Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

用核磁共振方法研究金属离子与蛋白质的相互作用

许多蛋白质含有金属离子,金属离子对蛋白质发挥生物学功能起着很大的作用. 金属离子与蛋白质的相互作用以及参与蛋白质功能调节的方式各种各样：有些金属离子高度专一性地与蛋白质紧密结合,对蛋白质发挥生物学功能起着关键性的作用;有些金属离子只是作为蛋白质发挥功能的辅助因子而瞬态地与蛋白质松散结合. 本文简要介绍目前国际上用NMR方法研究抗磁金属离子和顺磁金属离子与蛋白质相互作用的进展,并具体介绍了NMR方法在钙调蛋白、锌指蛋白、朊病毒蛋白等金属离子蛋白研究上的应用.     

Biological X‐ray absorption spectroscopy and metalloproteomics

In the past seven years the size of the known protein sequence universe has been rapidly expanding. At present, more then five million entries are included in the UniProtKB/TrEMBL protein database. In this context, a retrospective evaluation of recent X‐ray absorption studies is undertaken to assess its potential role in metalloproteomics. Metalloproteomics is the structural and functional characterization of metal‐binding proteins. This is a new area of active research which has particular relevance to biology and for which X‐ray absorption spectroscopy is ideally suited. In the last three years, biological X‐ray absorption spectroscopy (BioXAS) has been included among the techniques used in post‐genomics initiatives for metalloprotein characterization. The emphasis of this review is on the progress in BioXAS that has emerged from recent meetings in 2007–2008. Developments required to enable BioXAS studies to better contribute to metalloproteomics throughput are also discussed. Overall, this paper suggests that X‐ray absorption spectroscopy could have a higher impact on metalloproteomics, contributing significantly to the understanding of metal site structures and of reaction mechanisms for metalloproteins.     

Luminescencence determination of ecotoxicants in protein-based media

The structural changes in the protein macromolecules caused by polycyclic aromatic hydrocarbon (PAH) ecotoxicants were studied using the data on intrinsic fluorescence of proteins and fluorescence of PAH molecules introduced into proteins. A luminescence method for PAH determination in proteins was developed and used to study the interaction of two PAHs (pyrene and anthracene) with proteins of two types (bovine serum albumin and human serum albumin). The results were interpreted using the Stern–Volmer fluorescence quenching model. The association constants and the number of binding sites in the protein–ligand complexes were calculated. The binding of PAHs with proteins was described based on the static version of quenching with formation of nonfluorescent complexes of protein fluorophores with PAHs.     

Are there generic mechanisms governing interactions between nanoparticles and cells? Epitope mapping the outer layer of the protein–material interface

In this paper we discuss the possibility of a general paradigm for cell–biomaterial and cell–nanoparticle interactions. The basis of the paradigm is that the nature of the biomaterial or nanoparticle surface is not the important parameter, but rather the nature of the outermost layer of adsorbed proteins as well as long-lived misfolded proteins shed from the surfaces. If the adsorbed protein is irreversibly adsorbed onto the surface it may be sufficiently disrupted so that a variety of peptide units (here termed “cryptic epitopes”) not usually expressed in nature at the surface of the protein become exposed. Similarly, where there is a slow exchange time with the surface, surface-induced perturbations may lead to long-lived misfolded proteins being shed from the surface and continuing to express altered surface peptide sequences. In cases where the proteins have lost most of their tertiary structure, anomalous peptide sequences and geometries that are not displayed at the surface by the native protein may in fact be presented after surface adsorption of a protein. Such anomalous surface expressions could contain novel epitopes that trigger various signalling pathways or even diseases. Thus, future approaches to understanding cell–biomaterial and cell–nanoparticle interactions should focus on characterising the outer layer of the adsorbed proteins, or “epitope mapping” as well as examining the possibility of formation of essentially “new” proteins as a result of desorption of conformationally or geometrically altered proteins.     

In Situ Evaluation of Nanoparticle–Protein Interactions by Dynamic Magnetic Susceptibility Measurements

The use of dynamic magnetic susceptibility measurements is reported to study nanoparticle–protein interactions in situ. The technique consists of measuring the rotational diffusivity of thermally blocked magnetic nanoparticles (MNPs) in protein solutions. To illustrate the technique, the effect of nanoparticle zeta potential in carboxymethyl‐dextran‐coated MNPs and their interaction with model anionic and cationic proteins, such as bovine serum albumin (BSA), immunoglobulin G (IgG), fibrinogen (FIBR), apo‐transferrin (TRANS), lysozyme (LYZ), and histone (HIS), in a range of protein concentrations is studied. Experiments indicate that interactions between the negatively charged particles and the negatively charged proteins BSA, IgG, FIBR, and TRANS are negligible. However, positively charged proteins LYZ and HIS readily absorb onto the nanoparticles, as evidenced by an increase in size and eventual aggregation of the particles. Onset of this effect seems to happen at a lower concentration of HIS compared with LYZ. The technique could be applied to other particle surface coatings and to particles in complex protein mixtures, such as whole blood and serum, allowing systematic in situ studies of nanoparticle–protein interactions.     

