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Sample records for clustered yy1 binding

  1. Identification of clustered YY1 binding sites in Imprinting Control Regions

    SciTech Connect

    Kim, J D; Hinz, A; Bergmann, A; Huang, J; Ovcharenko, I; Stubbs, L; Kim, J

    2006-04-19

    Mammalian genomic imprinting is regulated by Imprinting Control Regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In the current study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) led us to identify three additional clustered YY1 binding sites, which are also localized within the DMRs of Xist, Tsix, and Nespas. These regions have been shown to play a critical role as ICRs for the regulation of surrounding genes. These ICRs have maintained a tandem array of YY1 binding sites during mammalian evolution. The in vivo binding of YY1 to these regions is allele-specific and only to the unmethylated active alleles. Promoter/enhancer assays suggest that a tandem array of YY1 binding sites function as a potential orientation-dependent enhancer. Insulator assays revealed that the enhancer-blocking activity is detected only in the YY1 binding sites of Peg3-DMR but not in the YY1 binding sites of other DMRs. Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting.

  2. Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

    PubMed

    Kim, Jeong Do; Faulk, Christopher; Kim, Joomyeong

    2007-01-01

    YY1 is a DNA-binding transcription factor found in both vertebrates and invertebrates. Database searches identified 62 YY1 related sequences from all the available genome sequences ranging from flying insects to human. These sequences are characterized by high levels of sequence conservation, ranging from 66% to 100% similarity, in the zinc finger DNA-binding domain of the predicted proteins. Phylogenetic analyses uncovered duplication events of YY1 in several different lineages, including flies, fish and mammals. Retroposition is responsible for generating one duplicate in flies, PHOL from PHO, and two duplicates in placental mammals, YY2 and Reduced Expression 1 (REX1) from YY1. DNA-binding motif studies have demonstrated that YY2 still binds to the same consensus sequence as YY1 but with much lower affinity. In contrast, REX1 binds to DNA motifs divergent from YY1, but the binding motifs of REX1 and YY1 share some similarity at their core regions (5'-CCAT-3'). This suggests that the two duplicates, YY2 and REX1, although generated through similar retroposition events have undergone different selection schemes to adapt to new roles in placental mammals. Overall, the conservation of YY2 and REX1 in all placental mammals predicts that each duplicate has co-evolved with some unique features of eutherian mammals. PMID:17478514

  3. A Common Variant at the 14q32 Endometrial Cancer Risk Locus Activates AKT1 through YY1 Binding.

    PubMed

    Painter, Jodie N; Kaufmann, Susanne; O'Mara, Tracy A; Hillman, Kristine M; Sivakumaran, Haran; Darabi, Hatef; Cheng, Timothy H T; Pearson, John; Kazakoff, Stephen; Waddell, Nicola; Hoivik, Erling A; Goode, Ellen L; Scott, Rodney J; Tomlinson, Ian; Dunning, Alison M; Easton, Douglas F; French, Juliet D; Salvesen, Helga B; Pollock, Pamela M; Thompson, Deborah J; Spurdle, Amanda B; Edwards, Stacey L

    2016-06-01

    A recent meta-analysis of multiple genome-wide association and follow-up endometrial cancer case-control datasets identified a novel genetic risk locus for this disease at chromosome 14q32.33. To prioritize the functional SNP(s) and target gene(s) at this locus, we employed an in silico fine-mapping approach using genotyped and imputed SNP data for 6,608 endometrial cancer cases and 37,925 controls of European ancestry. Association and functional analyses provide evidence that the best candidate causal SNP is rs2494737. Multiple experimental analyses show that SNP rs2494737 maps to a silencer element located within AKT1, a member of the PI3K/AKT/MTOR intracellular signaling pathway activated in endometrial tumors. The rs2494737 risk A allele creates a YY1 transcription factor-binding site and abrogates the silencer activity in luciferase assays, an effect mimicked by transfection of YY1 siRNA. Our findings suggest YY1 is a positive regulator of AKT1, mediating the stimulatory effects of rs2494737 increasing endometrial cancer risk. Identification of an endometrial cancer risk allele within a member of the PI3K/AKT signaling pathway, more commonly activated in tumors by somatic alterations, raises the possibility that well tolerated inhibitors targeting this pathway could be candidates for evaluation as chemopreventive agents in individuals at high risk of developing endometrial cancer.

  4. YY1 modulates taxane response in epithelial ovarian cancer

    SciTech Connect

    Matsumura, Noriomi; Huang, Zhiqing; Baba, Tsukasa; Lee, Paula S.; Barnett, Jason C.; Mori, Seiichi; Chang, Jeffrey T.; Kuo, Wen-Lin; Gusberg, Alison H.; Whitaker, Regina S.; Gray, JoeW.; Fujii, Shingo; Berchuck, Andrew; Murphy, Susan K.

    2008-10-10

    The results of this study show that a high YY1 gene signature (characterized by coordinate elevated expression of transcription factor YY1 and putative YY1 target genes) within serous epithelial ovarian cancers is associated with enhanced response to taxane-based chemotherapy and improved survival. If confirmed in a prospective study, these results have important implications for the potential future use of individualized therapy in treating patients with ovarian cancer. Identification of the YY1 gene signature profile within a tumor prior to initiation of chemotherapy may provide valuable information about the anticipated response of these tumors to taxane-based drugs, leading to better informed decisions regarding chemotherapeutic choice. Survival of ovarian cancer patients is largely dictated by their response to chemotherapy, which depends on underlying molecular features of the malignancy. We previously identified YIN YANG 1 (YY1) as a gene whose expression is positively correlated with ovarian cancer survival. Herein we investigated the mechanistic basis of this association. Epigenetic and genetic characteristics of YY1 in serous epithelial ovarian cancer (SEOC) were analyzed along with YY1 mRNA and protein. Patterns of gene expression in primary SEOC and in the NCI60 database were investigated using computational methods. YY1 function and modulation of chemotherapeutic response in vitro was studied using siRNA knockdown. Microarray analysis showed strong positive correlation between expression of YY1 and genes with YY1 and transcription factor E2F binding motifs in SEOC and in the NCI60 cancer cell lines. Clustering of microarray data for these genes revealed that high YY1/E2F3 activity positively correlates with survival of patients treated with the microtubule stabilizing drug paclitaxel. Increased sensitivity to taxanes, but not to DNA crosslinking platinum agents, was also characteristic of NCI60 cancer cell lines with a high YY1/E2F signature. YY1

  5. Binding of YY1 to a site overlapping a weak TATA box is essential for transcription from the uteroglobin promoter in endometrial cells.

    PubMed Central

    Klug, J; Beato, M

    1996-01-01

    The gene for rabbit uteroglobin codes for a small calcium-, steroid-, and biphenyl metabolite-binding homodimeric protein which is expressed in a variety of epithelial cell types such as Clara cells (lung) and the glandular and luminal cells of the endometrium. One important region mediating its efficient transcription in a human endometrium-derived cell line, Ishikawa, is centered around a noncanonical TATA box. Two factors, TATA core factor (TCF), expressed in cell lines derived from uteroglobin-expressing tissues, and the ubiquitously expressed TATA palindrome factor, bind to the DNA major groove at two adjacent sites within this region. Here, we report the identification of the TATA palindrome factor as the transcription/initiation factor YY1 by microsequencing of the biochemically purified factor from HeLa cells. The binding site for YY1 within the uteroglobin gene is unique in its sequence and its location overlapping a weak TATA box (TACA). Binding of YY1 was required for efficient transcription in TCF-positive Ishikawa cells, which responded only weakly to a change of TACA to TATA, although in vitro binding affinity for the TATA-box-binding protein increased by 1 order of magnitude. In contrast, in CV-1 cells, lacking TCF, binding of YY1 was not required for transcription in the context of a wild-type TACA box, whereas a change from TACA to TATA led to significantly increased reporter gene expression. DNA binding data exclude a role of YY1 in stabilizing the interaction of the TATA-box-binding protein with the uteroglobin promoter. We conclude that cell lines derived from uteroglobin-expressing tissues overcome the weak TATA box with the help of auxiliary factors, one of them being YY1. PMID:8887668

  6. Nucleophosmin/B23 regulates PCNA promoter through YY1

    SciTech Connect

    Weng, Jing J.; Yung, Benjamin Y.M. . E-mail: byung@mail.cgu.edu.tw

    2005-09-30

    Ectopic over-expression of nucleophosmin/B23 caused a marked up-regulation in the amounts of Yin Yang 1 (YY1) and proliferating cellular nuclear antigen (PCNA) proteins. Transfection with nucleophosmin/B23-targeting siRNA induced a decrease in the intracellular amounts of nucleophosmin/B23, YY1, and PCNA. PCNA expression and its promoter activity were attenuated either by nucleophosmin/B23-siRNA or YY1-siRNA. The ChIP assay showed that positive regulation of PCNA is achieved by binding of YY1 to the initiation site of PCNA promoter. The binding of YY1 to the PCNA promoter and histone H4 acetylation was significantly decreased in nucleophosmin/B23-siRNA-treated cells as compared to control vector-transfected cells. Mutation in YY1 binding site resulted in the loss of PCNA promoter activity and the binding of YY1 to the promoter. The results have indicated that YY1 binds to the initiation site of the PCNA promoter along with histone H4 acetylation, leading to transcriptional activity. We have demonstrated that nucleophosmin/B23 plays an important role in the regulation of PCNA through YY1.

  7. YY1 Is Required for Germinal Center B Cell Development

    PubMed Central

    Vuyyuru, Raja; Jha, Vibha; Hodewadekar, Suchita; Manser, Tim; Atchison, Michael L.

    2016-01-01

    YY1 has been implicated as a master regulator of germinal center B cell development as YY1 binding sites are frequently present in promoters of germinal center-expressed genes. YY1 is known to be important for other stages of B cell development including the pro-B and pre-B cells stages. To determine if YY1 plays a critical role in germinal center development, we evaluated YY1 expression during B cell development, and used a YY1 conditional knock-out approach for deletion of YY1 in germinal center B cells (CRE driven by the immunoglobulin heavy chain γ1 switch region promoter; γ1-CRE). We found that YY1 is most highly expressed in germinal center B cells and is increased 3 fold in splenic B cells activated by treatment with anti-IgM and anti-CD40. In addition, deletion of the yy1 gene by action of γ1-CRE recombinase resulted in significant loss of GC cells in both un-immunized and immunized contexts with corresponding loss of serum IgG1. Our results show a crucial role for YY1 in the germinal center reaction. PMID:27167731

  8. The YY1/MMP2 axis promotes trophoblast invasion at the maternal-fetal interface.

    PubMed

    Tian, Fu-Ju; Cheng, Yan-Xiang; Li, Xiao-Cui; Wang, Fa; Qin, Chuan-Mei; Ma, Xiao-Ling; Yang, Jing; Lin, Yi

    2016-05-01

    YY1 is a sequence-specific DNA-binding transcription factor that has many important biological roles. However, its function in trophoblasts at the maternal-fetal interface remains to be elucidated. In this study, we used an mRNA microarray and reverse transcription qPCR and compared the YY1 mRNA expression level in trophoblasts between patients with recurrent miscarriage (RM) and healthy control subjects. Our results revealed that YY1 mRNA expression was significantly lower in the trophoblasts of the RM group compared with the healthy control group. Furthermore, immunofluorescence and immunohistochemical data showed that YY1 was highly expressed in human placental villi during early pregnancy, especially in cytotrophoblast cells and invasive extravillous trophoblasts, and it was expressed at a much lower level in the placental villi of term pregnancy. YY1 overexpression enhanced, and knockdown repressed, the invasion and proliferation of trophoblasts. Antibody array screening revealed that YY1 significantly promoted MMP2 expression in trophoblasts. Bioinformatics analysis identified three YY1-binding sites in the MMP2 promoter region, and chromatin immunoprecipitation analysis verified that YY1 binds directly to its promoter region. Importantly, inhibition of YY1 by siRNA clearly decreased trophoblast invasion in an ex vivo explant culture model. Overall, our findings revealed a new regulatory pathway of YY1/MMP2 in trophoblast cell invasion during early pregnancy and indicated that YY1 may be involved in the pathogenesis of RM. PMID:27071480

  9. The YY1/MMP2 axis promotes trophoblast invasion at the maternal–fetal interface

    PubMed Central

    Tian, Fu‐Ju; Cheng, Yan‐Xiang; Li, Xiao‐Cui; Wang, Fa; Qin, Chuan‐Mei; Ma, Xiao‐Ling

    2016-01-01

    Abstract YY1 is a sequence‐specific DNA‐binding transcription factor that has many important biological roles. However, its function in trophoblasts at the maternal–fetal interface remains to be elucidated. In this study, we used an mRNA microarray and reverse transcription qPCR and compared the YY1 mRNA expression level in trophoblasts between patients with recurrent miscarriage (RM) and healthy control subjects. Our results revealed that YY1 mRNA expression was significantly lower in the trophoblasts of the RM group compared with the healthy control group. Furthermore, immunofluorescence and immunohistochemical data showed that YY1 was highly expressed in human placental villi during early pregnancy, especially in cytotrophoblast cells and invasive extravillous trophoblasts, and it was expressed at a much lower level in the placental villi of term pregnancy. YY1 overexpression enhanced, and knockdown repressed, the invasion and proliferation of trophoblasts. Antibody array screening revealed that YY1 significantly promoted MMP2 expression in trophoblasts. Bioinformatics analysis identified three YY1binding sites in the MMP2 promoter region, and chromatin immunoprecipitation analysis verified that YY1 binds directly to its promoter region. Importantly, inhibition of YY1 by siRNA clearly decreased trophoblast invasion in an ex vivo explant culture model. Overall, our findings revealed a new regulatory pathway of YY1/MMP2 in trophoblast cell invasion during early pregnancy and indicated that YY1 may be involved in the pathogenesis of RM. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. PMID:27071480

  10. YY1 positively regulates human UBIAD1 expression

    SciTech Connect

    Funahashi, Nobuaki; Hirota, Yoshihisa; Nakagawa, Kimie; Sawada, Natumi; Watanabe, Masato; Suhara, Yoshitomo; Okano, Toshio

    2015-05-01

    Vitamin K is involved in bone formation and blood coagulation. Natural vitamin K compounds are composed of the plant form phylloquinone (vitamin K{sub 1}) and a series of bacterial menaquionones (MK-n; vitamin K{sub 2}). Menadione (vitamin K{sub 3}) is an artificial vitamin K compound. MK-4 contains 4-isoprenyl as a side group in the 2-methyl-1,4-naphthoquinone common structure and has various bioactivities. UbiA prenyltransferase domain containing 1 (UBIAD1 or TERE1) is the menaquinone-4 biosynthetic enzyme. UBIAD1 transcript expression significantly decreases in patients with prostate carcinoma and overexpressing UBIAD1 inhibits proliferation of a tumour cell line. UBIAD1 mRNA expression is ubiquitous in mouse tissues, and higher UBIAD1 mRNA expression levels are detected in the brain, heart, kidneys and pancreas. Several functions of UBIAD1 have been reported; however, regulation of the human UBIAD1 gene has not been elucidated. Here we report cloning and characterisation of the human UBIAD1 promoter. A 5′ rapid amplification of cDNA ends analysis revealed that the main transcriptional start site was 306 nucleotides upstream of the translation initiation codon. Deletion and mutation analyses revealed the functional importance of the YY1 consensus motif. Electrophoretic gel mobility shift and chromatin immunoprecipitation assays demonstrated that YY1 binds the UBIAD1 promoter in vitro and in vivo. In addition, YY1 small interfering RNA decreased endogenous UBIAD1 mRNA expression and UBIAD1 conversion activity. These results suggest that YY1 up-regulates UBIAD1 expression and UBIAD1 conversion activity through the UBIAD1 promoter. - Highlights: • We cloned the human UBIAD1 promoter. • The functional importance of the YY1 motif was identified in the UBIAD1 promoter. • YY1 binds the UBIAD1 promoter in vitro and in vivo. • Knockdown of YY1 significantly decreased UBIAD1 expression. • YY1 up-regulates UBIAD1 conversion activity through the UBIAD1

  11. YY1 regulates the expression of snail through a distal enhancer

    PubMed Central

    Palmer, Matthew B.; Majumder, Parimal; Cooper, John C.; Yoon, Hyesuk; Wade, Paul A.; Boss, Jeremy M.

    2010-01-01

    Expression of the snail gene is required for the epithelial-mesenchymal transitions that accompany mammalian gastrulation, neural crest migration, and organ formation. Pathological expression of snail contributes to the migratory capacity of invasive tumors, including melanomas. To investigate the mechanism of snail up regulation in human melanoma cells, a conserved enhancer located 3’ of the snail gene was analyzed. An overlapping Ets and YY1 consensus sequence, in addition to a SOX consensus sequence, were required for full enhancer activity. Proteins specifically binding these sequences were detected by EMSA. The Ets/YY1 binding activity was purified by DNA affinity chromatography and identified as YY1. Although ubiquitously expressed, YY1 was bound at the snail 3’ enhancer in vivo in snail-expressing cells but not in cells that did not express snail. Knockdown of YY1 in A375 cells led to decreased snail expression. These results identify a role for YY1 in regulating transcription of snail in melanoma cells through binding to the snail 3’ enhancer. PMID:19208738

  12. Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis

    PubMed Central

    Lu, Leina; Sun, Kun; Chen, Xiaona; Zhao, Yu; Wang, Lijun; Zhou, Liang; Sun, Hao; Wang, Huating

    2013-01-01

    Skeletal muscle differentiation is orchestrated by a network of transcription factors, epigenetic regulators, and non-coding RNAs. The transcription factor Yin Yang 1 (YY1) silences multiple target genes in myoblasts (MBs) by recruiting Ezh2 (Enhancer of Zeste Homologue2). To elucidate genome-wide YY1 binding in MBs, we performed chromatin immunoprecipitation (ChIP)-seq and found 1820 specific binding sites in MBs with a large portion residing in intergenic regions. Detailed analysis demonstrated that YY1 acts as an activator for many loci in addition to its known repressor function. No significant co-occupancy was found between YY1 and Ezh2, suggesting an additional Ezh2-independent function for YY1 in MBs. Further analysis of intergenic binding sites showed that YY1 potentially regulates dozens of large intergenic non-coding RNAs (lincRNAs), whose function in myogenesis is underexplored. We characterized a novel muscle-associated lincRNA (Yam-1) that is positively regulated by YY1. Yam-1 is downregulated upon differentiation and acts as an inhibitor of myogenesis. We demonstrated that Yam-1 functions through in cis regulation of miR-715, which in turn targets Wnt7b. Our findings not only provide the first genome-wide picture of YY1 association in muscle cells, but also uncover the functional role of lincRNA Yam-1. PMID:23942234

  13. A prominent and conserved role for YY1 in Xist transcriptional activation

    PubMed Central

    Navarro, Pablo; Neuillet, Damien; Rougeulle, Claire

    2014-01-01

    Accumulation of the non-coding RNA Xist on one X chromosome in female cells is a hallmark of X-chromosome inactivation in eutherians. Here, we uncovered an essential function for the ubiquitous autosomal transcription factor Yin-Yang 1 (YY1) in the transcriptional activation of Xist in both human and mouse. We show that loss of YY1 prevents Xist up-regulation during the initiation and maintenance of X-inactivation, and that YY1 binds directly the Xist 5′ region to trigger the activity of the Xist promoter. Binding of YY1 to the Xist 5′ region prior to X-chromosome inactivation competes with the Xist repressor REX1 while DNA methylation controls mono-allelic fixation of YY1 to Xist at the onset of X-chromosome inactivation. YY1 is thus the first autosomal activating factor involved in a fundamental and conserved pathway of Xist regulation that ensures the asymmetric transcriptional up-regulation of the master regulator of X-chromosome inactivation. PMID:25209548

  14. YY1 inhibits differentiation and function of regulatory T cells by blocking Foxp3 expression and activity.

    PubMed

    Hwang, Soo Seok; Jang, Sung Woong; Kim, Min Kyung; Kim, Lark Kyun; Kim, Bong-Sung; Kim, Hyeong Su; Kim, Kiwan; Lee, Wonyong; Flavell, Richard A; Lee, Gap Ryol

    2016-01-01

    Regulatory T (T(reg)) cells are essential for maintenance of immune homeostasis. Foxp3 is the key transcription factor for T(reg)-cell differentiation and function; however, molecular mechanisms for its negative regulation are poorly understood. Here we show that YY1 expression is lower in T(reg) cells than T(conv) cells, and its overexpression causes a marked reduction of Foxp3 expression and abrogation of suppressive function of Treg cells. YY1 is increased in T(reg) cells under inflammatory conditions with concomitant decrease of suppressor activity in dextran sulfate-induced colitis model. YY1 inhibits Smad3/4 binding to and chromatin remodelling of the Foxp3 locus. In addition, YY1 interrupts Foxp3-dependent target gene expression by physically interacting with Foxp3 and by directly binding to the Foxp3 target genes. Thus, YY1 inhibits differentiation and function of T(reg) cells by blocking Foxp3. PMID:26892542

  15. Expression of YY1 in Differentiated Thyroid Cancer.

    PubMed

    Arribas, Jéssica; Castellví, Josep; Marcos, Ricard; Zafón, Carles; Velázquez, Antonia

    2015-05-01

    The transcription factor Yin Yang 1 (YY1) has an important regulatory role in tumorigenesis, but its implication in thyroid cancer has not been yet investigated. In the present study, we have analyzed the expression of YY1 in differentiated thyroid cancer and assessed the association of YY1 expression with clinical features. Expression of YY1 was evaluated in human thyroid cancer cell lines, a series of matched normal/tumor thyroid tissues and in a thyroid cancer tissue microarray, using real-time PCR, Western blot, and/or immunohistochemistry. YY1 was overexpressed in thyroid cancer cells, at transcription and protein levels. A significant increase of YY1 mRNA was also observed in tumor thyroid tissues. Moreover, immunohistochemical analysis of the thyroid cancer tissue microarray revealed that both papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC) present increased YY1 protein levels (48 and 19%, respectively). After stratification by the level of YY1 protein, positive YY1 expression identifies 88% of patients with PTC. The association of YY1 expression with clinicopathological features in PTC and FTC showed that YY1 expression was related with age at diagnosis. Our data indicates for the first time overexpression of YY1 in differentiated thyroid cancer, with YY1 being more frequently overexpressed in the PTC subtype.

  16. The Human Factors YY1 and LSF Repress the Human Immunodeficiency Virus Type 1 Long Terminal Repeat via Recruitment of Histone Deacetylase 1

    PubMed Central

    Coull, Jason J.; Romerio, Fabio; Sun, Jian-Min; Volker, Janet L.; Galvin, Katherine M.; Davie, James R.; Shi, Yang; Hansen, Ulla; Margolis, David M.

    2000-01-01

    Enigmatic mechanisms restore the resting state in activated lymphocytes following human immunodeficiency virus type 1 (HIV-1) infection, rarely allowing persistent nonproductive infection. We detail a mechanism whereby cellular factors could establish virological latency. The transcription factors YY1 and LSF cooperate in repression of transcription from the HIV-1 long terminal repeat (LTR). LSF recruits YY1 to the LTR via the zinc fingers of YY1. The first two zinc fingers were observed to be sufficient for this interaction in vitro. A mutant of LSF incapable of binding DNA blocked repression. Like other transcriptional repressors, YY1 can function via recruitment of histone deacetylase (HDAC). We find that HDAC1 copurifies with the LTR-binding YY1-LSF repressor complex, the domain of YY1 that interacts with HDAC1 is required to repress the HIV-1 promoter, expression of HDAC1 augments repression of the LTR by YY1, and the deacetylase inhibitor trichostatin A blocks repression mediated by YY1. This novel link between HDAC recruitment and inhibition of HIV-1 expression by YY1 and LSF, in the natural context of a viral promoter integrated into chromosomal DNA, is the first demonstration of a molecular mechanism of repression of HIV-1. YY1 and LSF may establish transcriptional and virological latency of HIV, a state that has recently been recognized in vivo and has significant implications for the long-term treatment of AIDS. PMID:10888618

  17. Cloning and identification of a YY-1 homolog as a potential transcription factor from Pinctada fucata.

    PubMed

    Zheng, Xiangnan; Cheng, Minzhang; Xiang, Liang; Su, Jingtan; Zhou, Yujuan; Xie, Liping; Zhang, Rongqing

    2015-11-01

    Biomineralization is an important and ubiquitous process in organisms. The shell formation of mollusks is a typical biomineral physical activity and is used as a canonical model in biomineralization research. Most recent studies focused on the identification of matrix proteins involved in shell formation; however, little is known about their transcriptional regulation mechanism, especially the transcription factors involved in shell formation. In this study, we identified a homolog of the YY-1 transcriptional factor from Pinctada fucata, named Pf-YY-1, and characterized its expression pattern and biological functions. Pf-YY-1 has a typical zinc finger motif highly similar to those in humans, mice, and other higher organisms, which indicated its DNA-binding capability and its function as a transcription factor. Pf-YY-1 is ubiquitously expressed in many tissues, but at a higher level in the mantle, which suggested a role in biomineralization. The expression pattern of Pf-YY-1 during pearl sac development was quite similar to, and was synchronized with, those of Prisilkin-39, ACCBP, and other genes involved in biomineralization, which also suggested its function in biomineralization.

  18. YY1-MIR372-SQSTM1 regulatory axis in autophagy.

    PubMed

    Feng, Lifeng; Ma, Yanning; Sun, Jie; Shen, Qi; Liu, Leiming; Lu, Haiqi; Wang, Faliang; Yue, Yongfang; Li, Jiaqiu; Zhang, Shenjie; Lin, Xiaoying; Chu, Jue; Han, Weidong; Wang, Xian; Jin, Hongchuan

    2014-08-01

    Autophagy is a self-proteolytic process that degrades intracellular material to enable cellular survival under unfavorable conditions. However, how autophagy is activated in human carcinogenesis remains largely unknown. Herein we report an epigenetic regulation of autophagy in human cancer cells. YY1 (YY1 transcription factor) is a well-known epigenetic regulator and is upregulated in many cancers. We found that YY1 knockdown inhibited cell viability and autophagy flux through downregulating SQSTM1 (sequestosome 1). YY1 regulated SQSTM1 expression through the epigenetic modulation of the transcription of MIR372 (microRNA 372) which was found to target SQSTM1 directly. During nutrient starvation, YY1 was stimulated to promote SQSTM1 expression and subsequent autophagy activation by suppressing MIR372 expression. Similar to YY1 depletion, MIR372 overexpression blocked autophagy activation and inhibited in vivo tumor growth. SQSTM1 upregulation and competent autophagy flux thus contributed to the oncogenic function of YY1. YY1-promoted SQSTM1 upregulation might be a useful histological marker for cancer detection and a potential target for drug development.

  19. YY1-MIR372-SQSTM1 regulatory axis in autophagy

    PubMed Central

    Feng, Lifeng; Ma, Yanning; Sun, Jie; Shen, Qi; Liu, Leiming; Lu, Haiqi; Wang, Faliang; Yue, Yongfang; Li, Jiaqiu; Zhang, Shenjie; Lin, Xiaoying; Chu, Jue; Han, Weidong; Wang, Xian; Jin, Hongchuan

    2014-01-01

    Autophagy is a self-proteolytic process that degrades intracellular material to enable cellular survival under unfavorable conditions. However, how autophagy is activated in human carcinogenesis remains largely unknown. Herein we report an epigenetic regulation of autophagy in human cancer cells. YY1 (YY1 transcription factor) is a well-known epigenetic regulator and is upregulated in many cancers. We found that YY1 knockdown inhibited cell viability and autophagy flux through downregulating SQSTM1 (sequestosome 1). YY1 regulated SQSTM1 expression through the epigenetic modulation of the transcription of MIR372 (microRNA 372) which was found to target SQSTM1 directly. During nutrient starvation, YY1 was stimulated to promote SQSTM1 expression and subsequent autophagy activation by suppressing MIR372 expression. Similar to YY1 depletion, MIR372 overexpression blocked autophagy activation and inhibited in vivo tumor growth. SQSTM1 upregulation and competent autophagy flux thus contributed to the oncogenic function of YY1. YY1-promoted SQSTM1 upregulation might be a useful histological marker for cancer detection and a potential target for drug development. PMID:24991827

  20. A Dual-Function Transcription Factor, AtYY1, Is a Novel Negative Regulator of the Arabidopsis ABA Response Network.

    PubMed

    Li, Tian; Wu, Xiu-Yun; Li, Hui; Song, Jian-Hui; Liu, Jin-Yuan

    2016-05-01

    Abscisic acid (ABA) plays crucial roles in plant growth and development, as well as in response to various environmental stresses. To date, many regulatory genes involved in the ABA response network have been identified; however, their roles have remained to be fully elucidated. In this study, we identified AtYY1, an Arabidopsis homolog of the mammalian C2H2 zinc-finger transcription factor Yin Yang 1 (YY1), as a novel negative regulator of the ABA response. AtYY1 is a dual-function transcription factor with both repression and activation domains. The expression of AtYY1 was induced by ABA and stress conditions including high salt and dehydration. The yy1 mutant was more sensitive to ABA and NaCl than the wild-type, while overexpressing AtYY1 plants were less sensitive. AtYY1 loss also enhanced ABA-induced stomatal closing and drought resistance. Moreover, AtYY1 can bind the ABA REPRESSOR1 (ABR1) promoter and directly upregulate ABR1 expression, as well as negatively regulate ABA- and salt-responsive gene expression. Additional analysis indicated that ABA INSENSITIVE4 (ABI4) might positively regulate AtYY1 expression and that ABR1 can antagonize this regulation. Our findings provide direct evidence that AtYY1 is a novel negative regulator of the ABA response network and that the ABI4-AtYY1-ABR1 regulatory pathway may fine-tune ABA-responsive gene expression in Arabidopsis. PMID:26961720

  1. PARP-1 and YY1 Are Important Novel Regulators of CXCL12 Gene Transcription in Rat Pancreatic Beta Cells

    PubMed Central

    Marković, Jelena; Grdović, Nevena; Dinić, Svetlana; Karan-Djurašević, Teodora; Uskoković, Aleksandra; Arambašić, Jelena; Mihailović, Mirjana; Pavlović, Sonja; Poznanović, Goran; Vidaković, Melita

    2013-01-01

    Despite significant progress, the molecular mechanisms responsible for pancreatic beta cell depletion and development of diabetes remain poorly defined. At present, there is no preventive measure against diabetes. The positive impact of CXCL12 expression on the pancreatic beta cell prosurvival phenotype initiated this study. Our aim was to provide novel insight into the regulation of rat CXCL12 gene (Cxcl12) transcription. The roles of poly(ADP-ribose) polymerase-1 (PARP-1) and transcription factor Yin Yang 1 (YY1) in Cxcl12 transcription were studied by examining their in vitro and in vivo binding affinities for the Cxcl12 promoter in a pancreatic beta cell line by the electrophoretic mobility shift assay and chromatin immunoprecipitation. The regulatory activities of PARP-1 and YY1 were assessed in transfection experiments using a reporter vector with a Cxcl12 promoter sequence driving luciferase gene expression. Experimental evidence for PARP-1 and YY1 revealed their trans-acting potential, wherein PARP-1 displayed an inhibitory, and YY1 a strong activating effect on Cxcl12 transcription. Streptozotocin (STZ)-induced general toxicity in pancreatic beta cells was followed by changes in Cxcl12 promoter regulation. PARP-1 binding to the Cxcl12 promoter during basal and in STZ-compromised conditions led us to conclude that PARP-1 regulates constitutive Cxcl12 expression. During the early stage of oxidative stress, YY1 exhibited less affinity toward the Cxcl12 promoter while PARP-1 displayed strong binding. These interactions were accompanied by Cxcl12 downregulation. In the later stages of oxidative stress and intensive pancreatic beta cell injury, YY1 was highly expressed and firmly bound to Cxcl12 promoter in contrast to PARP-1. These interactions resulted in higher Cxcl12 expression. The observed ability of PARP-1 to downregulate, and of YY1 to upregulate Cxcl12 promoter activity anticipates corresponding effects in the natural context where the functional

  2. The Polycomb Group Protein EED Interacts with YY1, and Both Proteins Induce Neural Tissue in Xenopus Embryos

    PubMed Central

    Satijn, David P. E.; Hamer, Karien M.; den Blaauwen, Jan; Otte, Arie P.

    2001-01-01

    Polycomb group (PcG) proteins form multimeric protein complexes which are involved in the heritable stable repression of genes. Previously, we identified two distinct human PcG protein complexes. The EED-EZH protein complex contains the EED and EZH2 PcG proteins, and the HPC-HPH PcG complex contains the HPC, HPH, BMI1, and RING1 PcG proteins. Here we show that YY1, a homolog of the Drosophila PcG protein pleiohomeotic (Pho), interacts specificially with the human PcG protein EED but not with proteins of the HPC-HPH PcG complex. Since YY1 and Pho are DNA-binding proteins, the interaction between YY1 and EED provides a direct link between the chromatin-associated EED-EZH PcG complex and the DNA of target genes. To study the functional significance of the interaction, we expressed the Xenopus homologs of EED and YY1 in Xenopus embryos. Both Xeed and XYY1 induce an ectopic neural axis but do not induce mesodermal tissues. In contrast, members of the HPC-HPH PcG complex do not induce neural tissue. The exclusive, direct neuralizing activity of both the Xeed and XYY1 proteins underlines the significance of the interaction between the two proteins. Our data also indicate a role for chromatin-associated proteins, such as PcG proteins, in Xenopus neural induction. PMID:11158321

  3. Genome-wide analysis of YY2 versus YY1 target genes

    PubMed Central

    Chen, Li; Shioda, Toshi; Coser, Kathryn R.; Lynch, Mary C.; Yang, Chuanwei; Schmidt, Emmett V.

    2010-01-01

    Yin Yang 1 (YY1) is a critical transcription factor controlling cell proliferation, development and DNA damage responses. Retrotranspositions have independently generated additional YY family members in multiple species. Although Drosophila YY1 [pleiohomeotic (Pho)] and its homolog [pleiohomeotic-like (Phol)] redundantly control homeotic gene expression, the regulatory contributions of YY1-homologs have not yet been examined in other species. Indeed, targets for the mammalian YY1 homolog YY2 are completely unknown. Using gene set enrichment analysis, we found that lentiviral constructs containing short hairpin loop inhibitory RNAs for human YY1 (shYY1) and its homolog YY2 (shYY2) caused significant changes in both shared and distinguishable gene sets in human cells. Ribosomal protein genes were the most significant gene set upregulated by both shYY1 and shYY2, although combined shYY1/2 knock downs were not additive. In contrast, shYY2 reversed the anti-proliferative effects of shYY1, and shYY2 particularly altered UV damage response, platelet-specific and mitochondrial function genes. We found that decreases in YY1 or YY2 caused inverse changes in UV sensitivity, and that their combined loss reversed their respective individual effects. Our studies show that human YY2 is not redundant to YY1, and YY2 is a significant regulator of genes previously identified as uniquely responding to YY1. PMID:20215434

  4. Expression of the Human Endogenous Retrovirus HTDV/HERV-K Is Enhanced by Cellular Transcription Factor YY1

    PubMed Central

    Knössl, Michael; Löwer, Roswitha; Löwer, Johannes

    1999-01-01

    The human endogenous retrovirus HTDV/HERV-K, which resides in moderate copy numbers in the human genome, is expressed in a cell-type-specific manner, predominantly in teratocarcinoma cells. We have analyzed the regulatory potential of the 5′ enhancer of the HERV-K long terminal repeat. Protein extracts of HERV-K-expressing teratocarcinoma cell lines (GH and Tera2) and nonexpressing HeLa and HepG2 cells form different protein complexes on the enhancer sequence as detected by electrophoretic mobility shift assays (EMSA). Using competition EMSAs, DNase I footprinting, and supershift experiments, we localized the binding site of these complexes to a 20-bp sequence within the enhancer and showed that the transcription factor YY1 is one component of the HERV-K enhancer complex. Replacement of the YY1 binding site with unrelated sequences reduced expression of the luciferase gene as a reporter in transient-transfection assays. PMID:9882329

  5. Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.

    PubMed

    Woo, Caroline J; Kharchenko, Peter V; Daheron, Laurence; Park, Peter J; Kingston, Robert E

    2013-08-01

    Polycomb group (PcG)-mediated repression is an evolutionarily conserved process critical for cell fate determination and maintenance of gene expression during embryonic development. However, the mechanisms underlying PcG recruitment in mammals remain unclear since few regulatory sites have been identified. We report two novel prospective PcG-dependent regulatory elements within the human HOXB and HOXC clusters and compare their repressive activities to a previously identified element in the HOXD cluster. These regions recruited the PcG proteins BMI1 and SUZ12 to a reporter construct in mesenchymal stem cells and conferred repression that was dependent upon PcG expression. Furthermore, we examined the potential of two DNA-binding proteins, JARID2 and YY1, to regulate PcG activity at these three elements. JARID2 has differential requirements, whereas YY1 appears to be required for repressive activity at all 3 sites. We conclude that distinct elements of the mammalian HOX clusters can recruit components of the PcG complexes and confer repression, similar to what has been seen in Drosophila. These elements, however, have diverse requirements for binding factors, which, combined with previous data on other loci, speaks to the complexity of PcG targeting in mammals.

