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PubMed2006

Structures and relative stability of medium-sized silicon clusters. V. Low-lying endohedral fullerenelike clusters Si31-Si40 and Si45.

We have performed unconstrained search for low-lying structures of medium-sized silicon clusters Si(31)-Si(40) and Si(45), by means of the minimum-hopping global optimization method coupled with a density-functional based tight-binding model of silicon. Subsequent geometric optimization by using density-functional theory with the PBE, BLYP, and B3LYP functionals was carried out to determine the relative stability of various candidate low-lying silicon clusters obtained from the unconstrained search. The low-lying characteristics of these clusters can be affirmed by comparing the binding energies per atom of these clusters with previously determined lowest-energy clusters(Si(n)) in the size range of 21</=n</=30. In view of the fact that there exist numerous low-lying "endohedral fullerenelike" isomers for each size in the range 30</=n</=40, we used the homologue carbon-fullerene cage to classify different families of isomers. This structural classification allows us to focus on generic features of various isomers and to group many apparently different isomers into a single family. In addition, we report a new family of low-lying clusters which have "Y-shaped three-arm" structures. Isomers in this "handmade" family can be energetically competitive as the endohedral fullerene isomers when the total energies are calculated with the BLYP or B3LYP functional.

Journal Article↗
PubMed1991

Transition from one revolving cluster to two revolving clusters in the ground-state rotational bands of nuclei in the lanthanon region.

Whereas 234(92)U142 and other actinon nuclei have ground-state bands that indicate that each nucleus consists of a sphere and a single revolving cluster with constant composition and with only a steady increase in the moment of inertia with increase in J, the angular-momentum quantum number, many of the lanthanon ground-state bands show discontinuities, usually with an initial slightly or strongly curved segment followed by one or two nearly straight segments. The transition to nearly straight segments is interpreted as a change in structure from one revolving cluster to two revolving clusters. The proton-neutron compositions of the clusters and the central sphere are assigned, leading to values of the radius of revolution. The approximation of the two-cluster sequences to linearity is attributed to the very small values of the quadrupole polarizability of the central sphere. Values of the nucleon numbers of clusters and spheres, of the radius of revolution, and of promotion energy are discussed.

Journal Article↗
PubMed2001

Characterization of the iron-sulfur cluster coordinated by a cysteine cluster motif (CXXCXXXCX27C) in the Nqo3 subunit in the proton-translocating NADH-quinone oxidoreductase (NDH-1) of Thermus thermophilus HB-8.

The proton-translocating NADH-quinone oxidoreductase (NDH-1) of Thermus thermophilus HB-8 is composed of 14 subunits (designated Nqo1-14). This NDH-1 houses nine putative iron-sulfur binding sites, eight of which are generally found in bacterial NDH-1 and its mitochondrial counterpart (complex I). The extra site contains a CXXCXXXCX(27)C motif and is located in the Nqo3 subunit. This motif was originally found in Escherichia coli NDH-1 and was assigned to a binuclear cluster (g(z, y, x) = 2.00, 1.95, 1.92) and named N1c. In this report, the Thermus Nqo3 fragment containing this motif was heterologously overexpressed, using a glutathione S-transferase fusion system. This fragment contained a small amount of iron-sulfur cluster, whose content was significantly increased by in vitro reconstitution. The UV-visible and EPR spectroscopic properties of this fragment indicate that the ligated iron-sulfur cluster is tetranuclear with nearly axial symmetry (g( parallel, perpendicular) = 2.045, approximately 1.94). Site-directed mutants show that all four cysteines participate in the ligation of a [4Fe-4S] cluster. Considering the fact that the same motif coordinates only tetranuclear clusters in other enzymes so far known, we propose that the CXXCXXXCX(27)C motif in the Nqo3 subunit most likely ligates the [4Fe-4S] cluster.

Amino Acid Sequence↗
PubMed2006

Iron-sulfur cluster biosynthesis: characterization of Escherichia coli CYaY as an iron donor for the assembly of [2Fe-2S] clusters in the scaffold IscU.

