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PubMed1997

Epidemic diseases and host clustering: an optimum cluster size ensures maximum survival.

The risk of infection is generally believed to increase with gregariousness. Using a discrete time spatial simulation model we tested the effect of host clustering on transmission of infection within a population. Over a large parameter range, an optimum cluster size was observed to ensure maximum probability of escaping infection. Although the within cluster transmission increased with cluster size, the between cluster distance increased thereby decreasing the probability of transmission across clusters. The probability of stochastic extinction of the pathogen also increased with increasing cluster size. Thus contrary to the popular belief, clustering can be an effective strategy to minimize the risk of infections.

Computer Simulation↗
PubMed1989

Complete nucleotide sequence of the rabbit beta-like globin gene cluster. Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster.

The nucleotide sequence of the entire beta-like globin gene cluster of rabbits has been determined. This sequence of a continuous stretch of 44.5 x 10(3) base-pairs (bp) starts about 6 x 10(3) bp upstream from epsilon (the 5'-most gene) and ends about 12 x 10(3) bp downstream from beta (the 3'-most gene). Analysis of the sequence reveals that: (1) the sequence is relatively A + T rich (about 60%); (2) regions with high G + C content are associated with OcC repeats, a short interspersed repeated DNA in rabbits; (3) the distribution of polypurines, polypyrimidines and alternating purine/pyrimidine tracts is not random within the cluster; (4) most open reading frames are associated with known globin coding regions, OcC repeats or long interspersed repeats (L1 repeats); (5) the most prominent open reading frames are found in the L1 repeats; (6) different strand asymmetries in base composition are associated with embyronic and adult genes as well as the tandem L1 repeats at the 3' end of the cluster; and (7) essentially all the repeats appear to have been inserted by a transposon mechanism. A comparison of the sequence with itself by a dot-plot analysis has revealed nine new members of the OcC family of repeats in addition to the six previously reported. The OcC repeats tend to be clustered, particularly in the epsilon-gamma and gamma-psi delta intergenic regions. Dot-plot comparisons between the rabbit and the human clusters have revealed extensive sequence matches. Homology starts about 6 x 10(3) bp 5' to epsilon or as far upstream as the rabbit sequence is available. It continues throughout the entire cluster and stops about 0.7 x 10(3) bp 3' to beta, at which point several repeats have inserted in both rabbits and humans. Throughout the gene cluster, the homology is interrupted mainly by insertions or deletions in either the rabbit or the human genome. Almost all of the insertions are of known short or long repeated DNAs. The positions of the insertions are different in the two gene clusters, which indicates that both short and long repeats have been transposing throughout the genome for the time since the mammalian radiation. An alignment of rabbit and human sequences allows the calculation of the substitution rate around epsilon. Sequences far removed from the gene are evolving at a rate equivalent to the pseudogene rate, although some short regions show an apparently higher rate.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2006

The asymmetric IscA homodimer with an exposed [2Fe-2S] cluster suggests the structural basis of the Fe-S cluster biosynthetic scaffold.

It has been shown that the so-called scaffold proteins are vital in Fe-S cluster biosynthesis by providing an intermediate site for the assembly of Fe-S clusters. However, since no structural information on such scaffold proteins with bound Fe-S cluster intermediates is available, the structural basis of the core of Fe-S cluster biosynthesis remains poorly understood. Here we report the first Fe-S cluster-bound crystal structure of a scaffold protein, IscA, from Thermosynechococcus elongatus, which carries three strictly conserved cysteine residues. Surprisingly, one partially exposed [2Fe-2S] cluster is coordinated by two conformationally distinct IscA protomers, termed alpha and beta, with asymmetric cysteinyl ligation by Cys37, Cys101, Cys103 from alpha and Cys103 from beta. In the crystal, two alphabeta dimers form an unusual domain-swapped tetramer via central domains of beta protomers. Together with additional biochemical data supporting its physiologically relevant configuration, we propose that the unique asymmetric Fe-S cluster coordination and the resulting distinct conformational stabilities of the two IscA protomers are central to the function of IscA-type Fe-S cluster biosynthetic scaffold.

