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At least 19 recordsLinked to original sources
PubMed2000

The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S].

Hybrid-cluster proteins ('prismane proteins') have previously been isolated and characterized from strictly anaerobic sulfate-reducing bacteria. These proteins contain two types of Fe/S clusters unique in biological systems: a [4Fe-4S] cubane cluster with spin-admixed S = 3/2 ground-state paramagnetism and a novel type of hybrid [4Fe-2S-2O] cluster, which can attain four redox states. Genomic sequencing reveals that genes encoding putative hybrid-cluster proteins are present in a range of bacterial and archaeal species. In this paper we describe the isolation and spectroscopic characterization of the hybrid-cluster protein from Escherichia coli. EPR spectroscopy shows the presence of a hybrid cluster in the E. coli protein with characteristics similar to those in the proteins of anaerobic sulfate reducers. EPR spectra of the reduced E. coli hybrid-cluster protein, however, give evidence for the presence of a [2Fe-2S] cluster instead of a [4Fe-4S] cluster. The hcp gene encoding the hybrid-cluster protein in E. coli and other facultative anaerobes occurs, in contrast with hcp genes in obligate anaerobic bacteria and archaea, in a small operon with a gene encoding a putative NADH oxidoreductase. This NADH oxidoreductase was also isolated and shown to contain FAD and a [2Fe-2S] cluster as cofactors. It catalysed the reduction of the hybrid-cluster protein with NADH as an electron donor. Midpoint potentials (25 degrees C, pH 7.5) for the Fe/S clusters in both proteins indicate that electrons derived from the oxidation of NADH (Em NADH/NAD+ couple: -320 mV) are transferred along the [2Fe-2S] cluster of the NADH oxidoreductase (Em = -220 mV) and the [2Fe-2S] cluster of the hybrid-cluster protein (Em = -35 mV) to the hybrid cluster (Em = -50, +85 and +365 mV for the three redox transitions). The physiological function of the hybrid-cluster protein has not yet been elucidated. The protein is only detected in the facultative anaerobes E. coli and Morganella morganii after cultivation under anaerobic conditions in the presence of nitrate or nitrite, suggesting a role in nitrate-and/or nitrite respiration.

Amino Acid Sequence↗
PubMed1991

Clusters of clusters: self-organization and self-similarity in the intermediate stages of cluster growth of Au-Ag supraclusters.

A systematic structural investigation of a new series of high-nuclearity Au-Ag clusters containing 25, 37, 38, and 46 metal atoms led to the description of these clusters as "clusters of clusters" based on vertex-sharing icosahedra as building blocks. Based on the observed structures, a growth sequence is proposed here for the formation of these secondary clusters (clusters of clusters) from a single 13-atom icosahedron to a 127-atom icosahedron of icosahedra via successive additions of vertex-sharing icosahedral units. This cluster-of-clusters growth mechanism parallels the atom-by-atom growth pathway for the primary clusters from a single atom to a 13-atom icosahedron. It is hypothesized that the formation of these clusters of clusters is a manifestation of the spontaneous self-organization and self-similarity processes often observed in nature. It is conceivable that the concept of cluster of clusters may be important in the intermediate stages of some cluster growth as exemplified by the polyicosahedral growth of Au-Ag supraclusters.

Journal Article↗
PubMed2003

Vanadium-iron-sulfur clusters containing the cubane-type [VFe3S4] core unit: synthesis of a cluster with the topology of the PN cluster of nitrogenase.