Inorganic biochemistry with short-lived radioisotopes as nuclear probes

Metal ions are ubiquitous in the biosphere. In living organisms metalloproteins with specifically designed metal cores perform vital chemical processes. On the other hand, several heavy metals are detrimental to living organisms and nature has developed effective enzymatic detoxification systems which convert toxic metal ions to less toxic species. The nuclear spectroscopy technique Time Differential Perturbed Angular Correlation (TDPAC) of γ-rays uses radioactive isotopes as nuclear probes in these metal cores to obtain a better understanding of the structural and functional significance of these metal cores by monitoring the nuclear quadrupole interaction of the TDPAC probe. Since this technique is based on the nuclear decay, it is also applicable under physiological conditions, i.e., especially at picomolar concentrations. For these studies an indispensable prerequisite is the production of the TDPAC probes with highest possible specific activity and purity as is done by the on-line mass separator ISOLDE at CERN in Geneva. This revised version was published online in July 2006 with corrections to the Cover Date.     

Spectroscopic investigations on the interaction between cadmium telluride semiconductor nanoparticle and bovine alkaline phosphatase

The interaction of enzymes with nanoparticles is important in the field of biotechnology and medicine. Due to the various uses of cadmium telluride nanoparticle in protein science, biotechnology and biophysical chemistry, drug delivery, and cellular imaging, study of this nanoparticle interaction with protein seems to be necessary. Therefore, the interaction between cadmium telluride semiconductor nanoparticle and bovine alkaline phosphatase, a clinical marker enzyme, were investigated by assaying kinetic parameters and fluorescence absorption, UV–vis absorption spectra, and circular dichroism spectroscopic techniques. Obtained results showed that cadmium telluride nanoparticle could quench the fluorescence signal of bovine alkaline phosphatase effectively with a static quenching mechanism. Moreover, the binding of cadmium telluride nanoparticle to the enzyme was spontaneous and van der Waals and hydrogen bonding forces played a key role in the complex stabilization. Circular dichroism spectra measurements indicated that cadmium telluride nanoparticle decreased α-helical content and increased the β-sheet structure of bovine alkaline phosphatase. These findings suggest that cadmium telluride nanoparticle changes the structure and activity of bovine alkaline phosphatase.     

Interaction of gold nanoparticles with bovine serum albumin

The interaction between gold nanoparticles and bovine serum albumin (BSA) in aqueous solutions was studied. The formation of nanoparticle—BSA associates was demonstrated, which is expressed in a bathochromic shift of the surface plasmon resonance band by 5–6 nm in the absorption spectrum. The results were approximated using the Drude model for metal spheres. The thickness of the dielectric (protein) shell of the nanoparticle and its permittivity (refractive index) were calculated.     

Exploring the anti-proliferative activity of <Emphasis Type="BoldItalic">Pelargonium sidoides</Emphasis> DC with in silico target identification and network pharmacology

Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated. The protein targets of the 12 phenolic compounds were identified using the target identification server PharmMapper and the server for predicting Drug Repositioning and Adverse Reactions via the Chemical–Protein Interactome (DRAR-CPI). Protein–protein and protein–pathway interaction networks were subsequently constructed with Cytoscape 3.4.0 to evaluate potential mechanisms of action. A total of 142 potential human target proteins were identified with the in silico target identification servers, and 90 of these were found to be related to cancer. The protein interaction network was constructed from 86 proteins involved in 209 interactions with each other, and two protein clusters were observed. A pathway enrichment analysis identified over 80 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with the protein targets and included several pathways specifically related to cancer as well as various signaling pathways that have been found to be dysregulated in cancer. These results indicate that the anti-proliferative activity of P. sidoides may be multifactorial and arises from the collective regulation of several interconnected cell signaling pathways.     

