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Giant platinum clusters: 2-nm covalent metal cluster labels.

A new class of covalently linkable platinum cluster reagents with core diameters close to 2 nm has been prepared. The new label offers the performance advantages and versatility of the 1.4-nm Nanogold in a larger label which is more clearly visualized against electron-dense regions of a specimen. Large platinum clusters were prepared by the reduction of platinum(II) acetate in the presence of 1,10-phenanthroline ligands which had been synthetically modified to include solubilizing and reactive cross-linkable functional groups. These were then conjugated site-specifically to antibody IgG molecules and to Fab' fragments and visualized by scanning transmission electron microscopy. The resulting conjugates may be autometallographically enhanced and show sensitivity similar to that of Nanogold conjugates in immunoblotting experiments. In preliminary experiments, they have also exhibited labeling of tissue antigens and penetrate to access nuclear targets.

Affinity Labels↗

The cps gene cluster of Salmonella strain LT2 includes a second mannose pathway: sequence of two genes and relationship to genes in the rfb gene cluster.

We report the presence in Salmonella enterica strain LT2 (serovar thyphimurium) of duplicate genes for two steps in the synthesis of GDP-mannose. The previously known genes, rfbK (phosphomannomutase) and rfbM (mannose-1-phosphate guanyltransferase), are part of the gene cluster for the O antigen. The two new genes, cpsB and cpsG, respectively, are thought to be part of the gene cluster for the M antigen capsular polysaccharide, present in many Enterobacteriaceae. The two genes have been sequenced and have a GC content of 0.61, suggesting an origin outside of Salmonella. Comparison of the inferred protein sequences for cpsB and rfbM shows 57% identity of amino acids whereas for cpsG and rfbK there is only 19% identity. It is suggested that the greater divergence between cpsG and rfbK may be due to a period of accelerated evolution, perhaps precipitated by transfer of the genes from another species.

Amino Acid Sequence↗

Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: translocation of the str cluster as an early event in the rhodophyte-chromophyte lineage of plastid evolution.

The nucleotide sequence of a cluster of ribosomal protein genes in the plastid genome of a unicellular red alga, Cyanidioschyzon merolae, which has been supposed to be the most primitive alga, was determined. The phylogenetic tree inferred from the amino acid sequence of ribosomal proteins of two rhodophytes, a chromophyte, a glaucophyte, two chlorophytes (land plants), a cyanobacterium, and three eubacteria suggested a close relationship between the cyanobacterium Synechocystis PCC6803 and the plastids of various species in the kingdom Plantae, which is consistent with the hypothesis of the endosymbiotic origin of plastids. In this tree, the two species of rhodophytes were grouped with the chromophyte, and the glaucophyte was grouped with the chlorophytes. Analysis of the organization of the genes encoding the ribosomal proteins suggested that the translocation of the str cluster occurred early in the lineage of rhodophytes and chromophytes after these groups had been separated from chlorophytes and glaucophytes.

Cyanobacteria↗

A gene cluster for biosynthesis of kanamycin from Streptomyces kanamyceticus: comparison with gentamicin biosynthetic gene cluster.

Gene clusters for the biosynthesis of kanamycin (Km) and gentamicin (Gm) were isolated from the genomic libraries of Streptomyces kanamyceticus and Micromonospora echinospora, respectively. The sequencing of the 47 kb-region of S. kanamyceticus genomic DNA revealed 40 putative open reading frames (ORFs) encoding Km biosynthetic proteins, regulatory proteins, and resistance and transport proteins. Similarly, the sequencing of 32.6 kb genomic DNA of M. echinospora revealed a Gm biosynthetic gene cluster flanked by resistant genes. Biosynthetic pathways for the formation of Km were proposed by the comparative study of biosynthetic genes. Out of 12 putative Km biosynthetic genes, kanA was expressed in Escherichia coli and determined its function as a 2-deoxy-scyllo-inosose synthase. Furthermore, the acetylations of aminoglycoside-aminocyclitols (AmAcs) by Km acetyltransferase (KanM) were also demonstrated. The acetylated derivatives completely lost their antibacterial activities against Bacillus subtilis. The comparative genetic studies of Gm, Km, tobramycin (Tm), and butirosin (Bn) reveal their similar biosynthetic routes and provide a framework for the further biosynthetic studies.

Base Sequence↗

Organization of a large gene cluster encoding ribosomal proteins in the cyanobacterium Synechococcus sp. strain PCC 6301: comparison of gene clusters among cyanobacteria, eubacteria and chloroplast genomes.