Amino Acid Sequence↗
PubMed2005

Deletion of N-terminal rapsyn domains disrupts clustering and has dominant negative effects on clustering of full-length rapsyn.

The peripheral muscle membrane protein rapsyn is essential for the formation and maintenance of high density acetylcholine receptor aggregates at the neuromuscular synapse. Rapsyn is concentrated at synaptic sites and is colocalized with acetylcholine receptors from the earliest stages of synaptogenesis. Previous studies have shown that recombinant rapsyn expressed in heterologous cells forms clusters, and acetylcholine receptors coexpressed with rapsyn are colocalized with rapsyn clusters. However, the molecular interactions involved in clustering of rapsyn are not well defined. To analyze the process of cluster formation by rapsyn we examined the formation of rapsyn clusters and complexes using mutant constructs specifically deleted for individual domains of rapsyn in the presence and absence of tagged, full-length rapsyn. Specific deletions of the tetratricopeptide repeat (TPR) domains 1 and 3 of rapsyn abrogated not only clustering of mutant rapsyns, but also, in a dominant negative fashion, the clustering of tagged, full-length rapsyn. We also analyzed rapsyn protein complexes isolated from cells transfected with tagged and untagged rapsyn. Our results show that both tagged and untagged rapsyn are present in immunoprecipitates of rapsyn from cotransfected cells, demonstrating that rapsyn molecules interact directly or indirectly to form oligomers. Mutants that were dominant negatives were also present in complexes containing tagged, full-length rapsyn. Together these results indicate that rapsyn forms clusters at the synapse by oligomerization, and suggest models for the mechanistic bases of this oligomerization via interactions mediated by TPRs 1 and 3.

Animals↗
PubMed2002

Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster.

The Escherichia coli DNA repair enzyme MutY plays an important role in the recognition and repair of 7,8-dihydro-8-oxo-2'-deoxyguanosine-2'-deoxyadenosine (OG*A) mismatches in DNA. MutY prevents DNA mutations caused by the misincorporation of A opposite OG by catalyzing the deglycosylation of the aberrant adenine. MutY is representative of a unique subfamily of DNA repair enzymes that also contain a [4Fe-4S]2+ cluster, which has been implicated in substrate recognition. Previously, we have used site-directed mutagenesis to individually replace the cysteine ligands to the [4Fe-4S]2+ cluster of E. coli MutY with serine, histidine, or alanine. These experiments suggested that histidine coordination to the iron-sulfur cluster may be accommodated in MutY at position 199. Purification and enzymatic analysis of C199H and C199S forms indicated that these forms behave nearly identical to the WT enzyme. Furthermore, introduction of the C199H mutation in a truncated form of MutY (C199HT) allowed for crystallization and structural characterization of the modified [4Fe-4S] cluster coordination. The C199HT structure showed that histidine coordinated to the iron cluster although comparison to the structure of the WT truncated enzyme indicated that the occupancy of iron at the modified position had been reduced to 60%. Electron paramagnetic resonance (EPR) spectroscopy on samples of C199HT indicates that a significant percentage (15-30%) of iron clusters were of the [3Fe-4S]1+ form. Oxidation of the C199HT enzyme with ferricyanide increases the amount of the 3Fe cluster by approximately 2-fold. Detailed kinetic analysis on samples containing a mixture of [3Fe-4S]1+ and [4Fe-4S]2+ forms indicated that the reactivity of the [3Fe-4S]1+ C199HT enzyme does not differ significantly from that of the WT truncated enzyme. The relative resistance of the [4Fe-4S]2+ cluster toward oxidation, as well as the retention of activity of the [3Fe-4S]1+ form, may be an important aspect of the role of MutY in repair of DNA damage resulting from oxidative stress.