The biogenesis of iron-sulfur [Fe-S] clusters requires the coordinated delivery of both iron and sulfide. Sulfide is provided by cysteine desulfurases that use L-cysteine as sulfur source. So far, the physiological iron donor has not been clearly identified. CyaY, the bacterial ortholog of frataxin, an iron binding protein thought to be involved in iron-sulfur cluster formation in eukaryotes, is a good candidate because it was shown to bind iron. Nevertheless, no functional in vitro studies showing an involvement of CyaY in [Fe-S] cluster biosynthesis have been reported so far. In this paper we demonstrate for the first time a specific interaction between CyaY and IscS, a cysteine desulfurase participating in iron-sulfur cluster assembly. Analysis of the iron-loaded CyaY protein demonstrated a strong binding of Fe(3+) and a weak binding of Fe(2+) by CyaY. Biochemical analysis showed that the CyaY-Fe(3+) protein corresponds to a mixture of monomer, intermediate forms (dimer-pentamers), and oligomers with the intermediate one corresponding to the only stable and soluble iron-containing form of CyaY. Using spectroscopic methods, this form was further demonstrated to be functional in vitro as an iron donor during [Fe-S] cluster assembly on the scaffold protein IscU in the presence of IscS and cysteine. All of these results point toward a link between CyaY and [Fe-S] cluster biosynthesis, and a possible mechanism for the process is discussed.

Bacterial Proteins↗
PubMed2003

Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters.

Medermycin is a Streptomyces aromatic C-glycoside antibiotic classified in the benzoisochromanequinones (BIQs), which presents several interesting biosynthetic problems concerning polyketide synthase (PKS), post-PKS tailoring and deoxysugar pathways. The biosynthetic gene cluster for medermycin (the med cluster) was cloned from Streptomyces sp. AM-7161. Completeness of the clone was proved by the heterologous expression of a cosmid carrying the entire med cluster in Streptomyces coelicolor CH999 to produce medermycin. The DNA sequence of the cosmid (36 202 bp) revealed 34 complete ORFs, with an incomplete ORF at either end. Functional assignment of the deduced products was made for PKS and biosynthetically related enzymes, tailoring steps including strereochemical control, oxidation, angolosamine pathway, C-glycosylation, and regulation. The med cluster was estimated to be about 30 kb long, covering 29 ORFs. An unusual characteristic of the cluster is the disconnected organization of the minimal PKS genes: med-ORF23 encoding the acyl carrier protein is 20 kb apart from med-ORF1 and med-ORF2 for the two ketosynthase components. Secondly, the six genes (med-ORF14, 15, 16, 17, 18 and 20) for the biosynthesis of the deoxysugar, angolosamine, are all contiguous. Finally, the finding of a glycosyltransferase gene, med-ORF8, suggests a possible involvement of conventional C-glycosylation in medermycin biosynthesis. Comparison among the three complete BIQ gene clusters - med and those for actinorhodin (act) and granaticin (gra) - revealed some common genes whose deduced functions are unavailable from database searches (the 'unknowns'). An example is med-ORF5, a homologue of actVI-ORF3 and gra-ORF18, which was highlighted by a recent proteomic analysis of S. coelicolor A3(2).

Amino Acid Sequence↗
PubMed2005

Attraction-limited cluster-cluster aggregation of Ising dipolar particles.

The attraction-limited cluster-cluster aggregation of two-dimensional Ising dipolar particles with or without particle-size dispersity is studied. The fast decrease of the number of even-sized clusters for relatively smaller clusters is observed. The threshold concentration is also determined, under which the dynamics of aggregation is explained using the well-known dynamic scaling theory of Vicsek and Family. Above the threshold concentration, the dynamics depends on particle-size dispersity. Furthermore, it is suggested that, even in the dilute limit, the dynamic exponents are affected by the screening of the surrounding clusters on collision between two clusters.

Journal Article↗
PubMed2004

Borderline magic clustering: the fabrication of tetravalent Pb cluster arrays on Si(111)-(7x7) surfaces.

Well-ordered arrays of identical Pb clusters have been fabricated on a Si(111)-(7x7) substrate by the temperature-mediated surface clustering method. Interestingly, these clusters can easily transform into other forms when the growth temperature deviates slightly from the optimal values. In accord with experiments, first-principle total-energy calculations reveal several cluster structures centered on a mixed cluster model involving surface Pb and Si exchange. This borderline Pb/Si(111) system provides a unique, controlled way to study surface magic cluster formation and breakup dynamics.