  6. Transcriptional Regulation of the Astrocytic Excitatory Amino Acid Transporter 1 (EAAT1) via NF-κB and Yin Yang 1 (YY1)*

    PubMed Central

    Karki, Pratap; Kim, Clifford; Smith, Keisha; Son, Deok-Soo; Aschner, Michael; Lee, Eunsook

    2015-01-01

    Astrocytic glutamate transporter excitatory amino acid transporter (EAAT) 1, also known as glutamate aspartate transporter (GLAST) in rodents, is one of two glial glutamate transporters that are responsible for removing excess glutamate from synaptic clefts to prevent excitotoxic neuronal death. Despite its important role in neurophysiological functions, the molecular mechanisms of EAAT1 regulation at the transcriptional level remain to be established. Here, we report that NF-κB is a main positive transcription factor for EAAT1, supported by the following: 1) EAAT1 contains two consensus sites for NF-κB, 2) mutation of NF-κB binding sites decreased EAAT1 promoter activity, and 3) activation of NF-κB increased, whereas inhibition of NF-κB decreased EAAT1 promoter activity and mRNA/protein levels. EGF increased EAAT1 mRNA/protein levels and glutamate uptake via NF-κB. The transcription factor yin yang 1 (YY1) plays a role as a critical negative regulator of EAAT1, supported by the following: 1) the EAAT1 promoter contains multiple consensus sites for YY1, 2) overexpression of YY1 decreased EAAT1 promoter activity and mRNA/protein levels, and 3) knockdown of YY1 increased EAAT1 promoter activity and mRNA/protein levels. Manganese decreased EAAT1 expression via YY1. Epigenetic modifiers histone deacetylases (HDACs) served as co-repressors of YY1 to further decrease EAAT1 promoter activity, whereas inhibition of HDACs reversed manganese-induced decrease of EAAT1 expression. Taken together, our findings suggest that NF-κB is a critical positive regulator of EAAT1, mediating the stimulatory effects of EGF, whereas YY1 is a negative regulator of EAAT1 with HDACs as co-repressors, mediating the inhibitory effects of manganese on EAAT1 regulation. PMID:26269591

  7. Overexpression of YY1 increases the protein production in mammalian cells.

    PubMed

    Tastanova, Aizhan; Schulz, Alexandra; Folcher, Marc; Tolstrup, Anne; Puklowski, Anja; Kaufmann, Hitto; Fussenegger, Martin

    2016-02-10

    The production of therapeutic antibodies using mammalian cells remains a high-priority in the biopharmaceutical manufacturing industry. Bioengineers have targeted different cellular processes, including transcription, translation, secretion and post-translational modifications, to overcome the metabolic bottlenecks limiting production capacity and create high-producing mammalian cell lines. The polycomb group (PcG) proteins belong to a family of chromatin regulators with important roles in multicellular development. By overexpressing and screening genes from the PcG family, we have identified an epigenetic key player for biopharmaceutical manufacturing enhancement: the transcription factor Yin Yang 1 (YY1). The overexpression of YY1 led to an increase in the production of several product genes (SEAP, VEGF165, IgG including Rituximab), provided that human YY1 (hYY1) was expressed in human cells (HeLa, HT-1080, HEK-293T, FreeStyle™ 293-F) and Chinese hamster ovary cell-derived YY1 (cYY1) was expressed in CHO cells (CHO-K1, CHO-easyC, FreeStyle™ CHO-S, CHO-B13-24, CHO-IgG1). Ectopic expression of cYY1 in the stable CHO-derived IgG producer cell lines CHO-B13-24 and CHO-IgG1 increased the antibody titer up to 6-fold, suggesting that epigenetic engineering of mammalian production cell lines could become a new strategy to improve the manufacturing of complex protein pharmaceuticals. PMID:26686315

  8. mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex.

    PubMed

    Cunningham, John T; Rodgers, Joseph T; Arlow, Daniel H; Vazquez, Francisca; Mootha, Vamsi K; Puigserver, Pere

    2007-11-29

    Transcriptional complexes that contain peroxisome-proliferator-activated receptor coactivator (PGC)-1alpha control mitochondrial oxidative function to maintain energy homeostasis in response to nutrient and hormonal signals. An important component in the energy and nutrient pathways is mammalian target of rapamycin (mTOR), a kinase that regulates cell growth, size and survival. However, it is unknown whether and how mTOR controls mitochondrial oxidative activities. Here we show that mTOR is necessary for the maintenance of mitochondrial oxidative function. In skeletal muscle tissues and cells, the mTOR inhibitor rapamycin decreased the gene expression of the mitochondrial transcriptional regulators PGC-1alpha, oestrogen-related receptor alpha and nuclear respiratory factors, resulting in a decrease in mitochondrial gene expression and oxygen consumption. Using computational genomics, we identified the transcription factor yin-yang 1 (YY1) as a common target of mTOR and PGC-1alpha. Knockdown of YY1 caused a significant decrease in mitochondrial gene expression and in respiration, and YY1 was required for rapamycin-dependent repression of those genes. Moreover, mTOR and raptor interacted with YY1, and inhibition of mTOR resulted in a failure of YY1 to interact with and be coactivated by PGC-1alpha. We have therefore identified a mechanism by which a nutrient sensor (mTOR) balances energy metabolism by means of the transcriptional control of mitochondrial oxidative function. These results have important implications for our understanding of how these pathways might be altered in metabolic diseases and cancer. PMID:18046414

  9. GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis.

    PubMed

    Agarwal, Neeraj; Dancik, Garrett M; Goodspeed, Andrew; Costello, James C; Owens, Charles; Duex, Jason E; Theodorescu, Dan

    2016-09-01

    In principle, the inhibition of candidate gain-of-function genes defined through genomic analyses of large patient cohorts offers an attractive therapeutic strategy. In this study, we focused on changes in expression of CD24, a well-validated clinical biomarker of poor prognosis and a driver of tumor growth and metastasis, as a benchmark to assess functional relevance. Through this approach, we identified GON4L as a regulator of CD24 from screening a pooled shRNA library of 176 candidate gain-of-function genes. GON4L depletion reduced CD24 expression in human bladder cancer cells and blocked cell proliferation in vitro and tumor xenograft growth in vivo Mechanistically, GON4L interacted with transcription factor YY1, promoting its association with the androgen receptor to drive CD24 expression and cell growth. In clinical bladder cancer specimens, expression of GON4L, YY1, and CD24 was elevated compared with normal bladder urothelium. This pathway is biologically relevant in other cancer types as well, where CD24 and the androgen receptor are clinically prognostic, given that silencing of GON4L and YY1 suppressed CD24 expression and growth of human lung, prostate, and breast cancer cells. Overall, our results define GON4L as a novel driver of cancer growth, offering new biomarker and therapeutic opportunities. Cancer Res; 76(17); 5175-85. ©2016 AACR.

  10. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism.

    PubMed

    Liu, Lian; Wang, Jian-Fei; Fan, Jie; Rao, Yi-Song; Liu, Fang; Yan, You-E; Wang, Hui

    2016-01-01

    Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression. PMID:27598153

  11. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism.

    PubMed

    Liu, Lian; Wang, Jian-Fei; Fan, Jie; Rao, Yi-Song; Liu, Fang; Yan, You-E; Wang, Hui

    2016-09-03

    Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression.

  12. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism

    PubMed Central

    Liu, Lian; Wang, Jian-Fei; Fan, Jie; Rao, Yi-Song; Liu, Fang; Yan, You-E; Wang, Hui

    2016-01-01

    Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression. PMID:27598153

  13. Promoter-region hypermethylation and expression downregulation of Yy1 (Yin yang 1) in preneoplastic liver lesions in a thioacetamide rat hepatocarcinogenesis model

    SciTech Connect

    Abe, Hajime; Ogawa, Takashi; Wang, Liyun; Kimura, Masayuki; Tanaka, Takeshi; Morita, Reiko; Yoshida, Toshinori; Shibutani, Makoto

    2014-11-01

    Thioacetamide (TAA) has been used to develop a rodent model for hepatocarcinogenesis. To determine the genes with epigenetic modifications in early hepatocarcinogenesis, we did a genome-wide scan for hypermethylated promoter regions using CpG island microarrays in TAA-promoted rat liver tissue. Eight genes were selected based on the microarray profile; of these, Yy1 and Wdr45b were confirmed to be hypermethylated by methylation-specific polymerase chain reaction (PCR) and pyrosequencing and downregulated by real-time reverse transcription PCR. Non-neoplastic liver cells had nuclear Yy1 immunoreactivity, while preneoplastic foci with glutathione S-transferase placental form (GST-P) immunoreactivity had decreased Yy1 immunoreactivity. The incidence of these foci was proportional to the dose of TAA administered. Co-expression analysis of gene products downstream of Yy1 revealed increased nuclear phospho-c-Myc{sup +} foci as well as nuclear and cytoplasmic p21{sup Cip1+} foci in Yy1{sup −} or GST-P{sup +} foci in response to TAA-promotion dose. Although the absolute number of cells was low, the incidence of death receptor 5{sup −} foci was increased in Yy1{sup −} foci in proportion to the TAA dose. Yy1{sup −}/GST-P{sup +} foci revealed a higher number of proliferating cell nuclear antigen (PCNA)-immunoreactive cells than Yy1{sup +}/GST-P{sup +} foci, while cleaved caspase-3{sup +} cells were unchanged between Yy1{sup –}/GST-P{sup +} and Yy1{sup +}/GST-P{sup +} foci. In the case of Wdr45b, most GST-P{sup +} foci were Wdr45b{sup –} and were not increased by TAA promotion. These results suggest involvement of Yy1 in the epigenetic gene regulation at the early stages of TAA promoted cell proliferation and concomitant cell cycle arrest in preneoplastic lesions. - Highlights: • Epigenetically downregulated genes were searched in TAA-promnoted rat livers. • Yy1 and Wdr45b showed promoter-region hypermethylation and mRNA downregulation. • TAA promoted

  14. Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity

    PubMed Central

    Verdeguer, Francisco; Soustek, Meghan S.; Hatting, Maximilian; Blättler, Sharon M.; McDonald, Devin; Barrow, Joeva J.

    2015-01-01

    Mitochondrial oxidative and thermogenic functions in brown and beige adipose tissues modulate rates of energy expenditure. It is unclear, however, how beige or white adipose tissue contributes to brown fat thermogenic function or compensates for partial deficiencies in this tissue and protects against obesity. Here, we show that the transcription factor Yin Yang 1 (YY1) in brown adipose tissue activates the canonical thermogenic and uncoupling gene expression program. In contrast, YY1 represses a series of secreted proteins, including fibroblast growth factor 21 (FGF21), bone morphogenetic protein 8b (BMP8b), growth differentiation factor 15 (GDF15), angiopoietin-like 6 (Angptl6), neuromedin B, and nesfatin, linked to energy expenditure. Despite substantial decreases in mitochondrial thermogenic proteins in brown fat, mice lacking YY1 in this tissue are strongly protected against diet-induced obesity and exhibit increased energy expenditure and oxygen consumption in beige and white fat depots. The increased expression of secreted proteins correlates with elevation of energy expenditure and promotion of beige and white fat activation. These results indicate that YY1 in brown adipose tissue controls antagonistic gene expression programs associated with energy balance and maintenance of body weight. PMID:26503783

  15. Transcriptional regulation of the human acid alpha-glucosidase gene. Identification of a repressor element and its transcription factors Hes-1 and YY1.

    PubMed

    Yan, B; Heus, J; Lu, N; Nichols, R C; Raben, N; Plotz, P H

    2001-01-19

    Acid alpha-glucosidase, the product of a housekeeping gene, is a lysosomal enzyme that degrades glycogen. A deficiency of this enzyme is responsible for a recessively inherited myopathy and cardiomyopathy, glycogenesis type II. We have previously demonstrated that the human acid alpha-glucosidase gene expression is regulated by a silencer within intron 1, which is located in the 5'-untranslated region. In this study, we have used deletion analysis, electrophoretic mobility shift assay, and footprint analysis to further localize the silencer to a 25-base pair element. The repressive effect on the TK promoter was about 50% in both orientations in expression plasmid, and two transcriptional factors were identified with antibodies binding specifically to the element. Mutagenesis and functional analyses of the element demonstrated that the mammalian homologue 1 of Drosophila hairy and Enhancer of split (Hes-1) binding to an E box (CACGCG) and global transcription factor-YY1 binding to its core site function as a transcriptional repressor. Furthermore, the overexpression of Hes-1 significantly enhanced the repressive effect of the silencer element. The data should be helpful in understanding the expression and regulation of the human acid alpha-glucosidase gene as well as other lysosomal enzyme genes.

  16. Antithetical regulation of α-myosin heavy chain between fetal and adult heart failure though shuttling of HDAC5 regulating YY-1 function.

    PubMed

    Fang, Jie; Li, Yifei; Zhou, Kaiyu; Hua, Yimin; Wang, Chuan; Mu, Dezhi

    2015-04-01

    Molecular switches of myosin isoforms are known to occur in various conditions. Here, we demonstrated the result from fetal heart failure and its potential mechanisms. Fetal and adult heart failure rat models were induced by injections of isoproterenol as previously described, and Go6976 was given to heart failing fetuses. Real-time PCR and Western blot were adopted to measure the expressions of α-MHC, β-MHC and YY-1. Co-immunoprecipitation was performed to analysis whether YY-1 interacts with HDAC5. Besides, histological immunofluorescence assessment was carried out to identify the location of HDAC5. α-MHC was recorded elevated in fetal heart failure which was decreased in adult heart failure. Besides, YY-1 was observed elevated both in fetal and adult failing hearts, but YY-1 could co-immunoprecipitation with HDAC5 only in adult hearts. Nuclear localization of HDAC5 was identified in adult cardiomyocytes, while cytoplasmic localization was identified in fetuses. After Go6976 supplied, HDAC5 shuttled into nucleuses interacted with YY-1. The myosin molecular switches were reversed with worsening cardiac functions and higher mortalities. Regulation of MHC in fetal heart failure was different from adult which provided a better compensation with increased α-MHC. This kind of transition was involved with shuttling of HDAC5 regulating YY-1 function.

  17. Predicting Ca2+ -binding sites using refined carbon clusters.

    PubMed

    Zhao, Kun; Wang, Xue; Wong, Hing C; Wohlhueter, Robert; Kirberger, Michael P; Chen, Guantao; Yang, Jenny J

    2012-12-01

    Identifying Ca(2+) -binding sites in proteins is the first step toward understanding the molecular basis of diseases related to Ca(2+) -binding proteins. Currently, these sites are identified in structures either through X-ray crystallography or NMR analysis. However, Ca(2+) -binding sites are not always visible in X-ray structures due to flexibility in the binding region or low occupancy in a Ca(2+) -binding site. Similarly, both Ca(2+) and its ligand oxygens are not directly observed in NMR structures. To improve our ability to predict Ca(2+) -binding sites in both X-ray and NMR structures, we report a new graph theory algorithm (MUG(C) ) to predict Ca(2+) -binding sites. Using carbon atoms covalently bonded to the chelating oxygen atoms, and without explicit reference to side-chain oxygen ligand co-ordinates, MUG(C) is able to achieve 94% sensitivity with 76% selectivity on a dataset of X-ray structures composed of 43 Ca(2+) -binding proteins. Additionally, prediction of Ca(2+) -binding sites in NMR structures was obtained by MUG(C) using a different set of parameters, which were determined by the analysis of both Ca(2+) -constrained and unconstrained Ca(2+) -loaded structures derived from NMR data. MUG(C) identified 20 of 21 Ca(2+) -binding sites in NMR structures inferred without the use of Ca(2+) constraints. MUG(C) predictions are also highly selective for Ca(2+) -binding sites as analyses of binding sites for Mg(2+) , Zn(2+) , and Pb(2+) were not identified as Ca(2+) -binding sites. These results indicate that the geometric arrangement of the second-shell carbon cluster is sufficient not only for accurate identification of Ca(2+) -binding sites in NMR and X-ray structures but also for selective differentiation between Ca(2+) and other relevant divalent cations.

  18. The Ubiquitin Carboxyl Hydrolase BAP1 Forms a Ternary Complex with YY1 and HCF-1 and Is a Critical Regulator of Gene Expression ▿

    PubMed Central

    Yu, Helen; Mashtalir, Nazar; Daou, Salima; Hammond-Martel, Ian; Ross, Julie; Sui, Guangchao; Hart, Gerald W.; Rauscher, Frank J.; Drobetsky, Elliot; Milot, Eric; Shi, Yang; Affar, El Bachir

    2010-01-01

    The candidate tumor suppressor BAP1 is a deubiquitinating enzyme (DUB) involved in the regulation of cell proliferation, although the molecular mechanisms governing its function remain poorly defined. BAP1 was recently shown to interact with and deubiquitinate the transcriptional regulator host cell factor 1 (HCF-1). Here we show that BAP1 assembles multiprotein complexes containing numerous transcription factors and cofactors, including HCF-1 and the transcription factor Yin Yang 1 (YY1). Through its coiled-coil motif, BAP1 directly interacts with the zinc fingers of YY1. Moreover, HCF-1 interacts with the middle region of YY1 encompassing the glycine-lysine-rich domain and is essential for the formation of a ternary complex with YY1 and BAP1 in vivo. BAP1 activates transcription in an enzymatic-activity-dependent manner and regulates the expression of a variety of genes involved in numerous cellular processes. We further show that BAP1 and HCF-1 are recruited by YY1 to the promoter of the cox7c gene, which encodes a mitochondrial protein used here as a model of BAP1-activated gene expression. Our findings (i) establish a direct link between BAP1 and the transcriptional control of genes regulating cell growth and proliferation and (ii) shed light on a novel mechanism of transcription regulation involving ubiquitin signaling. PMID:20805357

  19. Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide.

    PubMed

    Sommer, Dayn Joseph; Roy, Anindya; Astashkin, Andrei; Ghirlanda, Giovanna

    2015-07-01

    iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.

  20. Glutamate-dependent transcriptional regulation of GLAST/EAAT1: a role for YY1.

    PubMed

    Rosas, Sandra; Vargas, Miguel A; López-Bayghen, Esther; Ortega, Arturo

    2007-05-01

    Glutamate is the major excitatory transmitter in the vertebrate brain and its extracellular levels are tightly regulated to prevent excitotoxic effects. The Na(+)-dependent glutamate/aspartate transporter GLAST/EAAT1 is regulated in the short and in the long term by glutamate. A receptors-independent change in its membrane translocation rate, accounts for an acute modulation in GLAST/EAAT1 transport. In contrast, activation of the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate subtype of glutamate receptors represses the transcription of the chick glast gene. A glutamate responsive element has been mapped to the promoter region of this gene containing a bonafide binding site for the transcription factor Ying-Yang 1. Using cultured chick cerebellar Bergmann glia cells, glutamate elicited a time and dose-dependent increase in Ying-Yang 1 DNA binding consistent with the negative response generated in a reporter gene construct controlled for Ying-Yang 1. Over-expression of this transcription factor leads to a substantial reduction in GLAST/EAAT1 transporter uptake and an important decrease in mRNA levels, all associated with the transcriptional repression of the chick glast promoter activity. These results provide evidence for an involvement of Ying-Yang 1 in the transcriptional response to glutamate in glial cells and favor the notion of a relevant role of this factor in GLAST/EAAT1 transcriptional control.

  1. NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maternal-effect mutations in NLRP7 cause rare biparentally inherited hydatidiform moles (BiHMs), abnormal pregnancies containing hypertrophic vesicular trophoblast but no embryo. BiHM trophoblasts display abnormal DNA methylation patterns affecting maternally methylated germline differentially methy...

  2. The glycocalyx promotes cooperative binding and clustering of adhesion receptors.

    PubMed

    Xu, Guang-Kui; Qian, Jin; Hu, Jinglei

    2016-05-18

    Cell adhesion plays a pivotal role in various biological processes, e.g., immune responses, cancer metastasis, and stem cell differentiation. The adhesion behaviors depend subtly on the binding kinetics of receptors and ligands restricted at the cell-substrate interfaces. Although much effort has been directed toward investigating the kinetics of adhesion molecules, the role of the glycocalyx, anchored on cell surfaces as an exterior layer, is still unclear. In this paper, we propose a theoretical approach to study the collective binding kinetics of a few and a large number of binders in the presence of the glycocalyx, representing the cases of initial and mature adhesions of cells, respectively. The analytical results are validated by finding good agreement with our Monte Carlo simulations. In the force loading case, the on-rate and affinity increase as more bonds form, whereas this cooperative effect is not observed in the displacement loading case. The increased thickness and stiffness of the glycocalyx tend to decrease the affinity for a few bonds, while they have less influence on the affinity for a large number of bonds. Moreover, for a flexible membrane with thermally-excited shape fluctuations, the glycocalyx is exhibited to promote the formation of bond clusters, mainly due to the cooperative binding of binders. This study helps to understand the cooperative kinetics of adhesion receptors under physiologically relevant loading conditions and sheds light on the novel role of the glycocalyx in cell adhesion. PMID:27102288

  3. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

    PubMed

    Vockley, Christopher M; D'Ippolito, Anthony M; McDowell, Ian C; Majoros, William H; Safi, Alexias; Song, Lingyun; Crawford, Gregory E; Reddy, Timothy E

    2016-08-25

    The glucocorticoid receptor (GR) binds the human genome at >10,000 sites but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter-gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady-state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs and may therefore play a major role in driving gene activation in response to GCs. PMID:27565349

  4. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

    PubMed

    Vockley, Christopher M; D'Ippolito, Anthony M; McDowell, Ian C; Majoros, William H; Safi, Alexias; Song, Lingyun; Crawford, Gregory E; Reddy, Timothy E

    2016-08-25

    The glucocorticoid receptor (GR) binds the human genome at >10,000 sites but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter-gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady-state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs and may therefore play a major role in driving gene activation in response to GCs.

  5. A tight-binding/density functional search for the structures of Ge clusters

    NASA Astrophysics Data System (ADS)

    Ghosh, Nandini; Jackson, Koblar; Hajnal, Zoltan; Frauenheim, Thomas

    2001-03-01

    We have used a combined tight-binding/density functional theory approach to search for the optimal structures of small and intermediate-sized Gen clusters, with n <= 30. The approach uses a computationally fast tight-binding method to survey the cluster energy surface for candidate structures. The search employs a novel single-parent genetic algorithm (SPGA) that successfully located the global minima for Si clusters in the same size range (Rata et al., Phys. Rev. Lett. 85, 546 (2000)). Gradient-corrected density functional theory (DFT) calculations are then performed to study the candidate structures in more detail. We show that our tight-binding model and the DFT yield consistent global minima for clusters up to n=10. The initial results of the SPGA searches for larger clusters show that prolate Gen clusters remain more stable than compact structures beyond n=26, the size at which Si clusters are known to undergo a prolate to compact transition.

  6. Tight-Binding Calcium Clusters from Adaptive Tempering Monte Carlo Simulation

    NASA Astrophysics Data System (ADS)

    Dong, X.; Gatica, S. M.; Blaisten-Barojas, E.

    The most stable structure of calcium clusters with 14 to 32 atoms is optimized by the Adaptive Tempering Monte Carlo method. The binding energy of the clusters is obtained within the tight-binding approach parameterized in a previous work. The optimization process is started at about 800 K and the tempering brings the structure to the global minimum ending the process at 1 K. It is found that six cluster sizes, 15, 16, 18, 21, 23 and 25 have a global minimum structure not reported in the literature. In this size range, Ca15, Ca21 and Ca23 are the preferred geometries that can be identified as magic numbers. The tight-binding one-electron levels in the valence band display a large energy gap of 0.5 eV between the last occupied and first unoccupied levels for the magic number clusters. This band gap is 5 to 10 times smaller for other cluster sizes.

  7. Low affinity binding site clusters confer hox specificity and regulatory robustness.

    PubMed

    Crocker, Justin; Abe, Namiko; Rinaldi, Lucrezia; McGregor, Alistair P; Frankel, Nicolás; Wang, Shu; Alsawadi, Ahmad; Valenti, Philippe; Plaza, Serge; Payre, François; Mann, Richard S; Stern, David L

    2015-01-15

    In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression. PMID:25557079

  8. Crocin Upregulates CX3CR1 Expression by Suppressing NF-κB/YY1 Signaling and Inhibiting Lipopolysaccharide-Induced Microglial Activation.

    PubMed

    Lv, Bochang; Huo, Fuquan; Zhu, Zhongqiao; Xu, Zhiguo; Dang, Xiaojie; Chen, Tao; Zhang, Ting; Yang, Xinguang

    2016-08-01

    Glaucoma is a group of neurodegenerative diseases characterized by the progressive loss of retinal ganglion cells (RGCs) and optic nerve fibers. Microglial activation has been shown to be deleterious to RGCs and may participate in the progression of glaucoma. Crocin, one of the major active ingredients in saffron, has been found to inhibit microglial activation. However, the mechanism remains unclear. The aim of this study was to investigate whether crocin can inhibit lipopolysaccharide (LPS)-induced microglial activation and to clarify the mechanisms involved. The influence of crocin on primary RGCs and LPS-stimulated BV2 microglial cells survival was determined by the MTT and lactate dehydrogenase assays, or by flow cytometry. BV2 cells were pretreated with various concentrations of crocin for 2 h followed by 1 μg/mL LPS stimulation. Microglial markers and pro-inflammatory mediators were assessed by real-time PCR, western blot and ELISA. Furthermore, CX3CR1 expression was detected and the underlying mechanism was examined. The concentrations of crocin ranged from 0.1 to 1 μM, and did not show any cytotoxicity in RGC and BV2 cells. After crocin pretreatment, the expression of microglial markers (CD11b and Iba-1) and pro-inflammatory mediators (iNOS, COX-2, IL-1β, and TNF-α) induced by LPS were significantly decreased in a dose-dependent manner. Additionally, CX3CR1 expression was remarkably increased by crocin via the suppression of NF-κB/Yin Yang 1 (YY1) signaling in BV2 cells. In conclusion, crocin effectively suppresses microglial activation and upregulates CX3CR1 expression by suppressing NF-κB/YY1 signaling. PMID:27084772

  9. Binding of Reactive Oxygen Species at Fe-S Cubane Clusters.

    PubMed

    Bruska, Marta K; Stiebritz, Martin T; Reiher, Markus

    2015-12-21

    Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron-sulfur proteins are particularly oxygen-sensitive and their inorganic cofactors frequently undergo ROS-induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe4S4] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O2 to singlet O2 is required for binding to valence-saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H2O2 as attacking agents. The thermodynamic picture of ROS binding to iron-sulfur clusters established here can serve as a starting point for studying reactivity-modulating effects of the cluster-embedding protein environment on ROS-induced decomposition of iron-sulfur proteins. PMID:26585994

  10. Chondroitin sulfate cluster of epiphycan from salmon nasal cartilage defines binding specificity to collagens.

    PubMed

    Tatara, Yota; Kakizaki, Ikuko; Suto, Shinichiro; Ishioka, Haruna; Negishi, Mika; Endo, Masahiko

    2015-05-01

    Epiphycan (EPY) from salmon nasal cartilage has a glycosaminoglycan (GAG) domain that is heavily modified by chondroitin 4-sulfate and chondroitin 6-sulfate. The functional role of the GAG domain has not been investigated. The interaction of EPY with collagen was examined in vitro using surface plasmon resonance analysis. EPY was found to bind to type I collagen via clustered chondroitin sulfate (CS), while a single chain of CS was unable to bind. Types I, III, VII, VIII and X collagen showed high binding affinity with EPY, whereas types II, IV, V, VI and IX showed low binding affinities. Chemical modification of lysine residues in collagen decreased the affinity with the clustered CS. These results suggest that lysine residues of collagen are involved in the interaction with the clustered CS, and the difference in lysine modification defines the binding affinity to EPY. The clustered CS was also involved in an inter-saccharide interaction, and formed self-associated EPY. CS of EPY promoted fibril formation of type I collagen.

  11. Zinc fingers, zinc clusters, and zinc twists in DNA-binding protein domains.

    PubMed Central

    Vallee, B L; Coleman, J E; Auld, D S

    1991-01-01

    We now recognize three distinct motifs of DNA-binding zinc proteins: (i) zinc fingers, (ii) zinc clusters, and (iii) zinc twists. Until very recently, x-ray crystallographic or NMR three-dimensional structure analyses of DNA-binding zinc proteins have not been available to serve as standards of reference for the zinc binding sites of these families of proteins. Those of the DNA-binding domains of the fungal transcription factor GAL4 and the rat glucocorticoid receptor are the first to have been determined. Both proteins contain two zinc binding sites, and in both, cysteine residues are the sole zinc ligands. In GAL4, two zinc atoms are bound to six cysteine residues which form a "zinc cluster" akin to that of metallothionein; the distance between the two zinc atoms of GAL4 is approximately 3.5 A. In the glucocorticoid receptor, each zinc atom is bound to four cysteine residues; the interatomic zinc-zinc distance is approximately 13 A, and in this instance, a "zinc twist" is represented by a helical DNA recognition site located between the two zinc atoms. Zinc clusters and zinc twists are here recognized as two distinctive motifs in DNA-binding proteins containing multiple zinc atoms. For native "zinc fingers," structural data do not exist as yet; consequently, the interatomic distances between zinc atoms are not known. As further structural data become available, the structural and functional significance of these different motifs in their binding to DNA and other proteins participating in the transmission of the genetic message will become apparent. Images PMID:1846973

  12. Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions

    PubMed Central

    Lim, Ji-Hyun; Latysheva, Natasha S.; Iggo, Richard D.; Barker, Daniel

    2016-01-01

    p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. It functions as a tetramer, where each component dimer binds to a decameric DNA region known as a response element. We identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. We start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. When combined, they give rise to three types of p53 binding sites. We find that probabilistic and alignment-based assessments of cross-species conservation show no strong evidence of differential conservation between types of binding sites. In contrast, functional analysis of the genes most proximal to the binding sites provides strong bioinformatic evidence of functional differentiation between the three types of binding sites. Our results are consistent with recent structural data identifying two conformations of the L1 loop in the DNA binding domain, suggesting that they reflect biologically meaningful groups imposed by the p53 protein structure. PMID:27812278

  13. Trinuclear ruthenium clusters as bivalent electrochemical probes for ligand-receptor binding interactions.

    PubMed

    Feld, Daniel J; Hsu, Hsiao-Tieh; Eckermann, Amanda L; Meade, Thomas J

    2012-01-10

    Despite their popularity, electrochemical biosensors often suffer from low sensitivity. One possible approach to overcome low sensitivity in protein biosensors is to utilize multivalent ligand-receptor interactions. Controlling the spatial arrangement of ligands on surfaces is another crucial aspect of electrochemical biosensor design. We have synthesized and characterized five biotinylated trinuclear ruthenium clusters as potential new biosensor platforms: [Ru(3)O(OAc)(6)CO(4-BMP)(py)](0) (3), [Ru(3)O(OAc)(6)CO(4-BMP)(2)](0) (4), [Ru(3)O(OAc)(6)L(4-BMP)(py)](+) (8), [Ru(3)O(OAc)(6)L(4-BMP)(2)](+) (9), and [Ru(3)O(OAc)(6)L(py)(2)](+) (10) (OAc = acetate, 4-BMP = biotin aminomethylpyridine, py = pyridine, L = pyC16SH). HABA/avidin assays and isothermal titration calorimetry were used to evaluate the avidin binding properties of 3 and 4. The binding constants were found to range from (6.5-8.0) × 10(6) M(-1). Intermolecular protein binding of 4 in solution was determined by native gel electrophoresis. QM, MM, and MD calculations show the capability for the bivalent cluster, 4, to intramolecularly bind to avidin. Electrochemical measurements in solution of 3a and 4a show shifts in E(1/2) of -58 and -53 mV in the presence of avidin, respectively. Self-assembled monolayers formed with 8-10 were investigated as a model biosensor system. Diluent/cluster ratio and composition were found to have a significant effect on the ability of avidin to adequately bind to the cluster. Complexes 8 and 10 showed negligible changes in E(1/2), while complex 9 showed a shift in E(1/2) of -43 mV upon avidin addition. These results suggest that multivalent interactions can have a positive impact on the sensitivity of electrochemical protein biosensors.

  14. Compound hierarchical correlated beta mixture with an application to cluster mouse transcription factor DNA binding data.

    PubMed

    Dai, Hongying; Charnigo, Richard

    2015-10-01

    Modeling correlation structures is a challenge in bioinformatics, especially when dealing with high throughput genomic data. A compound hierarchical correlated beta mixture (CBM) with an exchangeable correlation structure is proposed to cluster genetic vectors into mixture components. The correlation coefficient, [Formula: see text], is homogenous within a mixture component and heterogeneous between mixture components. A random CBM with [Formula: see text] brings more flexibility in explaining correlation variations among genetic variables. Expectation-Maximization (EM) algorithm and Stochastic Expectation-Maximization (SEM) algorithm are used to estimate parameters of CBM. The number of mixture components can be determined using model selection criteria such as AIC, BIC and ICL-BIC. Extensive simulation studies were conducted to compare EM, SEM and model selection criteria. Simulation results suggest that CBM outperforms the traditional beta mixture model with lower estimation bias and higher classification accuracy. The proposed method is applied to cluster transcription factor-DNA binding probability in mouse genome data generated by Lahdesmaki and others (2008, Probabilistic inference of transcription factor binding from multiple data sources. PLoS One, 3: , e1820). The results reveal distinct clusters of transcription factors when binding to promoter regions of genes in JAK-STAT, MAPK and other two pathways.

  15. Functional analysis of transcription factor binding sites in human promoters

    PubMed Central

    2012-01-01

    Background The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1. Results In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif. Conclusions The genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions. PMID:22951020

  16. Investigating the structure and properties of Fen clusters: a tight-binding/density functional theory study

    NASA Astrophysics Data System (ADS)

    Bobadova-Parvanova, Petia; Horoi, Mihai; Jackson, Koblar; Srinivas, Sudha; Koehler, Christof; Seifert, Gotthard

    2001-03-01

    Combined density-functional tight-binding (DFTB) and density functional theory (DFT) calculations have been performed to investigate Fen clusters with n=2,4, 7, 10 and 13. A new single parent genetic algorithm (see Rata et al., Phys. Rev. Lett. 85, 546 (2000)) was used with the DFTB to search the cluster configuration space for candidate ground-state structures. Separate searches were conducted for different total spin states. The ten lowest-energy DFTB structures for each spin were studied further using the DFT. The performance of the DFTB model for Fe clusters will be discussed and the structures and properties of the lowest-lying structures will be presented and compared to recent experimental results.

  17. Cargo binding promotes KDEL receptor clustering at the mammalian cell surface

    PubMed Central

    Becker, Björn; Shaebani, M. Reza; Rammo, Domenik; Bubel, Tobias; Santen, Ludger; Schmitt, Manfred J.

    2016-01-01

    Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTAH/KDEL), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface. PMID:27353000

  18. Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

    SciTech Connect

    Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.; Laskin, Julia

    2015-01-01

    We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cy ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important

  19. Iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

    PubMed

    Landry, Aaron P; Cheng, Zishuo; Ding, Huangen

    2013-03-01

    Iron-sulphur cluster biogenesis requires coordinated delivery of iron and sulphur to scaffold proteins, followed by transfer of the assembled clusters from scaffold proteins to target proteins. This complex process is accomplished by a group of dedicated iron-sulphur cluster assembly proteins that are conserved from bacteria to humans. While sulphur in iron-sulphur clusters is provided by L-cysteine via cysteine desulfurase, the iron donor(s) for iron-sulphur cluster assembly remains largely elusive. Here we report that among the primary iron-sulphur cluster assembly proteins, IscA has a unique and strong binding activity for mononuclear iron in vitro and in vivo. Furthermore, the ferric iron centre tightly bound in IscA can be readily extruded by l-cysteine, followed by reduction to ferrous iron for iron-sulphur cluster biogenesis. Substitution of the highly conserved residue tyrosine 40 with phenylalanine (Y40F) in IscA results in a mutant protein that has a diminished iron binding affinity but retains the iron-sulphur cluster binding activity. Genetic complementation studies show that the IscA Y40F mutant is inactive in vivo, suggesting that the iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

  20. Small Al clusters. II - Structure and binding in Al(n) (n = 2-6, 13)

    NASA Technical Reports Server (NTRS)

    Pettersson, Lars G. M.; Bauschlicher, Charles W., Jr.; Halicioglu, Timur

    1987-01-01

    The structure and stability of aluminum clusters containing up to six atoms have been studied using correlated wave functions and extended basis sets. The lowest energy structure is planar for Al4 and Al5, but three dimensional for Al6. The icosahedral, hcp, fcc, and two planar structures of Al13 were considered at the SCF level. The lowest energy structure is the icosahedron, but the planar structures are fairly low lying even in this case. A simplified description using two- and three-body interaction potentials is found to agree well with the ab initio structures and binding energies.