Amino Acid Sequence↗
PubMed2002

Assessment of relative stabilities of positional isomers of polyhedral heteronuclear clusters via a simplified method of bond energy calculations based on tight-binding approach and adjacent matrix method: applications to binary icosahedral clusters.

A new and simple method for assessing the relative stabilities of various positional isomers of a given heteronuclear cluster is described. The method is based on a tight-binding approach in conjunction with an adjacent matrix methodology (TBAM). The usefulness of the method is illustrated by bond energy calculations of a number of binary icosahedral clusters, including noncentered icosahedral A(n)B(12)(-)n clusters comprising main-group elements B, C, N, and S as well as B- and A-centered icosahedral A(n)B(13)(-)n clusters that consist of transition metals, Au, Ag, Ni, and Pt atoms. The latter results are compared with the previously reported molecular mechanics calculations based on Lennard-Jones potential and with experimental results, whenever possible. The trends of the total bond energies obtained by the two methods are nearly parallel in all cases, indicating that the relative stabilities predicted by the two methods follow the same order. The TBAM approach provides a simple and efficient way of predicting the relative stabilities of various positional isomers of a given cluster, particularly for clusters where the number of positional isomers is so large that it cannot be handled manually. The total bond energies exhibit a stepwise progression. Each step is characterized by a set of A-A, B-B, and A-B bonds which uniquely determines the total bond energy and, hence, the stability. The step formation implies that positional isomers of a given cluster geometry can be categorized by sets of numbers of A-A, B-B, and A-B bonds, or simply the numbers of the minority (either A-A or B-B) bonds. Three site preference rules, the strong-bond rule, the heterobond rule, and the big-hole rule, were formulated based on these model calculations. These rules are useful in rationalizing and/or predicting the relative stabilities of various positional isomers of a given cluster geometry.

Journal Article↗
PubMed2003

Synthesis and reactions of cubane-type iron-sulfur-phosphine clusters, including soluble clusters of nuclearities 8 and 16.

A family of soluble, reduced iron-sulfur clusters with nuclearities 4, 8, and 16 having tertiary phosphine ligation and based on the Fe(4)S(4) cubane-type structural motif has been synthesized. The results of this investigation substantially extend and improve the results of our original work on iron-sulfur-phosphine clusters (Goh, C.; Segal, B. M.; Huang, J.; Long, J. R.; Holm, R. H. J. Am. Chem. Soc. 1996, 118, 11844). A general property of this cluster family is facile phosphine substitution. The clusters [Fe(4)S(4)(PR(3))(4)](+) are precursors to monosubstituted [Fe(4)S(4)(PR(3))(3)X] (X = Cl-, RS-), homoleptic [Fe(4)S(4)(SR)(4)](3-), and all-ferrous monocubanes [Fe(4)S(4)(PR(3))(4)] (R = Pr(i), Cy, Bu(t); generated in solution). In turn, [Fe(4)S(4)(PPr(i)()(3))(3)(SSiPh(3))] and [Fe(4)S(4)(PPr(i)(3))(4)] can be transformed into the dicubanes [Fe(8)S(8)(PPr(i)()(3))(4)(SSiPh(3))(2)] and [Fe(8)S(8)(PPr(i)((3))(6)], respectively. Further, the tetracubanes [Fe(16)S(16)(PR(3))(8)] are also accessible from [Fe(4)S(4)(PR(3))(4)] under different conditions. X-ray structures are described for [Fe(4)S(4)(PCy(3))(3)X] (X = Cl-, PhS-), [Fe(8)S(8)(PPr(i)(3))(4)(SSiPh(3))(2)], [Fe(8)S(8)(PPr(i)()(3))(6)], and [Fe(16)S(16)(PCy(3))(8)]. The monosubstituted clusters show different distortions of the [Fe(4)S(4)](+) cores from idealized cubic symmetry. The dicubanes possess edge-bridged double cubane structures with an Fe(2)(mu(4)-S)(2) bridge rhomb and idealized C(2)(h)() symmetry. The ready cleavage of these clusters into single cubanes is considered a probable consequence of strained bond angles at the mu(4)-S atoms. Tetracubanes contain four individual cubanes, each of which is implicated in two bridge rhombs so as to generate a cyclic structure of idealized D(4) symmetry. Redox properties and Mössbauer spectroscopic parameters are reported. The species [Fe(4)S(4)(PR(3))(4)] (in solution), [Fe(8)S(8)(PR(3))(6)], and [Fe(16)S(16)(PR(3))(8)] are the only synthetic all-ferrous clusters with tetrahedral iron sites that have been isolated. Their utility as precursors to other highly reduced iron-sulfur clusters is under investigation.