Analytical Expression for the Relaxation Rate of Emitter-Near-Metal Nanoparticles

We present a simple analytical expression for the full relaxation rate of the excited state of the two-level resonant emitter placed close to a metal nanoparticle with localized plasmon resonance excited by the emitter. We take into account the interaction of the emitter with all multipole polarization modes and the radiation absorption in the nanoparticle. Analytical and numerical estimations of the full relaxation rate are in good agreement. Thus, only two modes are sufficient for describing the electromagnetic interaction of the dipole emitter and the metal nanoparticle, namely, the dipole mode and the mode related to the emitter image under the nanoparticle surface. Such “two-mode” approximation can simplify the analysis of optical properties of nanoplasmonic structures. In particular, the proposed expression for the full relaxation rate is helpful in the modeling of plasmonic nanolasers.     

Atomic spectrometry and atomic mass spectrometry in bioanalytical chemistry

Abstract

Atomic spectrometry and atomic mass spectrometric (MS) techniques have been playing crucial roles in the field of biosciences. They detect elements with relatively high sensitivities and are thus applicable to a wide range of analytical targets. In the past decade, determination of bio-relevant metallic elements continues to be of interest, while particularly noteworthy are methods developed for small molecules, peptides, proteins, nucleic acids and even cells that well exploited the bio-analytical strengths of atomic spectrometry and atomic MS, either in a direct or indirect manner. Quantitation, as well as speciation and imaging analyses are all involved. The present review aims to assimilate recent advances in bio-analysis utilizing atomic spectrometry and atomic MS, primarily covering the period of 2013–2018, in an attempt to provide readers insight into the developing trends of this research frontier. Followed by concluding remarks and perspectives, the applications are divided into the following four catalogs: (i) toxicologically important metal-containing species, with an emphasis on quantitative and imaging analysis; (ii) quantitation of biomolecules using naturally occurring heteroatoms; (iii) exogenous metal ion or nanoparticle tagging-based strategies in bioassays; and (iv) label-free detection of biomolecules.     

Cation-mediated sandwich formation between benzene and pillar[5]arene: a DFT study

Cation–π interactions in alkali metal ion (Li⁺, Na⁺ and K⁺)–pillar[5]arene complexes and sandwiches of pillar[5]arene and benzene formed via alkali metal ions are studied in the light of density functional theory. Several possible modes of interaction between metal ions and pillar[5]arene have been studied. Results suggest that interaction is stronger in the complexes with the metal ion present inside the cavity of the pillar[5]arene as compared to that where the metal ion is outside the cavity. The calculated interaction energy further reveals that though cation–π complexes with larger number of alkali metal ions are unstable, however, corresponding sandwiches are stable, which further support the fact that pillar[5]arene–metal ion complexes can interact with other π–electron-rich species. Absorption spectra of the complexes formed undergo both blue and red shifts as compared to the pillar[5]arene.     

联用技术应用于生物分子中金属和类金属的形态分析

本文依据最近有关联用技术应用于生物样品中痕量金属和类金属形态分析的报道,扼要介绍高效液相色谱（HPLC）和毛细管电泳（CE）与电感耦合等离子质谱（ICP－MS）和电喷雾离子化质谱（ESI－MS）联用技术在砷、硒和镉等元素的形态分析中的应用。体积排阻色谱（SEC）与ICP－MS在线联用最常用的初步筛选未知试样中大分子化合物的方法。但由于SEC的分辨率差,需要应用另一种色谱法,如离子交换色谱法（IEC）或反相色谱法（RP－HPLC）分离以保证分离信号的纯度。在无标准可利用的情况下,电喷雾串联质谱（ES－MS／MS）是用以表征化合物的最佳手段。毛细管区带电泳（CZE）与ICP－MS联用是形态分析的有用工具。分析中需要注意的问题是避免沾污和防止在分离过程中蛋白质的分解。目前,由于缺少标准和参考物质,联用技术主要应用于寻找新的金属物 种,而并非测定已知化合物。需要解决的难题是检测的信号是否属于某一特定的化合物以及该化合物的表征。     

Metal‐nanoparticle plasmonics

The rapid emergence of nanoplasmonics as a novel technology has been driven by recent progress in the fabrication, characterization, and understanding of metal‐nanoparticle systems. In this review, we highlight some of the key advances in each of these areas. We emphasize the basic physical understanding and experimental techniques that will enable a new generation of applications in nano‐optics.     