Journal Article↗
PubMed1995

Identification of the iron-sulfur clusters in a ferredoxin from the archaeon Sulfolobus acidocaldarius. Evidence for a reduced [3Fe-4S] cluster with pH-dependent electronic properties.

A ferredoxin isolated from the archaeon Sulfolobus acidocaldarius strain DSM 639 has been shown to contain one [3Fe-4S]1 + 10 cluster with a reduction potential of -275 mV and one [4Fe-4S]2+/1+ cluster with a reduction potential of -529 mV at pH 6.4, in the temperature range 0-50 degrees C. The monomer molecular mass was confirmed to be 10907.5 +/- 1.0 Da by electrospray mass spectrometry, as calculated from the published amino acid sequence [Minami, Y. Wakabayashi. S., Wada, K., Matsubara, H., Kerscher, L. & Oesterhelt, D. (1985) J. Biochem. (Tokyo) 97, 745-751], while the holoprotein molecular mass was found to be 11,550 +/- 1.0 Da. The reduced [3Fe-4S]0 cluster was also shown by direct electrochemistry and magnetic circular dichroic spectroscopy to undergo a one-proton uptake reaction as first observed for Azotobacter chroococcum ferredoxin I [George, S. J., Richards, A. J. M., Thomson, A. J. & Yates, M. G. (1984) Biochem. J. 224, 247-251]. The pKa of the protonation step has been determined by a novel thin film electrochemical method to be 5.8. This is significantly different from the pKa of 7.7 determined for A. vinelandii ferredoxin I [Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, J. M., Stephens, P. J., LaMar, G. N., Gorst, C. M. & Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939] and indicates that the polypeptide chain around the [3Fe-4S] cluster controls this reaction. Although this appears to be only the second reported case of protonation at or near the reduced [3Fe-4S]0 cluster, its observation in S. acidocaldarius ferredoxin raises the question of the generality of this chemistry for 3Fe clusters. The similarity of the pKa to the estimated intracellular pH of S. acidocaldarius strongly suggests a physiological role for this process.

Amino Acid Sequence↗
PubMed1996

Evidence for Cu(I) clusters and Zn(II) clusters in neuronal growth-inhibitory factor isolated from bovine brain.

Neuronal growth-inhibitory factor (GIF), a central-nervous-system-specific metallothionein-like protein, has been isolated by means of an improved isolation procedure from bovine brain. The native protein contains 4-5 Cu+ and 2-2.5 Zn2+, which results in an overall stoichiometry of 6-7 mol metal ions/mol protein. Native Cu, ZN-GIF and the Zn2+ -substituted and Cd2+-substituted metalloforms have been characterized by means of electronic-absorption, CD, magnetic-circular-dichroism (MCD) and low-temperature (77 K) Cu(I)-luminescence spectroscopy. Analysis of the metal-induced-charge-transfer transitions below 300 nm in the electronic-absorption and CD spectra of Cu, ZN-GIF revealed spectral features characteristic of metal-thiolate coordination. The presence of formally spin-forbidden 3d --> 4s Cu(I)-cluster-centered transitions, above 300 nm in the corresponding CD and MCD spectra indicate the existence of a Cu(I) cluster. The 77-K luminescence spectrum of Cu, ZN-GIF revealed two emissive bands at approximately 420 nm and 570 nm, which were reported also for CU4 clusters in mammalian Cu8-metallothionein. By analogy with Cu8-metallothionein, we propose the presence of a Cu4 cluster with similar electronic structure in native GIF. However, the determined Cys/Cu+ ratio of approximately 2:1 in Cu, Zn-GIF is higher than the ratio found in mammalian Cu(I)-metallothionein forms (approximately 1.6:1 ), which implies that the coordination geometry of CU+-binding sites is different in the CU4 Cluster. The spectroscopic characterization of Zn2+-substituted and Cd2+-substituted GIF (6-7 metal ions/protein) showed CD and MCD features at positions identical to those reported for the well-characterized mammalian Zn7-metallothionein and Cd7-metallothionein. Therefore, it is inferred that the cluster organization in GIF with divalent metal ions is comparable to that found in mammalian metallothioneins. The effect of metal ions on the protein structure with regard to the biological function of GIF is discussed.

Amino Acid Sequence↗
PubMed2003

Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster.