Azotobacter vinelandii↗
PubMed2003

Electrochemistry of niobium(V) in sulfuric and methanesulfonic acids: formation of the Nb3O2(SO4)6(H2O)(3)(5-) cluster and designed electrochemical generation of "Nb3O2" core clusters by double potential pulse electrolysis.

The electrochemical and spectroelectrochemical properties of niobium(V) and the Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(5-) cluster in sulfuric acid and methanesulfonic acid were investigated using cyclic voltammetry, constant potential electrolysis, and spectroelectrochemistry. These chemical systems were suitable to probe the formation of "Nb(3)O(2)" core trinuclear clusters. In 9 M H(2)SO(4) the cluster Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(5-) exhibited a reversible 1-electron reduction peak at E(pc) = -1.30 V vs Hg/Hg(2)SO(4) electrode, as well as a 4-electron irreversible oxidation peak at E(pa) = -0.45 V. Controlled potential reduction at E = -1.40 V produced the green Nb(3.33+) cluster anion Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(6-). In 12 M H(2)SO(4) Nb(V) displayed two reduction peaks at E(pc) = -1.15 V and E(pc) = -1.30 V. It was determined that the first process involves a quasi-reversible 2-electron reduction. After reduction of Nb(V) to Nb(III) the following chemical step involves formation of [Nb(III)](2) dimer, which further reacts with Nb(V) to produce the Nb(3)O(2)(SO(4))(6(H(2)O)(3)(5-) cluster (ECC process). The second reduction peak at E(pc) = -1.30 V corresponds to further 2-electron reduction of Nb(III) to Nb(I). The electrogenerated Nb(I) species also chemically reacts with starting material Nb(V) to produce additional [Nb(III)](2). In 5 M H(2)SO(4), the rate of the second chemical step in the ECC process is relatively slower and reduction of Nb(V) at E = -1.45 V/-1.2 V produces a mixture of Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(5-) and [Nb(III)](2) dimer. [Nb(III)](2) can be selectively oxidized by two 2-electron steps at E = -0.65 V to Nb(V). However, if the oxidation is performed at E = -0.86 V, the product is Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(5-). A double potential pulse electrolysis waveform was developed to direct the reduction of Nb(V) toward selective formation of the Nb(3)O(2)(SO(4))(6)(H(2)O)(3)(5-) cluster. Proper application of dc-voltage pulses alternating between E(1) = -1.45 V and E(2) = -0.86 V yields only the target trinuclear cluster. Analogous double potential pulse electrolysis of Nb(V) in methanesulfonic acid generates the "Nb(3)O(2)" core cluster Nb(3)O(2)(CH(3)SO(3))(6)(H(2)O)(3)(+).

Journal Article↗
PubMed2006

Mixed-metal cluster chemistry. 29. Core expansion and ligand-driven metal exchange at group 6-iridium clusters.

