Assembly of an oxo-zirconium(IV) cluster in a protein cleft

Cooperative Self-Assembly Process Involving Giant Toroidal Polyoxometalate as a Membrane Building Block in Nanoscale Vesicles

The self-assembly of organic amphiphilic species into various aggregates such as spherical or elongated micelles and cylinders up to the formation of lyotropic hexagonal or lamellar phases results from cooperative processes orchestrated by the hydrophobic effect, while those involving ionic inorganic polynuclear entities and nonionic organic components are still intriguing. Herein, we report on the supramolecular behavior of giant toroidal molybdenum blue-type polyoxometalate, namely, the {Mo154} species in the presence of n-octyl-β-glucoside (C8G1), widely used as a surfactant in biochemistry. Structural investigations were carried out using a set of complementary multiscale methods including single-crystal X-ray diffraction analysis supported by molecular modeling, small-angle X-ray scattering and cryo-TEM observations. In addition, liquid NMR, viscosimetry, surface tension measurement, and isothermal titration calorimetry provided further information to decipher the complex aggregation pathway. Elucidation of the assembly process reveals a rich scenario where the presence of the large {Mo154} anion disrupts the self-assembly of the C8G1, well-known to produce micelles, and induces striking successive phase transitions from fluid-to-gel and from gel-to-fluid. Herein, intimate organic-inorganic primary interactions arising from the superchaotropic nature of the {Mo154} lead to versatile nanoscopic hybrid C8G1-{Mo154} aggregates including crystalline discrete assemblies, smectic lamellar liquid crystals, and large uni- or multilamellar vesicles where the large torus {Mo154} acts a trans-membrane component.

Superstoichiometric Binding of the Anticancer Agent Titanocene Dichloride by Human Serum Transferrin and the Accompanying Lobe Closure

Titanocene dichloride (TDC) is an anticancer agent that delivers Ti(IV) into each of the two Fe(III) binding sites of bilobal human serum transferrin (Tf). This protein has been implicated in the selective transport of Ti(IV) to cells. How Ti(IV) might be released from the Tf Fe(III) binding site has remained a question, and crystal structures have raised issues about lobe occupancy and lobe closure in Ti(IV)-loaded Tf, compared with the Fe(III)-loaded form. Here, inductively coupled plasma optical emission spectroscopy reveals that Tf can stabilize toward hydrolytic precipitation more than 2 equiv of Ti, implying superstoichiometric binding beyond the two Fe(III) binding sites. Further studies support the inability of TDC to induce a complete lobe closure of Tf. Fluorescence data for TDC binding at low equivalents of TDC support an initial protein conformational change and lobe closure upon Ti binding, whereas data at higher equivalents support an open lobe configuration. Spectroscopic titration reveals less intense protein-metal electronic transitions as TDC equivalents are increased. Denaturing urea-PAGE gels and small angle X-ray scattering studies support an open lobe conformation. The concentrations of bicarbonate used in some earlier studies are demonstrated here to cause a pH change over time, which may contribute to variation in the apparent molar absorptivity associated with Ti(IV) binding in the Fe binding site. Finally, Fe(III)-bound holo-Tf still stabilizes TDC toward hydrolytic precipitation, a finding that underscores the importance of the interactions of Tf and TDC outside the Fe(III) binding site and suggests possible new pathways of Ti introduction to cells.

Minerals in biology and medicine

Natural minerals ('stone drugs') have been used in traditional Chinese medicines for over 2000 years, but there is potential for modern-day use of inorganic minerals to combat viral infections, antimicrobial resistance, and for other areas in need of new therapies and diagnostic aids. Metal and mineral surfaces on scales from milli-to nanometres, either natural or synthetic, are patterned or can be modified with hydrophilic/hydrophobic and ionic/covalent target-recognition sites. They introduce new strategies for medical applications. Such surfaces have novel properties compared to single metal centres. Moreover, 3D mineral particles (including hybrid organo-minerals) can have reactive cavities, and some minerals have dynamic movement of metal ions, anions, and other molecules within their structures. Minerals have a unique ability to interact with viruses, microbes and macro-biomolecules through multipoint ionic and/or non-covalent contacts, with potential for novel applications in therapy and biotechnology. Investigations of mineral deposits in biology, with their often inherent heterogeneity and tendency to become chemically-modified on isolation, are highly challenging, but new methods for their study, including in intact tissues, hold promise for future advances.

Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters

Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.

Bioinspired nanoreactors for the biomineralisation of metallic-based nanoparticles for nanomedicine

This review explores the synthesis of inorganic metallic-based nanoparticles (MBNPs) (metals, alloys, metal oxides) using biological and biologically inspired nanoreactors for precipitation/crystallisation. Such nanoparticles exhibit a range of nanoscale properties such as surface plasmon resonance (nobel metals e.g. Au), fluorescence (semiconductor quantum dots e.g. CdSe) and nanomagnetism (magnetic alloys e.g. CoPt and iron oxides e.g. magnetite), which are currently the subject of intensive research for their applicability in diagnostic and therapeutic nanomedicine. For such applications, MBNPs are required to be biocompatible, of a precise size and shape for a consistent signal or output and be easily modified with biomolecules for applications. Ideally the MBNPs would be obtained via an environmentally-friendly synthetic route. A biological or biologically inspired nanoreactor synthesis of MBNPs is shown to address these issues. Biological nanoreactors for crystallizing MBNPs within cells (magnetosomes), protein cages (ferritin) and virus capsids (cowpea chlorotic mottle, cowpea mosaic and tobacco mosaic viruses), are discussed along with how these have been modified for applications and for the next generation of new materials. Biomimetic liposome, polymersome and even designed self-assembled proteinosome nanoreactors are also reviewed for MBNP crystallisation and further modification for applications. With the advent of synthetic biology, the research and understanding in this field is growing, with the goal of realising nanoreactor synthesis of MBNPs for biomedical applications within our grasp in the near future.

Binding of oxo-Cu2 clusters to ferric ion-binding protein A from Neisseria gonorrhoeae: a structural insight

The ferric ion-binding protein A (FbpA), a member of transferrin superfamily, is a periplasmic iron transporter employed by many Gram-negative pathogens. Our experiments indicated copper(ii) could bind with Neisseria gonorrhoeae FbpA (NgFbpA), and the binding constant reached up to (8.7 ± 0.2) × 10(8) M(-1)via UV-vis titration. The crystal structure of recombinant Cu-NgFbpA at 2.1 Å revealed that the oxo-Cu2 clusters (dinuclear centres) assembled in the iron binding cleft and were bound to the two adjacent tyrosine residues (Y195 and Y196) of the protein, two Cu ions coordinated with two tyrosines, Y195 and Y196, respectively, which was different from the binding model of Fe ion with FbpA, in which Y195 and Y196 coordinated together with one Fe ion. While this was similar to the binding of Zr and Hf ion clusters, Y195 and Y196 coordinated with two metal ions and the μ-oxo-bridges linking the metal ions. Structural superimposition demonstrated that oxo-Cu2-NgFbpA still keeping an open conformation, similar to the apo-form of NgFbpA. The structure presented additional information towards an understanding of the function of FbpA, and provided a detailed binding model for FbpA protein with the possible metal ions in a biological system.

From thioxo cluster to dithio cluster: exploring the chemistry of polynuclear zirconium complexes with S,O and S,S ligands

Three different zirconium thio and oxothio clusters, characterized by different coordination modes of dithioacetate and/or monothioacetate ligands, were obtained by the reaction of monothioacetic acid with zirconium n-butoxide, Zr(O(n)Bu)4, in different experimental conditions. In particular, we isolated the three polynuclear Zr3(μ3-SSSCCH3)2(SSCCH3)6·2(n)BuOH (Zr3), Zr4(μ3-O)2(μ-η(1)-SOCCH3)2(SOCCH3)8(O(n)Bu)2 (Zr4), and Zr6(μ3-O)5(μ-SOCCH3)2(μ-OOCCH3)(SOCCH3)11((n)BuOH) (Zr6) derivatives, presenting some peculiar characteristics. Zr6 has an unusual star-shaped structure. Only sulfur-based ligands, viz., chelating dithioacetate monoanions and an unusual ethane-1,1,1-trithiolate group μ3 coordinating the Zr ions, were observed in the case of Zr3. 1D and 2D NMR analyses confirmed the presence of differently coordinated ligands. Raman spectroscopy was further used to characterize the new polynuclear complexes. Time-resolved extended X-ray absorption fine structure measurements, devoted to unraveling the cluster formation mechanisms, evidenced a fast coordination of sulfur ligands and subsequent relatively rapid rearrangements.