A synthetic method affording a topological analogue of the electron-transfer P-cluster of nitrogenase (Fe(8)S(7)(mu(2)-S(Cys))(2)) in the P(N) state has been devised, based in part on our previous development of cubane-type VFe(3)S(4) clusters (Hauser, C.; Bill, E.; Holm, R. H. Inorg. Chem. 2002, 41, 1615-1624). The cluster [(Tp)VFe(3)S(4)Cl(3)](2-) (1) is converted to [(Tp)VFe(3)S(4)(PR(3))(3)](1+) (R = Et (2), Bu (3)) by reaction with R(3)P. The phosphine ligands are readily substituted, leading to [(Tp)VFe(3)S(4)(SR)(3)](2-) (R = Ph (4), H (5)). Reduction of 2 or 3 with cobaltocene produces the edge-bridged double cubanes [(Tp)(2)V(2)Fe(6)S(8)(PR(3))(4)] (R = Et (6), Bu (7)), which are readily converted to [(Tp)(2)V(2)Fe(6)S(8)(SPh)(4)](4-) (8). The structures of clusters 3-5 and 8 were proven crystallographically. Cluster 8 has the double-cubane structure previously shown for 6, in which two cubane units are bridged by two Fe-(mu(4)-S) bonds. (57)Fe isomer shifts are consistent with the formulation [VFe(2.33+)(3)S(4)](2+) for the single cubanes and the all-ferrous description 2[VFe(2+)(3)S(4)](1+) for the double cubanes. Reaction of 6 with 4 equiv of (Et(4)N)(HS) in acetonitrile results in the insertion of sulfide with concomitant structural rearrangement and the formation of [(Tp)(2)V(2)Fe(6)S(9)(SH)(2)](4-) (10), obtained in ca. 50% yield as the Et(4)N(+) salt. The cluster has C(2) symmetry, with two all-ferrous VFe(3)S(4) fragments bridged by a common mu(6)-S atom and two mu(2)-S atoms that simulate the bridging atoms in the two Fe-(mu(2)-S(Cys))-Fe bridges of the P(N) cluster. The bridge pattern V(2)Fe(6)(mu(2)-S)(2)(mu(3)-S)(6)(mu(6)-S) and cluster shape match those of the native cluster. A best-fit superposition of the cores of 10 and the P(N) cluster affords a weighted rms deviation in atom positions of 0.33 A. Cluster 10 and [(Tp)(2)Mo(2)Fe(6)S(9)(SH)(2)](3-), prepared by a related route (Zhang, Y.; Holm, R. H. J. Am. Chem. Soc. 2003, 125, 3910-3920), demonstrate that the topology of the P(N) cluster can be achieved in molecular form in the absence of protein structure (Tp = tris(pyrazolyl)hydroborate).

Crystallography, X-Ray↗
PubMed2004

Cluster-cluster aggregation controlled by the number of intercluster connections: kinetics of aggregation and cluster mass frequency.

The aggregation of colloids in the presence of hydrodynamic forces was investigated, employing a numerical model that took into account the masses of the individual clusters and the number of intercluster connections established when two clusters stuck together. The number of possible connections was determined by analyzing all the possible nonoverlapping configurations of stuck clusters. This operation was done for a couple of clusters of various masses, taking into account the assembly of clusters of even and uneven masses. The formulation of the constraints established a certain hierarchy in the sticking on a basis compatible with the irregular fracture model of Horwatt and co-workers. As a result, the permanent sticking of large clusters required the formation of a large number of connections, whereas that of small clusters might be realized even with a small number of connections. Thus, the aggregation started with the features of the standard reaction-limited process and this cluster growth became progressively inhibited as a result of the prevailing effects of the connection constraints. The cluster-mass frequency showed the emergence at least of a second population whose bell-shaped mass distribution was superimposed on the monotonically decreasing distribution resulting from the reaction-limited aggregation process. The results of the numerical study were confronted with those previously obtained in the aggregation of hydrated polystyrene latex particles dispersed in 1 M sodium chloride solution. The two striking features--the aggregate growth kinetics and the mass distribution function--were common to the computer-generated clusters and the latex aggregates.

Journal Article↗
PubMed2003

Cubane-type heterometallic sulfido clusters: incorporation of two metal fragments into a dinuclear ReS(mu-S)2ReS core affording bimetallic M2Re2(mu 3-S)4 clusters (M = Ru, Pt, Cu) or trimetallic MM'Re2(mu 3-S)4 clusters via incomplete cubane-type MRe2(mu 3-S)(mu 2-S)3 intermediates (M = Ru, Rh, Ir; M' = Mo, W, Pd, Ru, Rh).