Reactions of the tetrahedral clusters MoIr3(mu-CO)3(CO)8(eta-L) (L = C5HMe4, C5Me5) with the carbonylmetalate anions [Mo(CO)3(eta-L)]- afford the trigonal bipyramidal clusters Mo2Ir3(mu3-H)(mu-CO)2(CO)9(eta-L)2 (L = C5HMe4 (3c), 74%; L = C5Me5 (3d), 55%) in which the group 6 metal atoms occupy the apexes; reaction of the cyclopentadienylmolybdenum-containing analogues or their cyclopentadienyltungsten-containing homologues failed to afford analogous products. Reactions of MIr3(mu-CO)3(CO)8(eta-C5H5) (M = Mo, W) with [M(CO)3(eta-L)]- (L = C5HMe4, C5Me5) afford the core-expanded heteroapex clusters M2Ir3(mu3-H)(mu-CO)2(CO)9(eta-C5H5)(eta-L) (M = Mo, L = C5HMe4 (5c), 9%, L = C5Me5 (5d), 4%; M = W, L = C5Me5 (6d), 5%) in low yield, together with the homoapex clusters M2Ir3(mu3-H)(mu-CO)2(CO)9(eta-L)2 (M = Mo, L = C5HMe4 (3c), 81%, L = C5Me5 (3d), 60%; M = W, L = C5Me5 (4d), 5%) in much higher yield for the Mo-containing examples. The identities of clusters 3c,d, 4d, and 5c,d have been confirmed by single-crystal X-ray diffraction studies, with the same disposition of ligands about the trigonal bipyramidal cluster cores being observed in each case, a ligand arrangement that has been examined by complementary density functional theory studies. While cluster 5d is accessible as above, no reaction is observed from MoIr3(mu-CO)3(CO)8(eta-C5Me5) and [M(CO)3(eta-C5H5)]-. Treating MoIr3(mu-CO)3(CO)8(eta-C5H5) with 1 equiv of [M(CO)3(eta-C5Me5)]- affords 5d as the major product, a further 1 equiv affording some MoIr3(mu-CO)3(CO)8(eta-C5Me5) and a third 1 equiv giving a good yield of 3d. This is consistent with reaction proceeding by apex fragment addition, followed by apex fragment elimination, and finally a further apex fragment addition, the homometallic incoming apexes being distinguished from the departing vertices by their highly methylated cyclopentadienyl ligands. Spectroscopic data suggest that the electron density at these disparate-metal-containing cluster cores is tunable by progressive (conceptual) cyclopentadienyl alkylation.

Journal Article↗
PubMed1996

Kinetic Investigation of Homogeneous H(2)-D(2) Equilibration Catalyzed by Pt-Au Cluster Compounds. Characterization of the Cluster [(H)Pt(AuPPh(3))(9)](NO(3))(2).

The new Pt-Au hydrido cluster compound [(H)Pt(AuPPh(3))(9)](NO(3))(2) (3) has been synthesized and characterized by NMR, FABMS, and single-crystal X-ray diffraction [triclinic, P&onemacr;, a = 17.0452(1) Å, b = 17.4045(2) Å, c = 55.2353(1) Å, alpha = 89.891(1) degrees, beta = 85.287(1) degrees, gamma = 75.173(1) degrees, V = 15784.0(2) Å(3), Z = 4 (two molecules in asymmetric unit), residual R = 0.089 for 45 929 observed reflections and 3367 variables, Mo Kalpha radiation]. The Pt(AuP)(9) core geometry is a distorted icosahedron with three vertices vacant. The Pt-Au, Au-Au, and Au-P distances are within the normal ranges observed in other Pt-Au clusters. This cluster is a catalyst for H(2)-D(2) equilibration in homogeneous solution phase and has been used in a general mechanistic study of this reaction catalyzed by Pt-Au clusters. We previously proposed that a key step in the mechanism for catalytic H(2)-D(2) equilibration is the dissociation of a PPh(3) ligand to give a cluster with an open Au site for bonding of H(2) or D(2). This was based on qualitative observations that PPh(3) inhibited the rate of HD production with [Pt(AuPPh(3))(8)](NO(3))(2) (1) as catalyst. In order to test this hypothesis, phosphine inhibition (on the rate of HD production) and phosphine ligand exchange kinetic experiments were carried out with [(H)(PPh(3))Pt(AuPPh(3))(7)](NO(3))(2) (2) and 3. In this paper we show that the rate constant for phosphine dissociation determined from the PPh(3) inhibition rate study of H(2)-D(2) equilibration with cluster 2 is nearly identical to the rate constant for dissociative phosphine ligand exchange. The slower rate for H(2)-D(2) equilibration observed with 3 compared with 2 (5.5 x 10(-3) vs 7.7 x 10(-2) turnover s(-1)) is explained by its smaller rate constant for phosphine dissociation (2.8 x 10(-5) vs 2.9 x 10(-4) s(-1)). The fact that clusters 2 and 3 show similar kinetic behaviors suggests that the PPh(3) dissociation step in the catalytic H(2)-D(2) equilibration is general for 18-electron hydrido Pt-AuPPh(3) clusters.