  1. Identification and Characterization of a G Protein-binding Cluster in α7 Nicotinic Acetylcholine Receptors*

    PubMed Central

    King, Justin R.; Nordman, Jacob C.; Bridges, Samuel P.; Lin, Ming-Kuan; Kabbani, Nadine

    2015-01-01

    α7 nicotinic acetylcholine receptors (nAChRs) play an important role in synaptic transmission and inflammation. In response to ligands, this receptor channel opens to conduct cations into the cell but desensitizes rapidly. In recent studies we show that α7 nAChRs bind signaling proteins such as heterotrimeric GTP-binding proteins (G proteins). Here, we demonstrate that direct coupling of α7 nAChRs to G proteins enables a downstream calcium signaling response that can persist beyond the expected time course of channel activation. This process depends on a G protein-binding cluster (GPBC) in the M3-M4 loop of the receptor. A mutation of the GPBC in the α7 nAChR (α7345–348A) abolishes interaction with Gαq as well as Gβγ while having no effect on receptor synthesis, cell-surface trafficking, or α-bungarotoxin binding. Expression of α7345–348A, however, did significantly attenuate the α7 nAChR-induced Gαq calcium signaling response as evidenced by a decrease in PLC-β activation and IP3R-mediated calcium store release in the presence of the α7 selective agonist choline. Taken together, the data provides new evidence for the existence of a GPBC in nAChRs serving to promote intracellular signaling. PMID:26088141

  2. Binding inhibition of type 1 fimbriae to human granulocytes: a flow cytometric inhibition assay using trivalent cluster mannosides.

    PubMed

    Horst, A K; Kötter, S; Lindhorst, T K; Ludwig, A; Brandt, E; Wagener, C

    2001-12-01

    The binding of type 1 fimbriae from Escherichia coli to vital human neutrophilic granulocytes was inhibited by synthetic trivalent cluster mannosides. Binding of type 1 fimbriae was measured in a flow cytometric assay. Based on the molarity of mannosyl residues, the clusters exceed the inhibitory potency of methyl alpha-D-mannoside by a factor of more than 1,000 and the inhibitory potency of p-nitrophenyl alpha-D-mannoside by a factor of more than 10. The inhibition studies indicate that the trivalent cluster mannosides are very potent inhibitors of the binding of type 1 fimbriae to human neutrophilic granulocytes. Based on their defined structure, cluster mannosides are well suited for characterizing the molecular interactions of mannose-sensitive fimbriae with their cell membrane receptors.

  3. Auxins induce clustering of the auxin-binding protein at the surface of maize coleoptile protoplasts.

    PubMed Central

    Diekmann, W; Venis, M A; Robinson, D G

    1995-01-01

    The predominant localization of the major auxin-binding protein (ABP1) of maize is within the lumen of the endoplasmic reticulum. Nevertheless, all the electrophysiological evidence supporting a receptor role for ABP1 implies that a functionally important fraction of the protein must reside at the outer face of the plasma membrane. Using methods of protoplast preparation designed to minimize proteolysis, we report the detection of ABP at the surface of maize coleoptile protoplasts by the technique of silver-enhanced immunogold viewed by epipolarization microscopy. We also show that ABP clusters following auxin treatment and that this response is temperature-dependent and auxin-specific. Images Fig. 1 Fig. 2 Fig. 3 PMID:11607527

  4. Probing a Polar Cluster in the Retinal Binding Pocket of Bacteriorhodopsin by a Chemical Design Approach

    PubMed Central

    Simón-Vázquez, Rosana; Domínguez, Marta; Lórenz-Fonfría, Víctor A.; Álvarez, Susana; Bourdelande, José-Luís; de Lera, Ángel R.; Padrós, Esteve; Perálvarez-Marín, Alex

    2012-01-01

    Bacteriorhodopsin has a polar cluster of amino acids surrounding the retinal molecule, which is responsible for light harvesting to fuel proton pumping. From our previous studies, we have shown that threonine 90 is the pivotal amino acid in this polar cluster, both functionally and structurally. In an attempt to perform a phenotype rescue, we have chemically designed a retinal analogue molecule to compensate the drastic effects of the T90A mutation in bacteriorhodopsin. This analogue substitutes the methyl group at position C13 of the retinal hydrocarbon chain by and ethyl group (20-methyl retinal). We have analyzed the effect of reconstituting the wild-type and the T90A mutant apoproteins with all-trans-retinal and its 20-methyl derivative (hereafter, 13-ethyl retinal). Biophysical characterization indicates that recovering the steric interaction between the residue 90 and retinal, eases the accommodation of the chromophore, however it is not enough for a complete phenotype rescue. The characterization of these chemically engineered chromoproteins provides further insight into the role of the hydrogen bond network and the steric interactions involving the retinal binding pocket in bacteriorhodopsin and other microbial sensory rhodopsins. PMID:22879987

  5. Neuronal low-density lipoprotein receptor-related protein 1 binds and endocytoses prion fibrils via receptor cluster 4

    PubMed Central

    Jen, Angela; Parkyn, Celia J.; Mootoosamy, Roy C.; Ford, Melanie J.; Warley, Alice; Liu, Qiang; Bu, Guojun; Baskakov, Ilia V.; Moestrup, Søren; McGuinness, Lindsay; Emptage, Nigel; Morris, Roger J.

    2010-01-01

    For infectious prion protein (designated PrPSc) to act as a template to convert normal cellular protein (PrPC) to its distinctive pathogenic conformation, the two forms of prion protein (PrP) must interact closely. The neuronal receptor that rapidly endocytoses PrPC is the low-density lipoprotein receptor-related protein 1 (LRP1). We show here that on sensory neurons LRP1 is also the receptor that binds and rapidly endocytoses smaller oligomeric forms of infectious prion fibrils, and recombinant PrP fibrils. Although LRP1 binds two molecules of most ligands independently to its receptor clusters 2 and 4, PrPC and PrPSc fibrils bind only to receptor cluster 4. PrPSc fibrils out-compete PrPC for internalization. When endocytosed, PrPSc fibrils are routed to lysosomes, rather than recycled to the cell surface with PrPC. Thus, although LRP1 binds both forms of PrP, it traffics them to separate fates within sensory neurons. The binding of both to ligand cluster 4 should enable genetic modification of PrP binding without disrupting other roles of LRP1 essential to neuronal viability and function, thereby enabling in vivo analysis of the role of this interaction in controlling both prion and LRP1 biology. PMID:20048341

  6. Multivalent dendrimers presenting spatially controlled clusters of binding epitopes in thermoresponsive hyaluronan hydrogels.

    PubMed

    Seelbach, Ryan J; Fransen, Peter; Peroglio, Marianna; Pulido, Daniel; Lopez-Chicon, Patricia; Duttenhoefer, Fabian; Sauerbier, Sebastian; Freiman, Thomas; Niemeyer, Philipp; Semino, Carlos; Albericio, Fernando; Alini, Mauro; Royo, Miriam; Mata, Alvaro; Eglin, David

    2014-10-01

    The controlled presentation of biofunctionality is of key importance for hydrogel applications in cell-based regenerative medicine. Here, a versatile approach was demonstrated to present clustered binding epitopes in an injectable, thermoresponsive hydrogel. Well-defined multivalent dendrimers bearing four integrin binding sequences and an azido moiety were covalently grafted to propargylamine-derived hyaluronic acid (Hyal-pa) using copper-catalyzed alkyne-azide cycloaddition (CuAAC), and then combined with pN-modified hyaluronan (Hyal-pN). The dendrimers were prepared by synthesizing a bifunctional diethylenetriamine pentaacetic acid core with azido and NHBoc oligo(ethylene glycol) aminoethyl branches, then further conjugated with solid-phase synthesized RGDS and DGRS peptides. Azido terminated pN was synthesized by reversible addition-fragmentation chain transfer polymerization and reacted to Hyal-pa via CuAAC. Nuclear magnetic resonance (NMR), high performance liquid chromatography, size exclusion chromatography and mass spectroscopy proved that the dendrimers had well-defined size and were disubstituted. NMR and atomic absorption analysis confirmed the hyaluronan was affixed with dendrimers or pN. Rheological measurements demonstrated that dendrimers do not influence the elastic or viscous moduli of thermoresponsive hyaluronan compositions at a relevant biological concentration. Finally, human mesenchymal stromal cells were encapsulated in the biomaterial and cultured for 21days, demonstrating the faculty of this dendrimer-modified hydrogel as a molecular toolbox for tailoring the biofunctionality of thermoresponsive hyaluronan carriers for biomedical applications.

  7. Reciprocal control of RNA-binding and aconitase activity in the regulation of the iron-responsive element binding protein: role of the iron-sulfur cluster.

    PubMed

    Haile, D J; Rouault, T A; Tang, C K; Chin, J; Harford, J B; Klausner, R D

    1992-08-15

    Several mechanisms of posttranscriptional gene regulation are involved in regulation of the expression of essential proteins of iron metabolism. Coordinate regulation of ferritin and transferrin receptor expression is produced by binding of a cytosolic protein, the iron-responsive element binding protein (IRE-BP) to specific stem-loop structures present in target RNAs. The affinity of this protein for its cognate RNA is regulated by the cell in response to changes in iron availability. The IRE-BP demonstrates a striking level of amino acid sequence identity to the iron-sulfur (Fe-S) protein mitochondrial aconitase. Moreover, the recombinant IRE-BP has aconitase function. The lability of the Fe-S cluster in mitochondrial aconitase has led us to propose that the mechanism by which iron levels are sensed by the IRE-BP involves changes in an Fe-S cluster in the IRE-BP. In this study, we demonstrate that procedures aimed at altering the IRE-BP Fe-S cluster in vitro reciprocally alter the RNA binding and aconitase activity of the IRE-BP. The changes in the RNA binding of the protein produced in vitro appear to match the previously described alterations of the protein in response to iron availability in the cell. Furthermore, iron manipulation of cells correlates with the activation or inactivation of the IRE-BP aconitase activity. The results are consistent with a model for the posttranslational regulation of the IRE-BP in which the Fe-S cluster is altered in response to the availability of intracellular iron and this, in turn, regulates the RNA-binding activity. PMID:1502165

  8. A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans

    PubMed Central

    Fox, Ellen M.; Gardiner, Donald M.; Keller, Nancy P.; Howlett, Barbara J.

    2008-01-01

    A gene, sirZ, encoding a Zn(II)2Cys6 DNA binding protein is present in a cluster of genes responsible for the biosynthesis of the epipolythiodioxopiperazine (ETP) toxin, sirodesmin PL in the ascomycete plant pathogen, Leptosphaeria maculans. RNA-mediated silencing of sirZ gives rise to transformants that produce only residual amounts of sirodesmin PL and display a decrease in the transcription of several sirodesmin PL biosynthetic genes. This indicates that SirZ is a major regulator of this gene cluster. Proteins similar to SirZ are encoded in the gliotoxin biosynthetic gene cluster of Aspergillus fumigatus (gliZ) and in an ETP-like cluster in Penicillium lilacinoechinulatum (PlgliZ). Despite its high level of sequence similarity to gliZ, PlgliZ is unable to complement the gliotoxin-deficiency of a mutant of gliZ in A. fumigatus. Putative binding sites for these regulatory proteins in the promoters of genes in these clusters were predicted using bioinformatic analysis. These sites are similar to those commonly bound by other proteins with Zn(II)2Cys6 DNA binding domains. PMID:18023597

  9. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    SciTech Connect

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  10. Accurate calculation of binding energies for molecular clusters - Assessment of different models

    NASA Astrophysics Data System (ADS)

    Friedrich, Joachim; Fiedler, Benjamin

    2016-06-01

    In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.

  11. Regulation of Type VI Secretion Gene Clusters by σ54 and Cognate Enhancer Binding Proteins▿†

    PubMed Central

    Bernard, Christophe S.; Brunet, Yannick R.; Gavioli, Marthe; Lloubès, Roland; Cascales, Eric

    2011-01-01

    Type VI secretion systems (T6SS) are bacteriophage-derived macromolecular machines responsible for the release of at least two proteins in the milieu, which are thought to form an extracellular appendage. Although several T6SS have been shown to be involved in the virulence of animal and plant pathogens, clusters encoding these machines are found in the genomes of most species of Gram-negative bacteria, including soil, marine, and environmental isolates. T6SS have been associated with several phenotypes, ranging from virulence to biofilm formation or stress sensing. Their various environmental niches and large diversity of functions are correlated with their broad variety of regulatory mechanisms. Using a bioinformatic approach, we identified several clusters, including those of Vibrio cholerae, Aeromonas hydrophila, Pectobacterium atrosepticum, Pseudomonas aeruginosa, Pseudomonas syringae pv. tomato, and a Marinomonas sp., which possess typical −24/−12 sequences, recognized by the alternate sigma factor sigma 54 (σ54 or σN). σ54, which directs the RNA polymerase to these promoters, requires the action of a bacterial enhancer binding protein (bEBP), which binds to cis-acting upstream activating sequences. Putative bEBPs are encoded within the T6SS gene clusters possessing σ54 boxes. Using in vitro binding experiments and in vivo reporter fusion assays, we showed that the expression of these clusters is dependent on both σ54 and bEBPs. PMID:21378190

  12. A point mutation in the [2Fe–2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties

    SciTech Connect

    Tamir, Sagi; Eisenberg-Domovich, Yael; Conlan, Andrea R.; Stofleth, Jason T.; Lipper, Colin H.; Paddock, Mark L.; Mittler, Ron; Jennings, Patricia A.; Livnah, Oded Nechushtai, Rachel

    2014-06-01

    NAF-1 has been shown to be related with human health and disease, is upregulated in epithelial breast cancer and suppression of its expression significantly suppresses tumor growth. It is shown that replacement of the single His ligand with Cys resulted in dramatic changes to the properties of its 2Fe-2S clusters without any global crystal structural changes. NAF-1 is an important [2Fe–2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe–2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (R factor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe–2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (R factor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe–2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe–2S] cluster of NAF-1 in vivo.

  13. Microhydrated aromatic cluster cations: binding motifs of 4-aminobenzonitrile-(H₂O)n cluster cations with n ≤ 4.

    PubMed

    Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

    2014-12-01

    Infrared photodissociation (IRPD) spectra of mass-selected 4-aminobenzonitrile-(water)n cluster cations, ABN(+)-(H2O)n with n ≤ 4, recorded in the N-H and O-H stretch ranges are analyzed by quantum chemical calculations at the M06-2X/aug-cc-pVTZ level to determine the evolution of the initial microhydration process of this bifunctional aromatic cation in its ground electronic state. IRPD spectra of cold clusters tagged with Ar and N2 display higher resolution and allow for a clear-cut structural assignment. The clusters are generated in an electron impact source, which generates predominantly the most stable isomers. The IRPD spectra are assigned to single isomers for n = 1-3. The preferred cluster growth begins with sequential hydration of the two acidic NH protons of the amino group (n = 1-2), which is followed by attachment of secondary H2O ligands hydrogen-bonded to the first-shell ligands (n = 3-4). These symmetric and branched structures are more stable than those with a cyclic H-bonded solvent network. Moreover, in the size range n ≤ 4 the formation of a solvent network stabilized by strong cooperative effects is favored over interior ion hydration which is destabilized by noncooperative effects. The potential of the ABN(+)-H2O dimer is characterized in detail and supports the cluster growth derived from the IRPD spectra. Although the N-H bonds are destabilized by stepwise microhydration, which is accompanied by increasing charge transfer from ABN(+) to the solvent cluster, no proton transfer to the solvent is observed for n ≤ 4.

  14. A novel chemical footprinting approach identifies critical lysine residues involved in the binding of receptor-associated protein to cluster II of LDL receptor-related protein.

    PubMed

    Bloem, Esther; Ebberink, Eduard H T M; van den Biggelaar, Maartje; van der Zwaan, Carmen; Mertens, Koen; Meijer, Alexander B

    2015-05-15

    Tandem mass tags (TMTs) were utilized in a novel chemical footprinting approach to identify lysine residues that mediate the interaction of receptor-associated protein (RAP) with cluster II of LDL (low-density lipoprotein) receptor (LDLR)-related protein (LRP). The isolated RAP D3 domain was modified with TMT-126 and the D3 domain-cluster II complex with TMT-127. Nano-LC-MS analysis revealed reduced modification with TMT-127 of peptides including Lys(256), Lys(270) and Lys(305)-Lys(306) suggesting that these residues contribute to cluster II binding. This agrees with previous findings that Lys(256) and Lys(270) are critical for binding cluster II sub-domains [Fisher, Beglova and Blacklow (2006) Mol. Cell 22, 277-283]. Cluster II-binding studies utilizing D3 domain variants K(256)A, K(305)A and K(306)A now showed that Lys(306) contributes to cluster II binding as well. For full-length RAP, we observed that peptides including Lys(60), Lys(191), Lys(256), Lys(270) and Lys(305)-Lys(306) exhibited reduced modification with TMT in the RAP-cluster II complex. Notably, Lys(60) has previously been implicated to mediate D1 domain interaction with cluster II. Our results suggest that also Lys(191) of the D2 domain contributes to cluster II binding. Binding studies employing the RAP variants K(191)A, K(256)A, K(305)A and K(306)A, however, revealed a modest reduction in cluster II binding for the K(256)A variant only. This suggests that the other lysine residues can compensate for the absence of a single lysine residue for effective complex assembly. Collectively, novel insight has been obtained into the contribution of lysine residues of RAP to cluster II binding. In addition, we propose that TMTs can be utilized to identify lysine residues critical for protein complex formation. PMID:25728577

  15. Coordination-resolved local bond contraction and electron binding-energy entrapment of Si atomic clusters and solid skins

    SciTech Connect

    Bo, Maolin; Huang, Yongli; Zhang, Ting; Wang, Yan E-mail: ecqsun@ntu.edu.sg; Zhang, Xi; Li, Can; Sun, Chang Q. E-mail: ecqsun@ntu.edu.sg

    2014-04-14

    Consistency between x-ray photoelectron spectroscopy measurements and density-function theory calculations confirms our bond order-length-strength notation-incorporated tight-binding theory predictions on the quantum entrapment of Si solid skin and atomic clusters. It has been revealed that bond-order deficiency shortens and strengthens the Si-Si bond, which results in the local densification and quantum entrapment of the core and valence electrons. Unifying Si clusters and Si(001) and (111) skins, this mechanism has led to quantification of the 2p binding energy of 96.089 eV for an isolated Si atom, and their bulk shifts of 2.461 eV. Findings evidence the significance of atomic undercoordination that is of great importance to device performance.

  16. A point mutation in the [2Fe-2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties.

    PubMed

    Tamir, Sagi; Eisenberg-Domovich, Yael; Conlan, Andrea R; Stofleth, Jason T; Lipper, Colin H; Paddock, Mark L; Mittler, Ron; Jennings, Patricia A; Livnah, Oded; Nechushtai, Rachel

    2014-06-01

    NAF-1 is an important [2Fe-2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe-2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (R factor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe-2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (R factor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe-2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe-2S] cluster of NAF-1 in vivo.

  17. ADAP–SLP-76 Binding Differentially Regulates Supramolecular Activation Cluster (SMAC) Formation Relative to T Cell–APC Conjugation

    PubMed Central

    Wang, Hongyan; McCann, Fiona E.; Gordan, John D.; Wu, Xiang; Raab, Monika; Malik, Talat H.; Davis, Daniel M.; Rudd, Christopher E.

    2004-01-01

    T cell–APC conjugation as mediated by leukocyte function-associated antigen-1 (LFA-1)–intercellular adhesion molecule (ICAM)-1 binding is followed by formation of the supramolecular activation cluster (SMAC) at the immunological synapse. The intracellular processes that regulate SMAC formation and its influence on T cell function are important questions to be addressed. Here, using a mutational approach, we demonstrate that binding of adaptor adhesion and degranulation promoting adaptor protein (ADAP) to SLP-76 differentially regulates peripheral SMAC (pSMAC) formation relative to conjugation. Although mutation of the YDDV sites (termed M12) disrupted SLP-76 SH2 domain binding and prevented the ability of ADAP to increase conjugation and LFA-1 clustering, M12 acted selectively as a dominant negative (DN) inhibitor of pSMAC formation, an effect that was paralleled by a DN effect on interleukin-2 production. ADAP also colocalized with LFA-1 at the immunological synapse. Our findings identify ADAP–SLP-76 binding as a signaling event that differentially regulates SMAC formation, and support a role for SMAC formation in T cell cytokine production. PMID:15477347

  18. Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein

    PubMed Central

    Thompson, Michael C.; Wheatley, Nicole M.; Jorda, Julien; Sawaya, Michael R.; Gidaniyan, Soheil D.; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N.; Whitelegge, Julian P.; Yeates, Todd O.

    2014-01-01

    Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein, whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date. PMID:25102080

  19. Iron–Sulfur Cluster Binding by Mitochondrial Monothiol Glutaredoxin-1 of Trypanosoma brucei: Molecular Basis of Iron–Sulfur Cluster Coordination and Relevance for Parasite Infectivity

    PubMed Central

    Manta, Bruno; Pavan, Carlo; Sturlese, Mattia; Medeiros, Andrea; Crispo, Martina; Berndt, Carsten; Krauth-Siegel, R. Luise; Bellanda, Massimo

    2013-01-01

    Abstract Aims: Monothiol glutaredoxins (1-C-Grxs) are small proteins linked to the cellular iron and redox metabolism. Trypanosoma brucei brucei, model organism for human African trypanosomiasis, expresses three 1-C-Grxs. 1-C-Grx1 is a highly abundant mitochondrial protein capable to bind an iron–sulfur cluster (ISC) in vitro using glutathione (GSH) as cofactor. We here report on the functional and structural analysis of 1-C-Grx1 in relation to its ISC-binding properties. Results: An N-terminal extension unique to 1-C-Grx1 from trypanosomatids affects the oligomeric structure and the ISC-binding capacity of the protein. The active-site Cys104 is essential for ISC binding, and the parasite-specific glutathionylspermidine and trypanothione can replace GSH as the ligands of the ISC. Interestingly, trypanothione forms stable protein-free ISC species that in vitro are incorporated into the dithiol T. brucei 2-C-Grx1, but not 1-C-Grx1. Overexpression of the C104S mutant of 1-C-Grx1 impairs disease progression in a mouse model. The structure of the Grx-domain of 1-C-Grx1 was solved by nuclear magnetic resonance spectroscopy. Despite the fact that several residues—which in other 1-C-Grxs are involved in the noncovalent binding of GSH—are conserved, different physicochemical approaches did not reveal any specific interaction between 1-C-Grx1 and free thiol ligands. Innovation: Parasite Grxs are able to coordinate an ISC formed with trypanothione, suggesting a new mechanism of ISC binding and a novel function for the parasite-specific dithiol. The first 3D structure and in vivo relevance of a 1-C-Grx from a pathogenic protozoan are reported. Conclusion: T. brucei 1-C-Grx1 is indispensable for mammalian parasitism and utilizes a new mechanism for ISC binding. Antioxid. Redox Signal. 19, 665–682. PMID:23259530

  20. Influence of Molecular Structure on O2-Binding Properties and Blood Circulation of Hemoglobin‒Albumin Clusters

    PubMed Central

    Yamada, Kana; Yokomaku, Kyoko; Haruki, Risa; Taguchi, Kazuaki; Nagao, Saori; Maruyama, Toru; Otagiri, Masaki; Komatsu, Teruyuki

    2016-01-01

    A hemoglobin wrapped covalently by three human serum albumins, a Hb-HSA3 cluster, is an artificial O2-carrier with the potential to function as a red blood cell substitute. This paper describes the synthesis and O2-binding properties of new hemoglobin‒albumin clusters (i) bearing four HSA units at the periphery (Hb-HSA4, large-size variant) and (ii) containing an intramolecularly crosslinked Hb in the center (XLHb-HSA3, high O2-affinity variant). Dynamic light scattering measurements revealed that the Hb-HSA4 diameter is greater than that of either Hb-HSA3 or XLHb-HSA3. The XLHb-HSA3 showed moderately high O2-affinity compared to the others because of the chemical linkage between the Cys-93(β) residues in Hb. Furthermore, the blood circulation behavior of 125I-labeled clusters was investigated by assay of blood retention and tissue distribution after intravenous administration into anesthetized rats. The XLHb-HSA3 was metabolized faster than Hb-HSA3 and Hb-HSA4. Results suggest that the molecular structure of the protein cluster is a factor that can influence in vivo circulation behavior. PMID:26895315

  1. Influence of Molecular Structure on O2-Binding Properties and Blood Circulation of Hemoglobin‒Albumin Clusters.

    PubMed

    Yamada, Kana; Yokomaku, Kyoko; Haruki, Risa; Taguchi, Kazuaki; Nagao, Saori; Maruyama, Toru; Otagiri, Masaki; Komatsu, Teruyuki

    2016-01-01

    A hemoglobin wrapped covalently by three human serum albumins, a Hb-HSA3 cluster, is an artificial O2-carrier with the potential to function as a red blood cell substitute. This paper describes the synthesis and O2-binding properties of new hemoglobin‒albumin clusters (i) bearing four HSA units at the periphery (Hb-HSA4, large-size variant) and (ii) containing an intramolecularly crosslinked Hb in the center (XLHb-HSA3, high O2-affinity variant). Dynamic light scattering measurements revealed that the Hb-HSA4 diameter is greater than that of either Hb-HSA3 or XLHb-HSA3. The XLHb-HSA3 showed moderately high O2-affinity compared to the others because of the chemical linkage between the Cys-93(β) residues in Hb. Furthermore, the blood circulation behavior of 125I-labeled clusters was investigated by assay of blood retention and tissue distribution after intravenous administration into anesthetized rats. The XLHb-HSA3 was metabolized faster than Hb-HSA3 and Hb-HSA4. Results suggest that the molecular structure of the protein cluster is a factor that can influence in vivo circulation behavior.

  2. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features

    PubMed Central

    Ruiz, Duncan D. A.; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward’s, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  3. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D A; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  4. Mo-Cu metal cluster formation and binding in an orange protein isolated from Desulfovibrio gigas.

    PubMed

    Carepo, Marta S P; Pauleta, Sofia R; Wedd, Anthony G; Moura, José J G; Moura, Isabel

    2014-06-01

    The orange protein (ORP) isolated from the sulfate-reducing bacterium Desulfovibrio gigas (11.8 kDa) contains a mixed-metal sulfide cluster of the type [S2MoS2CuS2MoS2](3-) noncovalently bound to the polypeptide chain. The D. gigas ORP was heterologously produced in Escherichia coli in the apo form. Different strategies were used to reconstitute the metal cluster into apo-ORP and obtain insights into the metal cluster synthesis: (1) incorporation of a synthesized inorganic analogue of the native metal cluster and (2) the in situ synthesis of the metal cluster on the addition to apo-ORP of copper chloride and tetrathiomolybdate or tetrathiotungstate. This latter procedure was successful, and the visible spectrum of the Mo-Cu reconstituted ORP is identical to the one reported for the native protein with absorption maxima at 340 and 480 nm. The (1)H-(15)N heteronuclear single quantum coherence spectra of the reconstituted ORP obtained by strategy 2, in contrast to strategy 1, exhibited large changes, which required sequential assignment in order to identify, by chemical shift differences, the residues affected by the incorporation of the cluster, which is stabilized inside the protein by both electrostatic and hydrophobic interactions.

  5. Clusters in an intrinsically disordered protein create a protein-binding site: the TolB-binding region of colicin E9.

    PubMed

    Tozawa, Kaeko; Macdonald, Colin J; Penfold, Christopher N; James, Richard; Kleanthous, Colin; Clayden, Nigel J; Moore, Geoffrey R

    2005-08-30

    The 61-kDa colicin E9 protein toxin enters the cytoplasm of susceptible cells by interacting with outer membrane and periplasmic helper proteins and kills them by hydrolyzing their DNA. The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequence being a pentapeptide region that governs the interaction with the helper protein TolB (the TolB box). Previous NMR studies [Collins et al. (2002) J. Mol. Biol. 318, 787-904; MacDonald et al. (2004), J. Biomol. NMR 30, 81-96] have shown that the N-terminal 83 residues of colicin E9, which includes the TolB box, is intrinsically disordered and contains clusters of interacting side chains. To further define the properties of this region of colicin E9, we have investigated the effects on the dynamical and TolB-binding properties of three mutations of colicin E9 that inactivate it as a toxin. The mutations were contained in a fusion protein consisting of residues 1-61 of colicin E9 connected to the N terminus of the E9 DNase by an eight-residue linking sequence. The NMR data reveals that the mutations cause major alterations to the properties of some of the clusters, consistent with some form of association between them and other more distant parts of the amino acid sequence, particularly toward the N terminus of the protein. However, (15)N T(2) measurements indicates that residues 5-13 of the fusion protein bound to the 43-kDa TolB remain as flexible as they are in the free protein. The NMR data point to considerable dynamic ordering within the intrinsically disordered translocation domain of the colicin that is important for creating the TolB-binding site. Furthermore, amino acid sequence considerations suggest that the clusters of amino acids occur because of the size and polarities of the side chains forming them influenced by the propensities of the residues within the clusters and those immediately surrounding them in sequence space to form beta turns. PMID:16114886

  6. ORF13 in the Type III secretion system gene cluster of Edwardsiella tarda binds to the mammalian factor Cugbp2.

    PubMed

    Okuda, Jun; Takeuchi, Yusuke; Yasuda, Masashi; Nakai, Toshihiro

    2016-05-01

    The Type III secretion system (TTSS) is essential for the intracellular replication of Edwardsiella tarda in phagocytes of fish and mammals, and a hypothetical gene (orf13) located in the TTSS gene cluster is required for intracellular replication and virulence of E. tarda. Here, we show that under TTSS-inducing conditions, the protein ORF13 was secreted into culture supernatant. Then, using a yeast 2-hybrid screen, we show that the mammalian factor Cugbp2, which regulates apoptosis in breast cancer cells, directly interacts with ORF13. A pull-down assay revealed that ORF13 binds to the C-terminal region of Cugbp2. Our results suggest that ORF13 may facilitate E. tarda replication in phagocytes by binding to Cugbp2. PMID:27137075

  7. Competition of zinc ion for the [2Fe-2S] cluster binding site in the diabetes drug target protein mitoNEET.

    PubMed

    Tan, Guoqiang; Landry, Aaron P; Dai, Ruili; Wang, Li; Lu, Jianxin; Ding, Huangen

    2012-12-01

    Human mitochondrial protein mitoNEET is a novel target of type II diabetes drug pioglitazone, and contains a redox active [2Fe-2S] cluster that is hosted by a unique ligand arrangement of three cysteine and one histidine residues. Here we report that zinc ion can compete for the [2Fe-2S] cluster binding site in human mitoNEET and potentially modulate the physiological function of mitoNEET. When recombinant mitoNEET is expressed in Escherichia coli cells grown in M9 minimal media, purified mitoNEET contains very little or no iron-sulfur clusters. Addition of exogenous iron or zinc ion in the media produces mitoNEET bound with a [2Fe-2S] cluster or zinc, respectively. Mutations of the amino acid residues that hosting the [2Fe-2S] cluster in mitoNEET diminish the zinc binding activity, indicating that zinc ion and the [2Fe-2S] cluster may share the same binding site in mitoNEET. Finally, excess zinc ion effectively inhibits the [2Fe-2S] cluster assembly in mitoNEET in E. coli cells, suggesting that zinc ion may impede the function of mitoNEET by blocking the [2Fe-2S] cluster assembly in the protein.

  8. POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster.

    PubMed

    Farley, Brian M; Ryder, Sean P

    2012-12-01

    RNA-binding proteins (RBPs) coordinate cell fate specification and differentiation in a variety of systems. RNA regulation is critical during oocyte development and early embryogenesis, in which RBPs control expression from maternal mRNAs encoding key cell fate determinants. The Caenorhabditis elegans Notch homologue glp-1 coordinates germline progenitor cell proliferation and anterior fate specification in embryos. A network of sequence-specific RBPs is required to pattern GLP-1 translation. Here, we map the cis-regulatory elements that guide glp-1 regulation by the CCCH-type tandem zinc finger protein POS-1 and the STAR-domain protein GLD-1. Our results demonstrate that both proteins recognize the glp-1 3' untranslated region (UTR) through adjacent, overlapping binding sites and that POS-1 binding excludes GLD-1 binding. Both factors are required to repress glp-1 translation in the embryo, suggesting that they function in parallel regulatory pathways. It is intriguing that two equivalent POS-1-binding sites are present in the glp-1 3' UTR, but only one, which overlaps with a translational derepression element, is functional in vivo. We propose that POS-1 regulates glp-1 mRNA translation by blocking access of other RBPs to a key regulatory sequence.

  9. Monocarbon cationic cluster yields from N{sub 2}/CH{sub 4} mixtures embedded in He nanodroplets and their calculated binding energies

    SciTech Connect

    Tolbatov, Iogann; Ptasinska, Sylwia; Bartl, Peter; Scheier, Paul; Denifl, Stephan; Yurkovich, James; Chipman, Daniel M.

    2014-01-21

    The formation of monocarbon cluster ions has been investigated by electron ionization mass spectrometry of cold helium nanodroplets doped with nitrogen/methane mixtures. Ion yields for two groups of clusters, CH{sub m}N{sub 2}{sup +} or CH{sub m}N{sub 4}{sup +}, were determined for mixtures with different molecular ratios of CH{sub 4}. The possible geometrical structures of these clusters were analyzed using electronic structure computations. Little correlation between the ion yields and the associated binding energies has been observed indicating that in most cases kinetic control is more important than thermodynamic control for forming the clusters.

  10. A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

    PubMed

    Zhang, Chaolin; Xuan, Zhenyu; Otto, Stefanie; Hover, John R; McCorkle, Sean R; Mandel, Gail; Zhang, Michael Q

    2006-01-01

    Transcription factor binding sites (TFBSs) are short DNA sequences interacting with transcription factors (TFs), which regulate gene expression. Due to the relatively short length of such binding sites, it is largely unclear how the specificity of protein-DNA interaction is achieved. Here, we have performed a genome-wide analysis of TFBS-like sequences for the transcriptional repressor, RE1 Silencing Transcription Factor (REST), as well as for several other representative mammalian TFs (c-myc, p53, HNF-1 and CREB). We find a nonrandom distribution of inexact sites for these TFs, referred to as highly-degenerate TFBSs, that are enriched around the cognate binding sites. Comparisons among human, mouse and rat orthologous promoters reveal that these highly-degenerate sites are conserved significantly more than expected by random chance, suggesting their positive selection during evolution. We propose that this arrangement provides a favorable genomic landscape for functional target site selection.

  11. A Lipoprotein Receptor Cluster IV Mutant Preferentially Binds Amyloid-β and Regulates Its Clearance from the Mouse Brain*

    PubMed Central

    Sagare, Abhay P.; Bell, Robert D.; Srivastava, Alaka; Sengillo, Jesse D.; Singh, Itender; Nishida, Yoichiro; Chow, Nienwen; Zlokovic, Berislav V.

    2013-01-01

    Soluble low density lipoprotein receptor-related protein-1 (sLRP1) binds ∼70% of amyloid β-peptide (Aβ) in human plasma. In Alzheimer disease (AD) and individuals with mild cognitive impairment converting to AD, plasma sLRP1 levels are reduced and sLRP1 is oxidized, which results in diminished Aβ peripheral binding and higher levels of free Aβ in plasma. Experimental studies have shown that free circulating Aβ re-enters the brain and that sLRP1 and/or its recombinant wild type cluster IV (WT-LRPIV) prevent Aβ from entering the brain. Treatment of Alzheimer APPsw+/0 mice with WT-LRPIV has been shown to reduce brain Aβ pathology. In addition to Aβ, LRPIV binds multiple ligands. To enhance LRPIV binding for Aβ relative to other LRP1 ligands, we generated a library of LRPIV-derived fragments and full-length LRPIV variants with glycine replacing aspartic acid residues 3394, 3556, and 3674 in the calcium binding sites. Compared with WT-LRPIV, a lead LRPIV-D3674G mutant had 1.6- and 2.7-fold higher binding affinity for Aβ40 and Aβ42 in vitro, respectively, and a lower binding affinity for other LRP1 ligands (e.g. apolipoprotein E2, E3, and E4 (1.3–1.8-fold), tissue plasminogen activator (2.7-fold), matrix metalloproteinase-9 (4.1-fold), and Factor Xa (3.8-fold)). LRPIV-D3674G cleared mouse endogenous brain Aβ40 and Aβ42 25–27% better than WT-LRPIV. A 3-month subcutaneous treatment of APPsw+/0 mice with LRPIV-D3674G (40 μg/kg/day) reduced Aβ40 and Αβ42 levels in the hippocampus, cortex, and cerebrospinal fluid by 60–80% and improved cerebral blood flow responses and hippocampal function at 9 months of age. Thus, LRPIV-D3674G is an efficient new Aβ clearance therapy. PMID:23580652

  12. Halide binding and inhibition of laccase copper clusters: the role of reorganization energy.

    PubMed

    Kepp, Kasper P

    2015-01-20

    Laccase-like proteins are multicopper oxidases involved in several biological and industrial processes. Their application is commonly limited due to inhibition by fluoride and chloride, and as-isolated proteins are often substantially activated by heat, suggesting that multiple redox states can complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters in realistic models with ∼200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference. Antiferromagnetic coupling, assigned oxidation states, and general structures were consistent with known spectroscopic data. The computations show that (i) ligands bound to the T2 site substantially increase the reorganization energy of the second reduction of the resting state and reduce the redox potentials, providing a possible mechanism for inhibition; (ii) the reorganization energy is particularly large for F(-) but also high for Cl(-), consistent with the experimental tendency of inhibition; (iii) reduction leads to release of Cl(-) from the T2 site, suggesting a mechanism for heat/reduction activation of laccases by dissociation of inhibiting halides or hydroxide from T2. PMID:25532722

  13. Halide binding and inhibition of laccase copper clusters: the role of reorganization energy.

    PubMed

    Kepp, Kasper P

    2015-01-20

    Laccase-like proteins are multicopper oxidases involved in several biological and industrial processes. Their application is commonly limited due to inhibition by fluoride and chloride, and as-isolated proteins are often substantially activated by heat, suggesting that multiple redox states can complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters in realistic models with ∼200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference. Antiferromagnetic coupling, assigned oxidation states, and general structures were consistent with known spectroscopic data. The computations show that (i) ligands bound to the T2 site substantially increase the reorganization energy of the second reduction of the resting state and reduce the redox potentials, providing a possible mechanism for inhibition; (ii) the reorganization energy is particularly large for F(-) but also high for Cl(-), consistent with the experimental tendency of inhibition; (iii) reduction leads to release of Cl(-) from the T2 site, suggesting a mechanism for heat/reduction activation of laccases by dissociation of inhibiting halides or hydroxide from T2.

