of affinity tags for advanced biomaterials.

Site-directed fluorescence labeling of intrinsically disordered region of human transcription factor YY1: The inhibitory effect of zinc ions

Site-specific labeling of proteins with fluorescent dyes allows the study of protein structure and function using a wide variety of fluorescent techniques. However, specific labeling is not trivial in the case of proteins containing multiple cysteine residues. An example of such a protein is transcription factor Yin Yang 1, which comprises eight cysteine residues in four C2H2 type zinc fingers in the C-terminal region. Kinetic measurements of the labeling process allowed us to develop preparative labeling of three cysteine residues differently introduced to the N-terminal, disordered fragment of the protein. The protocol developed in the present study allows to prepare the protein with high recovery yield and high selectivity of the labeling. This was confirmed using proteolytic digestion and spectroscopic approach. The labeling process was significantly affected by the presence of zinc ions and was dependent on the localization of the engineered cysteine residue. This is the first known example of the use of cysteine metal protection and labeling (CyMPL) technology for the labeling of protein regions with no stable secondary structures.

Prediction of strong O-H/M hydrogen bonding between water and square-planar Ir and Rh complexes

Intermolecular O-H/M interactions, between a water molecule and square-planar acac complexes ([M(acac)L₂]), with different types of L ligands (en, H₂O, CO, CN^-, and OH^-) and different types of metal atoms (Ir(i), Rh(i), Pt(ii), and Pd(ii)) were studied by high level ab initio calculations. Among the studied neutral complexes, the [Pd(acac)(CN)(CO)] complex forms the weakest interaction, -0.62 kcal mol^-1, while the [Ir(acac)(en)] complex forms the strongest interaction, -9.83 kcal mol^-1, which is remarkably stronger than the conventional hydrogen bond between two water molecules (-4.84 kcal mol^-1).

Aberrant coordination geometries discovered in the most abundant metalloproteins

Metalloproteins bind and utilize metal ions for a variety of biological purposes. Due to the ubiquity of metalloprotein involvement throughout these processes across all domains of life, how proteins coordinate metal ions for different biochemical functions is of great relevance to understanding the implementation of these biological processes. Toward these ends, we have improved our methodology for structurally and functionally characterizing metal binding sites in metalloproteins. Our new ligand detection method is statistically much more robust, producing estimated false positive and false negative rates of ∼0.11% and ∼1.2%, respectively. Additional improvements expand both the range of metal ions and their coordination number that can be effectively analyzed. Also, the inclusion of additional quality control filters has significantly improved structure-function Spearman correlations as demonstrated by rho values greater than 0.90 for several metal coordination analyses and even one rho value above 0.95. Also, improvements in bond-length distributions have revealed bond-length modes specific to chemical functional groups involved in multidentation. Using these improved methods, we analyzed all single metal ion binding sites with Zn, Mg, Ca, Fe, and Na ions in the wwPDB, producing statistically rigorous results supporting the existence of both a significant number of unexpected compressed angles and subsequent aberrant metal ion coordination geometries (CGs) within structurally known metalloproteins. By recognizing these aberrant CGs in our clustering analyses, high correlations are achieved between structural and functional descriptions of metal ion coordination. Moreover, distinct biochemical functions are associated with aberrant CGs versus nonaberrant CGs. Proteins 2017; 85:885-907. © 2016 Wiley Periodicals, Inc.

Analytical approaches for the characterization of nickel proteome

Analytical strategies to study the nickel proteome and their advantages and limitations.

A survey of the mechanisms of action of anticancer transition metal complexes

Metal complexes have been the subject of numerous investigations in oncology but, despite the plethora of newly synthesized compounds, their precise mechanisms of action remain generally unknown or, for the best, incompletely determined. The continuous development of efficient and sensitive techniques in analytical chemistry and molecular biology gives scientists new tools to gather information on how metal complexes can be effective toward cancer. This review focuses on recent findings about the anticancer mechanism of action of metal complexes and how the ligands can be used to tune their pharmacological and physicochemical properties.

Electrostatic Deflection of a Molecular Beam of Massive Neutral Particles: Fully Field-Oriented Polar Molecules within Superfluid Nanodroplets

Electric deflection measurements on liquid helium nanodroplets doped with individual polar molecules demonstrate that the cold superfluid matrix enables full orientation of the molecular dipole along the external field. This translates into a deflection force that is increased enormously by comparison with typical deflection experiments, and it becomes possible to measurably deflect neutral doped droplets with masses of tens to hundreds of thousands of Daltons. By using continuous fluxes of fully oriented polar molecules and measuring the deflection of the doped nanodroplet beam, this approach makes it possible to directly determine the dipole moments of internally cryogenically cold molecules. The technique is broadly and generally applicable, including to complex and biological molecules.

The Eighth Central European Conference "Chemistry towards Biology": Snapshot

The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on August 28-September 1, 2016 to bring together experts in biology, chemistry and design of bioactive compounds; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topics of the conference covered "Chemistry towards Biology", meaning that the event welcomed chemists working on biology-related problems, biologists using chemical methods, and students and other researchers of the respective areas that fall within the common scope of chemistry and biology. The authors of this manuscript are plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting.

Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate

Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.

Nickel(ii), zinc(ii) and cadmium(ii) complexes of hexapeptides containing separate histidyl and cysteinyl binding sites

Hexapeptides containing separate histidyl and cysteinyl residues have outstanding metal binding ability but the binding sites of peptides reveal a significant specificity.

Protective Effect of Porcine Cerebral Hydrolysate Peptides on Learning and Memory Deficits and Oxidative Stress in Lead-Exposed Mice

In this study, lead acetate solution and porcine cerebral hydrolysate peptides (PCHPs) were administered to developing mice. Porcine cerebral protein pretreated by ultrasound was hydrolyzed with alcalase, and 11 peptide fragments were obtained by Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of PCHPs. Our data showed that PCHPs significantly decreased Pb2+-induced spontaneous locomotor activity, latencies to reach the platform, and the time in target quadrant. It also decreased the accumulation of lead in the blood and brain of Pb2+-exposed developing mice. Co-administration of PCHPs and dimercaptosuccinic acid (DMSA) did not only reduce the accumulation of lead in blood but also increased the absorption of zinc and iron in Pb2+-exposed mice. Administration of PCHPs individually significantly enhanced hematopoietic parameters compared with the Pb2+-exposed group. PCHPs significantly reduced the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) but increased glutathione (GSH) content and anti-oxidant enzymes and nitric oxide synthase (NOS) activities in Pb2+-exposed brain. Our findings suggest that PCHPs have the ability to protect against Pb2+-exposed learning and memory deficits and oxidative damage.

Chelating Surfaces for Native State Proteins Patterning: The Human Serum Albumin Case

The paper reports a new "soft" surface functionalization strategy, based on a highly selective ion metal chelation process. The proposed stepwise methodology implies at first the construction of a monolayer of terpyridine-based thiol (Tpy), whose highly packed structuring has been followed in situ by using quartz crystal microbalance (QCM-D) measurements, showing that the monolayers consist of about 2.7 × 10(14) Tpy/cm(2). Then, the tridentate sites of the each Tpy moiety are employed to partially chelate divalent metal ions, providing an effective platform to anchoring proteins by completing the metal ion coordination with an available site on the protein of interest. We report the case study of the application of the process to the HSA immobilization onto various surfaces, including Tpy-Fe(II) and Tpy-Cu(II) complexes, as well as hydrophilic bare gold substrates and hydrophobic self-assembled Tpy-based monolayers. It is shown that the chelation interaction between Tpy-Cu(II) complexes and HSA produces the highest and most robust HSA immobilization, with an adsorbed mass at the steady state of ∼800 ng/cm(2), with respect to an average adsorption of ∼350 ng/cm(2) for the other surfaces. Furthermore, Cu(II)-chelated surfaces seem to promote a sort of protein "soft" landing, preventing the ubiquitous surface-induced major unfolding and transmitting an orientation information to the protein, owing to the highly specific symmetry coordination of the Tpy-Cu(II)-protein complex. Indeed, the interaction with a specific monoclonal antiboby (anti-HSA) indicated the lack of a significant protein denaturation, while a massive reorientation/denaturation process was found for all the remaining surfaces, including the Tpy-Fe(II) complex. Finally, the metal-ion-dependent HSA immobilization selectivity has been exploited to obtain micropatterned surfaces, based on the strikingly different strength of interaction and stability observed for Fe(II) and Cu(II) complexes.

Prion Protein Does Not Confer Resistance to Hippocampus-Derived Zpl Cells against the Toxic Effects of Cu2+, Mn2+, Zn2+ and Co2+ Not Supporting a General Protective Role for PrP in Transition Metal Induced Toxicity

The interactions of transition metals with the prion protein (PrP) are well-documented and characterized, however, there is no consensus on their role in either the physiology of PrP or PrP-related neurodegenerative disorders. PrP has been reported to protect cells from the toxic stimuli of metals. By employing a cell viability assay, we examined the effects of various concentrations of Cu2+, Zn2+, Mn2+, and Co2+ on Zpl (Prnp-/-) and ZW (Prnp+/+) hippocampus-derived mouse neuronal cells. Prnp-/- Zpl cells were more sensitive to all four metals than PrP-expressing Zw cells. However, when we introduced PrP or only the empty vector into Zpl cells, we could not discern any protective effect associated with the presence of PrP. This observation was further corroborated when assessing the toxic effect of metals by propidium-iodide staining and fluorescence activated cell sorting analysis. Thus, our results on this mouse cell culture model do not seem to support a strong protective role for PrP against transition metal toxicity and also emphasize the necessity of extreme care when comparing cells derived from PrP knock-out and wild type mice.

Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor

Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba(2+) to Ca(2+)) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca(2+) to Mg(2+) to Ni(2+)) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal-nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba(2+) and Ca(2+) prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50-100 kJ mol(-1)) than the phenylalanine peptides.