Reactions of a dirhenium tetra(sulfido) complex [PPh(4)](2)[ReS(L)(mu-S)(2)ReS(L)] (L = S(2)C(2)(SiMe(3))(2)) with a series of group 8-11 metal complexes in MeCN at room temperature afforded either the cubane-type clusters [M(2)(ReL)(2)(mu(3)-S)(4)] (M = CpRu (2), PtMe(3), Cu(PPh(3)) (4); Cp = eta(5)-C(5)Me(5)) or the incomplete cubane-type clusters [M(ReL)(2)(mu(3)-S)(mu(2)-S)(3)] (M = (eta(6)-C(6)HMe(5))Ru (5), CpRh (6), CpIr (7)), depending on the nature of the metal complexes added. It has also been disclosed that the latter incomplete cubane-type clusters can serve as the good precursors to the trimetallic cubane-type clusters still poorly precedented. Thus, treatment of 5-7 with a range of metal complexes in THF at room temperature resulted in the formation of novel trimetallic cubane-type clusters, including the neutral clusters [[(eta(6)-C(6)HMe(5))Ru][W(CO)(3)](ReL)(2)(mu(3)-S)(4)], [(CpM)[W(CO)(3)](ReL)(2)(mu(3)-S)(4)] (M = Rh, Ir), [(Cp*Ir)[Mo(CO)(3)](ReL)(2)(mu(3)-S)(4)], [[(eta(6)-C(6)HMe(5))Ru][Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)], and [(Cp*Ir)[Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)] (13) along with the cationic clusters [(Cp*Ir)(CpRu)(ReL)(2)(mu(3)-S)(4)][PF(6)] (14) and [(Cp*Ir)[Rh(cod)](ReL)(2)(mu(3)-S)(4)][PF(6)] (cod = 1,5-cyclooctadiene). The X-ray analyses have been carried out for 2, 4, 7, 13, and the SbF(6) analogue of 14 (14') to confirm their bimetallic cubane-type, bimetallic incomplete cubane-type, or trimetallic cubane-type structures. Fluxional behavior of the incomplete cubane-type and trimetallic cubane-type clusters in solutions has been demonstrated by the variable-temperature (1)H NMR studies, which is ascribable to both the metal-metal bond migration in the cluster cores and the pseudorotation of the dithiolene ligand bonded to the square pyramidal Re centers, where the temperatures at which these processes proceed have been found to depend upon the nature of the metal centers included in the cluster cores.

Journal Article↗
PubMed1995

Mapping of the alpha 4 subunit gene (GABRA4) to human chromosome 4 defines an alpha 2-alpha 4-beta 1-gamma 1 gene cluster: further evidence that modern GABAA receptor gene clusters are derived from an ancestral cluster.

We demonstrated previously that an alpha 1-beta 2-gamma 2 gene cluster of the gamma-aminobutyric acid (GABAA) receptor is located on human chromosome 5q34-q35 and that an ancestral alpha-beta-gamma gene cluster probably spawned clusters on chromosomes 4, 5, and 15. Here, we report that the alpha 4 gene (GABRA4) maps to human chromosome 4p14-q12, defining a cluster comprising the alpha 2, alpha 4, beta 1, and gamma 1 genes. The existence of an alpha 2-alpha 4-beta 1-gamma 1 cluster on chromosome 4 and an alpha 1-alpha 6-beta 2-gamma 2 cluster on chromosome 5 provides further evidence that the number of ancestral GABAA receptor subunit genes has been expanded by duplication within an ancestral gene cluster. Moreover, if duplication of the alpha gene occurred before duplication of the ancestral gene cluster, then a heretofore undiscovered subtype of alpha subunit should be located on human chromosome 15q11-q13 within an alpha 5-alpha x-beta 3-gamma 3 gene cluster at the locus for Angelman and Prader-Willi syndromes.

Amino Acid Sequence↗
PubMed2005

Iron-sulfur cluster biosynthesis. Molecular chaperone DnaK promotes IscU-bound [2Fe-2S] cluster stability and inhibits cluster transfer activity.

IscU functions as a scaffold for Fe-S cluster assembly and transfer, and is known to be a substrate protein for molecular chaperones. Kinetic studies of Fe-S cluster transfer from holo IscU to apo Fd in the presence of chaperone DnaK demonstrate an inhibitory effect on the rate of Fe-S cluster transfer from IscU. Binding of DnaK reduces the rate of formation of the IscU-Fd complex (greater than 8-fold), but has little influence on the intrinsic rate of iron-sulfur cluster transfer to apo Fd. Apparently the molecular chaperone DnaK does not facilitate the process of Fe-S cluster transfer from IscU. Rather, DnaK has a modest influence on the stability of the IscU-bound Fe-S cluster that may reflect a more important role in promoting cluster assembly. In accord with prior observations the cochaperone DnaJ stimulates the ATPase activity of DnaK, but has a minimal influence on IscU cluster transfer activity, either alone or in concert with DnaK.