  14. High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

    PubMed Central

    Moller, Isabel; Marcus, Susan E.; Haeger, Ash; Verhertbruggen, Yves; Verhoef, Rene; Schols, Henk; Ulvskov, Peter; Mikkelsen, Jørn Dalgaard; Knox, J. Paul

    2007-01-01

    Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall glycans immobilized on nitrocellulose was assessed. Hierarchical clustering of microarray binding profiles from newly produced mAbs, together with the profiles for mAbs with previously defined specificities allowed the rapid assignments of mAb binding to antigen classes. mAb specificities were further investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls in plant materials. PMID:17629746

  15. SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster

    PubMed Central

    Mathai, Jinumary; Mittal, Smriti P. K.; Alam, Aftab; Ranade, Payal; Mogare, Devraj; Patel, Sonal; Saxena, Smita; Ghorai, Suvankar; Kulkarni, Abhijeet P.; Chattopadhyay, Samit

    2016-01-01

    Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373. PMID:27671416

  16. The Dipole Potential Modifies the Clustering and Ligand Binding Affinity of ErbB Proteins and Their Signaling Efficiency

    PubMed Central

    Kovács, Tamás; Batta, Gyula; Hajdu, Tímea; Szabó, Ágnes; Váradi, Tímea; Zákány, Florina; Csomós, István; Szöllősi, János; Nagy, Peter

    2016-01-01

    Although activation of the ErbB family of receptor tyrosine kinases (ErbB1-4) is driven by oligomerization mediated by intermolecular interactions between the extracellular, the kinase and the transmembrane domains, the transmembrane domain has been largely neglected in this regard. The largest contributor to the intramembrane electric field, the dipole potential, alters the conformation of transmembrane peptides, but its effect on ErbB proteins is unknown. Here, we show by Förster resonance energy transfer (FRET) and number and brightness (N&B) experiments that the epidermal growth factor (EGF)-induced increase in the homoassociation of ErbB1 and ErbB2 and their heteroassociation are augmented by increasing the dipole potential. These effects were even more pronounced for ErbB2 harboring an activating Val → Glu mutation in the transmembrane domain (NeuT). The signaling capacity of ErbB1 and ErbB2 was also correlated with the dipole potential. Since the dipole potential decreased the affinity of EGF to ErbB1, the augmented growth factor-induced effects at an elevated dipole potential were actually induced at lower receptor occupancy. We conclude that the dipole potential plays a permissive role in the clustering of ErbB receptors and that the effects of lipid rafts on ligand binding and receptor signaling can be partially attributed to the dipole potential. PMID:27775011

  17. Binding of HMG 17 to mononucleosomes of the avian beta-globin gene cluster in erythroid and non-erythroid cells.

    PubMed Central

    Brotherton, T W; Reneker, J; Ginder, G D

    1990-01-01

    The binding of HMG 17 to stripped core mononucleosomes containing DNA from the avian beta-globin gene cluster was examined to determine whether binding in vitro in this developmentally-regulated gene domain was associated with transcriptional activity or DNaseI-sensitivity in intact nuclei. Mononucleosomes were prepared from primitive and definitive stage embryonic red blood cells of chick embryos, adult reticulocytes, adult reticulocytes in which embryonic rho-globin transcription was induced, and adult thymus cells. Preferential binding by HMG 17 to mononucleosomes containing the beta-globin gene cluster was confined to erythroid-derived mononucleosomes that contain the embryonic rho-globin gene, the adult beta-globin gene, and DNA sequences located between these two genes, but not to those that contain the embryonic epsilon-globin gene. Comparison of these results to the known patterns of transcription and DNaseI-sensitivity within the beta-globin gene cluster shows that HMG 17 binding, although tissue-specific, does not correlate directly with either DNaseI-sensitivity or active gene transcription, but is dependent on other factors present in core mononucleosomes from this active gene domain. Images PMID:1692412

  18. The pH sensitivity of murine heat shock protein 47 (HSP47) binding to collagen is affected by mutations in the breach histidine cluster.

    PubMed

    Abdul-Wahab, Mohd Firdaus; Homma, Takayuki; Wright, Michael; Olerenshaw, Dee; Dafforn, Timothy R; Nagata, Kazuhiro; Miller, Andrew D

    2013-02-01

    Heat shock protein 47 (HSP47) is a single-substrate molecular chaperone crucial for collagen biosynthesis. Although its function is well established, the molecular mechanisms that govern binding to procollagen peptides and triple helices in the endoplasmic reticulum (followed by controlled release in the Golgi) are unclear. HSP47 binds procollagen at a neutral pH but releases at a pH similar to the pK(a) of the imidazole side chain of histidine residues. It thus seems likely that these residues are involved in this pH-dependent mechanism. Murine HSP47 has 14 histidine residues grouped into three clusters, known as the breach, gate, and shutter. Here, we report the use of histidine mutagenesis to demonstrate the relative contribution of these three clusters to HSP47 structure and the "pH switch." Many of the tested mutants are silent; however, breach mutants H197A and H198A show binding but no apparent pH switch and are unable to control release. Another breach mutant, H191A, shows perturbed collagen release characteristics, consistent with observed perturbations in pH-driven trans-conformational changes. Thus, His-198, His-197 and His-191 are important (if not central) to HSP47 mechanism of binding/release to collagen. This is consistent with the breach cluster residues being well conserved across the HSP47 family.

  19. Binding of phosphoinositide-specific phospholipase C-zeta (PLC-zeta) to phospholipid membranes: potential role of an unstructured cluster of basic residues.

    PubMed

    Nomikos, Michail; Mulgrew-Nesbitt, Anna; Pallavi, Payal; Mihalyne, Gyongyi; Zaitseva, Irina; Swann, Karl; Lai, F Anthony; Murray, Diana; McLaughlin, Stuart

    2007-06-01

    Phospholipase C-zeta (PLC-zeta) is a sperm-specific enzyme that initiates the Ca2+ oscillations in mammalian eggs that activate embryo development. It shares considerable sequence homology with PLC-delta1, but lacks the PH domain that anchors PLC-delta1 to phosphatidylinositol 4,5-bisphosphate, PIP2. Thus it is unclear how PLC-zeta interacts with membranes. The linker region between the X and Y catalytic domains of PLC-zeta, however, contains a cluster of basic residues not present in PLC-delta1. Application of electrostatic theory to a homology model of PLC-zeta suggests this basic cluster could interact with acidic lipids. We measured the binding of catalytically competent mouse PLC-zeta to phospholipid vesicles: for 2:1 phosphatidylcholine/phosphatidylserine (PC/PS) vesicles, the molar partition coefficient, K, is too weak to be of physiological significance. Incorporating 1% PIP2 into the 2:1 PC/PS vesicles increases K about 10-fold, to 5x10(3) M-1, a biologically relevant value. Expressed fragments corresponding to the PLC-zeta X-Y linker region also bind with higher affinity to polyvalent than monovalent phosphoinositides on nitrocellulose filters. A peptide corresponding to the basic cluster (charge=+7) within the linker region, PLC-zeta-(374-385), binds to PC/PS vesicles with higher affinity than PLC-zeta, but its binding is less sensitive to incorporating PIP2. The acidic residues flanking this basic cluster in PLC-zeta may account for both these phenomena. FRET experiments suggest the basic cluster could not only anchor the protein to the membrane, but also enhance the local concentration of PIP2 adjacent to the catalytic domain.

  20. FORMATION AND PROPERTIES OF ASTROPHYSICAL CARBONACEOUS DUST. I. AB-INITIO CALCULATIONS OF THE CONFIGURATION AND BINDING ENERGIES OF SMALL CARBON CLUSTERS

    SciTech Connect

    Mauney, Christopher; Lazzati, Davide; Buongiorno Nardelli, Marco

    2015-02-10

    The binding energies of n < 100 carbon clusters are calculated using the ab initio density functional theory code Quantum Espresso. Carbon cluster geometries are determined using several levels of classical techniques and further refined using density functional theory. The resulting energies are used to compute the work of cluster formation and the nucleation rate in a saturated, hydrogen-poor carbon gas. Compared to classical calculations that adopt the capillary approximation, we find that nucleation of carbon clusters is enhanced at low temperatures and depressed at high temperatures. This difference is ascribed to the different behavior of the critical cluster size. We find that the critical cluster size is at n = 27 or n = 8 for a broad range of temperatures and saturations, instead of being a smooth function of such parameters. The results of our calculations can be used to follow carbonaceous cluster/grain formation, stability, and growth in hydrogen-poor environments, such as the inner layers of core-collapse supernovae and supernova remnants.

  1. Mutational analysis of the [4Fe-4S]-cluster converting iron regulatory factor from its RNA-binding form to cytoplasmic aconitase.

    PubMed Central

    Hirling, H; Henderson, B R; Kühn, L C

    1994-01-01

    The control of cellular iron homeostasis involves the coordinate post-transcriptional regulation of ferritin mRNA translation and transferring receptor mRNA stability. These regulatory events are mediated by a soluble cytoplasmic protein, iron regulatory factor (IRF), which binds specifically to mRNA hairpin structures, termed iron-responsive elements (IREs), in the respective mRNAs. IRF is modulated by variations of cellular iron levels and exists as either an apo-protein or a [4Fe-4S]-cluster protein. The two conformations show distinct, mutually exclusive functions. High-affinity IRE binding is observed with the apo-form induced by iron deprivation, but is lost under high iron conditions when IRF is converted to the [4Fe-4S]-cluster form which shows cytoplasmic aconitase activity. Moreover, IRE binding is inactivated by the sulfhydryl-oxidizing agent diamide and fully activated in vitro by 2% 2-mercapto-ethanol, whereas alkylation of IRF inhibits IRE binding. In the present study, we analyzed each of the above features using site-directed mutants of recombinant human IRF. The results support the bifunctional nature of IRF. We conclude that cysteines 437, 503 and 506 anchor the [4Fe-4S]-cluster, and are essential to the aconitase activity. Mutagenesis changing any of the cysteines to serine leads to constitutive RNA binding in 0.02% 2-mercaptoethanol. Cysteine 437 is particularly critical to the RNA-protein interaction. The spontaneous or diamide-induced formation of disulfide bonds between cysteines 437 and 503 or 437 and 506, in apo-IRF, as well as its alkylation by N-ethylmaleimide, inhibit binding to the IRE.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:7508861

  2. Polygalacturonase-Inhibiting Protein Interacts with Pectin through a Binding Site Formed by Four Clustered Residues of Arginine and Lysine1

    PubMed Central

    Spadoni, Sara; Zabotina, Olga; Di Matteo, Adele; Mikkelsen, Jørn Dalgaard; Cervone, Felice; De Lorenzo, Giulia; Mattei, Benedetta; Bellincampi, Daniela

    2006-01-01

    Polygalacturonase-inhibiting protein (PGIP) is a cell wall protein that inhibits fungal polygalacturonases (PGs) and retards the invasion of plant tissues by phytopathogenic fungi. Here, we report the interaction of two PGIP isoforms from Phaseolus vulgaris (PvPGIP1 and PvPGIP2) with both polygalacturonic acid and cell wall fractions containing uronic acids. We identify in the three-dimensional structure of PvPGIP2 a motif of four clustered arginine and lysine residues (R183, R206, K230, and R252) responsible for this binding. The four residues were mutated and the protein variants were expressed in Pichia pastoris. The ability of both wild-type and mutated proteins to bind pectins was investigated by affinity chromatography. Single mutations impaired the binding and double mutations abolished the interaction, thus indicating that the four clustered residues form the pectin-binding site. Remarkably, the binding of PGIP to pectin is displaced in vitro by PGs, suggesting that PGIP interacts with pectin and PGs through overlapping although not identical regions. The specific interaction of PGIP with polygalacturonic acid may be strategic to protect pectins from the degrading activity of fungal PGs. PMID:16648220

  3. Sperm surface hyaluronan binding protein (HABP1) interacts with zona pellucida of water buffalo (Bubalus bubalis) through its clustered mannose residues.

    PubMed

    Ghosh, Ilora; Datta, Kasturi

    2003-02-01

    Sperm-oocyte interaction during fertilization is multiphasic, with multicomponent events, taking place between zona pellucida (ZP) glycoproteins and sperm surface receptor. d-mannosylated glycoproteins, the major constituents of ZP are considered to serve as ligands for sperm binding. The presence of hyaluronan binding protein 1 (HABP1) on sperm surface of different mammals including cattle and its possible involvement in sperm function is already reported. Recently, we have demonstrated the specificity of clustered mannose as another ligand for HABP1 (Kumar et al., 2001: J Biosci 26:325-332). Here, we report that only N-linked mannosylated zona-glycoproteins bind to sperm surface HABP1. Labeled HABP1 interacts with ZP of intact oocyte of Bubalus bubalis, which can be competed with unlabeled HABP1 or excess d-mannosylated albumin (DMA). This data suggests the specific interaction of HABP1 with ZP, through clustered mannose residues. In order to examine the physiological significance of such an interaction, the capacity of sperm binding to oocytes under in vitro fertilization plates was examined either in presence of DMA alone or in combination with HABP1. The number of sperms, bound to oocytes was observed to reduce significantly in presence of DMA, which could be reversed by the addition of purified recombinant HABP1 (rHABP1) in the same plate. This suggests that sperm surface HABP1 may act as mannose binding sites for zona recognition.

  4. Basis-set limit binding energies of Be{sub n} and Mg{sub n} (n=2,3,4) clusters

    SciTech Connect

    Lee, Jae Shin

    2003-10-01

    The general applicability of the basis set and correlation-dependent extrapolation method [J. Chem. Phys. 118, 3035 (2003)], which fits two successive correlation energies with correlation-consistent cc-pVXZ and cc-pV(X+1)Z basis sets [X=D(2),T(3),Q(4)] by (X+k){sup -3} with varying k according to basis-set quality and correlation level, was explored by examining the basis-set limit binding energies of the metallic clusters of Be{sub n} and Mg{sub n} (n=2,3,4) at the MP2 (second-order Moller-Plesset perturbation theory) and CCSD(T) (single and double coupled cluster method with perturbative triple correction) level. The comparison of the extrapolated basis-set limit estimates with the highly accurate reference basis-set limits suggests that the extrapolation of correlation contributions of binding energies with only cc-pVDZ and cc-pVTZ basis sets already yields the basis-set limit estimates close to the reference complete basis-set limits within 1 m-hartree in most cases, signifying the utility of this extrapolation method in the study of larger clusters. The natural extension of this extrapolation method to all electron correlated computations including core electrons with core-valence cc-pCVXZ basis sets is also made, which shows the similar accuracy of the extrapolated estimates for all electron correlated results as the valence electron only correlated results. The comparison of the MP2 and CCSD(T) basis-set limit binding energies with DFT (density-functional theory) results manifests the capability and limitation of the current DFT methods in studying the binding of such clusters.

  5. Overlapping binding sites of the frataxin homologue assembly factor and the heat shock protein 70 transfer factor on the Isu iron-sulfur cluster scaffold protein.

    PubMed

    Manicki, Mateusz; Majewska, Julia; Ciesielski, Szymon; Schilke, Brenda; Blenska, Anna; Kominek, Jacek; Marszalek, Jaroslaw; Craig, Elizabeth A; Dutkiewicz, Rafal

    2014-10-31

    In mitochondria FeS clusters, prosthetic groups critical for the activity of many proteins, are first assembled on Isu, a 14-kDa scaffold protein, and then transferred to recipient apoproteins. The assembly process involves interaction of Isu with both Nfs1, the cysteine desulfurase serving as a sulfur donor, and the yeast frataxin homolog (Yfh1) serving as a regulator of desulfurase activity and/or iron donor. Here, based on the results of biochemical experiments with purified wild-type and variant proteins, we report that interaction of Yfh1 with both Nfs1 and Isu are required for formation of a stable tripartite assembly complex. Disruption of either Yfh1-Isu or Nfs1-Isu interactions destabilizes the complex. Cluster transfer to recipient apoprotein is known to require the interaction of Isu with the J-protein/Hsp70 molecular chaperone pair, Jac1 and Ssq1. Here we show that the Yfh1 interaction with Isu involves the PVK sequence motif, which is also the site key for the interaction of Isu with Hsp70 Ssq1. Coupled with our previous observation that Nfs1 and Jac1 binding to Isu is mutually exclusive due to partially overlapping binding sites, we propose that such mutual exclusivity of cluster assembly factor (Nfs1/Yfh1) and cluster transfer factor (Jac1/Ssq1) binding to Isu has functional consequences for the transition from the assembly process to the transfer process, and thus regulation of the biogenesis of FeS cluster proteins.

  6. Pichia pastoris Fep1 is a [2Fe-2S] protein with a Zn finger that displays an unusual oxygen-dependent role in cluster binding.

    PubMed

    Cutone, Antimo; Howes, Barry D; Miele, Adriana E; Miele, Rossella; Giorgi, Alessandra; Battistoni, Andrea; Smulevich, Giulietta; Musci, Giovanni; di Patti, Maria Carmela Bonaccorsi

    2016-01-01

    Fep1, the iron-responsive GATA factor from the methylotrophic yeast Pichia pastoris, has been characterised both in vivo and in vitro. This protein has two Cys2-Cys2 type zinc fingers and a set of four conserved cysteines arranged in a Cys-X5-Cys-X8-Cys-X2-Cys motif located between the two zinc fingers. Electronic absorption and resonance Raman spectroscopic analyses in anaerobic and aerobic conditions indicate that Fep1 binds iron in the form of a [2Fe-2S] cluster. Site-directed mutagenesis shows that replacement of the four cysteines with serine inactivates this transcriptional repressor. Unexpectedly, the inactive mutant is still able to bind a [2Fe-2S] cluster, employing two cysteine residues belonging to the first zinc finger. These two cysteine residues can act as alternative cluster ligands selectively in aerobically purified Fep1 wild type, suggesting that oxygen could play a role in Fep1 function by causing differential localization of the [Fe-S] cluster. PMID:27546548

  7. Pichia pastoris Fep1 is a [2Fe-2S] protein with a Zn finger that displays an unusual oxygen-dependent role in cluster binding

    PubMed Central

    Cutone, Antimo; Howes, Barry D.; Miele, Adriana E.; Miele, Rossella; Giorgi, Alessandra; Battistoni, Andrea; Smulevich, Giulietta; Musci, Giovanni; di Patti, Maria Carmela Bonaccorsi

    2016-01-01

    Fep1, the iron-responsive GATA factor from the methylotrophic yeast Pichia pastoris, has been characterised both in vivo and in vitro. This protein has two Cys2-Cys2 type zinc fingers and a set of four conserved cysteines arranged in a Cys-X5-Cys-X8-Cys-X2-Cys motif located between the two zinc fingers. Electronic absorption and resonance Raman spectroscopic analyses in anaerobic and aerobic conditions indicate that Fep1 binds iron in the form of a [2Fe-2S] cluster. Site-directed mutagenesis shows that replacement of the four cysteines with serine inactivates this transcriptional repressor. Unexpectedly, the inactive mutant is still able to bind a [2Fe-2S] cluster, employing two cysteine residues belonging to the first zinc finger. These two cysteine residues can act as alternative cluster ligands selectively in aerobically purified Fep1 wild type, suggesting that oxygen could play a role in Fep1 function by causing differential localization of the [Fe-S] cluster. PMID:27546548

  8. Microhydrated aromatic cluster cations: Binding motifs of 4-aminobenzonitrile-(H2O)n cluster cations with n ≤ 4

    NASA Astrophysics Data System (ADS)

    Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

    2014-12-01

    Infrared photodissociation (IRPD) spectra of mass-selected 4-aminobenzonitrile-(water)n cluster cations, ABN+-(H2O)n with n ≤ 4, recorded in the N-H and O-H stretch ranges are analyzed by quantum chemical calculations at the M06-2X/aug-cc-pVTZ level to determine the evolution of the initial microhydration process of this bifunctional aromatic cation in its ground electronic state. IRPD spectra of cold clusters tagged with Ar and N2 display higher resolution and allow for a clear-cut structural assignment. The clusters are generated in an electron impact source, which generates predominantly the most stable isomers. The IRPD spectra are assigned to single isomers for n = 1-3. The preferred cluster growth begins with sequential hydration of the two acidic NH protons of the amino group (n = 1-2), which is followed by attachment of secondary H2O ligands hydrogen-bonded to the first-shell ligands (n = 3-4). These symmetric and branched structures are more stable than those with a cyclic H-bonded solvent network. Moreover, in the size range n ≤ 4 the formation of a solvent network stabilized by strong cooperative effects is favored over interior ion hydration which is destabilized by noncooperative effects. The potential of the ABN+-H2O dimer is characterized in detail and supports the cluster growth derived from the IRPD spectra. Although the N-H bonds are destabilized by stepwise microhydration, which is accompanied by increasing charge transfer from ABN+ to the solvent cluster, no proton transfer to the solvent is observed for n ≤ 4.

  9. Microhydrated aromatic cluster cations: Binding motifs of 4-aminobenzonitrile-(H{sub 2}O){sub n} cluster cations with n ≤ 4

    SciTech Connect

    Schmies, Matthias; Dopfer, Otto; Miyazaki, Mitsuhiko; Fujii, Masaaki

    2014-12-07

    Infrared photodissociation (IRPD) spectra of mass-selected 4-aminobenzonitrile-(water){sub n} cluster cations, ABN{sup +}-(H{sub 2}O){sub n} with n ≤ 4, recorded in the N–H and O–H stretch ranges are analyzed by quantum chemical calculations at the M06-2X/aug-cc-pVTZ level to determine the evolution of the initial microhydration process of this bifunctional aromatic cation in its ground electronic state. IRPD spectra of cold clusters tagged with Ar and N{sub 2} display higher resolution and allow for a clear-cut structural assignment. The clusters are generated in an electron impact source, which generates predominantly the most stable isomers. The IRPD spectra are assigned to single isomers for n = 1–3. The preferred cluster growth begins with sequential hydration of the two acidic NH protons of the amino group (n = 1–2), which is followed by attachment of secondary H{sub 2}O ligands hydrogen-bonded to the first-shell ligands (n = 3–4). These symmetric and branched structures are more stable than those with a cyclic H-bonded solvent network. Moreover, in the size range n ≤ 4 the formation of a solvent network stabilized by strong cooperative effects is favored over interior ion hydration which is destabilized by noncooperative effects. The potential of the ABN{sup +}-H{sub 2}O dimer is characterized in detail and supports the cluster growth derived from the IRPD spectra. Although the N–H bonds are destabilized by stepwise microhydration, which is accompanied by increasing charge transfer from ABN{sup +} to the solvent cluster, no proton transfer to the solvent is observed for n ≤ 4.

  10. Selective binding and lateral clustering of α5β1 and αvβ3 integrins: Unraveling the spatial requirements for cell spreading and focal adhesion assembly

    PubMed Central

    Schaufler, Viktoria; Czichos-Medda, Helmi; Hirschfeld-Warnecken, Vera; Neubauer, Stefanie; Rechenmacher, Florian; Medda, Rebecca; Kessler, Horst; Geiger, Benjamin; Spatz, Joachim P.; Cavalcanti-Adam, E. Ada

    2016-01-01

    ABSTRACT Coordination of the specific functions of α5β1 and αvβ3 integrins is crucial for the precise regulation of cell adhesion, spreading and migration, yet the contribution of differential integrin-specific crosstalk to these processes remains unclear. To determine the specific functions of αvβ3 and α5β1 integrins, we used nanoarrays of gold particles presenting immobilized, integrin-selective peptidomimetic ligands. Integrin binding to the peptidomimetics is highly selective, and cells can spread on both ligands. However, spreading is faster and the projected cell area is greater on α5β1 ligand; both depend on ligand spacing. Quantitative analysis of adhesion plaques shows that focal adhesion size is increased in cells adhering to αvβ3 ligand at 30 and 60 nm spacings. Analysis of αvβ3 and α5β1 integrin clusters indicates that fibrillar adhesions are more prominent in cells adhering to α5β1 ligand, while clusters are mostly localized at the cell margins in cells adhering to αvβ3 ligand. αvβ3 integrin clusters are more pronounced on αvβ3 ligand, though they can also be detected in cells adhering to α5β1 ligand. Furthermore, α5β1 integrin clusters are present in cells adhering to α5β1 ligand, and often colocalize with αvβ3 clusters. Taken together, these findings indicate that the activation of αvβ3 integrin by ligand binding is dispensable for initial adhesion and spreading, but essential to formation of stable focal adhesions. PMID:27003228

  11. The N-terminal Domain of the Drosophila Mitochondrial Replicative DNA Helicase Contains an Iron-Sulfur Cluster and Binds DNA*

    PubMed Central

    Stiban, Johnny; Farnum, Gregory A.; Hovde, Stacy L.; Kaguni, Laurie S.

    2014-01-01

    The metazoan mitochondrial DNA helicase is an integral part of the minimal mitochondrial replisome. It exhibits strong sequence homology with the bacteriophage T7 gene 4 protein primase-helicase (T7 gp4). Both proteins contain distinct N- and C-terminal domains separated by a flexible linker. The C-terminal domain catalyzes its characteristic DNA-dependent NTPase activity, and can unwind duplex DNA substrates independently of the N-terminal domain. Whereas the N-terminal domain in T7 gp4 contains a DNA primase activity, this function is lost in metazoan mtDNA helicase. Thus, although the functions of the C-terminal domain and the linker are partially understood, the role of the N-terminal region in the metazoan replicative mtDNA helicase remains elusive. Here, we show that the N-terminal domain of Drosophila melanogaster mtDNA helicase coordinates iron in a 2Fe-2S cluster that enhances protein stability in vitro. The N-terminal domain binds the cluster through conserved cysteine residues (Cys68, Cys71, Cys102, and Cys105) that are responsible for coordinating zinc in T7 gp4. Moreover, we show that the N-terminal domain binds both single- and double-stranded DNA oligomers, with an apparent Kd of ∼120 nm. These findings suggest a possible role for the N-terminal domain of metazoan mtDNA helicase in recruiting and binding DNA at the replication fork. PMID:25023283

  12. The N-terminal domain of the Drosophila mitochondrial replicative DNA helicase contains an iron-sulfur cluster and binds DNA.

    PubMed

    Stiban, Johnny; Farnum, Gregory A; Hovde, Stacy L; Kaguni, Laurie S

    2014-08-29

    The metazoan mitochondrial DNA helicase is an integral part of the minimal mitochondrial replisome. It exhibits strong sequence homology with the bacteriophage T7 gene 4 protein primase-helicase (T7 gp4). Both proteins contain distinct N- and C-terminal domains separated by a flexible linker. The C-terminal domain catalyzes its characteristic DNA-dependent NTPase activity, and can unwind duplex DNA substrates independently of the N-terminal domain. Whereas the N-terminal domain in T7 gp4 contains a DNA primase activity, this function is lost in metazoan mtDNA helicase. Thus, although the functions of the C-terminal domain and the linker are partially understood, the role of the N-terminal region in the metazoan replicative mtDNA helicase remains elusive. Here, we show that the N-terminal domain of Drosophila melanogaster mtDNA helicase coordinates iron in a 2Fe-2S cluster that enhances protein stability in vitro. The N-terminal domain binds the cluster through conserved cysteine residues (Cys(68), Cys(71), Cys(102), and Cys(105)) that are responsible for coordinating zinc in T7 gp4. Moreover, we show that the N-terminal domain binds both single- and double-stranded DNA oligomers, with an apparent Kd of ∼120 nm. These findings suggest a possible role for the N-terminal domain of metazoan mtDNA helicase in recruiting and binding DNA at the replication fork.

  13. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H2O)n clusters, n = 2-4

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Buchanan, Evan G.; Gord, Joseph R.; Zwier, Timothy S.

    2015-04-01

    The single-conformation infrared (IR) and ultraviolet (UV) spectroscopies of neutral 1,2-diphenoxyethane-(H2O)n clusters with n = 2-4 (labeled henceforth as 1:n) have been studied in a molecular beam using a combination of resonant two-photon ionization, IR-UV holeburning, and resonant ion-dip infrared (RIDIR) spectroscopies. Ground state RIDIR spectra in the OH and CH stretch regions were used to provide firm assignments for the structures of the clusters by comparing the experimental spectra with the predictions of calculations carried out at the density functional M05-2X/6-31+G(d) level of theory. At all sizes in this range, the water molecules form water clusters in which all water molecules engage in a single H-bonded network. Selective binding to the tgt monomer conformer of 1,2-diphenoxyethane (C6H5-O-CH2-CH2-O-C6H5, DPOE) occurs, since this conformer provides a binding pocket in which the two ether oxygens and two phenyl ring π clouds can be involved in stabilizing the water cluster. The 1:2 cluster incorporates a water dimer "chain" bound to DPOE much as it is in the 1:1 complex [E. G. Buchanan et al., J. Phys. Chem. Lett. 4, 1644 (2013)], with primary attachment via a double-donor water that bridges the ether oxygen of one phenoxy group and the π cloud of the other. Two conformers of the 1:3 cluster are observed and characterized, one that extends the water chain to a third molecule (1:3 chain) and the other incorporating a water trimer cycle (1:3 cycle). A cyclic water structure is also observed for the 1:4 cluster. These structural characterizations provide a necessary foundation for studies of the perturbations imposed on the two close-lying S1/S2 excited states of DPOE considered in the adjoining paper [P. S. Walsh et al., J. Chem. Phys. 142, 154304 (2015)].

  14. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H{sub 2}O){sub n} clusters, n = 2-4

    SciTech Connect

    Walsh, Patrick S.; Buchanan, Evan G.; Gord, Joseph R.; Zwier, Timothy S.

    2015-04-21

    The single-conformation infrared (IR) and ultraviolet (UV) spectroscopies of neutral 1,2-diphenoxyethane-(H{sub 2}O){sub n} clusters with n = 2-4 (labeled henceforth as 1:n) have been studied in a molecular beam using a combination of resonant two-photon ionization, IR-UV holeburning, and resonant ion-dip infrared (RIDIR) spectroscopies. Ground state RIDIR spectra in the OH and CH stretch regions were used to provide firm assignments for the structures of the clusters by comparing the experimental spectra with the predictions of calculations carried out at the density functional M05-2X/6-31+G(d) level of theory. At all sizes in this range, the water molecules form water clusters in which all water molecules engage in a single H-bonded network. Selective binding to the tgt monomer conformer of 1,2-diphenoxyethane (C{sub 6}H{sub 5}-O-CH{sub 2}-CH{sub 2}-O-C{sub 6}H{sub 5}, DPOE) occurs, since this conformer provides a binding pocket in which the two ether oxygens and two phenyl ring π clouds can be involved in stabilizing the water cluster. The 1:2 cluster incorporates a water dimer “chain” bound to DPOE much as it is in the 1:1 complex [E. G. Buchanan et al., J. Phys. Chem. Lett. 4, 1644 (2013)], with primary attachment via a double-donor water that bridges the ether oxygen of one phenoxy group and the π cloud of the other. Two conformers of the 1:3 cluster are observed and characterized, one that extends the water chain to a third molecule (1:3 chain) and the other incorporating a water trimer cycle (1:3 cycle). A cyclic water structure is also observed for the 1:4 cluster. These structural characterizations provide a necessary foundation for studies of the perturbations imposed on the two close-lying S{sub 1}/S{sub 2} excited states of DPOE considered in the adjoining paper [P. S. Walsh et al., J. Chem. Phys. 142, 154304 (2015)].

  15. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H₂O)n clusters, n = 2-4.

    PubMed

    Walsh, Patrick S; Buchanan, Evan G; Gord, Joseph R; Zwier, Timothy S

    2015-04-21

    The single-conformation infrared (IR) and ultraviolet (UV) spectroscopies of neutral 1,2-diphenoxyethane-(H2O)n clusters with n = 2-4 (labeled henceforth as 1:n) have been studied in a molecular beam using a combination of resonant two-photon ionization, IR-UV holeburning, and resonant ion-dip infrared (RIDIR) spectroscopies. Ground state RIDIR spectra in the OH and CH stretch regions were used to provide firm assignments for the structures of the clusters by comparing the experimental spectra with the predictions of calculations carried out at the density functional M05-2X/6-31+G(d) level of theory. At all sizes in this range, the water molecules form water clusters in which all water molecules engage in a single H-bonded network. Selective binding to the tgt monomer conformer of 1,2-diphenoxyethane (C6H5-O-CH2-CH2-O-C6H5, DPOE) occurs, since this conformer provides a binding pocket in which the two ether oxygens and two phenyl ring π clouds can be involved in stabilizing the water cluster. The 1:2 cluster incorporates a water dimer "chain" bound to DPOE much as it is in the 1:1 complex [E. G. Buchanan et al., J. Phys. Chem. Lett. 4, 1644 (2013)], with primary attachment via a double-donor water that bridges the ether oxygen of one phenoxy group and the π cloud of the other. Two conformers of the 1:3 cluster are observed and characterized, one that extends the water chain to a third molecule (1:3 chain) and the other incorporating a water trimer cycle (1:3 cycle). A cyclic water structure is also observed for the 1:4 cluster. These structural characterizations provide a necessary foundation for studies of the perturbations imposed on the two close-lying S1/S2 excited states of DPOE considered in the adjoining paper [P. S. Walsh et al., J. Chem. Phys. 142, 154304 (2015)].

  16. Binding water clusters to an aromatic-rich hydrophobic pocket: [2.2.2]paracyclophane-(H2O)n, n = 1-5.

    PubMed

    Buchanan, Evan G; Zwier, Timothy S

    2014-09-18

    [2.2.2]Paracylcophane (tricyclophane, TCP) is a macrocycle with three phenyl substituents linked by ethyl bridges (-CH2CH2-) in the para-position, forming an aromatic-rich pocket capable of binding various substituents, including nature's solvent, water. Building on previous work [Buchanan, E. G.; et al. J. Chem. Phys. 2013, 138, 064308] that reported on the ground state conformational preferences of TCP, the focus of the present study is on the infrared and ultraviolet spectroscopy of TCP-(H2O)n clusters with n = 1-5. Resonant two-photon ionization (R2PI) was used to interrogate the mass selected electronic spectrum of the clusters, reporting on the perturbations imposed on the electronic states of TCP as the size of the water clusters bound to it vary in size from n = 1-5. The TCP-(H2O)n S0-S1 origins are shifted to lower frequency from the monomer, indicating an increased binding energy of the water or water network in the excited state. Ground state resonant ion-dip infrared (RIDIR) spectra of TCP-(H2O)n (n = 1-5) clusters were recorded in the OH stretch region, which probes the H-bonded water networks present and the perturbations imposed on them by TCP. The experimental frequencies are compared with harmonic vibrational frequencies calculated using density functional theory (DFT) with the dispersion-corrected functional ωB97X-D and a 6-311+g(d,p) basis set, providing firm assignments for their H-bonding structures. The H2O molecule in TCP-(H2O)1 sits on top of the binding pocket, donating both of its hydrogen atoms to the aromatic-rich interior of the monomer. The antisymmetric stretch fundamental of H2O in the complex is composed of a closely spaced set of transitions that likely reflect contributions from both para- and ortho-forms of H2O due to internal rotation of the H2O in the binding pocket. TCP-(H2O)2 also exists in a single conformational isomer that retains the same double-donor binding motif for the first water molecule, with the second H2O acting

  17. Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

    NASA Astrophysics Data System (ADS)

    Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R.

    2016-03-01

    A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H2O)n (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculation MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%-65% saving of computational time. The methodology has a potential for application to molecular clusters containing ˜100 atoms.

  18. Essential role of the iron-sulfur cluster binding domain of the primase regulatory subunit Pri2 in DNA replication initiation.