Genes from the cytochrome P450 (CYP) superfamily encode a diverse group of monooxygenases that play important roles in both endogenous processes and in the metabolism of exogenous compounds, including most drugs. A cluster of Cyp2 genes on mouse chromosome 7 was mapped and analyzed in detail and compared with the homologous cluster on human chromosome 19. The mouse cluster includes 22 loci from the same six CYP2 subfamilies--Cyp2a, Cyp2b, Cyp2f, Cyp2g, Cyp2s, Cyp2t--that are found in the human cluster. Twelve of these loci are functional genes, and 10 are pseudogenes. Parts of the mouse and human gene clusters are similarly arranged, but the data indicate that a significantly different series of duplication events created the modern gene organizations in the two species. The comparison of the mouse and human clusters provides new insights into the evolution of gene families, whereas the detailed analysis provides background information that should be informative for future studies on the expression, regulation, and function of specific mouse Cyp2 genes.

Animals↗
PubMed2006

The receptor tyrosine kinase Met and its ligand hepatocyte growth factor are clustered at excitatory synapses and can enhance clustering of synaptic proteins.

The receptor protein tyrosine kinase Met and its ligand, hepatocyte growth factor, regulate cellular morphology, intercellular adhesion, and interactions among junctional proteins in numerous cell types. However, they have not been extensively studied in the central nervous system. We report that Met is clustered at excitatory synapses and that treatment of neurons with hepatocyte growth factor can enhance expression and clustering of synaptic proteins. We demonstrate that Met is present in clusters that strongly colocalize with the NR2B subunit of the N-methyl-D-aspartate receptor, PSD-95 and synapsin at excitatory synapses of hippocampal neurons in vitro. We also show that Met is clustered at the postsynaptic density of excitatory synapses in the CA1 region of the hippocampus with the use of immuno-electron microscopy. Hepatocyte growth factor also forms clusters that partially colocalize with PSD-95. Treatment of cultured neurons with exogenous hepatocyte growth factor increased expression of the NR2B subunit of the N-methyl-D-aspartate receptor, calcium/calmodulin-dependent protein kinase II, and the GluR1 subunit of the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate receptor. The size and number of clusters of these proteins were also increased at sites along dendrites in response to hepatocyte growth factor. These results suggest a novel role for Met and hepatocyte growth factor in regulating synapses.

Animals↗
PubMed1988

The state of cluster SH and S2- of aconitase during cluster interconversions and removal. A convenient preparation of apoenzyme.

During the interconversion of the various cluster types observed in aconitase ([4Fe-4S]1+,2+, [3Fe-4S]0,1+, cubane, or linear types) and production of apoenzyme, changes int he state of the sulfur ligands (RSH and S2-) are bound to occur. We have attempted to obtain information on such changes by interception of SH groups and/or by analysis of the resulting cluster or apoprotein for various forms of sulfur and enzymatic activity. During cluster interconversions no evidence was obtained for changes in SH titer that could be associated with cluster ligands. We conclude from this that the ligand exchange at the cluster is too rapid to allow trapping even by SH reagents of low Mr. The possibility that released SH becomes buried in the protein structure and unreactive cannot be entirely discounted. On formation of the apoenzyme by oxidation with ferricyanide, four SH groups per molecule became unavailable for reaction with 5,5'-dithiobis(2-nitrobenzoic acid); instead, while the holoenzyme contains no disulfides or S(0), two di- or polysulfides were found in the apoenzyme indicating that, on an average, four SH groups and three of the original four S(2-) ligands are trapped as RS-Sx-SR. In agreement with this conclusion is the fact that the apoenzyme can be reconstituted without addition of S(2-). A convenient preparative procedure for reconstitutable apoenzyme in 75% yield is [3Fe-4S] and [4Fe-4S] clusters with a variety of combinations of iron and sulfur isotopes as required for Mössbauer, resonance Raman, and electron nuclear double resonance studies.

Aconitate Hydratase↗
PubMed2004

The shark HoxN cluster is homologous to the human HoxD cluster.

The statistical analysis of phylogenetic footprints in the two known horn shark Hox clusters and the four mammalian clusters shows that the shark HoxN cluster is HoxD-like. This finding implies that the most recent common ancestor of jawed vertebrates had at least four Hox clusters, including those which are orthologous to the four mammalian Hox clusters.