The structure of a large gene cluster containing 22 ribosomal protein (r-protein) genes of the cyanobacterium Synechococcus sp. strain PCC6301 is presented. Based on DNA and protein sequence analyses, genes encoding r-proteins L3, L4, L23, L2, S19, L22, S3, L16, L29, S17, L14, L24, L5, S8, L6, L18, S5, L15, L36, S13, S11, L17, SecY, adenylate kinase (AK) and the alpha subunit of RNA polymerase were identified. The gene order is similar to that of the E. coli S10, spc and alpha operons. Unlike the corresponding E. coli operons, the genes for r-proteins S4, S10, S14 and L30 are not present in this cluster. The organization of Synechococcus r-protein genes also resembles that of chloroplast (cp) r-protein genes of red and brown algal species. This strongly supports the endosymbiotic theory that the cp genome evolved from an ancient photosynthetic bacterium.

Amino Acid Sequence↗

The mouse Ifi200 gene cluster: genomic sequence, analysis, and comparison with the human HIN-200 gene cluster.

The interferon-activatable Ifi200 gene cluster is located on mouse Chromosome 1q21-q23. We report here our analysis of two genomic regions encoding at least 10 closely related 200 family genes (Ifi201, Ifi202a, Ifi202b, Ifi202c, Ifi203a, Ifi203b, Ifi203c, Ifi203', Ifi204, and Ifi204') in 129/SvJ mice. Through a BAC-based sequencing approach, the exact structure and organization of these highly similar Ifi200 genes were obtained. A high degree of conservation (99% identity) was observed between Ifi202a and b and between Ifi203a and b. The presence of an additional transcribed region in intron 4 of Ifi203a and b suggests the possibility of alternative splicing, and a spliced variant of the Ifi204' mRNA exhibits 91% sequence identity with a related but unmapped D3 mRNA. Comparative analysis of the mouse and human clusters indicates an absence of significant sequence conservation in noncoding sequences, suggesting that the 200 family emerged prior to human-mouse speciation and subsequently diverged after gene duplication.

Amino Acid Sequence↗

Solution NMR characterization of the thermodynamics of the disulfide bond orientational isomerism and its effect of cluster electronic properties for the hyperthermostable three-iron cluster ferredoxin from the archaeon Pyrococcus furiosus.

The thermodynamics and dynamics of the Cys21-Cys48 disulfide "S" if "R" conformational isomerism in the three-iron, single cubane cluster ferredoxin (Fd) from the hyperthermophilic archaeon Pyrococcus furiosus (Pf) have been characterized by (1)H NMR spectroscopy in both water and water/methanol mixed solvents. The mean interconversion rate at 25 degrees C is 3 x 10(3) s(-1) and DeltaG(298) = -0.2 kcal/mol [DeltaH = 4.0 kcal/mol; DeltaS = 14 cal/(mol.K)], with the S orientation as the more stable form at low temperature (< 0 degrees C) but the R orientation predominating at >100 degrees C, where the organism thrives. The distinct pattern of ligated Cys beta-proton contact shifts for the resolved signals and their characteristic temperature behavior for the forms of the 3Fe Fd with alternate disulfide orientations have been analyzed to determine the influences of disulfide orientation and methanol cosolvent on the topology of the inter-iron spin coupling in the 3Fe cluster. The Cys21-Cys48 disulfide orientation influences primarily the spin couplings involving the iron ligated to Cys17, whose carbonyl oxygen is a hydrogen bond acceptor to the Cys21 peptide proton. Comparison of the Cys beta-proton contact shift pattern for the alternate disulfide orientations with the pattern exhibited upon cleaving the disulfide bridge confirms an earlier [Wang, P.-L., Calzolai, L., Bren, K. L., Teng, Q., Jenney, F. E., Jr., Brereton, P. S., Howard, J. B., Adams, M. W. W., and La Mar, G. N. (1999) Biochemistry 38, 8167-8178] proposal that the structure of the same Fd with the R disulfide orientation resembles that of the Fd upon cleaving the disulfide bond.

Amino Acid Sequence↗

Conversion of a Re(IV) tetrahedral cluster to a Re(III) octahedral cluster: synthesis of [(CH3)C(NH2)(2)](4)[Re(6)Se(8)(CN)(6)] by a solvothermal route.

The compound [(CH(3))C(NH(2))(2)](4)[Re(6)Se(8)(CN)(6)] has been synthesized by the reaction at 200 degrees C for 3 days of Re(4)Te(4)(TeCl(2))(4)Cl(8), KSeCN, and NH(4)Cl in superheated acetonitrile. This compound crystallizes in the space group C2/c of the monoclinic system with four formula units in a cell of dimensions a = 20.3113(14) A, b = 10.1332(7) A, c = 19.9981(14) A, beta = 106.754(1) degrees, V = 3941.3(5) A(3) (T = 153 K). The [Re(6)Se(8)(CN)(6)](4-) anion comprises an Re(6) octahedron face capped by mu(3)-Se atoms, with each Re atom liganded by a CN group. The anions and cations are connected by an extensive network of hydrogen bonds. The conversion of a Re(IV) tetrahedral cluster to a Re(III) octahedral cluster appears to be unprecedented.