Journal Article↗
PubMed2002

Pushing up the size limit of chalcogenide supertetrahedral clusters: two- and three-dimensional photoluminescent open frameworks from (Cu(5)In(30)S(54))(13-) clusters.

Direct band gap copper indium chalcogenides are of great technological importance in part because of their high photovoltaic conversion efficiency. Covalent superlattices constructed from copper indium chalcogenide clusters are of particular interest because they may combine open framework architecture with semiconducting properties. Here two photoluminescent covalent superlattices built from core-shell type copper indium sulfide supertetrahedral clusters are reported. Each cluster consists of 35 metal cations and is so far the largest known supertetrahedral cluster with a metal-to-metal distance of 1.6 nm. In addition, this is the first example of supertetrahedral clusters in heterometallic copper indium chalcogenides. The preparation of these large clusters has narrowed down the size gap between colloidal nanoclusters and small supertetrahedral clusters and revealed new possibilities in the construction of nanoporous semiconducting superlattices with tunable pore size. Through the combination of metal ions with different oxidation states to provide both overall and local charge neutrality, an effective approach has been demonstrated in the rational synthesis of chalcogenide open framework materials with large and unprecedented supertetrahedral clusters.

Journal Article↗
PubMed2003

A dimer of the FeS cluster biosynthesis protein IscA from cyanobacteria binds a [2Fe2S] cluster between two protomers and transfers it to [2Fe2S] and [4Fe4S] apo proteins.

Two proteins with similarity to IscA are encoded in the genome of the cyanobacterium Synechocystis PCC 6803. One of them, the product of slr1417 which accounts for 0.025% of the total soluble protein of Synechocystis was over-expressed in E. coli and purified. The purified protein was found to be mainly dimeric and did not contain any cofactor. Incubation with iron ions, cysteine and Synechocystis IscS led to the formation of one [2Fe2S] cluster at an IscA dimer as demonstrated (by the binding of about one iron and one sulfide ion per IscA monomer) by UV/Vis, EPR and Mössbauer spectroscopy. Mössbauer spectroscopy further indicated that the FeS cluster was bound by four cysteine residues. Site-directed mutagenesis revealed that of the five cysteine residues only C110 and C112 were involved in cluster binding. It was therefore concluded that the [2Fe2S] cluster is located between the two protomers of the IscA dimer and ligated by C110 and C112 of both protomers. The cluster could be transferred to apo ferredoxin, a [2Fe2S] protein, with a half-time of 10 min. Surprisingly, incubation of cluster-containing IscA with apo adenosine 5'-phosphosulfate reductase led to a reactivation of the enzyme which requires the presence of a [4Fe4S] cluster. This demonstrates that it is possible to build [4Fe4S] clusters from [2Fe2S] units.

Amino Acid Sequence↗
PubMed2006

Electronic structures of size-selected single-layered platinum clusters on silicon(111)-7x7 surface at a single cluster level by tunneling spectroscopy.