    PubMed

    Liu, Lili; Huang, Mingxia

    2015-03-01

    DNA primase catalyzes de novo synthesis of a short RNA primer that is further extended by replicative DNA polymerases during initiation of DNA replication. The eukaryotic primase is a heterodimeric enzyme comprising a catalytic subunit Pri1 and a regulatory subunit Pri2. Pri2 is responsible for facilitating optimal RNA primer synthesis by Pri1 and mediating interaction between Pri1 and DNA polymerase α for transition from RNA synthesis to DNA elongation. All eukaryotic Pri2 proteins contain a conserved C-terminal iron-sulfur (Fe-S) cluster-binding domain that is critical for primase catalytic activity in vitro. Here we show that mutations at conserved cysteine ligands for the Pri2 Fe-S cluster markedly decrease the protein stability, thereby causing S phase arrest at the restrictive temperature. Furthermore, Pri2 cysteine mutants are defective in loading of the entire DNA pol α-primase complex onto early replication origins resulting in defective initiation. Importantly, assembly of the Fe-S cluster in Pri2 is impaired not only by mutations at the conserved cysteine ligands but also by increased oxidative stress in the sod1Δ mutant lacking the Cu/Zn superoxide dismutase. Together these findings highlight the critical role of Pri2's Fe-S cluster domain in replication initiation in vivo and suggest a molecular basis for how DNA replication can be influenced by changes in cellular redox state.

  19. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.

    PubMed

    Lee, Brian M; Buck-Koehntop, Bethany A; Martinez-Yamout, Maria A; Dyson, H Jane; Wright, Peter E

    2007-08-31

    Churchill is a zinc-containing protein that is involved in neural induction during embryogenesis. At the time of its discovery, it was thought on the basis of sequence alignment to contain two zinc fingers of the C4 type. Further, binding of an N-terminal GST-Churchill fusion protein to a particular DNA sequence was demonstrated by immunoprecipitation selection assay, suggesting that Churchill may function as a transcriptional regulator by sequence-specific DNA binding. We show by NMR solution structure determination that, far from containing canonical C4 zinc fingers, the protein contains three bound zinc ions in novel coordination sites, including an unusual binuclear zinc cluster. The secondary structure of Churchill is also unusual, consisting of a highly solvent-exposed single-layer beta-sheet. Hydrogen-deuterium exchange and backbone relaxation measurements reveal that Churchill is unusually dynamic on a number of time scales, with the exception of regions surrounding the zinc coordinating sites, which serve to stabilize the otherwise unstructured N terminus and the single-layer beta-sheet. No binding of Churchill to the previously identified DNA sequence could be detected, and extensive searches using DNA sequence selection techniques could find no other DNA sequence that was bound by Churchill. Since the N-terminal amino acids of Churchill form part of the zinc-binding motif, the addition of a fusion protein at the N terminus causes loss of zinc and unfolding of Churchill. This observation most likely explains the published DNA-binding results, which would arise due to non-specific interaction of the unfolded protein in the immunoprecipitation selection assay. Since Churchill does not appear to bind DNA, we suggest that it may function in embryogenesis as a protein-interaction factor.

  20. Frataxin directly stimulates mitochondrial cysteine desulfurase by exposing substrate-binding sites, and a mutant Fe-S cluster scaffold protein with frataxin-bypassing ability acts similarly.

    PubMed

    Pandey, Alok; Gordon, Donna M; Pain, Jayashree; Stemmler, Timothy L; Dancis, Andrew; Pain, Debkumar

    2013-12-27

    For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the "buried" substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation.

  1. Strategies for maximizing ATP supply in the microsporidian Encephalitozoon cuniculi: direct binding of mitochondria to the parasitophorous vacuole and clustering of the mitochondrial porin VDAC

    PubMed Central

    Hacker, Christian; Howell, Matthew; Bhella, David; Lucocq, John

    2013-01-01

    Summary Microsporidia are obligate intracellular parasites with extremely reduced genomes and a dependence on host-derived ATP. The microsporidium Encephalitozoon cuniculi proliferates within a membranous vacuole and we investigated how the ATP supply is optimized at the vacuole–host interface. Using spatial EM quantification (stereology), we found a single layer of mitochondria coating substantial proportions of the parasitophorous vacuole. Mitochondrial binding occurred preferentially over the vegetative ‘meront’ stages of the parasite, which bulged into the cytoplasm, thereby increasing the membrane surface available for mitochondrial interaction. In a broken cell system mitochondrial binding was maintained and was typified by electron dense structures (< 10 nm long) bridging between outer mitochondrial and vacuole membranes. In broken cells mitochondrial binding was sensitive to a range of protease treatments. The function of directly bound mitochondria, as measured by the membrane potential sensitive dye JC-1, was indistinguishable from other mitochondria in the cell although there was a generalized depression of the membrane potential in infected cells. Finally, quantitative immuno-EM revealed that the ATP-delivering mitochondrial porin, VDAC, was concentrated atthe mitochondria-vacuole interaction site. Thus E. cuniculi appears to maximize ATP supply by direct binding of mitochondria to the parasitophorous vacuole bringing this organelle within 0.020 microns of the growing vegetative form of the parasite. ATP-delivery is further enhanced by clustering of ATP transporting porins in those regions of the outer mitochondrial membrane lying closest to the parasite. PMID:24245785

  2. Strategies for maximizing ATP supply in the microsporidian Encephalitozoon cuniculi: direct binding of mitochondria to the parasitophorous vacuole and clustering of the mitochondrial porin VDAC.

    PubMed

    Hacker, Christian; Howell, Matthew; Bhella, David; Lucocq, John

    2014-04-01

    Microsporidia are obligate intracellular parasites with extremely reduced genomes and a dependence on host-derived ATP. The microsporidium Encephalitozoon cuniculi proliferates within a membranous vacuole and we investigated how the ATP supply is optimized at the vacuole-host interface. Using spatial EM quantification (stereology), we found a single layer of mitochondria coating substantial proportions of the parasitophorous vacuole. Mitochondrial binding occurred preferentially over the vegetative 'meront' stages of the parasite, which bulged into the cytoplasm, thereby increasing the membrane surface available for mitochondrial interaction. In a broken cell system mitochondrial binding was maintained and was typified by electron dense structures (< 10 nm long) bridging between outer mitochondrial and vacuole membranes. In broken cells mitochondrial binding was sensitive to a range of protease treatments. The function of directly bound mitochondria, as measured by the membrane potential sensitive dye JC-1, was indistinguishable from other mitochondria in the cell although there was a generalized depression of the membrane potential in infected cells. Finally, quantitative immuno-EM revealed that the ATP-delivering mitochondrial porin, VDAC, was concentrated atthe mitochondria-vacuole interaction site. Thus E. cuniculi appears to maximize ATP supply by direct binding of mitochondria to the parasitophorous vacuole bringing this organelle within 0.020 microns of the growing vegetative form of the parasite. ATP-delivery is further enhanced by clustering of ATP transporting porins in those regions of the outer mitochondrial membrane lying closest to the parasite.

  3. The small iron-sulfur protein from the ORP operon binds a [2Fe-2S] cluster.

    PubMed

    Maiti, Biplab K; Moura, Isabel; Moura, José J G; Pauleta, Sofia R

    2016-09-01

    A linear cluster formulated as [S2MoS2CuS2MoS2](3-), a unique heterometallic cluster found in biological systems, was identified in a small monomeric protein (named as Orange Protein). The gene coding for this protein is part of an operon mainly present in strict anaerobic bacteria, which is composed (in its core) by genes coding for the Orange Protein and two ATPase proposed to contain Fe-S clusters. In Desulfovibrio desulfuricans G20, there is an ORF, Dde_3197 that encodes a small protein containing several cysteine residues in its primary sequence. The heterologously produced Dde_3197 aggregates mostly in inclusion bodies and was isolated by unfolding with a chaotropic agent and refolding by dialysis. The refolded protein contained sub-stoichiometric amounts of iron atoms/protein (0.5±0.2), but after reconstitution with iron and sulfide, high iron load contents were detected (1.8±0.1 or 3.4±0.2) using 2- and 4-fold iron excess. The visible absorption spectral features of the iron-sulfur clusters in refolded and reconstituted Dde_3197 are similar and resemble the ones of [2Fe-2S] cluster containing proteins. The refolded and reconstituted [2Fe-2S] Dde_3197 are EPR silent, but after reduction with dithionite, a rhombic signal is observed with gmax=2.00, gmed=1.95 and gmin=1.92, consistent with a one-electron reduction of a [2Fe-2S](2+) cluster into a [2Fe-2S](1+) state, with an electron spin of S=½. The data suggests that Dde_3197 can harbor one or two [2Fe-2S] clusters, one being stable and the other labile, with quite identical spectroscopic properties, but stable to oxygen. PMID:27240719

  4. The small iron-sulfur protein from the ORP operon binds a [2Fe-2S] cluster.

    PubMed

    Maiti, Biplab K; Moura, Isabel; Moura, José J G; Pauleta, Sofia R

    2016-09-01

    A linear cluster formulated as [S2MoS2CuS2MoS2](3-), a unique heterometallic cluster found in biological systems, was identified in a small monomeric protein (named as Orange Protein). The gene coding for this protein is part of an operon mainly present in strict anaerobic bacteria, which is composed (in its core) by genes coding for the Orange Protein and two ATPase proposed to contain Fe-S clusters. In Desulfovibrio desulfuricans G20, there is an ORF, Dde_3197 that encodes a small protein containing several cysteine residues in its primary sequence. The heterologously produced Dde_3197 aggregates mostly in inclusion bodies and was isolated by unfolding with a chaotropic agent and refolding by dialysis. The refolded protein contained sub-stoichiometric amounts of iron atoms/protein (0.5±0.2), but after reconstitution with iron and sulfide, high iron load contents were detected (1.8±0.1 or 3.4±0.2) using 2- and 4-fold iron excess. The visible absorption spectral features of the iron-sulfur clusters in refolded and reconstituted Dde_3197 are similar and resemble the ones of [2Fe-2S] cluster containing proteins. The refolded and reconstituted [2Fe-2S] Dde_3197 are EPR silent, but after reduction with dithionite, a rhombic signal is observed with gmax=2.00, gmed=1.95 and gmin=1.92, consistent with a one-electron reduction of a [2Fe-2S](2+) cluster into a [2Fe-2S](1+) state, with an electron spin of S=½. The data suggests that Dde_3197 can harbor one or two [2Fe-2S] clusters, one being stable and the other labile, with quite identical spectroscopic properties, but stable to oxygen.

  5. Ligand Binding Site of Tear Lipocalin: Contribution of a Trigonal Cluster of Charged Residues Probed by 8-Anilino-1-naphthalenesulfonic Acid†

    PubMed Central

    Gasymov, Oktay K.; Abduragimov, Adil R.; Glasgow, Ben J.

    2010-01-01

    Human tear lipocalin (TL) exhibits diverse functions, most of which are linked to ligand binding. To map the binding site of TL for some amphiphilic ligands, we capitalized on the hydrophobic and hydrophilic properties of 8-anilino-1-naphthalenesulfonic acid (ANS). In single Trp mutants, resonance energy transfer from Trp to ANS indicates that the naphthalene group of ANS is proximate to Leu105 in the cavity. Binding energies of TL to ANS and its analogues reveal contributions from electrostatic interactions. The sulfonate group of ANS interacts strongly with the nonconserved intracavitary residue Lys114 and less with neighboring residues His84 and Glu34. This trigonal cluster of residues may play a role in the ligand recognition site for some negatively charged ligands. Because many drugs possess sulfonate groups, the trigonal cluster–sulfonate interaction can also be exploited as a lipocalin-based drug delivery mechanism. The binding of lauric acid and its analogues shows that fatty acids assume heterogeneous orientations in the cavity of TL. Predominantly, the hydrocarbon tail is buried in the cavity of TL and the carboxyl group is oriented toward the mouth. However, TL can also interact, albeit relatively weakly, with fatty acids oriented in the opposite direction. As the major lipid binding protein of tears, the ability to accommodate fatty acids in two opposing orientations may have functional implications for TL. At the aqueous–lipid interface, fatty acids whose carboxyl groups are positioned toward the aqueous phase are available for interaction with TL that could augment stability of the tear film. PMID:18179255

  6. Binding of Hyaluronan to the Native Lymphatic Vessel Endothelial Receptor LYVE-1 Is Critically Dependent on Receptor Clustering and Hyaluronan Organization*

    PubMed Central

    Lawrance, William; Banerji, Suneale; Day, Anthony J.; Bhattacharjee, Shaumick; Jackson, David G.

    2016-01-01

    The lymphatic endothelial receptor LYVE-1 has been implicated in both uptake of hyaluronan (HA) from tissue matrix and in facilitating transit of leukocytes and tumor cells through lymphatic vessels based largely on in vitro studies with recombinant receptor in transfected fibroblasts. Curiously, however, LYVE-1 in lymphatic endothelium displays little if any binding to HA in vitro, and this has led to the conclusion that the native receptor is functionally silenced, a feature that is difficult to reconcile with its proposed in vivo functions. Nonetheless, as we reported recently, LYVE-1 can function as a receptor for HA-encapsulated Group A streptococci and mediate lymphatic dissemination in mice. Here we resolve these paradoxical findings and show that the capacity of LYVE-1 to bind HA is strictly dependent on avidity, demanding appropriate receptor self-association and/or HA multimerization. In particular, we demonstrate the prerequisite of a critical LYVE-1 threshold density and show that HA binding may be elicited in lymphatic endothelium by surface clustering with divalent LYVE-1 mAbs. In addition, we show that cross-linking of biotinylated HA in streptavidin multimers or supramolecular complexes with the inflammation-induced protein TSG-6 enables binding even in the absence of LYVE-1 cross-linking. Finally, we show that endogenous HA on the surface of macrophages can engage LYVE-1, facilitating their adhesion and transit across lymphatic endothelium. These results reveal LYVE-1 as a low affinity receptor tuned to discriminate between different HA configurations through avidity and establish a new mechanistic basis for the functions ascribed to LYVE-1 in matrix HA binding and leukocyte trafficking in vivo. PMID:26823460

  7. FRET analysis using sperm-activating peptides tagged with fluorescent proteins reveals that ligand-binding sites exist as clusters.

    PubMed

    Arcos-Hernández, César; Romero, Francisco; Sánchez-Guevara, Yoloxochitl; Beltrán, Carmen; Nishigaki, Takuya

    2016-02-01

    Long-range cellular communication between the sperm and egg is critical for external fertilization. Sperm-activating peptides (SAPs) are diffusible components of the outer layer of eggs in echinoderms, and function as chemoattractants for spermatozoa. The decapeptide named speract is the best-characterized sea urchin SAP. Biochemical and physiological actions of speract have been studied with purified or chemically synthesized peptides. In this work, we prepared recombinant speract fused to a fluorescent protein (FP; FP-speract) using three color variants: a cyan (eCFP), a yellow (mVenus) and a large Stokes shift yellow (mAmetrine) FP. Although these fluorescence tags are 20 times larger than speract, competitive binding experiments using mAmetrine-speract revealed that this FP-speract has binding affinity to the receptor that is comparable (7.6-fold less) to that of non-labeled speract. Indeed, 10 nmol l(-1) eCFP-speract induces physiological sperm responses such as membrane potential changes and increases in intracellular pH and Ca(2+) concentrations similar to those triggered by 10 nmol l(-1) speract. Furthermore, FP-speract maintains its fluorescence upon binding to its receptor. Using this property, we performed fluorescence resonance energy transfer (FRET) measurements with eCFP-speract and mVenus-speract as probes and obtained a positive FRET signal upon binding to the receptor, which suggests that the speract receptor exists as an oligomer, at least as a dimer, or alternatively that a single speract receptor protein possesses multiple binding sites. This property could partially account for the positive and/or negative cooperative binding of speract to the receptor.

  8. Asp1 from Schizosaccharomyces pombe binds a [2Fe-2S](2+) cluster which inhibits inositol pyrophosphate 1-phosphatase activity.

    PubMed

    Wang, Huanchen; Nair, Vasudha S; Holland, Ashley A; Capolicchio, Samanta; Jessen, Henning J; Johnson, Michael K; Shears, Stephen B

    2015-10-27

    Iron-sulfur (Fe-S) clusters are widely distributed protein cofactors that are vital to cellular biochemistry and the maintenance of bioenergetic homeostasis, but to our knowledge, they have never been identified in any phosphatase. Here, we describe an iron-sulfur cluster in Asp1, a dual-function kinase/phosphatase that regulates cell morphogenesis in Schizosaccharomyces pombe. Full-length Asp1, and its phosphatase domain (Asp1(371-920)), were each heterologously expressed in Escherichia coli. The phosphatase activity is exquisitely specific: it hydrolyzes the 1-diphosphate from just two members of the inositol pyrophosphate (PP-InsP) signaling family, namely, 1-InsP7 and 1,5-InsP8. We demonstrate that Asp1 does not hydrolyze either InsP6, 2-InsP7, 3-InsP7, 4-InsP7, 5-InsP7, 6-InsP7, or 3,5-InsP8. We also recorded 1-phosphatase activity in a human homologue of Asp1, hPPIP5K1, which was heterologously expressed in Drosophila S3 cells with a biotinylated N-terminal tag, and then isolated from cell lysates with avidin beads. Purified, recombinant Asp1(371-920) contained iron and acid-labile sulfide, but the stoichiometry (0.8 atoms of each per protein molecule) indicates incomplete iron-sulfur cluster assembly. We reconstituted the Fe-S cluster in vitro under anaerobic conditions, which increased the stoichiometry to approximately 2 atoms of iron and acid-labile sulfide per Asp1 molecule. The presence of a [2Fe-2S](2+) cluster in Asp1(371-920) was demonstrated by UV-visible absorption, resonance Raman spectroscopy, and electron paramagnetic resonance spectroscopy. We determined that this [2Fe-2S](2+) cluster is unlikely to participate in redox chemistry, since it rapidly degraded upon reduction by dithionite. Biochemical and mutagenic studies demonstrated that the [2Fe-2S](2+) cluster substantially inhibits the phosphatase activity of Asp1, thereby increasing its net kinase activity.

  9. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential.

    PubMed

    Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand

    2015-03-19

    The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the

  10. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential.

    PubMed

    Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand

    2015-03-19

    The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the

  11. Two novel monothiol glutaredoxins from Saccharomyces cerevisiae provide further insight into iron-sulfur cluster binding, oligomerization, and enzymatic activity of glutaredoxins.

    PubMed

    Mesecke, Nikola; Mittler, Sarah; Eckers, Elisabeth; Herrmann, Johannes M; Deponte, Marcel

    2008-02-01

    Two novel monothiol glutaredoxins from yeast (ScGrx6 and ScGrx7) were identified and analyzed in vitro. Both proteins are highly suited to study structure-function relationships of glutaredoxin subclasses because they differ from all monothiol glutaredoxins investigated so far and share features with dithiol glutaredoxins. ScGrx6 and ScGrx7 are, for example, the first monothiol glutaredoxins showing an activity in the standard glutaredoxin transhydrogenase assay with glutathione and bis-(2-hydroxyethyl)-disulfide. Steady-state kinetics of ScGrx7 with glutathione and cysteine-glutathione disulfide are similar to dithiol glutaredoxins and are consistent with a ping-pong mechanism. In contrast to most other glutaredoxins, ScGrx7 and ScGrx6 are able to dimerize noncovalently. Furthermore, ScGrx6 is the first monothiol glutaredoxin shown to directly bind an iron-sulfur cluster. The cluster can be stabilized by reduced glutathione, and its loss results in the conversion of tetramers to dimers. ScGrx7 does not bind metal ions but can be covalently modified in Escherichia coli leading to a mass shift of 1090 +/- 14 Da. What might be the structural requirements that cause the different properties? We hypothesize that a G(S/T)x3 insertion between a highly conserved lysine residue and the active site cysteine residue could be responsible for the abrogated transhydrogenase activity of many monothiol glutaredoxins. In addition, we suggest an active site motif without proline residues that could lead to the identification of further metal binding glutaredoxins. Such different properties presumably reflect diverse functions in vivo and might therefore explain why there are at least seven glutaredoxins in yeast. PMID:18171082

  12. Homotypic clustering of OsMYB4 binding site motifs in promoters of the rice genome and cellular-level implications on sheath blight disease resistance.

    PubMed

    Pooja, Singh; Sweta, Kumari; Mohanapriya, A; Sudandiradoss, C; Siva, Ramamoorthy; Gothandam, Kodiveri M; Babu, Subramanian

    2015-05-01

    The promoter regions (1 kb upstream sequences) of 45,836 annotated genes of rice were analyzed for the presence of OsMYB4 binding sites using a Perl program algorithm. Based on the homotypic clustering concept, 113 promoters were found to have more than 4 binding site motifs. Among the downstream genes of these promoters, five genes which are known to have a role in disease resistance were selected and the binding capacity of OsMYB4 protein in the promoter regions was analyzed by docking studies. Expression level of these genes was analyzed by RT-PCR in Rhizoctonia solani infected rice seedlings. Upon pathogen challenge, higher expression of aminotransferase, ankyrin and WRKY 12 genes was observed corresponding to higher expression of Osmyb4. Over-expression of Osmyb4 cDNA in rice leaf tissues by agro-infection failed to result in similar over-expression of aminotransferase, ankyrin and WRKY 12 as expected. Although the role of OsMYB4 in sheath blight resistance was found to be definitive based on our initial results, artificial over-expression of this TF was observed to be insufficient in regulating the disease resistance related genes.

  13. A phosphoinositide-binding cluster in cavin1 acts as a molecular sensor for cavin1 degradation

    PubMed Central

    Tillu, Vikas A.; Kovtun, Oleksiy; McMahon, Kerrie-Ann; Collins, Brett M.; Parton, Robert G.

    2015-01-01

    Caveolae are abundant surface organelles implicated in a range of cellular processes. Two classes of proteins work together to generate caveolae: integral membrane proteins termed caveolins and cytoplasmic coat proteins called cavins. Caveolae respond to membrane stress by releasing cavins into the cytosol. A crucial aspect of this model is tight regulation of cytosolic pools of cavin under resting conditions. We now show that a recently identified region of cavin1 that can bind phosphoinositide (PI) lipids is also a major site of ubiquitylation. Ubiquitylation of lysines within this site leads to rapid proteasomal degradation. In cells that lack caveolins and caveolae, cavin1 is cytosolic and rapidly degraded as compared with cells in which cavin1 is associated with caveolae. Membrane stretching causes caveolar disassembly, release of cavin complexes into the cytosol, and increased proteasomal degradation of wild-type cavin1 but not mutant cavin1 lacking the major ubiquitylation site. Release of cavin1 from caveolae thus leads to exposure of key lysine residues in the PI-binding region, acting as a trigger for cavin1 ubiquitylation and down-regulation. This mutually exclusive PI-binding/ubiquitylation mechanism may help maintain low levels of cytosolic cavin1 in resting cells, a prerequisite for cavins acting as signaling modules following release from caveolae. PMID:26269585

  14. Binding of Trivalent Arsenic onto the Tetrahedral Au20 and Au19Pt Clusters: Implications in Adsorption and Sensing.

    PubMed

    Cortés-Arriagada, Diego; Oyarzún, María Paz; Sanhueza, Luis; Toro-Labbé, Alejandro

    2015-07-01

    The interaction of arsenic(III) onto the tetrahedral Au20 cluster was studied computationally to get insights into the interaction of arsenic traces (presented in polluted waters) onto embedded electrodes with gold nanostructures. Pollutant interactions onto the vertex, edge, or inner gold atoms of Au20 were observed to have a covalent character by forming metal-arsenic or metal-oxygen bonding, with adsorption energies ranging from 0.5 to 0.8 eV, even with a stable physisorption; however, in aqueous media, the Au-vertex-pollutant interaction was found to be disadvantageous. The substituent effect of a platinum atom onto the Au20 cluster was evaluated to get insights into the changes in the adsorption and electronic properties of the adsorbent-adsorbate systems due to chemical doping. It was found that the dopant atom increases both the metal-pollutant adsorption energy and stability onto the support in a water media for all interaction modes; adsorption energies were found to be in a range of 0.6 to 1.8 eV. All interactions were determined to be accompanied by electron transfer as well as changes in the local reactivity that determine the amount of transferred charge and a decrease in the HOMO-LUMO energy gap with respect to the isolated substrate.

  15. Binding of Trivalent Arsenic onto the Tetrahedral Au20 and Au19Pt Clusters: Implications in Adsorption and Sensing.

    PubMed

    Cortés-Arriagada, Diego; Oyarzún, María Paz; Sanhueza, Luis; Toro-Labbé, Alejandro

    2015-07-01

    The interaction of arsenic(III) onto the tetrahedral Au20 cluster was studied computationally to get insights into the interaction of arsenic traces (presented in polluted waters) onto embedded electrodes with gold nanostructures. Pollutant interactions onto the vertex, edge, or inner gold atoms of Au20 were observed to have a covalent character by forming metal-arsenic or metal-oxygen bonding, with adsorption energies ranging from 0.5 to 0.8 eV, even with a stable physisorption; however, in aqueous media, the Au-vertex-pollutant interaction was found to be disadvantageous. The substituent effect of a platinum atom onto the Au20 cluster was evaluated to get insights into the changes in the adsorption and electronic properties of the adsorbent-adsorbate systems due to chemical doping. It was found that the dopant atom increases both the metal-pollutant adsorption energy and stability onto the support in a water media for all interaction modes; adsorption energies were found to be in a range of 0.6 to 1.8 eV. All interactions were determined to be accompanied by electron transfer as well as changes in the local reactivity that determine the amount of transferred charge and a decrease in the HOMO-LUMO energy gap with respect to the isolated substrate. PMID:26061641

  16. A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters

    SciTech Connect

    Iftner, Christophe; Simon, Aude; Korchagina, Kseniia; Rapacioli, Mathias; Spiegelman, Fernand

    2014-01-21

    We propose in the present paper a SCC-DFTB/FF (Self-Consistent-Charge Density Functional based Tight Binding/Force-Field) scheme adapted to the investigation of molecules trapped in rare gas environments. With respect to usual FF descriptions, the model involves the interaction of quantum electrons in a molecule with rare gas atoms in an anisotropic scheme. It includes polarization and dispersion contributions and can be used for both neutral and charged species. Parameters for this model are determined for hydrocarbon-argon complexes and the model is validated for small hydrocarbons. With the future aim of studying polycyclic aromatic hydrocarbons in Ar matrices, extensive benchmark calculations are performed on (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters against DFT and CCSD(T) calculations for the smaller sizes, and more generally against other experimental and theoretical data. Results on the structures and energetics (isomer ordering and energy separation, cohesion energy per Ar atom) are presented in detail for n = 1–8, 13, 20, 27, and 30, for both neutrals and cations. We confirm that the clustering of Ar atoms leads to a monotonous decrease of the ionization potential of benzene for n ⩽ 20, in line with previous experimental and FF data.

  17. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    PubMed

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  18. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    SciTech Connect

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  19. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    PubMed Central

    2016-01-01

    Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

  20. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    PubMed Central

    2016-01-01

    Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666

  1. The zinc binuclear cluster activator AlcR is able to bind to single sites but requires multiple repeated sites for synergistic activation of the alcA gene in Aspergillus nidulans.

    PubMed

    Panozzo, C; Capuano, V; Fillinger, S; Felenbok, B

    1997-09-01

    The alcA gene which is part of the recently identified ethanol regulon, is one of the most strongly inducible genes in Aspergillus nidulans. Its transcriptional activation is mediated by the AlcR transactivator which contains a DNA-binding domain belonging to the C6 zinc binuclear cluster family. AlcR differs from the other members of this family by several features, the most striking characteristic being its binding to both symmetric and asymmetric DNA sites with the same apparent affinity. However, AlcR is also able to bind to a single site with high affinity, suggesting that unlike the other C6 proteins, AlcR binds as a monomer. In this report, we show that AlcR targets, to be functional in vivo, have to be organized as inverted or direct repeats. In addition, we show a strong synergistic activation of alcA transcription in which the number and the position of the AlcR-binding sites are crucial. The fact that the AlcR unit for in vitro binding is a single site whereas the in vivo functional unit is a repeat opens the question of the mechanism of the strong alcA transactivation. These results show that AlcR displays both in vitro and in vivo a new range of binding specificity and provides a novel example in the C6 zinc cluster protein family.

  2. A novel polynuclear Cu(I)-sulfur cluster with 1,2-dithiolate-o-carborane ligands as a potential in vitro antitumour agent and its DNA binding properties.

    PubMed

    Han, Zhong; Jiang, Jin; Lu, Jing; Li, Dacheng; Cheng, Shuang; Dou, Jianmin

    2013-04-14

    A novel polynuclear Cu(I)-sulfur cluster, (C54H62B30Cu6N8S6), bearing 1,2-dithiolate-o-carborane and 1,10-phenanthroline ligands was synthesized. The complex displayed rapid, low micromolar in vitro cytotoxicity against a range of epithelial tumour cells and efficient CT-DNA binding. PMID:23426331

  3. A Structural Snapshot of CYP2B4 in Complex with Paroxetine Provides Insights into Ligand Binding and Clusters of Conformational States

    PubMed Central

    Kufareva, Irina; Pascual, Jaime; Zhang, Qinghai; Stout, C. David; Halpert, James R.

    2013-01-01

    An X-ray crystal structure of CYP2B4 in complex with the drug paroxetine [(3S,4R)-3-[(2H-1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine] was solved at 2.14 Å resolution. The structure revealed a conformation intermediate to that of the recently solved complex with amlodipine and that of the more compact complex with 4-(4-chlorophenyl)imidazole in terms of the placement of the F-G cassette. Moreover, comparison of the new structure with 15 previously solved structures of CYP2B4 revealed some new insights into the determinants of active-site size and shape. The 2B4-paroxetine structure is nearly superimposable on a previously solved closed structure in a ligand-free state. Despite the overall conformational similarity among multiple closed structures, the active-site cavity volume of the paroxetine complex is enlarged. Further analysis of the accessible space and binding pocket near the heme reveals a new subchamber that resulted from the movement of secondary structural elements and rearrangements of active-site side chains. Overall, the results from the comparison of all 16 structures of CYP2B4 demonstrate a cluster of protein conformations that were observed in the presence or absence of various ligands. PMID:23633618

  4. De novo design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled-coil with a four-iron four-sulfur cluster binding site in its central core.

    PubMed

    Grzyb, Joanna; Xu, Fei; Weiner, Lev; Reijerse, Eduard J; Lubitz, Wolfgang; Nanda, Vikas; Noy, Dror

    2010-03-01

    Using a 'metal-first' approach, we computationally designed, prepared, and characterized a four-iron four-sulfur (Fe(4)S(4)) cluster protein with a non-natural alpha-helical coiled-coil fold. The novelty of this fold lies in the placement of a Fe(4)S(4) cluster within the hydrophobic core of a four-helix bundle, making it unique among previous iron-sulfur (FeS) protein designs, and different from known natural FeS proteins. The apoprotein, recombinantly expressed and purified from E. coli, readily self-assembles with Fe(4)S(4) clusters in vitro. UV-Vis absorption and CD spectroscopy, elemental analysis, gel filtration, and analytical ultracentrifugation confirm that the protein is folded and assembled as designed, namely, alpha-helical coiled-coil binding a single Fe(4)S(4) cluster. Dithionite-reduced holoprotein samples have characteristic rhombic EPR spectra, typical of low-potential, [Fe(4)S(4)](+) (S=1/2), with g values of g(zy)=(1.970, 1.975), and g(x)=2.053. The temperature, and power dependence of the signal intensity were also characteristic of [Fe(4)S(4)](+) clusters with very efficient spin relaxation, but almost without any interaction between adjacent clusters. The new design is very promising although optimization is required, particularly for preventing aggregation, and adding second shell interactions to stabilize the reduced state. Its main advantage is its extendibility into a multi-FeS cluster protein by simply duplicating and translating the binding site along the coiled-coil axis. This opens new possibilities for designing protein-embedded redox chains that may be used as "wires" for coupling any given set of redox enzymes. PMID:20035711

  5. Monothiol Glutaredoxins Can Bind Linear [Fe3S4]+ and [Fe4S4]2+ Clusters in Addition to [Fe2S2]2+ Clusters: Spectroscopic Characterization and Functional Implications

    PubMed Central

    Zhang, Bo; Bandyopadhyay, Sibali; Shakamuri, Priyanka; Naik, Sunil G.; Huynh, Boi Hanh; Couturier, Jérémy; Rouhier, Nicolas; Johnson, Michael K.

    2013-01-01

    Saccharomyces cerevisiae mitochondrial glutaredoxin 5 (Grx5) is the archetypical member of a ubiquitous class of monothiol glutaredoxins with a strictly conserved CGFS active-site sequence that has been shown to function in biological [Fe2S2]2+ cluster trafficking. In this work, we show that recombinant S. cerevisiae Grx5 purified aerobically after prolonged exposure of the cell-free extract to air or after anaerobic reconstitution in the presence of glutathione, predominantly contains a linear [Fe3S4]+ cluster. The excited state electronic properties and ground state electronic and vibrational properties of the linear [Fe3S4]+ cluster have been characterized using UV-visible absorption/CD/MCD, EPR, Mössbauer and resonance Raman spectroscopies. The results reveal a rhombic S = 5/2 linear [Fe3S4]+ cluster with properties similar to those reported for synthetic linear [Fe3S4]+ clusters and the linear [Fe3S4]+ clusters in purple aconitase. Moreover, the results indicate that the Fe-S cluster content previously reported for many monothiol Grxs has been misinterpreted exclusively in terms of [Fe2S2]2+ clusters, rather than linear [Fe3S4]+ clusters or mixtures of linear [Fe3S4]+ and [Fe2S2]2+ clusters. In the absence of GSH, anaerobic reconstitution of Grx5 yields a dimeric form containing one [Fe4S4]2+ cluster that competent for in vitro activation of apo-aconitase, via intact cluster transfer. The ligation of the linear [Fe3S4]+ and [Fe4S4]2+ clusters in Grx5 has been assessed by spectroscopic, mutational and analytical studies. Potential roles for monothiol Grx5 in scavenging and recycling linear [Fe3S4]+ clusters released during protein unfolding under oxidative stress conditions and in maturation of [Fe4S4]2+ cluster-containing proteins are discussed in light of these results. PMID:24032439

  6. Structure-function relationship in the globular type III antifreeze protein: identification of a cluster of surface residues required for binding to ice.

    PubMed Central

    Chao, H.; Sönnichsen, F. D.; DeLuca, C. I.; Sykes, B. D.; Davies, P. L.

    1994-01-01

    Antifreeze proteins (AFPs) depress the freezing point of aqueous solutions by binding to and inhibiting the growth of ice. Whereas the ice-binding surface of some fish AFPs is suggested by their linear, repetitive, hydrogen bonding motifs, the 66-amino-acid-long Type III AFP has a compact, globular fold without any obvious periodicity. In the structure, 9 beta-strands are paired to form 2 triple-stranded antiparallel sheets and 1 double-stranded antiparallel sheet, with the 2 triple sheets arranged as an orthogonal beta-sandwich (Sönnichsen FD, Sykes BD, Chao H, Davies PL, 1993, Science 259:1154-1157). Based on its structure and an alignment of Type III AFP isoform sequences, a cluster of conserved, polar, surface-accessible amino acids (N14, T18, Q44, and N46) was noted on and around the triple-stranded sheet near the C-terminus. At 3 of these sites, mutations that switched amide and hydroxyl groups caused a large decrease in antifreeze activity, but amide to carboxylic acid changes produced AFPs that were fully active at pH 3 and pH 6. This is consistent with the observation that Type III AFP is optimally active from pH 2 to pH 11. At a concentration of 1 mg/mL, Q44T, N14S, and T18N had 50%, 25%, and 10% of the activity of wild-type antifreeze, respectively. The effects of the mutations were cumulative, such that the double mutant N14S/Q44T had 10% of the wild-type activity and the triple mutant N14S/T18N/Q44T had no activity. All mutants with reduced activity were shown to be correctly folded by NMR spectroscopy. Moreover, a complete characterization of the triple mutant by 2-dimensional NMR spectroscopy indicated that the individual and combined mutations did not significantly alter the structure of these proteins. These results suggest that the C-terminal beta-sheet of Type III AFP is primarily responsible for antifreeze activity, and they identify N14, T18, and Q44 as key residues for the AFP-ice interaction. PMID:7849594

  7. Identification of okadaic acid binding protein 2 in reconstituted sponge cell clusters from Halichondria okadai and its contribution to the detoxification of okadaic acid.

    PubMed

    Konoki, Keiichi; Okada, Kayo; Kohama, Mami; Matsuura, Hiroki; Saito, Kaori; Cho, Yuko; Nishitani, Goh; Miyamoto, Tomofumi; Fukuzawa, Seketsu; Tachibana, Kazuo; Yotsu-Yamashita, Mari

    2015-12-15

    Okadaic acid (OA) and OA binding protein 2 (OABP2) were previously isolated from the marine sponge Halichondria okadai. Because the amino acid sequence of OABP2 is completely different from that of protein phosphatase 2A, a well-known target of OA, we have been investigating the production and function of OABP2. In the present study, we hypothesized that OABP2 plays a role in the detoxification of OA in H. okadai and that the OA concentrations are in proportional to the OABP2 concentrations in the sponge specimens. Based on the OA concentrations and the OABP2 concentrations in the sponge specimens collected in various places and in different seasons, however, we could not determine a positive correlation between OA and OABP2. We then attempted to determine distribution of OA and OABP2 in the sponge specimen. When the mixture of dissociated sponge cells and symbiotic species were separated with various pore-sized nylon meshes, most of the OA and OABP2 was detected from the same 0-10 μm fraction. Next, when sponge cell clusters were prepared from a mixture of dissociated sponge cells and symbiotic species in the presence of penicillin and streptomycin, we identified the 18S rDNA of H. okadai and the gene of OABP2 in the analysis of genomic DNA but could not detect OA by LC-MS/MS. We thus concluded that the sponge cells express OABP2, and that OA was not apparently present in the sponge cells but could be colocalized with OABP2 in the sponge cells at a concentration less than the limit of detection.