Journal Article↗

Density functional theory study of nine-atom germanium clusters: effect of electron count on cluster geometry.

Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge(9)(z) clusters (z = -6, -4, -3, -2, 0, +2, and +4) starting from three different initial configurations. Double-zeta quality LANL2DZ basis functions extended by adding one set of polarization (d) and one set of diffuse (p) functions were used. The global minimum for Ge(9)(2)(-) is the tricapped trigonal prism expected by Wade's rules for a 2n + 2 skeletal electron structure. An elongated tricapped trigonal prism is the global minimum for Ge(9)(4)(-) similar to the experimentally found structure for the isoelectronic Bi(9)(5+). However, the capped square antiprism predicted by Wade's rules for a 2n + 4 skeletal electron structure is only 0.21 kcal/mol above this global minimum indicating that these two nine-vertex polyhedra have very similar energies in this system. Tricapped trigonal prismatic structures are found for both singlet and triplet Ge(9)(6)(-), with the latter being lower in energy by 3.66 kcal/mol and far less distorted. The global minimum for the hypoelectronic Ge(9) is a bicapped pentagonal bipyramid. However, a second structure for Ge(9) only 4.54 kcal/mol above this global minimum is the C(2)(v)() flattened tricapped trigonal prism structure found experimentally for the isoelectronic Tl(9)(9)(-). For the even more hypoelectronic Ge(9)(2+), the lowest energy structure consists of an octahedron fused to two trigonal bipyramids. For Ge(9)(4+), the global minimum is an oblate (squashed) pentagonal bipyramid with two pendant Ge vertices.

Journal Article↗

Assembly of heterometallic clusters and coordination polymers by combining Mo-S-based clusters with Mn2+.

Addition of [Mo(V)2O2S2(edt)2]2- (edt =1,2-ethanedithiolate) to acetonitrile and/or methanol solutions of MnII containing bipyridines [4,4'-trimethylenedipyridine (TDP), 4,4'-bipyridine (4,4'-bpy), 2,2'-bipyridine (2,2'-bpy)] or 15-crown-5 produces three new heterometallic cluster coordination polymers, [Mn2[Mo2O2S2(edt)2]2(TDP)3(CH3OH)2(NCMe)2].3CH3OH.0.25MeCN (1), [Mn(TDP)2(H2O)2]2+[Mn[Mo2O2S2(edt)2)2(TDP)2]]2-.6CH3OH (2), [Mn[Mo2O2S2(edt)2](TDP)2(CH3OH)(H2O)].CH3OH (3), and three new multinuclear clusters, [Mn[Mo2O2S2(edt)2](4,4'-bpy)(CH3OH)4].0.5(4,4'-bpy) (4), [Mn[Mo2O2S2(edt)2](2,2'-bpy)2].2CH3OH (5), and (NEt4)2[Mn(15-crown-5)[Mo2O2S2(edt)2]2] (6). All compounds were characterized by X-ray crystallography. The coordination mode of Mn in these compounds depends on the ligands and the crystallization conditions. Compound 2 readily converts to 1 or 3 depending on the reaction and solvent conditions. Compounds 1 and 2 were analyzed using thermogravimetric analysis combined with mass spectroscopy (TG-MS) in the temperature range 25-500 degrees C. The room-temperature magnetic moments for compounds 1-6 were determined.

Journal Article↗

Chalcogen-rich lanthanide clusters: cluster reactivity and the influence of ancillary ligands on structure.