Amino Acid Sequence↗
PubMed2006

HF in clusters of molecular hydrogen: II. Quantum solvation by H2 isotopomers, cluster rigidity, and comparison with CO-doped parahydrogen clusters.

We present a comprehensive theoretical study of the quantum solvation of the HF molecule by small clusters of the H2 isotopomers, p-H2, HD, and o-D2, with up to 13 hydrogen solvent molecules. This complements our earlier work on the HF-doped parahydrogen clusters [H. Jiang and Z. Bacic, J. Chem. Phys. 122, 244306 (2005)]. The ground-state properties of the clusters are calculated exactly using the diffusion Monte Carlo method. Detailed information is obtained regarding the size and isotopomer dependences of the energetics, vibrationally averaged structures, and their rigidity. The rigidity of these clusters is investigated further by analyzing the distributions of their principal moments of inertia from the diffusion Monte Carlo simulations. The clusters are found to be rather rigid, especially when compared with the pure parahydrogen clusters of the same size. Extensive comparison is made with the quantum Monte Carlo results for the CO-doped parahydrogen clusters and significant differences are observed in the size evolution of certain properties, notably the chemical potential.

Journal Article↗
PubMed2001

One-year follow-up of patients with cluster C personality disorders: a prospective study comparing patients with "pure" and comorbid conditions within cluster C, and "pure" C with "pure" cluster A or B conditions.

This one-year, post-treatment prospective study of consecutively admitted patients to a national psychiatric in-patient clinic, compares patients belonging to four subgroups of DSM-III-R personality disorder (PDs): "pure cluster A (N = 21), "pure" B (N = 67), "pure" C (N = 251), and Axis II "comorbid" C (N = 138). Outcome was measured by SCl-90 and occupational status. Axis I disorders were controlled for in all analyses. Contrary to our hypothesis, patients in pure cluster C had no better outcome than either Axis II comorbid cluster C patients or patients with pure cluster A or B. Although pure C patients relapsed in symptom distress after discharge, comorbid C patients did not. C patients with an additional Histrionic PD were less at risk to be a case at follow up (GSI level > 1.00). Cluster C disorders as a whole had negative impact upon outcome in the total sample. These findings suggest the need for better treatment of patients with cluster C conditions.

Cluster Analysis↗
PubMedDate not supplied

Cluster analysis: significance, empty space, clustering tendency, non-uniformity. I--Statistical tests on the significance of clusters.

The agglomerative clustering methods and the tests usually applied to evaluate the significance of clusters are critically evaluated. Many clustering techniques can provide erroneous information about the existence of clusters. The single linkage technique is suggested to identify natural, well separated, clusters. The existing statistical tests on the significance of clusters are not satisfactory. A new statistical test, based on the distribution of the distances between the objects and their first nearest neighbor, is presented. The performances of the test are compared with those of the Sneath test and of the variance-ratio test on some artificial and real data sets.

Chemistry Techniques, Analytical↗
PubMed2006

Precursors to clusters with the topology of the P(N) cluster of nitrogenase: edge-bridged double cubane clusters [(Tp)2Mo2Fe6S8L4]z: synthesis, structures, and electron transfer series.