Tunneling spectra of size-selected single-layered platinum clusters (size range of 5-40) deposited on a silicon(111)-7x7 surface were measured individually at a temperature of 77 K by means of a scanning tunneling microscope (STM), and the local electronic densities of states of individual clusters were derived from their tunneling spectra measured by placing an STM tip on the clusters. In a bias-voltage (V(s)) range from -3 to 3 V, each tunneling spectrum exhibits several peaks assignable to electronic states associated with 5d states of a constituent platinum atom and an energy gap of 0.1-0.6 eV in the vicinity of V(s)=0. Even when platinum cluster ions having the same size were deposited on the silicon(111)-7x7 surface, the tunneling spectra and the energy gaps of the deposited clusters are not all the same but can be classified in shape into several different groups; this finding is consistent with the observation of the geometrical structures of platinum clusters on the silicon(111)-7x7 surface. The mean energy gap of approximately 0.4 eV drops to approximately 0.25 eV at the size of 20 and then decreases gradually as the size increases, consistent with our previous finding that the cluster diameter remains unchanged, but the number density of Pt atoms increases below the size of 20 while the diameter increases, but the density does not change above it. It is concluded that the mean energy gap tends to decrease gradually with the mean cluster diameter. The dependence of the mean energy gap on the mean Pt-Pt distance shows that the mean energy gap decreases sharply when the mean Pt-Pt distance exceeds that of a platinum metal (0.28 nm).

Journal Article↗
PubMed2006

Search for global-minimum geometries of medium-sized germanium clusters. II. Motif-based low-lying clusters Ge21-Ge29.

We performed a constrained search for the geometries of low-lying neutral germanium clusters Ge(N) in the size range of 21 < or = N < or = 29. The basin-hopping global optimization method is employed for the search. The potential-energy surface is computed based on the plane-wave pseudopotential density functional theory. A new series of low-lying clusters is found on the basis of several generic structural motifs identified previously for silicon clusters [S. Yoo and X. C. Zeng, J. Chem. Phys. 124, 054304 (2006)] as well as for smaller-sized germanium clusters [S. Bulusu et al., J. Chem. Phys. 122, 164305 (2005)]. Among the generic motifs examined, we found that two motifs stand out in producing most low-lying clusters, namely, the six/nine motif, a puckered-hexagonal-ring Ge6 unit attached to a tricapped trigonal prism Ge9, and the six/ten motif, a puckered-hexagonal-ring Ge6 unit attached to a bicapped antiprism Ge10. The low-lying clusters obtained are all prolate in shape and their energies are appreciably lower than the near-spherical low-energy clusters. This result is consistent with the ion-mobility measurement in that medium-sized germanium clusters detected are all prolate in shape until the size N approximately 65.

Journal Article↗
PubMed1983

Iron-sulfur stoichiometry and structure of iron-sulfur clusters in three-iron proteins: evidence for [3Fe-4S] clusters.

Beef heart aconitase contains 3Fe clusters in its inactive and 4Fe clusters in its active form. The fully active form can be restored from the inactive one by insertion of Fe(2+), whereas S(2-) is not required. Chemical analyses for iron and labile sulfide yield Fe/S(2-) ratios of 0.66-0.74 for the inactive and 0.90-1.03 for the active form. Sulfane sulfur (S(0)) was not detected. We propose on the basis of these data that the inactive form may arise from the active one by loss of one iron only per cluster with the sulfur remaining as S(2-) in a [3Fe-4S] structure. Measurements by extended x-ray absorption fine structure (EXAFS) spectroscopy on the 3Fe form of aconitase yield a Fe..S distance of 2.24 A and a Fe..Fe distance of 2.71 A. This Fe..Fe distance is in agreement with that obtained by EXAFS on ferredoxin II of Desulfovibrio gigas, another 3Fe protein, but disagrees with Fe..Fe distances observed for the 3Fe cluster of Azotobacter vinelandii ferredoxin I by x-ray diffraction-namely, 4.1 A. We suggest that this difference may be due to the presence of a [3Fe-3S] structure in the Azotobacter ferredoxin I crystals vs. a [3Fe-4S] structure in liquid or frozen solutions of aconitase. The [3Fe-3S] cluster has been shown to have a relatively flat twist-boat structure, whereas a [3Fe-4S] cluster could be expected to essentially maintain the compact structure of the [4Fe-4S] cluster. This would explain the differences in Fe..Fe distances. Two possible structural models for a [3Fe-4S] cluster are discussed.