Ytterbium metal reacts with PhEEPh (E = S, Se, Te) and elemental Se in pyridine to give (pyridine)(8)Yb(4)(SeSe)(2)(Se)(2)(mu(2)-SPh)(2)(SPh)(2), (py)(8)Yb(4)Se(SeSe)(3)(SeSeSePh)(Se(0.38)SePh), and (py)(8)Yb(4)Se(SeSe)(3)(SeSeTePh)(SeTePh), respectively. The SePh and TePh compounds contain a square array of Ln(III) ions all connected to a central Se(2)(-) ligand. Three edges of the square are bridged by diselenide ligands, with the fourth SeSe unit coordinating to an EPh ligand that has been displaced from an inner Yb coordination sphere. Differences in the two compounds have their origin in the relative strength of the Yb-E(Ph) bond. In the TePh compound, there is a complete insertion of Se into the remaining Yb-Te(Ph) bond to give a terminal SeTePh ligand, while in the SePh compound there is a compositional disorder in the structure comprised of a terminal SePh ligand and a minor component that has Se inserted into the Yb-Se(Ph) bond to give a terminal SeSePh ligand. The thiolate compound differs dramatically, crystallizing as a rhombohedral array of four Yb(III) ions connected by a pair of mu(3)-Se(2)(-) ligands, with the edges of the rhombus spanned by alternating diselenide and SPh. The SPh coordinate directly to Yb(III) ions in terminal or bridging modes. Cluster interconversion is facile: (py)(4)Yb(SePh)(2) reduces (py)(8)Yb(4)Se(SeSe)(3)(SeSeSePh)(Se(0.38)SePh) to give the cubane cluster [(py)(2)YbSe(SePh)](4), and the cubane reacts with elemental Se to give (py)(8)Yb(4)Se(SeSe)(3)(SeSeSePh)(Se(0.38)SePh). Upon thermolysis, these compounds give YbSe(x)().

Journal Article↗

Iron-sulfur cluster biosynthesis: characterization of iron nucleation sites for assembly of the [2Fe-2S]2+ cluster core in IscU proteins.

ISU (eukaryotes) and IscU (prokaryotes) are a homologous family of proteins that appear to provide a platform for assembly of [2Fe-2S] centers prior to delivery to a target apoprotein. The intermediate [2Fe-2S] IscU-bound cluster is formed by delivery of iron and sulfur to the apo-IscU, with the latter delivered through an IscS-mediated reaction. The identity of the iron donor is not yet established. In this report we characterize iron-binding sites on IscU that appear to nucleate [2Fe-2S] cluster assembly. This iron-bound form of IscU is shown to be viable for subsequent IscS-mediated assembly of holo-IscU. Following on recent reports, we demonstrate the persulfide form of IscU to be a dead-end complex that is incapable of forming holoprotein after addition of ferrous or ferric ion. The latter observation reflects the low binding affinity of persulfido IscU for iron ion.

Bacterial Proteins↗

Probing cooperative effects in bimetallic clusters: indications of C-N coupling of CH4 and NH3 mediated by the cluster ion PtAu+ in the gas phase.

The bimetallic cluster ion PtAu+ activates methane in the gas-phase, yielding the carbene PtAuCH2+ which further reacts with ammonia under C-N coupling. In contrast, neither Pt2+ nor Au2+ mediates C-N bond formation. This example demonstrates how bond activation in the gas phase can be tuned by cooperative effects in bimetallic clusters.

Journal Article↗

The influence of metal cluster size on adsorption energies: CO adsorbed on Au clusters supported on TiO2.

Infrared reflection absorption spectroscopy (IRAS) has been used to study CO adsorption on Au clusters ranging in size from 1.8 to 3.1 nm, supported on TiO(2). The adsorbed CO vibrational frequency blue-shifts slightly (approximately 4 cm(-)(1)) compared to that adsorbed on bulk Au, whereas the heats of adsorption (-DeltaH(ads)) increase sharply with decreasing cluster size, from 12.5 to 18.3 kcal/mol.

Journal Article↗

Bimetallic cluster complexes: the synthesis, structures, and bonding of ruthenium carbonyl cluster complexes containing palladium and platinum with the bulky tri-tert-butyl-phosphine ligand.

The bis-phosphine compounds M(PBut3)2, M = Pd and Pt, readily eliminate one PBut3 ligand and transfer MPBut3 groups to the ruthenium-ruthenium bonds in the compounds Ru3(CO)12, Ru6(CO)17(micro6-C), and Ru6(CO)14(eta6-C6H6)(micro6-C) without displacement of any of the ligands on the ruthenium complexes. The new compounds, Ru3(CO)12[Pd(PBut3)]3, 10, and Ru6(CO)17(micro6-C)[Pd(PBut3)]2, 11, Ru6(CO)17(micro6-C)[Pt(PBut3)]n, n = 1 (12), n = 2 (13), and Ru6(CO)14(eta6-C6H6)(micro6-C)[Pd(PBut3)]n, n = 1 (15), n = 2 (16), have been prepared and structurally characterized. In most cases the MPBut3 groups bridge a pair of mutually bonded ruthenium atoms, and the associated Ru-Ru bond distance increases in length. Fenske-Hall calculations were performed on 10 and 11 to develop an understanding of the electron deficient metal-metal bonding. 10 undergoes a Jahn-Teller distortion to increase bonding interactions between neighboring Ru(CO)4 and Pd(PBut3) fragments. 11 has seven molecular orbitals important to cluster bonding in accord with cluster electron-counting rules.