  8. The Amyloid Precursor Protein of Alzheimer's Disease Clusters at the Organelle/Microtubule Interface on Organelles that Bind Microtubules in an ATP Dependent Manner.

    PubMed

    Stevenson, James W; Conaty, Eliza A; Walsh, Rylie B; Poidomani, Paul J; Samoriski, Colin M; Scollins, Brianne J; DeGiorgis, Joseph A

    2016-01-01

    The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer's disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer's protein tau has a microtubule-based function.

  9. Six S100 genes are clustered on human chromosome 1q21: Identification of two genes coding for the two previously unreported calcium-binding proteins S100D and S100E

    SciTech Connect

    Engelkamp, D.; Schaefer, B.W.; Heizmann, C.W. ); Mattei, M.G. ); Erne, P. )

    1993-07-15

    The human genome contains large regions that are highly structured. Sequence-related members of multigene families are often found in a clustered organization. Here the authors describe a previously unrecognized gene cluster composed of genes coding for calcium-binding proteins of the S100 family. The linkage of six S100 genes was established by pulsed-field gel electrophoresis, and a contiguous DNA sequence of 15 kilobases containing the full coding region of four different S100 genes was characterized. This is the tightest mammalian gene cluster discovered so far to the authors' knowledge. Two additional S100 genes are located within the cluster, both of which exhibit unique structural features when compared with other S100 genes. The product of S100E is cysteine-rich, whereas that of S100D contains a long hydrophobic N-terminal tail. The gene cluster was assigned to chromosome 1q21, one of the bands showing rearrangements in neoplasms at high frequency. The deregulated expression of some S100 genes in the cluster during tumor progression suggests that chromosomal abnormalities may influence the expression of S100 genes in late stages of cancer, particularly in association with the formation of metastases. 43 refs., 3 figs., 1 tab.

  10. A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced From Studies With Subunit B of Heterodisulfide Reductase From Methanothermobacter Marburgensis

    SciTech Connect

    Hamann, N.; Mander, G.J.; Shokes, J.E.; Scott, R.A.; Bennati, M.; Hedderich, R.

    2009-06-01

    Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]{sup 3+} cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX{sub 31-39}CCX{sub 35-36}CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusual [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (g{sub zyx} = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. {sup 57}Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with {sup 57}Fe hyperfine couplings very similar to that of CoM-HDR. CoM-{sup 33}SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S{sub 3}(O/N){sub 1} geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn

  11. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution.

    PubMed

    Howard, E I; Guillot, B; Blakeley, M P; Haertlein, M; Moulin, M; Mitschler, A; Cousido-Siah, A; Fadel, F; Valsecchi, W M; Tomizaki, Takashi; Petrova, T; Claudot, J; Podjarny, A

    2016-03-01

    Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface. PMID:27006775

  12. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution.

    PubMed

    Howard, E I; Guillot, B; Blakeley, M P; Haertlein, M; Moulin, M; Mitschler, A; Cousido-Siah, A; Fadel, F; Valsecchi, W M; Tomizaki, Takashi; Petrova, T; Claudot, J; Podjarny, A

    2016-03-01

    Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

  13. Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis.

    PubMed

    Hirabayashi, Kei; Yuda, Eiki; Tanaka, Naoyuki; Katayama, Sumie; Iwasaki, Kenji; Matsumoto, Takashi; Kurisu, Genji; Outten, F Wayne; Fukuyama, Keiichi; Takahashi, Yasuhiro; Wada, Kei

    2015-12-11

    ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.

  14. High Mannose-binding Lectin with Preference for the Cluster of α1–2-Mannose from the Green Alga Boodlea coacta Is a Potent Entry Inhibitor of HIV-1 and Influenza Viruses*

    PubMed Central

    Sato, Yuichiro; Hirayama, Makoto; Morimoto, Kinjiro; Yamamoto, Naoki; Okuyama, Satomi; Hori, Kanji

    2011-01-01

    The complete amino acid sequence of a lectin from the green alga Boodlea coacta (BCA), which was determined by a combination of Edman degradation of its peptide fragments and cDNA cloning, revealed the following: 1) B. coacta used a noncanonical genetic code (where TAA and TAG codons encode glutamine rather than a translation termination), and 2) BCA consisted of three internal tandem-repeated domains, each of which contains the sequence motif similar to the carbohydrate-binding site of Galanthus nivalis agglutinin-related lectins. Carbohydrate binding specificity of BCA was examined by a centrifugal ultrafiltration-HPLC assay using 42 pyridylaminated oligosaccharides. BCA bound to high mannose-type N-glycans but not to the complex-type, hybrid-type core structure of N-glycans or oligosaccharides from glycolipids. This lectin had exclusive specificity for α1–2-linked mannose at the nonreducing terminus. The binding activity was enhanced as the number of terminal α1–2-linked mannose substitutions increased. Mannobiose, mannotriose, and mannopentaose were incapable of binding to BCA. Thus, BCA preferentially recognized the nonreducing terminal α1–2-mannose cluster as a primary target. As predicted from carbohydrate-binding propensity, this lectin inhibited the HIV-1 entry into the host cells at a half-maximal effective concentration of 8.2 nm. A high association constant (3.71 × 108 m−1) of BCA with the HIV envelope glycoprotein gp120 was demonstrated by surface plasmon resonance analysis. Moreover, BCA showed the potent anti-influenza activity by directly binding to viral envelope hemagglutinin against various strains, including a clinical isolate of pandemic H1N1-2009 virus, revealing its potential as an antiviral reagent. PMID:21460211

  15. Position of the ATP-binding site of the Fe-protein relative to the iron-sulfur clusters 4Fe-4S and the iron-molybdenum-containing cofactor

    SciTech Connect

    Kondrat'eva, T.A.; Gvozdev, R.I.; Mitsova, I.Z.

    1986-06-10

    Nitrogenase was affinity labeled with epsilon-ATP at the ATP-binding sites and separated into protein components by ion exchange chromatography. In spectrofluorometric titration of the labeled Fe-protein with the native MoFe-protein from the wild strain of Azotobacter and the MoFe-protein not containing iron-sulfur clusters 4Fe-4S, a 4-6-fold quenching of the fluorescence of immobilized epsilon-ATP was observed. When the labeled Fe-protein was titrated with MoFe-protein from the Azotobacter mutant UW-45, on the contrary, there was a four-fold increase in the fluorescence of immobilized epsilon-ATP. Since the MoFe-protein of the Azotobacter mutant UW-45 differs from the MoFe-protein from the wild strain of Azotobacter only by the absence of an iron-molybdenum-containing cofactor (Fe-Mo-cofactor), it is suggested that the ATP-binding site of the Fe-protein is situated next to the FeMo-cofactor and at a distance from the iron-sulfur clusters 4Fe-4S when a complex is formed with the MoFe-protein. The formation of a complex is accompanied by a change in the conformation of the Fe-protein.

  16. UME6, a negative regulator of meiosis in Saccharomyces cerevisiae, contains a C-terminal Zn2Cys6 binuclear cluster that binds the URS1 DNA sequence in a zinc-dependent manner.

    PubMed Central

    Anderson, S. F.; Steber, C. M.; Esposito, R. E.; Coleman, J. E.

    1995-01-01

    UME6 is a protein of 836 amino acids from Saccharomyces cerevisiae that acts as a repressor and activator of several early meiotic genes. UME6 contains, near the C-terminus, the amino acid sequence-771C-X2-C-X6-C-X6-C-X2-C-X6-C-, in which the spacings of the six Cys residues are identical to those found in 39 N-terminal Cys-rich DNA binding subdomains of fungal transcription factors. This sequence has been shown in GAL4 and other proteins to form a zinc binuclear cluster. In spite of the different location, the C-rich sequence, cloned and over-produced within the last 111 amino acid residues of UME6, UME6(111), forms a binuclear cluster and exhibits a Zn-dependent binding to the URS1 DNA sequence. The latter, TAGCCGCCGA, is required for the repression or activation of meiosis-specific genes by UME6. UME6(111) contains 1.8 +/- 0.4 mol Zn/mol protein and the Zn can be exchanged for Cd to yield a protein containing 1.9 +/- 0.1 mol Cd/mol protein. At 5 degrees C, 113Cd2UME6(111) shows two 113Cd NMR signals, with chemical shifts of 699 and 689 ppm, similar to those observed for 113Cd2GAL4(149). The magnitude of these chemical shifts suggests that each 113Cd nucleus is coordinated to four -S- ligands, compatible with a 113Cd2 cluster structure in which two thiolates from bridging ligands. The entire UME6 gene has been cloned and overexpressed and binds more tightly to the URS1 sequence than the zinc binuclear cluster domain alone. DNase I footprints of UME6 on URS1-containing DNA show that the protein protects the phosphodiesters of the 5'-CCGCCG-3' region within the URS1 sequence. PMID:8528081

  17. Identification of 70 calcium-sensing receptor mutations in hyper- and hypo-calcaemic patients: evidence for clustering of extracellular domain mutations at calcium-binding sites.

    PubMed

    Hannan, Fadil M; Nesbit, M Andrew; Zhang, Chen; Cranston, Treena; Curley, Alan J; Harding, Brian; Fratter, Carl; Rust, Nigel; Christie, Paul T; Turner, Jeremy J O; Lemos, Manuel C; Bowl, Michael R; Bouillon, Roger; Brain, Caroline; Bridges, Nicola; Burren, Christine; Connell, John M; Jung, Heike; Marks, Eileen; McCredie, David; Mughal, Zulf; Rodda, Christine; Tollefsen, Sherida; Brown, Edward M; Yang, Jenny J; Thakker, Rajesh V

    2012-06-15

    The calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that has an extracellular bilobed venus flytrap domain (VFTD) predicted to contain five calcium (Ca(2+))-binding sites. To elucidate the structure-function relationships of the VFTD, we investigated 294 unrelated probands with familial hypocalciuric hypercalcaemia (FHH), neonatal severe primary hyperparathyroidism (NSHPT) or autosomal dominant hypocalcaemic hypercalciuria (ADHH) for CaSR mutations and performed in vitro functional expression studies and three-dimensional modelling of mutations involving the VFTD. A total of 70 different CaSR mutations were identified: 35 in FHH, 10 in NSHPT and 25 in ADHH patients. Furthermore, a CaSR variant (Glu250Lys) was identified in FHH and ADHH probands and demonstrated to represent a functionally neutral polymorphism. NSHPT was associated with a large proportion of truncating CaSR mutations that occurred in the homozygous or compound heterozygous state. Thirty-four VFTD missense mutations were identified, and 18 mutations were located within 10 Å of one or more of the predicted Ca(2+)-binding sites, particularly at the VFTD cleft, which is the principal site of Ca(2+) binding. Mutations of residues 173 and 221, which are located at the entrance to the VFTD cleft binding site, were associated with both receptor activation (Leu173Phe and Pro221Leu) and inactivation (Leu173Pro and Pro221Gln), thereby highlighting the importance of these residues for entry and binding of Ca(2+) by the CaSR. Thus, these studies of disease-associated CaSR mutations have further elucidated the role of the VFTD cleft region in Ca(2+) binding and the function of the CaSR. PMID:22422767

  18. Identification of 70 calcium-sensing receptor mutations in hyper- and hypo-calcaemic patients: evidence for clustering of extracellular domain mutations at calcium-binding sites.

    PubMed

    Hannan, Fadil M; Nesbit, M Andrew; Zhang, Chen; Cranston, Treena; Curley, Alan J; Harding, Brian; Fratter, Carl; Rust, Nigel; Christie, Paul T; Turner, Jeremy J O; Lemos, Manuel C; Bowl, Michael R; Bouillon, Roger; Brain, Caroline; Bridges, Nicola; Burren, Christine; Connell, John M; Jung, Heike; Marks, Eileen; McCredie, David; Mughal, Zulf; Rodda, Christine; Tollefsen, Sherida; Brown, Edward M; Yang, Jenny J; Thakker, Rajesh V

    2012-06-15

    The calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that has an extracellular bilobed venus flytrap domain (VFTD) predicted to contain five calcium (Ca(2+))-binding sites. To elucidate the structure-function relationships of the VFTD, we investigated 294 unrelated probands with familial hypocalciuric hypercalcaemia (FHH), neonatal severe primary hyperparathyroidism (NSHPT) or autosomal dominant hypocalcaemic hypercalciuria (ADHH) for CaSR mutations and performed in vitro functional expression studies and three-dimensional modelling of mutations involving the VFTD. A total of 70 different CaSR mutations were identified: 35 in FHH, 10 in NSHPT and 25 in ADHH patients. Furthermore, a CaSR variant (Glu250Lys) was identified in FHH and ADHH probands and demonstrated to represent a functionally neutral polymorphism. NSHPT was associated with a large proportion of truncating CaSR mutations that occurred in the homozygous or compound heterozygous state. Thirty-four VFTD missense mutations were identified, and 18 mutations were located within 10 Å of one or more of the predicted Ca(2+)-binding sites, particularly at the VFTD cleft, which is the principal site of Ca(2+) binding. Mutations of residues 173 and 221, which are located at the entrance to the VFTD cleft binding site, were associated with both receptor activation (Leu173Phe and Pro221Leu) and inactivation (Leu173Pro and Pro221Gln), thereby highlighting the importance of these residues for entry and binding of Ca(2+) by the CaSR. Thus, these studies of disease-associated CaSR mutations have further elucidated the role of the VFTD cleft region in Ca(2+) binding and the function of the CaSR.

  19. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

    PubMed Central

    Howard, E. I.; Guillot, B.; Blakeley, M. P.; Haertlein, M.; Moulin, M.; Mitschler, A.; Cousido-Siah, A.; Fadel, F.; Valsecchi, W. M.; Tomizaki, Takashi; Petrova, T.; Claudot, J.; Podjarny, A.

    2016-01-01

    Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader’s quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface. PMID:27006775

  20. (S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro−Metal Coordination Interactions in the Binuclear Manganese Cluster

    SciTech Connect

    Zakharian, T.; Di Costanzo, L; Christianson, D

    2008-01-01

    The binding affinity of (S)-2-amino-6-nitrohexanoic acid to human arginase I was studied using surface plasmon resonance (K{sub d} = 60 {mu}M), and the X-ray crystal structure of the enzyme-inhibitor complex was determined at 1.6 {angstrom} resolution to reveal multiple nitro-metal coordination interactions.

  1. Transcriptional activation is a conserved feature of the early embryonic factor Zelda that requires a cluster of four zinc fingers for DNA binding and a low-complexity activation domain.

    PubMed

    Hamm, Danielle C; Bondra, Eliana R; Harrison, Melissa M

    2015-02-01

    Delayed transcriptional activation of the zygotic genome is a nearly universal phenomenon in metazoans. Immediately following fertilization, development is controlled by maternally deposited products, and it is not until later stages that widespread activation of the zygotic genome occurs. Although the mechanisms driving this genome activation are currently unknown, the transcriptional activator Zelda (ZLD) has been shown to be instrumental in driving this process in Drosophila melanogaster. Here we define functional domains of ZLD required for both DNA binding and transcriptional activation. We show that the C-terminal cluster of four zinc fingers mediates binding to TAGteam DNA elements in the promoters of early expressed genes. All four zinc fingers are required for this activity, and splice isoforms lacking three of the four zinc fingers fail to activate transcription. These truncated splice isoforms dominantly suppress activation by the full-length, embryonically expressed isoform. We map the transcriptional activation domain of ZLD to a central region characterized by low complexity. Despite relatively little sequence conservation within this domain, ZLD orthologs from Drosophila virilis, Anopheles gambiae, and Nasonia vitripennis activate transcription in D. melanogaster cells. Transcriptional activation by these ZLD orthologs suggests that ZLD functions through conserved interactions with a protein cofactor(s). We have identified distinct DNA-binding and activation domains within the critical transcription factor ZLD that controls the initial activation of the zygotic genome.

  2. Diffusion Monte Carlo studies of MB-pol (H2O)2-6 and (D2O)2-6 clusters: Structures and binding energies

    NASA Astrophysics Data System (ADS)

    Mallory, Joel D.; Mandelshtam, Vladimir A.

    2016-08-01

    We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.

  3. Functional characterization of the nucleotide binding domain of the Cryptosporidium parvum CpABC4 transporter: an iron-sulfur cluster transporter homolog.

    PubMed

    Benitez, Alvaro J; Arrowood, Michael J; Mead, Jan R

    2009-06-01

    In a previous study, we showed that the Cryptosporidium parvum ATP half-transporter CpABC4 (cgd1_1350) transcript was up-regulated in response to drug treatment with paromomycin and cyclosporine A in an in vitro infection model. CpABC4 may be directly or indirectly involved in the metabolic interactions between host and parasite in response to drug treatment and/or be involved in the intrinsic resistance to chemotherapy. In order to characterize the catalytic site of this transporter, an extended region of the nucleotide-binding domain of CpABC4 (H6-1350NBD) was expressed and purified as an N-terminal hexahistidine-tagged protein in E. coli. The presence of a single tryptophan residue enabled the intrinsic fluorescence to be monitored in response to binding of different compounds. A dose-dependent quenching of the domain's intrinsic fluorescence was observed with its natural substrate, ATP and the fluorescent analogue TNP-ATP. A similar effect was observed with progesterone as well as the flavonoids quercetin and silibinin, previously shown to inhibit parasite development in a cell-based assay. The purified domain also exhibited ATPase activity in the nanomolar range, which further confirmed correct folding and activity of the recombinant domain. The H6-1350NBD serves as a tool to test and design stereospecific inhibitors of the catalytic site, as well as other compounds that bind elsewhere in the domain that may indirectly interact with the catalytic site of the NBD of the CpABC4 transporter.

  4. Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.

    PubMed

    Chatterjee, Debashree; Sanchez, Ana M; Goldgur, Yehuda; Shuman, Stewart; Schwer, Beate

    2016-07-01

    Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.

  5. Experimental measurement of the van der Waals binding energy of X-O{sub 2} clusters (X=Xe,CH{sub 3}I,C{sub 3}H{sub 6},C{sub 6}H{sub 12})

    SciTech Connect

    Vidma, Konstantin V.; Bogdanchikov, Georgii A.; Baklanov, Alexey V.; Chestakov, Dmitri A.; Parker, David H.

    2010-11-21

    Van der Waals binding energies for the X-O{sub 2} complexes (X=Xe,CH{sub 3}I,C{sub 3}H{sub 6},C{sub 6}H{sub 12}) are determined by analysis of experimental velocity map imaging data for O({sup 3}P{sub 2}) atoms arising from UV-photodissociation of the complex [A. V. Baklanov et al., J. Chem. Phys. 126, 124316 (2007)]. Several dissociation pathways have been observed, we focus on the channel corresponding to prompt dissociation of X-O{sub 2} into X+2O({sup 3}P) fragments, which is present for complexes of O{sub 2} with all partners X. Our method is based on analysis of the kinetic energy of all three photofragments, where the O atom kinetic energy was directly measured in the experiment and the kinetic energy of the X partner was calculated using momentum conservation, along with the measured angular anisotropy for O atom recoil. We exploit the fact that the clusters are all T-shaped or nearly T-shaped, which we also confirm by ab initio calculations, along with knowledge of the transition dipole governing radiative absorption by the complex. The effect of partitioning the kinetic energy between translation along the X-O{sub 2} and O-O coordinates on the angular anisotropy of the O atom recoil direction is discussed. Van der Waals binding energies of 110{+-}20 cm{sup -1}, 280{+-}20 cm{sup -1}, 135{+-}30 cm{sup -1}, and 585{+-}20 cm{sup -1} are determined for Xe-O{sub 2}, CH{sub 3}I-O{sub 2}, C{sub 3}H{sub 6}-O{sub 2}, and C{sub 6}H{sub 12}-O{sub 2} clusters, respectively.

  6. Symbolic clustering

    SciTech Connect

    Reinke, R.E.

    1991-01-01

    Clustering is the problem of finding a good organization for data. Because there are many kinds of clustering problems, and because there are many possible clusterings for any data set, clustering programs use knowledge and assumptions about individual problems to make clustering tractable. Cluster-analysis techniques allow knowledge to be expressed in the choice of a pairwise distance measure and in the choice of clustering algorithm. Conceptual clustering adds knowledge and preferences about cluster descriptions. In this study the author describes symbolic clustering, which adds representation choice to the set of ways a data analyst can use problem-specific knowledge. He develops an informal model for symbolic clustering, and uses it to suggest where and how knowledge can be expressed in clustering. A language for creating symbolic clusters, based on the model, was developed and tested on three real clustering problems. The study concludes with a discussion of the implications of the model and the results for clustering in general.

  7. Critical interpretation of CH– and OH– stretching regions for infrared spectra of methanol clusters (CH{sub 3}OH){sub n} (n = 2–5) using self-consistent-charge density functional tight-binding molecular dynamics simulations

    SciTech Connect

    Nishimura, Yoshifumi; Lee, Yuan-Pern; Irle, Stephan; Witek, Henryk A.

    2014-09-07

    Vibrational infrared (IR) spectra of gas-phase O–H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C–H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C–H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν{sub 3}, ν{sub 9}, and ν{sub 2} C–H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.

  8. Conformation-Specific Infrared and Ultraviolet Spectroscopy of DIBENZO-15-CROWN-5-(H2O)1-CLUSTER: Reshaping a Binding Pocket

    NASA Astrophysics Data System (ADS)

    Buchanan, Evan G.; Rodrigo, Chirantha P.; Gutberlet, Anna K.; Zwier, Timothy S.

    2010-06-01

    Crown ethers are oxygen containing macrocycles noted for their ability to preferentially bind substrates such as ions and water. Despite the high symmetry inherent to the chemical structure, crown ethers are remarkably flexible, adapting their conformation to the substrate to which they are bound. Here, we present the conformational preferences of the singly hydrated dibenzo-15-crown-5 ether (DB15C) complex formed and cooled in a supersonic jet. The resonance enhanced two-photon ionization, UV-UV Hole-burning, and resonant ion-dip infrared spectra lead to the identification of a single DB15C-(H2O)1 conformer with the water doubly hydrogen bonded to the crown. Single vibronic level dispersed fluorescence identified both electronic origins and the coupling between the two chromophores. Finally, infrared population transfer spectroscopy is used to study the monomer conformer populations formed by infrared photodissocation of the complex via the water OH stretch transitions, providing unique insight to the energy flow between water and crown.

  9. The Lon protease from the haloalkaliphilic archaeon Natrialba magadii is transcriptionally linked to a cluster of putative membrane proteases and displays DNA-binding activity.

    PubMed

    Sastre, Diego E; Paggi, Roberto A; De Castro, Rosana E

    2011-05-20

    The ATP-dependent Lon protease is universally distributed in bacteria, eukaryotic organelles and archaea. In comparison with bacterial and eukaryal Lon proteases, the biology of the archaeal Lon has been studied to a limited extent. In this study, the gene encoding the Lon protease of the alkaliphilic haloarchaeon Natrialba magadii (Nmlon) was cloned and sequenced, and the genetic organization of Nmlon was examined at the transcriptional level. Nmlon encodes a 84 kDa polypeptide with a pI of 4.42 which contains the ATPase, protease and membrane targeting domains of the archaeal-type LonB proteases. Nmlon is part of an operon that encodes membrane proteases and it is transcribed as a polycistronic mRNA in N. magadii cells at different growth stages. Accordingly, NmLon was detected in cell membranes of N. magadii throughout growth by Western blot analysis using specific anti-NmLon antibodies. Interestingly, in electrophoretic mobility shift assays, purified NmLon bound double stranded as well as single stranded DNA in the presence of elevated salt concentrations. This finding shows that DNA-binding is conserved in the LonA and LonB subfamilies and suggests that Lon-DNA interaction may be relevant for its function in haloarchaea.

  10. Accessory Interaction Motifs in the Atg19 Cargo Receptor Enable Strong Binding to the Clustered Ubiquitin-related Atg8 Protein*

    PubMed Central

    Abert, Christine; Kontaxis, Georg

    2016-01-01

    Selective autophagy contributes to cellular homeostasis by delivering harmful material into the lysosomal system for degradation via vesicular intermediates referred to as autophagosomes. The cytoplasm-to-vacuole targeting pathway is a variant of selective autophagy in Saccharomyces cerevisiae during which hydrolases such as prApe1 are transported into the vacuole. In general, selectivity is achieved by autophagic cargo receptors that link the cargo to autophagosomal membranes because of their ability to simultaneously interact with the cargo and Atg8 proteins that coat the membrane. The Atg19 receptor contains multiple Atg8 interaction sites in its C terminus in addition to a canonical Atg8-interacting LC3-interacting region (LIR, with LC3 being a homolog of Atg8) motif, but their mode of interaction with Atg8 is unclear. Here we show, using a combination of NMR, microscopy-based interaction assays, and prApe1 processing experiments, that two additional sites interact with Atg8 in a LIR-like and thus mutually exclusive manner. We term these motifs accessory LIR motifs because their affinities are lower than that of the canonical LIR motif. Thus, one Atg19 molecule has the ability to interact with multiple Atg8 proteins simultaneously, resulting in a high-avidity interaction that may confer specific binding to the Atg8-coated autophagosomal membrane on which Atg8 is concentrated. PMID:27402840

  11. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  12. Water's Role in Reshaping a Macrocycle's Binding Pocket: Conformation-Specific Infrared and Ultraviolet Spectroscopy of BENZO-15-CROWN-5-(H_{2}O)_{n}-CLUSTERS (n = 1, 2)

    NASA Astrophysics Data System (ADS)

    Shubert, V. Alvin; Müller, Christian W.; James, William H. James, III; Zwier, Timothy S.

    2009-06-01

    Crown ethers are well-studied examples of flexible macrocycles with a high binding selectivity for substrates, especially cations. We investigated the conformational preferences of the singly and doubly complexed water clusters of the crown ethers benzo-15-crown-5 (B15C) and its amino-derivative 4'-aminobenzo-15-crown-5 (ABC) cooled in a supersonic jet expansion. The fluorescence excitation, resonance enhanced two-photon ionization (R2PI), UV-UV holeburning (UVHB), fluorescence-dip infrared (FDIR), resonant ion-dip infrared (RIDIR) and novel IR-IR-UV holeburning^{1} spectra allowed for the identification of two B15C-(H_{2}O)_{1} conformers and one ABC-(H_{2}O)_{1} conformer. These conformers are characterized by an all-planar arrangement of the atoms directly bound to the benzene ring in which the crown ether macrocycle opens up to a symmetric structure and accomodates a doubly and triply H-bonded H_{2}O molecule in two distinct ways, respectively. Two B15C-(H_{2}O)_{2} conformers and one ABC-(H_{2}O)_{2} conformer were identified. One of the B15C-(H_{2}O)_{2} conformers contains a macrocycle configuration identical to that found in the monohydrated clusters with an H-bonding topology in which the H_{2}O molecules occupy both available sites simultaneously. The second B15C-(H_{2}O)_{2} conformer is assigned to an H-bond pattern in which the two H_{2}O molecules are concatenated to form an H-bonded bridge involving only three of the four available O-H-bonds (see figure). (1) V. A. Shubert and T. S. Zwier, J. Phys. Chem. A, 2007, 111, 13283.

  13. Rhodobacter sphaeroides rdxA, a homolog of Rhizobium meliloti fixG, encodes a membrane protein which may bind cytoplasmic [4Fe-4S] clusters.

    PubMed Central

    Neidle, E L; Kaplan, S

    1992-01-01

    In the photosynthetic bacterium Rhodobacter sphaeroides, a chromosomal gene, rdxA, which encodes a 52-kDa protein, was found to be homologous to fixG, the first gene of a Rhizobium meliloti nitrogen fixation operon on the pSym plasmid (D. Kahn, M. David, O. Domergue, M.-L. Daveran, J. Ghai, P. R. Hirsch, and J. Batut, J. Bacteriol. 171:929-939, 1989). The deduced amino acid sequences of RdxA and FixG are 53% identical and 73% similar; sequence analyses suggested that each has five transmembrane helices and a central region resembling bacterial-type ferredoxins. Translational fusion proteins with an alkaline phosphatase reporter group were expressed in both R. sphaeroides and Escherichia coli and were used to assess the membrane topology of RdxA. Its ferredoxinlike sequence, which may bind two [4Fe-4S] centers, was found to be cytoplasmically located. Genetic disruptions showed that rdxA is not essential for nitrogen fixation in R. sphaeroides. Immediately downstream of rdxA, an open reading frame (ORFT2) that encoded a 48-kDa protein was found. This DNA sequence was not homologous to any region of the R. meliloti fixG operon. The N-terminal sequence of the ORFT2 gene product resembled amino acid sequences found in members of the GntR family of regulatory proteins (D. J. Haydon and J. R. Guest, FEMS Microbiol. Lett. 79:291-296, 1991). The rdxA gene was localized to the smaller of two R. sphaeroides chromosomes, upstream of and divergently transcribed from hemT, which encodes one of two 5-aminolevulinate synthase isozymes. The rdxA and hemT genes may share a transcriptional regulatory region. Southern hybridization analysis demonstrated the presence of an rdxA homolog on the R. sphaeroides large chromosome. The functions of this homolog, like those of rdxA, remain to be determined, but roles in oxidation-reduction processes are likely. Images PMID:1400197

  14. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... be related to the body's sudden release of histamine (chemical in the body released during an allergic ...

  15. Meaningful Clusters

    SciTech Connect

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  16. Abell Clusters

    NASA Astrophysics Data System (ADS)

    Katgert, P.; Murdin, P.

    2000-11-01

    Abell clusters are the most conspicuous groupings of galaxies identified by George Abell on the plates of the first photographic survey made with the SCHMIDT TELESCOPE at Mount Palomar in the 1950s. Sometimes, the term Abell clusters is used as a synonym of nearby, optically selected galaxy clusters....

  17. Carbamate-linked lactose: design of clusters and evidence for selectivity to block binding of human lectins to (neo)glycoproteins with increasing degree of branching and to tumor cells.

    PubMed

    André, Sabine; Specker, Daniel; Bovin, Nicolai V; Lensch, Martin; Kaltner, Herbert; Gabius, Hans-Joachim; Wittmann, Valentin

    2009-09-01

    Various pathogenic processes are driven by protein(lectin)-glycan interactions, especially involving beta-galactosides at branch ends of cellular glycans. These emerging insights fuel the interest to design potent inhibitors to block lectins. As a step toward this aim, we prepared a series of ten mono- to tetravalent glycocompounds with lactose as a common headgroup. To obtain activated carbonate for ensuing carbamate formation, conditions for the facile synthesis of pure isomers from anomerically unprotected lactose were identified. To probe for the often encountered intrafamily diversity of human lectins, we selected representative members from the three subgroups of adhesion/growth-regulatory galectins as receptors. Diversity of the glycan display was accounted for by using four (neo)glycoproteins with different degrees of glycan branching as matrices in solid-phase assays. Cases of increased inhibitory potency of lactose clusters compared to free lactose were revealed. Extent of relative inhibition was not directly associated with valency in the glycocompound and depended on the lectin type. Of note for screening protocols, efficacy of blocking appeared to decrease with increased degree of glycan branching in matrix glycoproteins. Binding to tumor cells was impaired with selectivity for galectins-3 and -4. Representative compounds did not impair growth of carcinoma cells up to a concentration of 5 mM of lactose moieties (valence-corrected value) per assay. The reported bioactivity and the delineation of its modulation by structural parameters of lectins and glycans set instructive examples for the further design of selective inhibitors and assay procedures. PMID:19715307

  18. An accurate and efficient computational protocol for obtaining the complete basis set limits of the binding energies of water clusters at the MP2 and CCSD(T) levels of theory: Application to (H2O)m, m = 2-6, 8, 11, 16, and 17.

    PubMed

    Miliordos, Evangelos; Xantheas, Sotiris S

    2015-06-21

    We report MP2 and Coupled Cluster Singles, Doubles, and perturbative Triples [CCSD(T)] binding energies with basis sets up to pentuple zeta quality for the (H2O)m=2-6,8 water clusters. Our best CCSD(T)/Complete Basis Set (CBS) estimates are -4.99 ± 0.04 kcal/mol (dimer), -15.8 ± 0.1 kcal/mol (trimer), -27.4 ± 0.1 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer), and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (De) and basis set superposition error-corrected (De (CP)) binding energies recovered with respect to the CBS limit falls into a narrow range on either sides of the CBS limit for each basis set for all clusters. In addition, this range decreases upon increasing the basis set. Relatively accurate estimates (within <0.5%) of the CBS limits can be obtained when using the "23, 13" (for the AVDZ set) or the "12, 12" (for the AVTZ, AVQZ, and AV5Z sets) mixing ratio between De and De (CP). These mixing rations are determined via a least-mean-squares approach from a dataset that encompasses clusters of various sizes. Based on those findings, we propose an accurate and efficient computational protocol that can be presently used to estimate accurate binding energies of water clusters containing up to 30 molecules (for CCSD(T)) and up to 100 molecules (for MP2).

  19. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

  20. Thermodynamic prediction of glass formation tendency, cluster-in-jellium model for metallic glasses, ab initio tight-binding calculations, and new density functional theory development for systems with strong electron correlation

    SciTech Connect

    Yao, Yongxin

    2009-01-01

    Solidification of liquid is a very rich and complicated field, although there is always a famous homogeneous nucleation theory in a standard physics or materials science text book. Depending on the material and processing condition, liquid may solidify to single crystalline, polycrystalline with different texture, quasi-crystalline, amorphous solid or glass (Glass is a kind of amorphous solid in general, which has short-range and medium-range order). Traditional oxide glass may easily be formed since the covalent directional bonded network is apt to be disturbed. In other words, the energy landcape of the oxide glass is so complicated that system need extremely long time to explore the whole configuration space. On the other hand, metallic liquid usually crystalize upon cooling because of the metallic bonding nature. However, Klement et.al., (1960) reported that Au-Si liquid underwent an amorphous or “glassy” phase transformation with rapid quenching. In recent two decades, bulk metallic glasses have also been found in several multicomponent alloys[Inoue et al., (2002)]. Both thermodynamic factors (e.g., free energy of various competitive phase, interfacial free energy, free energy of local clusters, etc.) and kinetic factors (e.g., long range mass transport, local atomic position rearrangement, etc.) play important roles in the metallic glass formation process. Metallic glass is fundamentally different from nanocrystalline alloys. Metallic glasses have to undergo a nucleation process upon heating in order to crystallize. Thus the short-range and medium-range order of metallic glasses have to be completely different from crystal. Hence a method to calculate the energetics of different local clusters in the undercooled liquid or glasses become important to set up a statistic model to describe metalllic glass formation. Scattering techniques like x-ray and neutron have widely been used to study the structues of metallic glasses. Meanwhile, computer simulation

  1. The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT.

    PubMed

    Noguchi, Yasunori; Katayama, Tsutomu

    2016-01-01

    The initiation of bacterial chromosomal replication is regulated by multiple pathways. To explore novel regulators, we isolated multicopy suppressors for the cold-sensitive hda-185 ΔsfiA(sulA) mutant. Hda is crucial for the negative regulation of the initiator DnaA and the hda-185 mutation causes severe replication overinitiation at the replication origin oriC. The SOS-associated division inhibitor SfiA inhibits FtsZ ring formation, an essential step for cell division regulation during the SOS response, and ΔsfiA enhances the cold sensitivity of hda-185 cells in colony formation. One of the suppressors comprised the yfdQ-yfdR-yfdS-yfdT gene cluster carried on a cryptic prophage. Increased copy numbers of yfdQRT or yfdQRS inhibited not only hda-185-dependent overinitiation, but also replication overinitiation in a hyperactive dnaA mutant, and in a mutant lacking an oriC-binding initiation-inhibitor SeqA. In addition, increasing the copy number of the gene set inhibited the growth of cells bearing specific, initiation-impairing dnaA mutations. In wild-type cells, multicopy supply of yfdQRT or yfdQRS also inhibited replication initiation and increased hydroxyurea (HU)-resistance, as seen in cells lacking DiaA, a stimulator of DnaA assembly on oriC. Deletion of the yfdQ-yfdR-yfdS-yfdT genes did not affect either HU resistance or initiation regulation. Furthermore, we found that DnaA bound specifically to YfdR in soluble protein extracts oversupplied with YfdQRST. Purified YfdR also bound to DnaA, and DnaA Phe46, an amino acid residue crucial for DnaA interactions with DiaA and DnaB replicative helicase was important for this interaction. Consistently, YfdR moderately inhibited DiaA-DnaA and DnaB-DnaA interactions. In addition, protein extracts oversupplied with YfdQRST inhibited replication initiation in vitro. Given the roles of yfdQ and yfdS in cell tolerance to specific environmental stresses, the yfdQ-yfdR-yfdS-yfdT genes might downregulate the initiator Dna

  2. Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation

    PubMed Central

    Zhang, Wen-juan; Wu, Xiao-nan; Shi, Tao-tao; Xu, Huan-teng; Yi, Jia; Shen, Hai-feng; Huang, Ming-feng; Shu, Xing-yi; Wang, Fei-fei; Peng, Bing-ling; Xiao, Rong-quan; Gao, Wei-wei; Ding, Jian-cheng; Liu, Wen

    2016-01-01

    Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it is regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remains completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. Functional studies revealed that SET7/9-mediated YY1 methylation regulated YY1 DNA-binding activity both in vitro and at specific genomic loci in cultured cells. Consistently, SET7/9-mediated YY1 methylation was shown to involve in YY1-regulated gene transcription and cell proliferation. Our findings revealed a novel regulatory strategy, methylation by lysine methyltransferase, imposed on YY1 protein, and linked YY1 methylation with its biological functions. PMID:26902152

  3. Binding Procurement

    NASA Technical Reports Server (NTRS)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  4. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

  5. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  6. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  7. Hydrated hydride anion clusters

    NASA Astrophysics Data System (ADS)

    Lee, Han Myoung; Kim, Dongwook; Singh, N. Jiten; Kołaski, Maciej; Kim, Kwang S.