Niobium uptake and release by bacterial ferric ion binding protein

Ferric ion binding proteins (Fbps) transport Fe^III across the periplasm and are vital for the virulence of many Gram negative bacteria. Iron(III) is tightly bound in a hinged binding cleft with octahedral coordination geometry involving binding to protein side chains (including tyrosinate residues) together with a synergistic anion such as phosphate. Niobium compounds are of interest for their potential biological activity, which has been little explored. We have studied the binding of cyclopentadienyl and nitrilotriacetato Nb^V complexes to the Fbp from Neisseria gonorrhoeae by UV-vis spectroscopy, chromatography, ICP-OES, mass spectrometry, and Nb K-edge X-ray absorption spectroscopy. These data suggest that Nb^V binds strongly to Fbp and that a dinuclear Nb^V centre can be readily accommodated in the interdomain binding cleft. The possibility of designing niobium-based antibiotics which block iron uptake by pathogenic bacteria is discussed.

Comprehensive analysis of the helix-X-helix motif in soluble proteins

Alpha-helices are the most common secondary structures found in globular proteins. In this report, we analyze the stereochemical and sequence properties of helix-X-helix (HXH) motifs in which two alpha-helices are linked by a single residue, in search of characteristic structures and sequence signals. The analysis is carried out on a database of 837 nonredundant HXH motifs. The kinks are characterized by the bend angle between the axes of the N-terminal and C-terminal helices and the wobble angle corresponding to the rotation of C-terminal helix axis on the plane perpendicular to the N-terminal one. The phi-psi dihedral angles of the linker residue are clustered in six distinct areas of the Ramachandran plot: two areas are located in the additional allowed alpha region (alpha(1) and alpha(2)), two areas are in the additional allowed beta region (beta(1) and beta(2)) and two areas have positive phi values (alpha(L) and beta(M)). Each phi/psi region corresponds to characteristic bend and wobble angles and amino acid distributions. Bend angles can vary from 0 degrees to 160 degrees. Most wobble angles correspond to a counter-clockwise rotation of the C-terminal helix. Proline residues are rigorously excluded from the linker position X but have a high propensity at position X+1 of the beta(1) and beta(2) motifs (12 and 7, respectively) and at position X+3 of the alpha(1) motifs (9). Glycine linkers are located either in the alpha(L) region (20%) or in the beta(M) region (80%). This latter conformation is characterized by a marked bend angle (124 degrees +/- 18 degrees) and a clockwise wobble. Among other amino acids, Asn is remarkable for its high propensity (>3) at the linker position of the alpha(2), beta(1), and beta(2) motifs. Stabilization of HXH motifs by H-bonds between polar side chains of the linker and polar groups of the backbone is determined. A method based on position-specific scoring matrices is developed for conformational prediction. The accuracy of the predictions reaches 80% when the method is applied to proline-induced kinks or to kinks with bend angles in the 50 degrees-100 degrees range.

Crystal structure based design of functional metal/protein hybrids

Preparation of metal/protein hybrids is growing into important topics in the field of bioinorganic chemistry. X-ray crystal structure analyses of them provide direct information on unique interactions of metal cations or metal cofactors to understand and design enzymatic functions. In this mini review, the authors focus on the recent studies on the metal/protein hybrids concerning crystal structure analyses since 2002 and our related works. The precise structural determination promise us to deeply understand coordination chemistry in protein scaffold and shows intriguing suggestions on rational design and application use for biocatalysts, metal drugs and so on.

Metals in membranes

In this critical review we discuss recent advances in understanding the modes of interaction of metal ions with membrane proteins, including channels, pumps, transporters, ATP-binding cassette proteins, G-protein coupled receptors, kinases and respiratory enzymes. Such knowledge provides a basis for elucidating the mechanism of action of some classes of metallodrugs, and a stimulus for the further exploration of the coordination chemistry of metal ions in membranes. Such research offers promise for the discovery of new drugs with unusual modes of action. The article will be of interest to bioinorganic chemists, chemical biologists, biochemists, pharmacologists and medicinal chemists. (247 references).