Members of the cluster set [(Tp)2Mo2Fe6S8L4]z contain the core unit M2Fe6(mu3-S)6(mu4-S)2 in which two MoFe3S4 cubanes are coupled by two Fe-(mu4-S) interactions to form a centrosymmetric edge-bridged double cubane cluster. Some of these clusters are synthetic precursors to [(Tp)2Mo2Fe6S9L2]3-, which possess the same core topology as the P(N) cluster of nitrogenase. In this work, the existence of a three-member electron-transfer series of single cubanes [(Tp)MoFe3S4L3](z) (z = 3-, 2-, 1-) and a four-member series of double cubanes [(Tp)2Mo2Fe6S8L4]z (z = 4-, 3-, 2-, 1-) with L = F-, Cl-, N3, PhS- is demonstrated by electrochemical methods, cluster synthesis, and X-ray structure determinations. The potential of the [4-/3-] couple is extremely low (<-1.5 V vs SCE in acetonitrile) such that the 4- state cannot be maintained in solution under normal anaerobic conditions. The chloride double cubane redox series was examined in detail. The members [(Tp)2Mo2Fe6S8Cl4]4-,3-,2- were isolated and structurally characterized. The redox series includes the reversible steps [4-/3-] and [3-/2-]. Under oxidizing conditions, [(Tp)2Mo2Fe6S8Cl4]2- cleaves with the formation of single cubane [(Tp)MoFe3S4Cl3]1-. The quasireversible [2-/1-] couple is observed at more positive potentials than those of the single cubane redox step. Structure comparison of nine double cubanes suggests that significant dimensional changes pursuant to redox reactions are mainly confined to the Fe2(mu4-S)2 bridge rhomb. The synthesis and structure of [(Tp)2Mo2Fe6S9F2.H2O]3-, a new topological analogue of the P(N) cluster of nitrogenase, is described. (Tp = hydrotris(pyrazolyl)borate(1-)).

Azides↗
PubMed2002

Cluster persistence in one-dimensional diffusion-limited cluster-cluster aggregation.

The persistence probability, P(C)(t), of a cluster to remain unaggregated is studied in cluster-cluster aggregation, when the diffusion coefficient of a cluster depends on its size s as D(s) approximately s(gamma). In the mean field the problem maps to the survival of three annihilating random walkers with time-dependent noise correlations. For gamma> or =0 the motion of persistent clusters becomes asymptotically irrelevant and the mean-field theory provides a correct description. For gamma<0 the spatial fluctuations remain relevant and the persistence probability is overestimated by the random walk theory. The decay of persistence determines the small size tail of the cluster size distribution. For 0<gamma<2 the distribution is flat and, surprisingly, independent of gamma.

Journal Article↗
PubMed2006

From simple monopyridine clusters [Mo6Br13(Py-R)][n-Bu4N] and hexapyridine clusters [Mo6X8(Py-R)6][OSO2CF3]4 (X = Br or I) to cluster-cored organometallic stars, dendrons, and dendrimers.

Hexasubstitution of apical triflate ligands in the octahedral clusters [M]2[Mo6X8(CF3SO3)6] (M = n-Bu4N or Cs, X = Br or I) and monosubstitution in [n-Bu4N]2[Mo6Br13(CF3SO3)] was carried out in tetrahydrofuran at 60 degrees C with simple pyridines and then extended to organometallic pyridines, yielding cluster-cored stars, and to dendronic polyallyl- and polyferrocenylpyridines, yielding cluster-cored polyallyl and polyferrocenyl dendrimers and dendrons. The orange pyridine-substituted clusters, whose pyridine protons are deshielded in 1H NMR (a practical tool for characterization), are air-stable and thermally stable with simple pyridines, light- and air-sensitive with organometallic pyridines, and air-fragile and thermally fragile with large dendronized pyridines.

Journal Article↗
PubMed2003

Preparation and precise structural determination of a second Ga84 cluster compound. A first hint for cluster doping and its fundamental consequences in the field of chemistry and physics of nanoscaled metalloid cluster material.

The Ga(84)R(20)(4-) [R = N(SiMe(3))(2)] species, which represents the largest metalloid cluster entity structurally characterized so far, has been electronically and topologically modified: Via changing the redox potential of the reaction solution, crystals different from those containing the Ga(84)R(20)(4-) anion can be isolated, featuring similar Ga(84)R(20)(3-) entities. An accurate crystal structure analysis via synchrotron radiation is presented, which might be the first step toward an understanding of the metallic conductivity and superconductivity of the Ga(84)R(20)(4-) cluster compound, physical properties which are singular in the field of metalloid clusters so far.

Journal Article↗
PubMed2005

Image analysis of irregularity of cluster shape in cytological diagnosis of breast tumors: cluster analysis with 2D-fractal dimension.