    2007-10-01

    On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.

  8. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  9. Guanylate binding protein-1 mediates EGFRvIII and promotes glioblastoma growth in vivo but not in vitro

    PubMed Central

    Cheng, Yanwei; Mukasa, Akitaki; Ma, Jiawei; Hong, Lei; Yu, Shuye; Sun, Lili; Huang, Qiang; Purow, Benjamin; Li, Ming

    2016-01-01

    Glioblastoma multiforme (GBM) is the most common and deadly primary brain tumor in adults. Epidermal growth factor receptor (EGFR) is frequently amplified and mutated in GBM. We previously reported that Guanylate binding protein-1 (GBP1) is a novel transcriptional target gene of EGFR and plays a role in GBM invasion. Here we demonstrate that GBP1 can also be induced by EGFRvIII at the transcriptional level through the p38 MAPK/Yin Yang 1 (YY1) signaling pathway. Silencing of GBP1 by RNA interference significantly inhibits EGFRvIII-mediated GBM cell proliferation in vitro and in a mouse model. Overexpression of GBP1 has no obvious effect on glioblastoma cell proliferation in vitro. In contrast, in an orthotopic glioma mouse model GBP1 overexpression significantly promotes glioma growth and reduces survival rate of glioma-bearing mice by increasing cell proliferation and decreasing cell apoptosis in tumor. Clinically, GBP1 expression is elevated in human GBM tumors and positively correlates with EGFRvIII status in GBM specimens, and its expression is inversely correlated with the survival rate of GBM patients. Taken together, these results reveal that GBP1 may serve as a potential therapeutic target for GBMs with EGFRvIII mutation. PMID:26848767

  10. Architecture of Eph receptor clusters

    SciTech Connect

    Himanen, Juha P.; Yermekbayeva, Laila; Janes, Peter W.; Walker, John R.; Xu, Kai; Atapattu, Lakmali; Rajashankar, Kanagalaghatta R.; Mensinga, Anneloes; Lackmann, Martin; Nikolov, Dimitar B.; Dhe-Paganon, Sirano

    2010-10-04

    Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanism underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.

  11. Expression of the helix-loop-helix protein inhibitor of DNA binding-1 (ID-1) is activated by all-trans retinoic acid in normal human keratinocytes

    SciTech Connect

    Villano, C.M.; White, L.A. . E-mail: lawhite@aesop.rutgers.edu

    2006-08-01

    The ID (inhibitor of differentiation or DNA binding) helix-loop-helix proteins are important mediators of cellular differentiation and proliferation in a variety of cell types through regulation of gene expression. Overexpression of the ID proteins in normal human keratinocytes results in extension of culture lifespan, indicating that these proteins are important for epidermal differentiation. Our hypothesis is that the ID proteins are targets of the retinoic acid signaling pathway in keratinocytes. Retinoids, vitamin A analogues, are powerful regulators of cell growth and differentiation and are widely used in the prevention and treatment of a variety of cancers in humans. Furthermore, retinoic acid is necessary for the maintenance of epithelial differentiation and demonstrates an inhibitory action on skin carcinogenesis. We examined the effect of all-trans retinoic acid on expression of ID-1, -2, -3, and -4 in normal human keratinocytes and found that exposure of these cells to all-trans retinoic acid causes an increase in both ID-1 and ID-3 gene expression. Furthermore, our data show that this increase is mediated by increased transcription involving several cis-acting elements in the distal portion of the promoter, including a CREB-binding site, an Egr1 element, and an YY1 site. These data demonstrate that the ID proteins are direct targets of the retinoic acid signaling pathway. Given the importance of the ID proteins to epidermal differentiation, these results suggest that IDs may be mediating some of the effects of all-trans retinoic acid in normal human keratinocytes.

  12. Solvation at nanoscale: Alkali-halides in water clusters

    SciTech Connect

    Partanen, Leena; Mikkelae, Mikko-Heikki; Huttula, Marko; Tchaplyguine, Maxim; Zhang Chaofan; Andersson, Tomas; Bjoerneholm, Olle

    2013-01-28

    The solvation of alkali-halides in water clusters at nanoscale is studied by photoelectron spectroscopy using synchrotron radiation. The Na 2p, K 3p, Cl 2p, Br 3d, and I 4d core level binding energies have been measured for salt-containing water clusters. The results have been compared to those of alkali halide clusters and the dilute aqueous salt solutions. It is found that the alkali halides dissolve in small water clusters as ions.

  13. Unit charge on supported gold clusters in photoemission final state

    NASA Astrophysics Data System (ADS)

    Wertheim, G. K.; Dicenzo, S. B.; Youngquist, S. E.

    1983-12-01

    The large, positive core-level shifts seen in photoemission from Au clusters on poorly conducting substrates result from a unit positive charge left on a cluster during the photoemission final state. The case of clusters supported on a poorly conducting carbon substrate is intermediate between the case of free clusters and that of clusters supported on metallic substrates. The identification of a macroscopic Coulomb effect removes the apparent conflict between positive core-level shifts and the expected initial state band-structure effect, whereby increased localization in small clusters should increase the density in Au and decrease the Au core electron binding energy.

  14. Nature of multiple-nucleus cluster galaxies

    SciTech Connect

    Merritt, D.

    1984-05-01

    In models for the evolution of galaxy clusters which include dynamical friction with the dark binding matter, the distribution of galaxies becomes more concentrated to the cluster center with time. In a cluster like Coma, this evolution could increase by a factor of approximately 3 the probability of finding a galaxy very close to the cluster center, without decreasing the typical velocity of such a galaxy significantly below the cluster mean. Such an enhancement is roughly what is needed to explain the large number of first-ranked cluster galaxies which are observed to have extra ''nuclei''; it is also consistent with the high velocities typically measured for these ''nuclei.'' Unlike the cannibalism model, this model predicts that the majority of multiple-nucleus systems are transient phenomena, and not galaxies in the process of merging.

  15. Yin Yang-1 increases apoptosis through Bax activation in pancreatic cancer cells

    PubMed Central

    Yang, Chuang; Liu, Xian; Peng, Yun-Peng; Jiang, Kui-Rong; Miao, Yi; Xu, Ze-Kuan

    2016-01-01

    The transcriptional regulator Yin Yang-1 (YY1) is a tumor suppressor known to be overexpressed in pancreatic cancer. We found that overexpression of YY1 promoted apoptosis and increased the expression and mitochondrial localization of the pro-apoptotic Bax protein in pancreatic cancer cell lines. Luciferase reporter, electrophoretic mobility shift (EMSA), and chromatin immunoprecipitation (ChIP) assays revealed binding of YY1 to the BAX promoter. Moreover, YY1 promoted pancreatic cancer cell apoptosis through Bax transcriptional activation and subsequent translocation of Bax to the mitochondrial membrane, leading to cytochrome c release, and caspase activation.YY1 and BAX are co-expressed in pancreatic cancer tissues and higher BAX expression predicts better outcomes for patients. The ability of YY1 to promote apoptosis in pancreatic cancer cells suggests it may represent a valuable diagnostic and therapeutic target. PMID:27074573

  16. Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters.

    PubMed

    Obara, Isaiah; Nielsen, Morten; Jeschek, Marie; Nijhof, Ard; Mazzoni, Camila J; Svitek, Nicholas; Steinaa, Lucilla; Awino, Elias; Olds, Cassandra; Jabbar, Ahmed; Clausen, Peter-Henning; Bishop, Richard P

    2016-05-01

    There is strong evidence that the immunity induced by live vaccination for control of the protozoan parasite Theileria parva is mediated by class I MHC-restricted CD8(+) T cells directed against the schizont stage of the parasite that infects bovine lymphocytes. The functional competency of class I MHC genes is dependent on the presence of codons specifying certain critical amino acid residues that line the peptide binding groove. Compared with European Bos taurus in which class I MHC allelic polymorphisms have been examined extensively, published data on class I MHC transcripts in African taurines in T. parva endemic areas is very limited. We utilized the multiplexing capabilities of 454 pyrosequencing to make an initial assessment of class I MHC allelic diversity in a population of Ankole cattle. We also typed a population of exotic Holstein cattle from an African ranch for class I MHC and investigated the extent, if any, that their peptide-binding motifs overlapped with those of Ankole cattle. We report the identification of 18 novel allelic sequences in Ankole cattle and provide evidence of positive selection for sequence diversity, including in residues that predominantly interact with peptides. In silico functional analysis resulted in peptide binding specificities that were largely distinct between the two breeds. We also demonstrate that CD8(+) T cells derived from Ankole cattle that are seropositive for T. parva do not recognize vaccine candidate antigens originally identified in Holstein and Boran (Bos indicus) cattle breeds. PMID:26852329

  17. Evidence for chemoreceptors with bimodular ligand-binding regions harboring two signal-binding sites

    PubMed Central

    Pineda-Molina, Estela; Reyes-Darias, José-Antonio; Lacal, Jesús; Ramos, Juan L.; García-Ruiz, Juan Manuel; Gavira, Jose A.; Krell, Tino

    2012-01-01

    Chemoreceptor-based signaling is a central mechanism in bacterial signal transduction. Receptors are classified according to the size of their ligand-binding region. The well-studied cluster I proteins have a 100- to 150-residue ligand-binding region that contains a single site for chemoattractant recognition. Cluster II receptors, which contain a 220- to 300-residue ligand-binding region and which are almost as abundant as cluster I receptors, remain largely uncharacterized. Here, we report high-resolution structures of the ligand-binding region of the cluster II McpS chemotaxis receptor (McpS-LBR) of Pseudomonas putida KT2440 in complex with different chemoattractants. The structure of McpS-LBR represents a small-molecule binding domain composed of two modules, each able to bind different signal molecules. Malate and succinate were found to bind to the membrane-proximal module, whereas acetate binds to the membrane-distal module. A structural alignment of the two modules revealed that the ligand-binding sites could be superimposed and that amino acids involved in ligand recognition are conserved in both binding sites. Ligand binding to both modules was shown to trigger chemotactic responses. Further analysis showed that McpS-like receptors were found in different classes of proteobacteria, indicating that this mode of response to different carbon sources may be universally distributed. The physiological relevance of the McpS architecture may lie in its capacity to respond with high sensitivity to the preferred carbon sources malate and succinate and, at the same time, mediate lower sensitivity responses to the less preferred but very abundant carbon source acetate. PMID:23112148

  18. Formation of [4Fe-4S] clusters in the mitochondrial iron-sulfur cluster assembly machinery.

    PubMed

    Brancaccio, Diego; Gallo, Angelo; Mikolajczyk, Maciej; Zovo, Kairit; Palumaa, Peep; Novellino, Ettore; Piccioli, Mario; Ciofi-Baffoni, Simone; Banci, Lucia

    2014-11-19

    The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins (in mammals named ISCA1 and ISCA2), which perform a nonredundant functional role forming in vivo a heterocomplex. The molecular function of ISCA1 and ISCA2 proteins, i.e., how these proteins help in generating [4Fe-4S] clusters, is still unknown. In this work we have structurally characterized the Fe/S cluster binding properties of human ISCA2 and investigated in vitro whether and how a [4Fe-4S] cluster is assembled when human ISCA1 and ISCA2 interact with the physiological [2Fe-2S](2+) cluster-donor human GRX5. We found that (i) ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex. This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster. The formation of the same [4Fe-4S](2+) cluster-bound heterodimeric species is also observed by having first one [2Fe-2S](2+) cluster transferred from GRX5 to each individual ISCA1 and ISCA2 proteins to form [2Fe-2S](2+) ISCA2 and [2Fe-2S](2+) ISCA1, and then mixing them together. These findings imply that such heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins.

  19. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity.

    PubMed

    Jose, Davis; Weitzel, Steven E; Baase, Walter A; Michael, Miya M; von Hippel, Peter H

    2015-10-30

    We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5'-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex.

  20. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity.

    PubMed

    Jose, Davis; Weitzel, Steven E; Baase, Walter A; Michael, Miya M; von Hippel, Peter H

    2015-10-30

    We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5'-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. PMID:26275774

  1. Cluster headache

    PubMed Central

    2010-01-01

    Introduction The revised International Headache Society (IHS) criteria for cluster headache are: attacks of severe or very severe, strictly unilateral pain, which is orbital, supraorbital, or temporal pain, lasting 15 to 180 minutes and occurring from once every other day to eight times daily. Methods and outcomes We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of interventions to abort cluster headache? What are the effects of interventions to prevent cluster headache? We searched: Medline, Embase, The Cochrane Library, and other important databases up to June 2009 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations, such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). Results We found 23 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. Conclusions In this systematic review, we present information relating to the effectiveness and safety of the following interventions: baclofen (oral); botulinum toxin (intramuscular); capsaicin (intranasal); chlorpromazine; civamide (intranasal); clonidine (transdermal); corticosteroids; ergotamine and dihydroergotamine (oral or intranasal); gabapentin (oral); greater occipital nerve injections (betamethasone plus xylocaine); high-dose and high-flow-rate oxygen; hyperbaric oxygen; leuprolide; lidocaine (intranasal); lithium (oral); melatonin; methysergide (oral); octreotide (subcutaneous); pizotifen (oral); sodium valproate (oral); sumatriptan (oral, subcutaneous, and intranasal); topiramate (oral); tricyclic antidepressants (TCAs); verapamil; and zolmitriptan (oral and intranasal). PMID:21718584

  2. CcaR Is an Autoregulatory Protein That Binds to the ccaR and cefD-cmcI Promoters of the Cephamycin C-Clavulanic Acid Cluster in Streptomyces clavuligerus

    PubMed Central

    Santamarta, Irene; Rodríguez-García, Antonio; Pérez-Redondo, Rosario; Martín, Juan F.; Liras, Paloma

    2002-01-01

    The putative regulatory CcaR protein, which is encoded in the β-lactam supercluster of Streptomyces clavuligerus, has been partially purified by ammonium sulfate precipitation and heparin affinity chromatography. In addition, it was expressed in Escherichia coli, purified as a His-tagged recombinant protein (rCcaR), and used to raise anti-rCcaR antibodies. The partially purified CcaR protein from S. clavuligerus was able to bind DNA fragments containing the promoter regions of the ccaR gene itself and the bidirectional cefD-cmcI promoter region. In contrast, CcaR did not bind to DNA fragments with the promoter regions of other genes of the cephamycin-clavulanic acid supercluster including lat, blp, claR, car-cyp, and the unlinked argR gene. The DNA shifts obtained with CcaR were prevented by anti-rCcaR immunoglobulin G (IgG) antibodies but not by anti-rabbit IgG antibodies. ccaR and the bidirectional cefD-cmcI promoter region were fused to the xylE reporter gene and expressed in Streptomyces lividans and S. clavuligerus. These constructs produced low catechol dioxygenase activity in the absence of CcaR; activity was increased 1.7- to 4.6-fold in cultures expressing CcaR. Amplification of the ccaR promoter region lacking its coding sequence in a high-copy-number plasmid in S. clavuligerus ATCC 27064 resulted in a reduced production of cephamycin C and clavulanic acid, by 12 to 20% and 40 to 60%, respectively, due to titration of the CcaR regulator. These findings confirm that CcaR is a positively acting autoregulatory protein able to bind to its own promoter as well as to the cefD-cmcI bidirectional promoter region. PMID:12003953

  3. CcaR is an autoregulatory protein that binds to the ccaR and cefD-cmcI promoters of the cephamycin C-clavulanic acid cluster in Streptomyces clavuligerus.

    PubMed

    Santamarta, Irene; Rodríguez-García, Antonio; Pérez-Redondo, Rosario; Martín, Juan F; Liras, Paloma

    2002-06-01

    The putative regulatory CcaR protein, which is encoded in the beta-lactam supercluster of Streptomyces clavuligerus, has been partially purified by ammonium sulfate precipitation and heparin affinity chromatography. In addition, it was expressed in Escherichia coli, purified as a His-tagged recombinant protein (rCcaR), and used to raise anti-rCcaR antibodies. The partially purified CcaR protein from S. clavuligerus was able to bind DNA fragments containing the promoter regions of the ccaR gene itself and the bidirectional cefD-cmcI promoter region. In contrast, CcaR did not bind to DNA fragments with the promoter regions of other genes of the cephamycin-clavulanic acid supercluster including lat, blp, claR, car-cyp, and the unlinked argR gene. The DNA shifts obtained with CcaR were prevented by anti-rCcaR immunoglobulin G (IgG) antibodies but not by anti-rabbit IgG antibodies. ccaR and the bidirectional cefD-cmcI promoter region were fused to the xylE reporter gene and expressed in Streptomyces lividans and S. clavuligerus. These constructs produced low catechol dioxygenase activity in the absence of CcaR; activity was increased 1.7- to 4.6-fold in cultures expressing CcaR. Amplification of the ccaR promoter region lacking its coding sequence in a high-copy-number plasmid in S. clavuligerus ATCC 27064 resulted in a reduced production of cephamycin C and clavulanic acid, by 12 to 20% and 40 to 60%, respectively, due to titration of the CcaR regulator. These findings confirm that CcaR is a positively acting autoregulatory protein able to bind to its own promoter as well as to the cefD-cmcI bidirectional promoter region.

  4. Tight-Binding Configuration Interaction (TBCI): A Noniterative Approach to Incorporating Electrostatics into Tight Binding.

    PubMed

    Iron, Mark A; Heyden, Andreas; Staszewska, Grażyna; Truhlar, Donald G

    2008-05-01

    We present a new electronic structure approximation called Tight Binding Configuration Interaction. It uses a tight-binding Hamiltonian to obtain orbitals that are used in a configuration interaction calculation that includes explicit charge interactions. This new method is better capable of predicting energies, ionization potentials, and fragmentation charges than the Wolfsberg-Helmholz Tight-Binding and Many-Body Tight-Binding models reported earlier (Staszewska, G.; Staszewski, P.; Schultz, N. E.; Truhlar, D. Phys. Rev. B 2005, 71, 045423). The method is illustrated for clusters and nanoparticles containing aluminum.

  5. Coupled Cluster Evaluation of the Stability of Atmospheric Acid-Base Clusters with up to 10 Molecules.

    PubMed

    Myllys, Nanna; Elm, Jonas; Halonen, Roope; Kurtén, Theo; Vehkamäki, Hanna

    2016-02-01

    We investigate the utilization of the domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method for calculating binding energies of atmospherical molecular clusters. Applied to small complexes of atmospherical relevance we find that the DLPNO method significantly reduces the scatter in the binding energy, which is commonly present in DFT calculations. For medium sized clusters consisting of sulfuric acid and bases the DLPNO method yields a systematic underestimation of the binding energy compared to canonical coupled cluster results. The errors in the DFT binding energies appear to be more random, while the systematic nature of the DLPNO results allows the establishment of a scaling factor, to better mimic the canonical coupled cluster calculations. Based on the trends identified for the small and medium sized systems, we further extend the application of the DLPNO method to large acid - base clusters consisting of up to 10 molecules, which have previously been out of reach with accurate coupled cluster methods. Using the Atmospheric Cluster Dynamics Code (ACDC) we compare the sulfuric acid dimer formation based on the new DLPNO binding energies with previously published RI-CC2/aug-cc-pV(T+d)Z results. We also compare the simulated sulfuric acid dimer concentration as a function of the base concentration with measurement data from the CLOUD chamber and flow tube experiments. The DLPNO method, even after scaling, underpredicts the dimer concentration significantly. Reasons for this are discussed.

  6. Coupled Cluster Evaluation of the Stability of Atmospheric Acid-Base Clusters with up to 10 Molecules.

    PubMed

    Myllys, Nanna; Elm, Jonas; Halonen, Roope; Kurtén, Theo; Vehkamäki, Hanna

    2016-02-01

    We investigate the utilization of the domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method for calculating binding energies of atmospherical molecular clusters. Applied to small complexes of atmospherical relevance we find that the DLPNO method significantly reduces the scatter in the binding energy, which is commonly present in DFT calculations. For medium sized clusters consisting of sulfuric acid and bases the DLPNO method yields a systematic underestimation of the binding energy compared to canonical coupled cluster results. The errors in the DFT binding energies appear to be more random, while the systematic nature of the DLPNO results allows the establishment of a scaling factor, to better mimic the canonical coupled cluster calculations. Based on the trends identified for the small and medium sized systems, we further extend the application of the DLPNO method to large acid - base clusters consisting of up to 10 molecules, which have previously been out of reach with accurate coupled cluster methods. Using the Atmospheric Cluster Dynamics Code (ACDC) we compare the sulfuric acid dimer formation based on the new DLPNO binding energies with previously published RI-CC2/aug-cc-pV(T+d)Z results. We also compare the simulated sulfuric acid dimer concentration as a function of the base concentration with measurement data from the CLOUD chamber and flow tube experiments. The DLPNO method, even after scaling, underpredicts the dimer concentration significantly. Reasons for this are discussed. PMID:26771121

  7. Cluster growth processes by direct simulation monte carlo method

    NASA Astrophysics Data System (ADS)

    Mizuseki, H.; Jin, Y.; Kawazoe, Y.; Wille, L. T.

    Thin films obtained by cluster deposition have attracted strong attention both as a new manufacturing technique to realize high-density magnetic recording media and to create systems with unique magnetic properties. Because the film's features are influenced by the cluster properties during the flight path, the relevant physical scale to be studied is as large as centimeters. In this paper, a new model of cluster growth processes based on a combination of the Direct Simulation Monte Carlo (DSMC) method and the cluster growth model is introduced to examine the effects of experimental conditions on cluster growth by an adiabatic expansion process. From the macroscopic viewpoint, we simulate the behavior of clusters and inert gas in the flight path under different experimental conditions. The internal energy of the cluster, which consists of rotational and vibrational energies, is limited by the binding energy which depends on the cluster size. These internal and binding energies are used as criteria of the cluster growth. The binding energy is estimated by surface and volume terms. Several types of size distribution of generated clusters under various conditions are obtained by the present model. The results of the present numerical simulations reveal that the size distribution is strongly related to the experimental conditions and can be controlled.

  8. Preferential site occupancy observed in coexpanded argon-krypton clusters

    SciTech Connect

    Lundwall, M.; Bergersen, H.; Lindblad, A.; Oehrwall, G.; Svensson, S.; Bjoerneholm, O.; Tchaplyguine, M.

    2006-10-15

    Free heterogeneous argon-krypton clusters have been produced by coexpansion and investigated by means of x-ray photoelectron spectroscopy. By examining cluster surface and bulk binding energy shifts, relative intensities, and peak widths, we show that in the mixed argon-krypton clusters the krypton atoms favor the bulk and argon atoms are pushed to the surface. Furthermore, we show that krypton atoms in the surface layer occupy high-coordination sites and that heterogeneous argon-krypton clusters produced by coexpansion show the same surface structure as argon host clusters doped with krypton. These observations are supported by site-dependent calculations of chemical shifts.

  9. Yin Yang 1: a multifaceted protein beyond a transcription factor.

    PubMed

    Deng, Zhiyong; Cao, Paul; Wan, Mei Mei; Sui, Guangchao

    2010-01-01

    As a transcription factor, Yin Yang 1 (YY1) regulates the transcription of a dazzling list of genes and the number of its targets still mounts. Recent studies revealed that YY1 possesses functions independent of its DNA binding activity and its regulatory role in tumorigenesis has started to emerge.

  10. Quantum Monte Carlo methods and lithium cluster properties. [Atomic clusters

    SciTech Connect

    Owen, R.K.

    1990-12-01

    Properties of small lithium clusters with sizes ranging from n = 1 to 5 atoms were investigated using quantum Monte Carlo (QMC) methods. Cluster geometries were found from complete active space self consistent field (CASSCF) calculations. A detailed development of the QMC method leading to the variational QMC (V-QMC) and diffusion QMC (D-QMC) methods is shown. The many-body aspect of electron correlation is introduced into the QMC importance sampling electron-electron correlation functions by using density dependent parameters, and are shown to increase the amount of correlation energy obtained in V-QMC calculations. A detailed analysis of D-QMC time-step bias is made and is found to be at least linear with respect to the time-step. The D-QMC calculations determined the lithium cluster ionization potentials to be 0.1982(14) (0.1981), 0.1895(9) (0.1874(4)), 0.1530(34) (0.1599(73)), 0.1664(37) (0.1724(110)), 0.1613(43) (0.1675(110)) Hartrees for lithium clusters n = 1 through 5, respectively; in good agreement with experimental results shown in the brackets. Also, the binding energies per atom was computed to be 0.0177(8) (0.0203(12)), 0.0188(10) (0.0220(21)), 0.0247(8) (0.0310(12)), 0.0253(8) (0.0351(8)) Hartrees for lithium clusters n = 2 through 5, respectively. The lithium cluster one-electron density is shown to have charge concentrations corresponding to nonnuclear attractors. The overall shape of the electronic charge density also bears a remarkable similarity with the anisotropic harmonic oscillator model shape for the given number of valence electrons.

  11. Theoretical studies of binding of mannose-binding protein to monosaccharides

    NASA Astrophysics Data System (ADS)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  12. A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The B4 resistance (R)-gene cluster, located in subtelomeric region of chromosome 4, is one of the largest clusters known in common bean (Phaseolus vulgaris, Pv). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-coil-Nucleotide-Binding-Site-Leucine-Rich...

  13. Ion-pair binding: is binding both binding better?

    PubMed

    Roelens, Stefano; Vacca, Alberto; Francesconi, Oscar; Venturi, Chiara

    2009-08-17

    It is often tempting to explain chemical phenomena on the basis of intuitive principles, but this practice can frequently lead to biased analysis of data and incorrect conclusions. One such intuitive principle is brought into play in the binding of salts by synthetic receptors. Following the heuristic concept that "binding both is binding better", it is widely believed that ditopic receptors capable of binding both ionic partners of a salt are more effective than monotopic receptors because of a cooperative effect. Using a newly designed ditopic receptor and a generalized binding descriptor, we show here that, when the problem is correctly formulated and the appropriate algorithm is derived, the cooperativity principle is neither general nor predictable, and that competition between ion binding and ion pairing may even lead to inhibition rather than enhancement of the binding of an ion to a ditopic receptor.

  14. Electron spectra and structure of atomic and molecular clusters

    SciTech Connect

    Dehmer, Patricia M.

    1980-01-01

    Changes in electronic structure that occur during the stepwise transition from gas phase monomers to large clusters which resemble the condensed phase were studied. This basic information on weakly bound clusters is critical to the understanding of such phenomena as nucleation, aerosol formation, catalysis, and gas-to-particle conversion, yet there exist almost no experimental data on neutral particle energy levels or binding energies as a function of cluster size. (GHT)

  15. Analyzing binding data.

    PubMed

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  16. Water may inhibit oxygen binding in hemoprotein models

    PubMed Central

    Collman, James P.; Decréau, Richard A.; Dey, Abhishek; Yang, Ying

    2009-01-01

    Three distal imidazole pickets in a cytochrome c oxidase (CcO) model form a pocket hosting a cluster of water molecules. The cluster makes the ferrous heme low spin, and consequently the O2 binding slow. The nature of the rigid proximal imidazole tail favors a high spin/low spin cross-over. The O2 binding rate is enhanced either by removing the water, increasing the hydrophobicity of the gas binding pocket, or inserting a metal ion that coordinates to the 3 distal imidazole pickets. PMID:19246375

  17. PREFACE: Nuclear Cluster Conference; Cluster'07

    NASA Astrophysics Data System (ADS)

    Freer, Martin

    2008-05-01

    The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

  18. The Structure and Stability of B(n)H(+) Clusters

    NASA Technical Reports Server (NTRS)

    Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

    1996-01-01

    The geometries of the B(n)H(+) clusters for n=1-13 have been optimized at the B3LYP level of theory. Excluding B2H(+) all clusters are low-spin coupled. The structures appear to be related to the bare B(+)(n) clusters in two ways: 1) an H atom is added to the B(+)(n) cluster or 2) a BH is added to the B(+)(n-1) cluster. The B(+)(n)-H binding energies are computed at the B3LYP level of theory, and calibrated n using the CCSD(T) level of theory. The computed results tend to fall between the experimental best estimates and the experimental lower bounds. The B(+)(n)-H binding energies show an inverse correspondence with the B+(n-1)-B values) while the B(+)(n-1)-B and B(+)(n-1)-BH results tend to parallel each other.

  19. Simulation of water cluster assembly on a graphite surface.

    PubMed

    Lin, C S; Zhang, R Q; Lee, S T; Elstner, M; Frauenheim, Th; Wan, L J

    2005-07-28

    The assembly of small water clusters (H2O)n, n = 1-6, on a graphite surface is studied using a density functional tight-binding method complemented with an empirical van der Waals force correction, with confirmation using second-order Møller-Plesset perturbation theory. It is shown that the optimized geometry of the water hexamer may change its original structure to an isoenergy one when interacting with a graphite surface in some specific orientation, while the smaller water cluster will maintain its cyclic or linear configurations (for the water dimer). The binding energy of water clusters interacting with graphite is dependent on the number of water molecules that form hydrogen bonds, but is independent of the water cluster size. These physically adsorbed water clusters show little change in their IR peak position and leave an almost perfect graphite surface.

  20. A Molecular Full-Potential LMTO Calculation for Copper Clusters

    NASA Astrophysics Data System (ADS)

    Datta, Radhika Prosad; Banerjea, Amitava; Mookerjee, Abhijit; Bhattacharyya, A. K.

    We study the electronic properties of small (10-20 atoms) copper clusters using the newly-developed molecular full-potential linearized muffin-tin orbital two-centre-fit (TCF) method of Methfessel and van Schilfgaarde. The geometric structures of the clusters had earlier been determined by us through simulated annealing using the Equivalent Crystal Theory to compute total energies. We report the variation of the binding energy, as obtained from the TCF calculations, with cluster size and compare these to the binding energies determined, for the same structures, from the ECT. We also show the variation of the HOMO-LUMO gap with cluster size, and the pseudo-density of states for select cluster sizes.

  1. Influence of different liquid-drop-based bindings on lighter mass fragments and entropy production

    NASA Astrophysics Data System (ADS)

    Kumar, Rohit; Shivani; Gautam, Sakshi

    2016-04-01

    We study the production of lighter fragments and associated phenomena within the Quantum Molecular Dynamics (QMD) model. The Minimum Spanning Tree (MST) method is used to identify the pre-clusters. The final stable fragments were identified by imposing binding energy criteria on the fragments formed using the MST method. The effect of different binding energy criteria was investigated by employing various liquid-drop-based binding energy formulae. Though light clusters show significant effect of different binding energies, their associated phenomenon, i.e. entropy production is insensitive towards different binding energy criteria.

  2. Survey on granularity clustering.

    PubMed

    Ding, Shifei; Du, Mingjing; Zhu, Hong

    2015-12-01

    With the rapid development of uncertain artificial intelligent and the arrival of big data era, conventional clustering analysis and granular computing fail to satisfy the requirements of intelligent information processing in this new case. There is the essential relationship between granular computing and clustering analysis, so some researchers try to combine granular computing with clustering analysis. In the idea of granularity, the researchers expand the researches in clustering analysis and look for the best clustering results with the help of the basic theories and methods of granular computing. Granularity clustering method which is proposed and studied has attracted more and more attention. This paper firstly summarizes the background of granularity clustering and the intrinsic connection between granular computing and clustering analysis, and then mainly reviews the research status and various methods of granularity clustering. Finally, we analyze existing problem and propose further research.

  3. Cluster automorphism groups of cluster algebras with coefficients

    NASA Astrophysics Data System (ADS)

    Chang, Wen; Zhu, Bin

    2016-10-01

    We study the cluster automorphism group of a skew-symmetric cluster algebra with geometric coefficients. For this, we introduce the notion of gluing free cluster algebra, and show that under a weak condition the cluster automorphism group of a gluing free cluster algebra is a subgroup of the cluster automorphism group of its principal part cluster algebra (i.e. the corresponding cluster algebra without coefficients). We show that several classes of cluster algebras with coefficients are gluing free, for example, cluster algebras with principal coefficients, cluster algebras with universal geometric coefficients, and cluster algebras from surfaces (except a 4-gon) with coefficients from boundaries. Moreover, except four kinds of surfaces, the cluster automorphism group of a cluster algebra from a surface with coefficients from boundaries is isomorphic to the cluster automorphism group of its principal part cluster algebra; for a cluster algebra with principal coefficients, its cluster automorphism group is isomorphic to the automorphism group of its initial quiver.

  4. Blackbody-induced radiative dissociation of cationic SF6 clusters

    NASA Astrophysics Data System (ADS)

    Toker, Y.; Rahinov, I.; Schwalm, D.; Even, U.; Heber, O.; Rappaport, M. L.; Strasser, D.; Zajfman, D.

    2012-08-01

    The stability of cationic SF5+(SF6)n-1 clusters was investigated by measuring their blackbody-induced radiative dissociation (BIRD) rates. The clusters were produced in a supersonic expansion ion source and stored in an electrostatic ion-beam trap at room temperature, where their abundances and lifetimes were measured. Using the “master equation” approach, relative binding energies of an SF6 unit in the clusters could be extracted from the storage-time dependence of the survival probabilities. The results allow for a deeper insight into the effect of a localized charge on the structure and stability of SF6-based clusters.

  5. Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

    PubMed Central

    Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

  6. Chemiluminescence in the Agglomeration of Metal Clusters

    PubMed

    König; Rabin; Schulze; Ertl

    1996-11-22

    The agglomeration of copper or silver atoms in a matrix of noble gas atoms to form small clusters may be accompanied by the emission of visible light. Spectral analysis reveals the intermediate formation of electronically excited atoms and dimers as the source of the chemiluminescence. A mechanism is proposed, according to which the gain in binding energy upon cluster formation may even lead to the ejection of excited fragments as a result of unstable intermediate configurations. A similar concept was introduced in the field of nuclear reactions by Niels Bohr 60 years ago.

  7. Photoelectron spectroscopy of nitromethane anion clusters

    NASA Astrophysics Data System (ADS)

    Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

    2016-08-01

    Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

  8. STABILITY OF SMALL SELF-INTERSTITIAL CLUSTERS IN TUNGSTEN

    SciTech Connect

    Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

    2015-12-31

    Density functional theory was employed to explore the stability of interstitial clusters in W up to size seven. For each cluster size, the most stable configuration consists of parallel dumbbells. For clusters larger than size three, parallel dumbbells prefer to form in a multilayer fashion, instead of a planar structure. For size-7 clusters, the most stable configuration is a complete octahedron. The binding energy of a [111] dumbbell to the most stable cluster increases with cluster size, namely 2.49, 3.68, 4.76, 4.82, 5.47, and 6.85 eV for clusters of size 1, 2, 3, 4, 5, and 6, respectively. For a size-2 cluster, collinear dumbbells are still repulsive at the maximum allowable distance of 13.8 Å (the fifth neighbor along [111]). On the other hand, parallel dumbbells are strongly bound together. Two parallel dumbbells in which the axis-to-axis distance is within a cylindrical radius of 5.2 Å still exhibit a considerable binding of 0.28 eV. The most stable cluster in each size will be used to explore interactions with transmutation products.

  9. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  10. Computer simulation structure and vibrations of small metal cluster on the Cu (111) surface

    SciTech Connect

    Borisova, Svetlana D. Rusina, Galina G.

    2015-10-27

    Vibrational properties of the small tetrahedral cluster of Co on the Cu (111) surface are studied by using tight-binding second moment approximation interatomic interaction potentials. It was shown that interaction of the clusters with substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The Co{sub 4} cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations.

  11. Preferential site occupancy of krypton atoms on free argon-cluster surfaces.

    PubMed

    Lundwall, M; Lindblad, A; Bergersen, H; Rander, T; Ohrwall, G; Tchaplyguine, M; Svensson, S; Björneholm, O

    2006-07-01

    Argon clusters have been doped with krypton atoms in a pick-up setup and investigated by means of ultraviolet and x-ray photoelectron spectroscopy (UPS and XPS). The width of the krypton surface feature in the XPS spectra from mixed krypton/argon clusters has been studied and found to be narrower than in the case of homogeneous krypton clusters. By considering known spectral broadening mechanisms of the cluster features and the electron binding energy shift of the cluster surface feature relative to the atomic signal, we conclude that krypton ad-atoms preferentially occupy high-coordination surface sites on the argon host-cluster.