Aconitate Hydratase↗
PubMed2005

Multiple turnover transfer of [2Fe2S] clusters by the iron-sulfur cluster assembly scaffold proteins IscU and IscA.

IscU/Isu and IscA/Isa (and related NifU and SufA proteins) have been proposed to serve as molecular scaffolds for preassembly of [FeS] clusters to be used in the biogenesis of iron-sulfur proteins. In vitro studies demonstrating transfer of preformed scaffold-[FeS] complexes to apoprotein acceptors have provided experimental support for this hypothesis, but investigations to date have yielded only single-cluster transfer events. We describe an in vitro assay system that allows for real-time monitoring of [FeS] cluster formation using circular dichroism spectroscopy and use this to investigate de novo [FeS] cluster formation and transfer from Escherichia coli IscU and IscA to apo-ferredoxin. Both IscU and IscA were found to be capable of multiple cycles of [2Fe2S] cluster formation and transfer suggesting that these scaffold proteins are capable of acting "catalytically." Kinetic studies further showed that cluster transfer exhibits Michaelis-Menten behavior indicative of complex formation of holo-IscU and holo-IscA with apoferredoxin and consistent with a direct [FeS] cluster transfer mechanism. Analysis of the dependence of the rate of cluster transfer, however, revealed enhanced efficiency at low ratios of scaffold to acceptor protein suggesting participation of a transient, labile scaffold-[FeS] species in the transfer process.

Carrier Proteins↗
PubMed1988

Dendritic cell-lymphocyte clusters that form spontaneously in rheumatoid arthritis synovial effusions differ from clusters formed in human mixed leukocyte reactions.

Lymphocytes cluster about dendritic cells (DC) spontaneously in 48 h cultures of rheumatoid arthritis synovial fluid (RA SF) mononuclear cells and in peripheral blood autologous or allogeneic mixed leukocyte reactions. In the latter case, the clusters are predominantly CD4+ T cells (T4/T8 greater than 5) and with time progress in blastic cells that express IL-2 (Tac) and/or transferrin (T9) receptors. In contrast, the clusters in RA SF cultures have a T4/T8 ratio of less than 1 and a majority of the T8 cells coexpress the Leu 7 marker. T cells in these clusters remain inert and with time the clusters disintegrate. Addition of IL-1, IL-2, or IFN-gamma alone or in combination had no effect on RA SF clusters but T cells became blastic when exposed to 10% RA SF. Mixing experiments using RA SF DC with normal T cells and RA T cells with normal DC show that both RA SF DC and T cells are immunofunctional. In addition, clusters of RA SF from a patient with active tuberculosis proliferated vigorously to PPD. Therefore, the unique RA SF cluster profile may reflect the memory nature of the RA SF T cells resulting in a paucity of T cells that are responsive to autologous stimulation. However, an immunosuppressive role for the double-labeled (CD8 and Leu 7) cells has not been excluded.

Antigens, Differentiation↗
PubMed1989

Six clustering algorithms applied to the WAIS-R: the problem of dissimilar cluster results.

Clusterings of the Wechsler Adult Intelligence Scale-Revised subtests were obtained from the application of six hierarchical clustering methods (N = 113). These sets of clusters were compared for similarities using the Rand index. The calculated indices suggested similarities of cluster group membership between the Complete Linkage and Centroid methods; Complete Linkage and Ward's methods; Centroid and Ward's methods; and Single Linkage and Average Linkage Between Groups methods. Cautious use of single clustering methods is implied, though the authors suggest some advantages of knowing specific similarities and differences. If between-method comparisons consistently reveal similar cluster membership, a choice could be made from those algorithms that tend to produce similar partitions, thereby enhancing cluster interpretation.

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