To establish diagnostic criteria using comparison of cell cluster shapes, between benign and malignant tumors, breast tumors demonstrating weak cellular atypia in low grade invasive ductal carcinoma (IDC) were compared. Fine-needle aspiration (FNA) specimens of breast tumors were obtained from 37 patients. Among these, 16 were histologically diagnosed as IDC low-grade and the other 21 as benign fibroadenoma (FA). For evaluation, we examined 740 clusters from these 37 FNA specimens. Nine image morphometric parameters were studied, including the cluster area, circumference, maximal length, maximal breadth, ratio of length to breadth, cluster roundness, cluster size, and the edge and distribution image fractal dimensions for cluster analysis. We evaluated the irregularity in cell cluster shape using fractal dimension analysis, and determined the correlation to cluster size. The irregularity in the IDC cluster shape was higher than that in the FA cluster shape. However, six cases (28.5%) of 21 FA clusters showed high fractal dimensions similar to those for IDC. The clusters were classified by cluster analysis into three types: IDC clusters, FA with irregular cluster shape, and FA with no irregular clusters. The average cell cluster area of the FA with irregular shape was found to be about three times larger than that of IDC clusters. When the differential diagnosis between IDC and FA is difficult, it is important to focus on irregularities in the shape and on overall size of the cell clusters. For accurate diagnosis, the cell cluster shape is as important as the individual cellular atypia.

Adenofibroma↗
PubMed2004

Selection of informative clusters from hierarchical cluster tree with gene classes.

BACKGROUND: A common clustering method in the analysis of gene expression data has been hierarchical clustering. Usually the analysis involves selection of clusters by cutting the tree at a suitable level and/or analysis of a sorted gene list that is obtained with the tree. Cutting of the hierarchical tree requires the selection of a suitable level and it results in the loss of information on the other level. Sorted gene lists depend on the sorting method of the joined clusters. Author proposes that the clusters should be selected using the gene classifications. RESULTS: This article presents a simple method for searching for clusters with the strongest enrichment of gene classes from a cluster tree. The clusters found are presented in the estimated order of importance. The method is demonstrated with a yeast gene expression data set and with two database classifications. The obtained clusters demonstrated a very strong enrichment of functional classes. The obtained clusters are also able to present similar gene groups to those that were observed from the data set in the original analysis and also many gene groups that were not reported in the original analysis. Visualization of the results on top of a cluster tree shows that the method finds informative clusters from several levels of the cluster tree and indicates that the clusters found could not have been obtained by simply cutting the cluster tree. Results were also used in the comparison of cluster trees from different clustering methods. CONCLUSION: The presented method should facilitate the exploratory analysis of big data sets when the associated categorical data is available.

Cluster Analysis↗
PubMed1986

Elimination of preexistent acetylcholine receptor clusters induced by the formation of new clusters in the absence of nerve.

Acetylcholine receptors (AChRs) form clusters spontaneously in cultured Xenopus myotomal muscle cells in the absence of innervation. Innervation causes a dispersal of these clusters, as well as the formation of new clusters along the neuromuscular contact. To examine whether this dispersal process is dependent upon the presence of the nerve or can be effected by the formation of new clusters alone, we examined the stability of the preexistent clusters during the formation of new AChR clusters induced by basic polypeptide-coated latex beads. These beads cause a rapid development of clusters in cultured Xenopus muscle cells, and the size and the number of clusters can be experimentally manipulated by varying the size and number of beads applied to the culture. Accompanying the bead-induced formation of new clusters was an observed suppression of preexistent clusters, as shown by fluorescence microscopy after staining with rhodamine-conjugated alpha-bungarotoxin. This process of extra-bead cluster removal can be speeded up by treating the cultures with more beads or using beads of larger diameter. Furthermore, if the beads are applied before the spontaneous AChR clustering, no extra-bead clusters are formed. Thus, the latex beads can mimic the nerve in both causing the formation of new clusters and the dispersal of preexistent clusters. Although the receptor clusters are dispersed by the beads, the density of diffuse receptors, as shown by autoradiography with 125I-conjugated alpha-bungarotoxin does not decrease in the short-term cultures under study. This indicates that the dispersal of preexistent clusters is not due to a depletion of the surface pool of AChRs.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