Amino Acid Sequence↗
PubMed2006

Shape resonances in molecular clusters: the 2t(2g) shape resonances in S 2p-excited sulfur hexafluoride clusters.

Sulfur hexafluoride clusters are investigated in the S 2p excitation regime. For the first time special emphasis is put on high-energy resolution spectroscopy of shape resonances in free clusters. We have investigated the 2t(2g)-shape resonance occurring above the S 2p threshold as one typical example to study size effects that are related to shape resonances. A small redshift of this resonance of 30 +/- 5 meV occurs in clusters relative to the free molecule and changes in line shape are observed. A double-barrier optical potential model is applied for the analysis of intra- and intermolecular effects occurring in SF6 clusters, which is suitable for rationalizing the experimentally observed spectral changes. The experimental and theoretical results are briefly discussed in comparison to previous work on core-excited van der Waals clusters containing diatomic molecules.

Cluster Analysis↗
PubMed2004

Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites.

SUMMARY: We have developed a program, Cluster Analyzer for Transcription Sites (CATS), which identifies clusters of transcription factor binding sites in any genome sequence. The program searches for clusters of the consensus sequence for DNA binding within a window (length of DNA). The window size and the cluster size (number of consensus sequences within a given window) can be varied. CATS can be used for single or multiple transcription factors for which consensus sequences have been deduced based on biochemical and mutational analysis, or by comparative genomics. The use of CATS for clusters of different transcription factor binding sites may facilitate the identification of genes that are co-regulated in a cell type-specific or developmental stage-specific manner. CATS is simple to install and use on computers running any Windows NT-platforms. AVAILABILITY: http://www.healthsciences.columbia.edu/dept/greenwaldlab/links.html

Binding Sites↗
PubMed2003

Marginal analyses of clustered data when cluster size is informative.

We propose a new approach to fitting marginal models to clustered data when cluster size is informative. This approach uses a generalized estimating equation (GEE) that is weighted inversely with the cluster size. We show that our approach is asymptotically equivalent to within-cluster resampling (Hoffman, Sen, and Weinberg, 2001, Biometrika 73, 13-22), a computationally intensive approach in which replicate data sets containing a randomly selected observation from each cluster are analyzed, and the resulting estimates averaged. Using simulated data and an example involving dental health, we show the superior performance of our approach compared to unweighted GEE, the equivalence of our approach with WCR for large sample sizes, and the superior performance of our approach compared with WCR when sample sizes are small.

Cluster Analysis↗
PubMed1991

Ionization of clusters. IV. Cooperativity and allosterism derived from shared clusters in macromolecules.

Clusters of ionizable groups are examined for conditions that develop cooperativity (1) on the binding of protons, and (2) on the binding of an associated ligand when the clusters are shared between domains or subunits in macromolecules. Cooperative binding isotherms for protons have long been observed (but not emphasized as cooperative binding) when studies have been done on clusters for the evaluation of metal ion complexation [A. E. Martell & M. Calvin (1952) Chemistry of the Metal Chelate Compounds, Prentice-Hall, Englewood Cliffs, New Jersey]. Reactions are formulated in this paper to show that anions, chelating to positively charged clusters, are also capable of developing the cooperative binding of protons. Extension of these simple reactions to those where clusters of ionizable groups are shared between domains of macromolecules provides models for cooperative binding, which include the allosteric, Bohr, anion, and cation effects in proteins.

Electrochemistry↗
PubMed1993

Genetic evidence for the interaction between cluster I and cluster III rifampicin resistant mutations.

Rifampicin-resistant (Rifr) mutations of Escherichia coli map to the central portion of the rpoB gene, which encodes the beta subunit of RNA polymerase. These mutations are located in three distinct clusters, designated I, II and III. Three intragenic suppressors of the cluster III Rifr mutation, rpoB3406(RH687), restore the ability of the mutant strain to grow at low and high temperatures and map to a single locus in cluster I. These suppressors are identical to two previously characterized Rifr alleles, rpoB3401(RC529) and rpoB3402(RS529). None of the other 14 previously identified Rifr mutations that we have characterized confers this phenotype. We suggest that this allele-specific suppression results from interaction between Cluster I and Cluster III of the beta subunit.

Alleles↗