Bimetallic Nanoparticles with Exotic Facet Structures via Iodide‐Assisted Reduction of Palladium

Iodide is arguably the most challenging halide to control as a shape‐directing additive in metal nanoparticle synthesis and the addition of iodide during bimetallic nanoparticle growth often leads to inhomogeneously stellated products. Through judicious control of low micromolar concentrations of iodide ions in solution in a seed‐mediated approach, alloyed gold–palladium tetradecapod nanoparticles have been synthesized with a mixture of both well‐defined convex and concave surfaces. Notably, these particles are uniform and symmetrical, and this unusual combination of convex and concave features in a single nanostructure is not simply an artifact of intersecting spikes, as would be the case with stellated particles. Further, an important new role for iodide in catalyzing the reduction of palladium ions is identified, particularly at the edge sites of the growing gold nanoparticles. This differs from the commonly accepted theory that iodide slows metal ion reduction, and thus opens up promising new routes to the synthesis of other bimetallic nanoparticles with exotic shapes and surface structures.     

Electronic and magnetic properties of Fe-, Co-, and Ni-decorated BC3: A first-principles study

The electronic and magnetic properties of Fe-, Co-, and Ni-decorated two dimensional (2D) BC₃ are systematically investigated by first-principles calculations. We find that the Fe, Co, and Ni atoms can be strongly adsorbed on the hollow sites of 2D BC₃. Fe and Co adatoms are more stable when adsorbed on the hollow sites of the carbon rings in the 2D BC₃, while the hollow sites of boron-carbon rings in the 2D BC₃ are the most stable sites for the adsorption of Ni adatoms. These proposed metal–BC₃ complexes exhibit interesting electronic and magnetic behaviors. In particular, the Fe–BC₃ and Co–BC₃ complexes are metals with magnetic ground states , while the Ni–BC₃ complex behaves as a nonmagnetic semiconductor with a direct bandgap. Furthermore, our magnetic analysis reveals that induced magnetism in the Fe–BC₃ and Co–BC₃ complexes arises from their local magnetic moments. Functionalization of 2D BC₃ through these metal–adatom adsorption appears to be a promising way to extend its applications.     

Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes

The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino N? H bond, side chain thiol group S? H bond, hydroxyl O? H bond, and Carbonyl C?O bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Formation and manipulation of regular metallic nanoparticle arrays on bacterial surface layers: an advanced TEM study

The template-directed formation of regular nanoparticle arrays on two-dimensional crystalline protein layers after their treatment with metal salt complexes was studied by transmission electron microscopy. For these investigations, bacterial surface layers (S layers), recrystallized in vitro into sheets and tube-shaped protein crystals with typical dimensions in the micrometer range, were used as the template. As identified by electron holography and scanning force microscopy, the S-layer tubes form alternating double layers when deposited onto a solid substrate surface. Two distinct pathways for the metal particle formation at the templates have been found: the site-specific growth of metal clusters by chemical reduction of the metal salt complexes, and the electron-beam induced growth of nanoparticles in the transmission electron microscope. Both mechanisms lead to regular arrays with particle densities > 6×10¹¹ cm ^-2. Nanoparticle formation by electron exposure takes exclusively place in the flat-lying double-layered protein tubes, where a sufficient amount of metal complexes can be accumulated during sample preparation. Received 6 December 2000     

Probing Zinc–Protein–Chelant Interactions Using Gold Nanoparticles Functionalized with Zinc‐Responsive Polypeptides

The coordination of zinc by proteins and various other organic molecules is essential for numerous biological processes, such as in enzymatic catalysis, metabolism, and signal transduction. Presence of small molecular chelants can have a profound effect on the bioavailability of zinc and affect critical Zn²⁺–protein interactions. Zn²⁺ chelators are also emerging therapeutics for Alzheimer's disease because of their preventive effect on zinc‐promoted amyloid formation. Despite the importance of zinc–protein–chelant interactions in biology and medicine, probing such interactions is challenging. Here, an innovative approach is introduced for real‐time characterization of zinc–protein–chelant interactions using gold nanoparticles (AuNPs) functionalized with a zinc‐responsive protein mimetic polypeptide. The peptide‐functionalized AuNPs aggregate extensively in the presence of Zn²⁺, triggered by specific Zn²⁺‐mediated polypeptide dimerization and folding, causing a massive red shift of the plasmon band. Chelants affects the Zn²⁺–polypeptide interaction and thus the aggregation differently depending on their concentrations, zinc‐binding affinities, and coordination numbers, which affect the position of the plasmon band. This system is a simple and powerful tool that provides extensive information about the interactions of chelants in the formation of Zn²⁺ coordination complexes, and an interesting platform for development of bioanalytical techniques, and characterization of chelation‐based therapeutics.