Journal Article↗

Novel rhodium and ruthenium carbonyl cluster complexes with face- and edge-bridging GaCp* ligands. Synthesis and structural characterization of the Rh6(CO)12(mu3-GaCp*)4 and Ru6(eta6-C)(mu2-CO)(CO)13(mu3-GaCp*)2(mu2-GaCp*) clusters.

Reactions of hexanuclear carbonyl clusters of rhodium Rh(6)(CO)(16) and ruthenium Ru(6)(eta(6)-C)(micro(2)-CO)(CO)(16) with GaCp*(Cp*= C(5)Me(5)) in the mild conditions result in substitution of CO ligands and formation of the Rh(6)(CO)(12)(micro(3)-GaCp*)(4) and the Ru(6)(eta(6)-C)(micro(2)-CO)(CO)(13)(micro(3)-GaCp*)(2)(micro(2)-GaCp*) cluster derivatives.

Journal Article↗

The isolable matryoshka nesting doll icosahedral cluster [As@Ni12@As20]3- as a "superatom": analogy with the jellium cluster Al13- generated in the gas phase by laser vaporization.

The valence electrons in the recently reported icosahedral cluster [As@Ni(12)@As(20)](3-) with a Russian matryoshka nesting doll structure can be partitioned so that the central As atom has the rare gas configuration, as As(3-), and the intermediate Ni(12) icosahedron receives 40 electrons from the lone pairs of the outer As(20) dodecahedron to be isoelectronic with the Al(13)(-) jellium cluster found in molecular beam experiments.

Journal Article↗

Stoichiometry and cluster specificity of copper binding to metallothionein: homogeneous metal clusters.

Experiments were done to define the stoichiometry of binding of Cu(I) to metallothionein (MT) and to determine its sites of binding in mixed-metal species. Spectrophotometric titrations of rabbit liver Cd7-MT 2, apoMT, and Cd4-alpha-domain with Cu(I) revealed endpoints of 3-4, 4 and 8, and 4 and 6-7 added Cu(I)/mol of MT for the three species respectively. Observed endpoints depended on conditions of the titration and the wavelength chosen for absorbance measurement. Nevertheless, from metal and sulphydryl analyses of titrated proteins that were pretreated with Chelex-100 to remove metal ions from solution, almost all of the cadmium was displaced from Cd7-MT by the addition of 7 Cu(I)/mol of MT. Similarly, 4 Cu(I)/mol of Cd4-alpha-domain completely displaced bound cadmium. The Cu4-alpha-domain was converted into a Cu6-alpha species upon addition of two equivalents of Cu(I)/mol of alpha-domain. Reaction of Cd7-MT with 7, 12 and 20 Cu/mol of MT, followed by reaction with Chelex resin, generated protein samples in each case with about 7 Cu/mol of MT. 111Cd-NMR analysis of the reaction of 111Cd7-MT with Cu(I) showed that nearly co-operative one-for-one replacement of 111Cd occurred and that the beta-domain cluster reacted before the alpha-domain cluster. Two mixed-metal MTs with Cu to Zn ratios approximating 3 to 4 and 6 to 4 were isolated from calf liver. After substitution of Zn with 111Cd, NMR spectra of each protein showed that 111Cd was confined almost completely to the alpha-domain. By inference, about 3 or 6 Cu were bound in the beta-domain of these proteins. Supporting this segregation of metal ions into domains, reaction of Cu6, Zn4-MT with nitrilotriacetate removed zinc exclusively, whereas reaction of Cu6,Cd4-MT with 4,7-phenylsulphonyl-2,9-dimethyl-1,10-phenanthroline extracted only Cu(I). Proteolytic digestion of both products followed by gel filtration demonstrated that Cu(I) and Cd were bound to fragments of the intact protein. Finally, reaction of rabbit liver 111Cd7-MT 2 with Cu10-MT 2 resulted in interprotein metal exchange in which 111Cd-moved from the beta- to the alpha-domain according to NMR analysis. In contrast with the prevalent view that six Cu(I) bind to each domain of MT, the present results show that Cu(I) binds to MT with a minimum stoichiometry of about 7 Cu(I)/mol of MT and can bind to the alpha-domain with stoichiometries of 4 or 6 Cu(I)/mol of MT. Although MTs interacting with 12 or 20 Cu(I)/mol of MT are less stable than that binding about 7 Cu(I)/mol, it appears that MT can bind Cu(I) in multiple stoichiometries.

Acetonitriles↗