  12. Star cluster dynamics.

    PubMed

    Vesperini, Enrico

    2010-02-28

    Dynamical evolution plays a key role in shaping the current properties of star clusters and star cluster systems. A detailed understanding of the effects of evolutionary processes is essential to be able to disentangle the properties that result from dynamical evolution from those imprinted at the time of cluster formation. In this review, I focus my attention on globular clusters, and review the main physical ingredients driving their early and long-term evolution, describe the possible evolutionary routes and show how cluster structure and stellar content are affected by dynamical evolution.

  13. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  14. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  15. Simulation of metastable CL-20 cluster structures

    NASA Astrophysics Data System (ADS)

    Degtyarenko, N. N.; Katin, K. P.; Maslov, M. M.

    2014-07-01

    Ensembles of C6H6N12O12 (CL-20) clusters with different types of intercluster bonds have been studied theoretically. The stability of such cluster has been investigated and the heights of potential barriers preventing their decomposition or isomerization have been determined by means of quantum-mechanical calculations based on the density functional theory and nonorthogonal tight-binding model. From the analysis of molecular dynamics data and potential energy hypersurface of these metastable configurations, it has been established that dimers and tetramers of CL-20 clusters are characterized by sufficiently high kinetic stability, which suggests the theoretical possibility of creation of high-energy covalent crystals on their basis.

  16. Analyzing radioligand binding data.

    PubMed

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  17. Structural transitions of tin clusters: Snn (n = 34-44)

    NASA Astrophysics Data System (ADS)

    Zang, Qing-Jun; Chen, Guang-Ju; Lu, Wen-Cai

    2012-11-01

    Snn (n = 34-44) clusters were studied using a combined method of the genetic algorithm/tight-binding search and the DFT-PBEPBE calculations. Snn (n = 34-44) clusters are shown to favor an assembly motif composed of small stable Sn9 and Sn10 subunits which are connected by cohesive linkages of smaller clusters (Sn1-5). Snn (n = 34-44) clusters were found to transform from a prolate pattern for Sn34,35 to a 'Y' pattern for Sn36-39 to a plate motif for Sn40-44. Obvious structural transitions would easily occur at the cross points of binding energy curves when isomers become competitive.

  18. Clustering aspects in nuclear structure functions

    SciTech Connect

    Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

    2011-03-15

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the {sup 9}Be nucleus consists of two {alpha}-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F{sub 2} of {sup 9}Be along with studies for other light nuclei. We found that nuclear modifications of F{sub 2} are similar in both AMD and shell models within our simple convolution description although there are slight differences in {sup 9}Be. It indicates that the anomalous {sup 9}Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F{sub 2}{sup A}/F{sub 2}{sup D})/dx are shown by the maximum local densities, the {sup 9}Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in {sup 9}Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

  19. Orientation-dependent binding energy of graphene on palladium

    NASA Astrophysics Data System (ADS)

    Kappes, Branden B.; Ebnonnasir, Abbas; Kodambaka, Suneel; Ciobanu, Cristian V.

    2013-02-01

    Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

  20. Orientation-dependent binding energy of graphene on palladium

    SciTech Connect

    Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V.; Kodambaka, Suneel

    2013-02-04

    Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

  1. Binding energy effects in cascade evolution and sputtering

    SciTech Connect

    Robinson, M.T.

    1995-06-01

    The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced {approximately}8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced {approximately}9% at 1 keV and {approximately}15% at 100 keV. In sputtering, the mean binding energy is reduced {approximately}8% in Cu and {approximately}15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits.

  2. Nanophase materials assembled from clusters

    SciTech Connect

    Siegel, R.W.

    1992-02-01

    The preparation of metal and ceramic atom clusters by means of the gas-condensation method, followed by their in situ collection and consolidation under high-vacuum conditions, has recently led to the synthesis of a new class of ultrafine-grained materials. These nanophase materials, with typical average grain sizes of 5 to 50 nm and, hence, a large fraction of their atoms in interfaces, exhibit properties that are often considerably improved relative to those of conventional materials. Furthermore, their synthesis and processing characteristics should enable the design of new materials with unique properties. Some examples are ductile ceramics that can be formed and sintered to full density at low temperatures without the need for binding or sintering aids, and metals with dramatically increased strength. The synthesis of these materials is briefly described along with what is presently known of their structure and properties. Their future impact on materials science and technology is also considered.

  3. Geometries, stabilities, and electronic properties of Pt-group-doped gold clusters, their relationship to cluster size, and comparison with pure gold clusters.

    PubMed

    Wang, Su Juan; Kuang, Xiao Yu; Lu, Cheng; Li, Yan Fang; Zhao, Ya Ru

    2011-06-01

    A systematic study of bimetallic Au(n)M(2) (n = 1-6, M = Ni, Pd, and Pt) clusters is performed by using density functional theory at the B3LYP level. The geometric structures, relative stabilities, HOMO-LUMO gaps, natural charges and electronic magnetic moments of these clusters are investigated, and compared with pure gold clusters. The results indicate that the properties of Au(n)M(2) clusters for n = 1-3 diverge more from pure gold clusters, while those for n = 4-6 show good agreement with Au(n) clusters. The dissociation energies, the second-order difference of energies, and HOMO-LUMO energy gaps, exhibiting an odd-even alternation, indicate that the Au(4)M(2) clusters are the most stable structures for Au(n)M(2) (n = 1-6, M = Ni, Pd, and Pt) clusters. Moreover, we predict that the average atomic binding energies of these clusters should tend to a limit in the range 1.56-2.00 eV.

  4. Infrared spectroscopic probing of dimethylamine clusters in an Ar matrix.

    PubMed

    Li, Siyang; Kjaergaard, Henrik G; Du, Lin

    2016-02-01

    Amines have many atmospheric sources and their clusters play an important role in aerosol nucleation processes. Clusters of a typical amine, dimethylamine (DMA), of different sizes were measured with matrix isolation IR (infrared) and NIR (near infrared) spectroscopy. The NIR vibrations are more separated and therefore it is easier to distinguish different sizes of clusters in this region. The DMA clusters, up to DMA tetramer, have been optimized using density functional methods, and the geometries, binding energies and thermodynamic properties of DMA clusters were obtained. The computed frequencies and intensities of NH-stretching vibrations in the DMA clusters were used to interpret the experimental spectra. We have identified the fundamental transitions of the bonded NH-stretching vibration and the first overtone transitions of the bonded and free NH-stretching vibration in the DMA clusters. Based on the changes in vibrational intensities during the annealing processes, the growth of clusters was clearly observed. The results of annealing processes indicate that DMA molecules tend to form larger clusters with lower energies under matrix temperatures, which is also supported by the calculated reaction energies of cluster formation. PMID:26969545

  5. Characterization of iron-sulfur cluster assembly protein IscA from Acidithiobacillus ferrooxidans.

    PubMed

    Qian, Lin; Zheng, Chunli; Liu, Jianshe

    2013-03-01

    IscA is a key member of the iron-sulfur cluster assembly machinery found in bacteria and eukaryotes, but the mechanism of its function in the biogenesis of iron-sulfur cluster remains elusive. In this paper, we demonstrate that Acidithiobacillus ferrooxidans IscA is a [4Fe-4S] cluster binding protein, and it can bind iron in the presence of DTT with an apparent iron association constant of 4·10(20) M(-1). The iron binding in IscA can be promoted by oxygen through oxidizing ferrous iron to ferric iron. Furthermore, we show that the iron bound form of IscA can be converted to iron-sulfur cluster bound form in the presence of IscS and L-cysteine in vitro. Substitution of the invariant cysteine residues Cys35, Cys99, or Cys101 in IscA abolishes the iron binding activity of the protein; the IscA mutants that fail to bind iron are unable to assemble the iron-sulfur clusters. Further studies indicate that the iron-loaded IscA could act as an iron donor for the assembly of iron-sulfur clusters in the scaffold protein IscU in vitro. Taken together, these findings suggest that A. ferrooxidans IscA is not only an iron-sulfur protein, but also an iron binding protein that can act as an iron donor for biogenesis of iron-sulfur clusters. PMID:23586717

  6. Information-based clustering

    PubMed Central

    Slonim, Noam; Atwal, Gurinder Singh; Tkačik, Gašper; Bialek, William

    2005-01-01

    In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster “prototype,” does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. PMID:16352721

  7. Convex Discriminative Multitask Clustering.

    PubMed

    Zhang, Xiao-Lei

    2015-01-01

    Multitask clustering tries to improve the clustering performance of multiple tasks simultaneously by taking their relationship into account. Most existing multitask clustering algorithms fall into the type of generative clustering, and none are formulated as convex optimization problems. In this paper, we propose two convex Discriminative Multitask Clustering (DMTC) objectives to address the problems. The first one aims to learn a shared feature representation, which can be seen as a technical combination of the convex multitask feature learning and the convex Multiclass Maximum Margin Clustering (M3C). The second one aims to learn the task relationship, which can be seen as a combination of the convex multitask relationship learning and M3C. The objectives of the two algorithms are solved in a uniform procedure by the efficient cutting-plane algorithm and further unified in the Bayesian framework. Experimental results on a toy problem and two benchmark data sets demonstrate the effectiveness of the proposed algorithms. PMID:26353206

  8. Clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Vikhlinin, A. A.; Kravtsov, A. V.; Markevich, M. L.; Sunyaev, R. A.; Churazov, E. M.

    2014-04-01

    Galaxy clusters are formed via nonlinear growth of primordial density fluctuations and are the most massive gravitationally bound objects in the present Universe. Their number density at different epochs and their properties depend strongly on the properties of dark matter and dark energy, making clusters a powerful tool for observational cosmology. Observations of the hot gas filling the gravitational potential well of a cluster allows studying gasdynamic and plasma effects and the effect of supermassive black holes on the heating and cooling of gas on cluster scales. The work of Yakov Borisovich Zeldovich has had a profound impact on virtually all cosmological and astrophysical studies of galaxy clusters, introducing concepts such as the Harrison-Zeldovich spectrum, the Zeldovich approximation, baryon acoustic peaks, and the Sunyaev-Zeldovich effect. Here, we review the most basic properties of clusters and their role in modern astrophysics and cosmology.

  9. Protein Binding Pocket Dynamics.

    PubMed

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  10. Protein Binding Pocket Dynamics.

    PubMed

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  11. Mini-clusters

    NASA Technical Reports Server (NTRS)

    Chinellato, J. A.; Dobrigkeit, C.; Bellandifilho, J.; Lattes, C. M. G.; Menon, M. J.; Navia, C. E.; Pamilaju, A.; Sawayanagi, K.; Shibuya, E. H.; Turtelli, A., Jr.

    1985-01-01

    Experimental results of mini-clusters observed in Chacaltaya emulsion chamber no.19 are summarized. The study was made on 54 single core shower upper and 91 shower clusters of E(gamma) 10 TeV from 30 families which are visible energy greater than 80 TeV and penetrate through both upper and lower detectors of the two-story chamber. The association of hadrons in mini-cluster is made clear from their penetrative nature and microscopic observation of shower continuation in lower chamber. Small P sub t (gamma) of hadrons in mini-clusters remained in puzzle.

  12. Reactions of intermetallic clusters

    NASA Astrophysics Data System (ADS)

    Farley, R. W.; Castleman, A. W., Jr.

    1990-02-01

    Reaction of bismuth-alkali clusters with closed-shell HX acids provides insight into the structures, formation, and stabilities of these intermetallic species. HC1 and HI are observed to quantitatively strip BixNay and BixKy, respectively, of their alkali component, leaving bare bismuth clusters as the only bismuth-containing species detected. Product bismuth clusters exhibit the same distribution observed when pure bismuth is evaporated in the source. Though evaporated simultaneously from the same crucible, this suggests alkali atoms condense onto existing bismuth clusters and have negligible effect on their formation and consequent distribution. The indistinguishibility of reacted and pure bismuth cluster distributions further argues against the simple replacement of alkali atoms with hydrogen in these reactions. This is considered further evidence that the alkali atoms are external to the stable bismuth Zintl anionic structures. Reactivities of BixNay clusters with HC1 are estimated to lie between 3×10-13 for Bi4Na, to greater than 4×10-11 for clusters possessing large numbers of alkali atoms. Bare bismuth clusters are observed in separate experiments to react significantly more slowly with rates of 1-9×10-14 and exhibit little variation of reactivity with size. The bismuth clusters may thus be considered a relatively inert substrate upon which the alkali overlayer reacts.

  13. Management of cluster headache.

    PubMed

    Tfelt-Hansen, Peer C; Jensen, Rigmor H

    2012-07-01

    The prevalence of cluster headache is 0.1% and cluster headache is often not diagnosed or misdiagnosed as migraine or sinusitis. In cluster headache there is often a considerable diagnostic delay - an average of 7 years in a population-based survey. Cluster headache is characterized by very severe or severe orbital or periorbital pain with a duration of 15-180 minutes. The cluster headache attacks are accompanied by characteristic associated unilateral symptoms such as tearing, nasal congestion and/or rhinorrhoea, eyelid oedema, miosis and/or ptosis. In addition, there is a sense of restlessness and agitation. Patients may have up to eight attacks per day. Episodic cluster headache (ECH) occurs in clusters of weeks to months duration, whereas chronic cluster headache (CCH) attacks occur for more than 1 year without remissions. Management of cluster headache is divided into acute attack treatment and prophylactic treatment. In ECH and CCH the attacks can be treated with oxygen (12 L/min) or subcutaneous sumatriptan 6 mg. For both oxygen and sumatriptan there are two randomized, placebo-controlled trials demonstrating efficacy. In both ECH and CCH, verapamil is the prophylactic drug of choice. Verapamil 360 mg/day was found to be superior to placebo in one clinical trial. In clinical practice, daily doses of 480-720 mg are mostly used. Thus, the dose of verapamil used in cluster headache treatment may be double the dose used in cardiology, and with the higher doses the PR interval should be checked with an ECG. At the start of a cluster, transitional preventive treatment such as corticosteroids or greater occipital nerve blockade can be given. In CCH and in long-standing clusters of ECH, lithium, methysergide, topiramate, valproic acid and ergotamine tartrate can be used as add-on prophylactic treatment. In drug-resistant CCH, neuromodulation with either occipital nerve stimulation or deep brain stimulation of the hypothalamus is an alternative treatment strategy

  14. The youngest globular clusters

    NASA Astrophysics Data System (ADS)

    Beck, Sara

    2015-11-01

    It is likely that all stars are born in clusters, but most clusters are not bound and disperse. None of the many protoclusters in our Galaxy are likely to develop into long-lived bound clusters. The super star clusters (SSCs) seen in starburst galaxies are more massive and compact and have better chances of survival. The birth and early development of SSCs takes place deep in molecular clouds, and during this crucial stage the embedded clusters are invisible to optical or UV observations but are studied via the radio-infrared supernebulae (RISN) they excite. We review observations of embedded clusters and identify RISN within 10 Mpc whose exciting clusters have ≈ 106 M⊙ or more in volumes of a few pc3 and which are likely to not only survive as bound clusters, but to evolve into objects as massive and compact as Galactic globulars. These clusters are distinguished by very high star formation efficiency η, at least a factor of 10 higher than the few percent seen in the Galaxy, probably due to the violent disturbances their host galaxies have undergone. We review recent observations of the kinematics of the ionized gas in RISN showing outflows through low-density channels in the ambient molecular cloud; this may protect the cloud from feedback by the embedded H II region.

  15. Clustering versus non-clustering phase synchronizations

    SciTech Connect

    Liu, Shuai; Zhan, Meng

    2014-03-15

    Clustering phase synchronization (CPS) is a common scenario to the global phase synchronization of coupled dynamical systems. In this work, a novel scenario, the non-clustering phase synchronization (NPS), is reported. It is found that coupled systems do not transit to the global synchronization until a certain sufficiently large coupling is attained, and there is no clustering prior to the global synchronization. To reveal the relationship between CPS and NPS, we further analyze the noise effect on coupled phase oscillators and find that the coupled oscillator system can change from CPS to NPS with the increase of noise intensity or system disorder. These findings are expected to shed light on the mechanism of various intriguing self-organized behaviors in coupled systems.

  16. Analyzing radioligand binding data.

    PubMed

    Motulsky, H; Neubig, R

    2001-05-01

    A radioligand is a radioactively labeled drug that can associate with a receptor, transporter, enzyme, or any protein of interest. Measuring the rate and extent of binding provides information on the number of binding sites, and their affinity and accessibility for various drugs. Radioligand binding experiments are easy to perform, and provide useful data in many fields. For example, radioligand binding studies are used to study receptor regulation, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  17. Evolving nucleotide binding surfaces

    NASA Technical Reports Server (NTRS)

    Kieber-Emmons, T.; Rein, R.

    1981-01-01

    An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

  18. Theoretical studies of the electronic structure of small metal clusters

    NASA Technical Reports Server (NTRS)

    Jordan, K. D.

    1982-01-01

    Theoretical studies of the electronic structure of metal clusters, in particular clusters of Group IIA and IIB atoms were conducted. Early in the project it became clear that electron correlation involving d orbitals plays a more important role in the binding of these clusters than had been previously anticipated. This necessitated that computer codes for calculating two electron integrals and for constructing the resulting CI Hamiltonions be replaced with newer, more efficient procedures. Program modification, interfacing and testing were performed. Results of both plans are reported.

  19. A nonparametric clustering technique which estimates the number of clusters

    NASA Technical Reports Server (NTRS)

    Ramey, D. B.

    1983-01-01

    In applications of cluster analysis, one usually needs to determine the number of clusters, K, and the assignment of observations to each cluster. A clustering technique based on recursive application of a multivariate test of bimodality which automatically estimates both K and the cluster assignments is presented.

  20. Dynamical Analyses of Galaxy Clusters With Large Redshift Samples

    NASA Astrophysics Data System (ADS)

    Mohr, J. J.; Richstone, D. O.; Wegner, G.

    1998-12-01

    We construct equilibrium models of galaxy orbits in five nearby galaxy clusters to study the distribution of binding mass, the nature of galaxy orbits and the kinematic differences between cluster populations of emission-line and non emission-line galaxies. We avail ourselves of 1718 galaxy redshifts (and 1203 cluster member redshifts) in this Jeans analysis; most of these redshifts are new, coming from multifiber spectroscopic runs on the MDM 2.4m with the Decaspec and queue observing on WIYN with Hydra. In addition to the spectroscopic data we have V and R band CCD mosaics (obtained with the MDM 1.3m) of the Abell region in each of these clusters. Our scientific goals include: (i) a quantitative estimate of the range of binding masses M500 consistent with the optical and X-ray data, (ii) an estimate of the typical galaxy oribital anisotropies required to make the galaxy data consistent with the NFW expectation for the cluster potential, (iii) a better understanding of the systematics inherent in the process of rescaling and ``stacking'' galaxy cluster observations, (iv) a reexamination of the recent CNOC results implying that emission-line (blue) galaxies are an equilibrium population with a more extended radial distribution than their non emission-line (red) galaxy counterparts and (v) a measure of the galaxy contribution to the cluster mass of baryons.

  1. Theoretical Study of Chemisorption on Small Palladium Clusters

    NASA Astrophysics Data System (ADS)

    Hira, Ajit; Naranjo, Frank; Munoz, Felipe; Jaramillo, Danelle

    2015-03-01

    We continue our interest in the chemisorption of different atomic and molecular species on small clusters of metallic elements, by examining the interactions of H, H2, Li and O adsorbates with Pdn clusters (n = 2 thru 20). Transition-metal clusters are specially suited for the study of quantum size effects and for formation of metallic states, and are ideal candidates for catalytic processes. Hybrid ab initio methods of quantum chemistry (particularly the DFT-B3LYP model) are used to derive optimal geometries for the clusters of interest. We compare calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps for the clusters. Of particular interest are the comparisons of binding strengths at the three important types of sites: edge (E), hollow (H), on-top (T), threefold sites and fourfold sites. Effects of crystal symmetries corresponding to the bulk structures are investigated. The capacity of Pd clusters to adsorb H atoms will be compared to Ni clusters. Research Supported by National Science Foundation.

  2. Thermal stability of structure in small gold clusters

    NASA Astrophysics Data System (ADS)

    Goloven'ko, Zh. V.; Gafner, Yu. Ya.; Gafner, S. L.; Redel', L. V.

    2013-12-01

    Limits of thermal stability of the original fcc phase in gold clusters up to 3.5 nm in diameter have been studied. The simulation carried out by the molecular-dynamics method using a modified TB-SMA tight-binding potential has shown that in small Au clusters under the effect of the temperature factor there occurs a transition from the original fcc phase to other structural modifications, including those with a pentagonal symmetry. As the size of gold nanoparticles increases, the polytypic-transition temperature shifts toward the melting temperature of the cluster. The results obtained are compared with the data for copper and nickel nanoparticles with similar sizes. It has been shown that, in the case of nickel and copper clusters, it is the transition from the fcc phase into structures with a pentagonal symmetry, which are not found in the bulk state, that is the governing factor; the gold clusters demonstrate a much more intricate behavior.

  3. Quantum and classical simulations of molecular clusters

    NASA Astrophysics Data System (ADS)

    Dong, Xiao

    Calcium nanoclusters are studied by several computational approaches with the goal of obtaining information about their energetic, stability and thermodynamic properties. Clusters with 32 to 84 calcium atoms are modeled by a tight-binding (TB) model and their structures are optimized with molecular dynamics simulated annealing, whereas clusters containing 14 to 34 atoms are optimized with the Adaptive Tempering Monte Carlo method (ATMC). Magic number clusters are determined to be of 15, 21, 23, 34, 37, 39, 45, 53, 57, and 82 atoms, in good agreement with experiments. These clusters range in size between 1 and 2 nm. The structures of clusters containing 15, 16, 18, 21, 23, 25, 35, 28, 43, 50, 58, 59, 62, 63, 76-84 atoms are new---not reported as minimum energy structures in the literature. In this cluster size range there is an enhanced ratio of surface to bulk atoms that favors an expansion of the surface bond lengths. Within the harmonic approximation, the calculated Helmhotz free energy indicates that the structures of the magic number clusters are maintained even at temperatures around 700 K. Based on TB molecular dynamics results of the mean-squared displacement as function of temperature, a premelting of the surface occurs around 600 K. The energy gap between occupied and empty states in the valence band is cluster-size-dependent and significantly larger for Ca15, Ca21, Ca23, Ca35, Ca 42, and Ca45. Calcium nanoclusters with more than 49 atoms display an incipient metallic character at temperatures higher than 500 K. The ATMC is a newly developed optimization method based on a multi-canonical Monte Carlo approach. This new method was designed to obtain the most ordered state of a system. In the simulation, the MC temperature is changed adaptively to sample configuration space in an efficient manner. The various canonical ensembles are connected along the simulation by a super-Markov chain, which allows for the adaptive excursion in configuration space leading

  4. Mixed-Initiative Clustering

    ERIC Educational Resources Information Center

    Huang, Yifen

    2010-01-01

    Mixed-initiative clustering is a task where a user and a machine work collaboratively to analyze a large set of documents. We hypothesize that a user and a machine can both learn better clustering models through enriched communication and interactive learning from each other. The first contribution or this thesis is providing a framework of…

  5. Cluster Interest Inventory.

    ERIC Educational Resources Information Center

    Herzog, Douglas

    The Cluster Interest Inventory is designed to familiarize students with representative occupations in 13 career clusters: (1) agribusiness and natural resources, (2) business marketing, and office occupations, (3) communications and media, (4) consumer and homemaker, (5) fine arts and humanities, (6) health, (7) manufacturing and processing, (8)…

  6. Matlab Cluster Ensemble Toolbox

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. Withmore » regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.« less

  7. [Cluster headache differential diagnosis].

    PubMed

    Guégan-Massardier, Evelyne; Laubier, Cécile

    2015-11-01

    Cluster headache is characterized by disabling stereotyped headache. Early diagnosis allows appropriate treatment, unfortunately diagnostic errors are frequent. The main differential diagnoses are other primary or essential headaches. Migraine, more frequent and whose diagnosis is carried by excess, trigeminal neuralgia or other trigemino-autonomic cephalgia. Vascular or tumoral underlying condition can mimic cluster headache, neck and brain imaging is recommended, ideally MRI.

  8. Blue emitting undecaplatinum clusters

    NASA Astrophysics Data System (ADS)

    Chakraborty, Indranath; Bhuin, Radha Gobinda; Bhat, Shridevi; Pradeep, T.

    2014-07-01

    A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents.A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents. Electronic supplementary information (ESI) available: Details of experimental procedures, instrumentation, chromatogram of the crude cluster; SEM/EDAX, DLS, PXRD, TEM, FT-IR, and XPS of the isolated Pt11 cluster; UV/Vis, MALDI MS and SEM/EDAX of isolated 2 and 3; and 195Pt NMR of the K2PtCl6 standard. See DOI: 10.1039/c4nr02778g

  9. Muster: Massively Scalable Clustering

    2010-05-20

    Muster is a framework for scalable cluster analysis. It includes implementations of classic K-Medoids partitioning algorithms, as well as infrastructure for making these algorithms run scalably on very large systems. In particular, Muster contains algorithms such as CAPEK (described in reference 1) that are capable of clustering highly distributed data sets in-place on a hundred thousand or more processes.

  10. Illinois' Career Cluster Model

    ERIC Educational Resources Information Center

    Jankowski, Natasha A.; Kirby, Catherine L.; Bragg, Debra D.; Taylor, Jason L.; Oertle, Kathleen M.

    2009-01-01

    This booklet provides information to multiple stakeholders on the implementation of career clusters in Illinois. The booklet is an extension of the previous edition titled "An Introduction to Illinois CTE Programs of Study" (2008), and provides a resource for partners to understand Illinois' Career Cluster Model as its own adaptation of the…

  11. Brightest Cluster Galaxy Identification

    NASA Astrophysics Data System (ADS)

    Leisman, Luke; Haarsma, D. B.; Sebald, D. A.; ACCEPT Team

    2011-01-01

    Brightest cluster galaxies (BCGs) play an important role in several fields of astronomical research. The literature includes many different methods and criteria for identifying the BCG in the cluster, such as choosing the brightest galaxy, the galaxy nearest the X-ray peak, or the galaxy with the most extended profile. Here we examine a sample of 75 clusters from the Archive of Chandra Cluster Entropy Profile Tables (ACCEPT) and the Sloan Digital Sky Survey (SDSS), measuring masked magnitudes and profiles for BCG candidates in each cluster. We first identified galaxies by hand; in 15% of clusters at least one team member selected a different galaxy than the others.We also applied 6 other identification methods to the ACCEPT sample; in 30% of clusters at least one of these methods selected a different galaxy than the other methods. We then developed an algorithm that weighs brightness, profile, and proximity to the X-ray peak and centroid. This algorithm incorporates the advantages of by-hand identification (weighing multiple properties) and automated selection (repeatable and consistent). The BCG population chosen by the algorithm is more uniform in its properties than populations selected by other methods, particularly in the relation between absolute magnitude (a proxy for galaxy mass) and average gas temperature (a proxy for cluster mass). This work supported by a Barry M. Goldwater Scholarship and a Sid Jansma Summer Research Fellowship.

  12. Marketing Occupations. Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    This cluster guide, which is designed to show teachers what specific knowledge and skills qualify high school students for entry-level employment (or postsecondary training) in marketing occupations, is organized into three sections: (1) cluster organization and implementation, (2) instructional emphasis areas, and (3) assessment. The first…

  13. Probability and Cancer Clusters

    ERIC Educational Resources Information Center

    Hamilton-Keene, Rachael; Lenard, Christoper T.; Mills, Terry M.

    2009-01-01

    Recently there have been several news items about possible cancer clusters in the Australian media. The term "cancer cluster" is used when an unusually large number of people in one geographic area, often a workplace, are diagnosed with cancer in a short space of time. In this paper the authors explore this important health issue using probability…

  14. Cosmology with galaxy clusters

    NASA Astrophysics Data System (ADS)

    Sartoris, Barbara

    2015-08-01

    Clusters of galaxies are powerful probes to constrain parameters that describe the cosmological models and to distinguish among different models. Since, the evolution of the cluster mass function and large-scale clustering contain the informations about the linear growth rate of perturbations and the expansion history of the Universe, clusters have played an important role in establishing the current cosmological paradigm. It is crucial to know how to determine the cluster mass from observational quantities when using clusters as cosmological tools. For this, numerical simulations are helpful to define and study robust cluster mass proxies that have minimal and well understood scatter across the mass and redshift ranges of interest. Additionally, the bias in cluster mass determination can be constrained via observations of the strong and weak lensing effect, X-ray emission, the Sunyaev- Zel’dovic effect, and the dynamics of galaxies.A major advantage of X-ray surveys is that the observable-mass relation is tight. Moreover, clusters can be easily identified in X-ray as continuous, extended sources. As of today, interesting cosmological constraints have been obtained from relatively small cluster samples (~102), X-ray selected by the ROSAT satellite over a wide redshift range (0clusters, the ROSAT All-Sky Survey.The next generation of X-ray telescopes will enhance the statistics of detected clusters and enlarge their redshift coverage. In particular, eROSITA will produce a catalog of >105 clusters with photometric redshifts from multi-band optical surveys (e.g. PanSTARRS, DES, and LSST). This will vastly improve upon current cosmological constraints, especially by the synergy with other cluster surveys that

  15. Cool Cluster Correctly Correlated

    SciTech Connect

    Varganov, Sergey Aleksandrovich

    2005-01-01

    Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, since empirical and semiempirical methods rely on simple models with many parameters, it is often difficult to estimate the quantitative and even qualitative accuracy of the results. On the other hand, because of significant advances in quantum chemical methods and computer capabilities, it is now possible to do high quality ab-initio calculations not only on systems of few atoms but on clusters of practical interest as well. In addition to accurate results for specific clusters, such methods can be used for benchmarking of different empirical and semiempirical approaches. The atomic clusters studied in this work contain from a few atoms to

  16. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box.

    PubMed Central

    Kiledjian, M; Dreyfuss, G

    1992-01-01

    Heterogeneous nuclear ribonucleoproteins (hnRNPs) are thought to influence the structure of hnRNA and participate in the processing of hnRNA to mRNA. The hnRNP U protein is an abundant nucleoplasmic phosphoprotein that is the largest of the major hnRNP proteins (120 kDa by SDS-PAGE). HnRNP U binds pre-mRNA in vivo and binds both RNA and ssDNA in vitro. Here we describe the cloning and sequencing of a cDNA encoding the hnRNP U protein, the determination of its amino acid sequence and the delineation of a region in this protein that confers RNA binding. The predicted amino acid sequence of hnRNP U contains 806 amino acids (88,939 Daltons), and shows no extensive homology to any known proteins. The N-terminus is rich in acidic residues and the C-terminus is glycine-rich. In addition, a glutamine-rich stretch, a putative NTP binding site and a putative nuclear localization signal are present. It could not be defined from the sequence what segment of the protein confers its RNA binding activity. We identified an RNA binding activity within the C-terminal glycine-rich 112 amino acids. This region, designated U protein glycine-rich RNA binding region (U-gly), can by itself bind RNA. Furthermore, fusion of U-gly to a heterologous bacterial protein (maltose binding protein) converts this fusion protein into an RNA binding protein. A 26 amino acid peptide within U-gly is necessary for the RNA binding activity of the U protein. Interestingly, this peptide contains a cluster of RGG repeats with characteristic spacing and this motif is found also in several other RNA binding proteins. We have termed this region the RGG box and propose that it is an RNA binding motif and a predictor of RNA binding activity. Images PMID:1628625

  17. Melanin-binding radiopharmaceuticals

    SciTech Connect

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  18. Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

    DOEpatents

    Sanfilippo, Antonio; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2009-12-22

    Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

  19. ATOMIC AND MOLECULAR PHYSICS: Structures and Electronic Properties of CuN (N <= 13) Clusters

    NASA Astrophysics Data System (ADS)

    Feng, Cui-Ju; Zhang, Xiao-Yan

    2009-10-01

    A systematic study on the structures and electronic properties of copper clusters has been performed using the density functional theory. In the calculation, there are many isomers near the ground state for small copper clusters. Our results show that the three-dimensional isomers of copper clusters start from Cu7 cluster and then show a tendency to form more compact structures. The results of the formation energy and the second derivative of binding energy with cluster size show that besides N = 8, N = 11 is also a magic number. Furthermore, it is the first time to find that the ground state of 11-atom clusters is a biplanar structure as same as the 13-atom cluster. The clear odd-even alternation as cluster size for the formation energy indicates the stability of electronic close shell existed in the range studied.

  20. Studies in clustering theory

    NASA Astrophysics Data System (ADS)

    Stell, George

    In recent years the properties of percolation models have been studied intensively. The purpose of our project was to develop a general theory of percolation and clustering between particles of arbitrary size and shape, with arbitrary correlations between them. The goal of such a theory includes the treatment of continuum percolation as well as a novel treatment of lattice percolation. We made substantial progress toward this goal. The quantities basic to a description of clustering, the mean cluster size, mean number of clusters, etc., were developed. Concise formulas were given for the terms in such series, and proved, at least for sufficiently low densities, that the series are absolutely convergent. These series can now be used to construct Pade approximants that will allow one to probe the percolation transition. A scaled-particle theory of percolation was developed which gives analytic approximants for the mean number of clusters in a large class of two and three dimensional percolation models. Although this quantity is essential in many applications, e.g., explaining colligative properties, and interpreting low-angle light-scattering data, no systematic studies of it have been done before this work. Recently carried out detailed computer simulations show that the mean number of clusters is given to high accuracy by several of there approximations. Extensions of this work will allow calculation of the complete cluster size distribution.

  1. Directed Assembly of Hierarchically Ordered Clusters from Anisotropic Microparticles

    NASA Astrophysics Data System (ADS)

    Han, Koohee; Bharti, Bhuvnesh; Shields, C. Wyatt, IV; Lopez, Gabriel P.; Velev, Orlin D.

    The directed assembly of colloidal particles with specific connectivity, symmetry, and directional response requires controlled interactions and means of programmable binding force. We will show how patchy microparticles can be hierarchically assembled into ordered clusters, resulting from directional interactions between metal-coated facets. First, we introduce lipid mediated capillary bridging as a new class of binding force for directed assembly of metallo-dielectric patchy microspheres. Iron oxide surface patches on latex microspheres were selectively wetted with liquid lipids, guiding the particle assembly into well-defined 2D and 3D clusters. The temperature driven fluid-to-gel phase transition of the fatty acids acts as a thermal switch for cluster assembly and disassembly. Secondly, we used external fields to bind patchy microcubes based on their polarization configuration and interparticle interaction. We present assembled clusters of cobalt-coated patchy microcubes that can be dynamically reconfigured using external magnetic field. The residual polarization of ferromagnetic cobalt patches allows for preserving the assembled sequence even in the absence of the field and drives dynamic reconfiguration of assembled clusters. NSF Grant #DMR-1121107.

  2. Temporal Clustering and Sequencing in Short-Term Memory and Episodic Memory

    ERIC Educational Resources Information Center

    Farrell, Simon

    2012-01-01

    A model of short-term memory and episodic memory is presented, with the core assumptions that (a) people parse their continuous experience into episodic clusters and (b) items are clustered together in memory as episodes by binding information within an episode to a common temporal context. Along with the additional assumption that information…

  3. Extending Beowulf Clusters

    USGS Publications Warehouse

    Steinwand, Daniel R.; Maddox, Brian; Beckmann, Tim; Hamer, George

    2003-01-01

    Beowulf clusters can provide a cost-effective way to compute numerical models and process large amounts of remote sensing image data. Usually a Beowulf cluster is designed to accomplish a specific set of processing goals, and processing is very efficient when the problem remains inside the constraints of the original design. There are cases, however, when one might wish to compute a problem that is beyond the capacity of the local Beowulf system. In these cases, spreading the problem to multiple clusters or to other machines on the network may provide a cost-effective solution.

  4. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    Content-based multimedia indexing, retrieval, and processing as well as multimedia databases demand the structuring of the media content (image, audio, video, text, etc.), one significant goal being to associate the identity of the content to the individual segments of the signals. In this paper, we specifically address the problem of speaker clustering, the task of assigning every speech utterance in an audio stream to its speaker. We offer a complete treatment to the idea of partially supervised speaker clustering, which refers to the use of our prior knowledge of speakers in general to assist the unsupervised speaker clustering process. By means of an independent training data set, we encode the prior knowledge at the various stages of the speaker clustering pipeline via 1) learning a speaker-discriminative acoustic feature transformation, 2) learning a universal speaker prior model, and 3) learning a discriminative speaker subspace, or equivalently, a speaker-discriminative distance metric. We study the directional scattering property of the Gaussian mixture model (GMM) mean supervector representation of utterances in the high-dimensional space, and advocate exploiting this property by using the cosine distance metric instead of the euclidean distance metric for speaker clustering in the GMM mean supervector space. We propose to perform discriminant analysis based on the cosine distance metric, which leads to a novel distance metric learning algorithm—linear spherical discriminant analysis (LSDA). We show that the proposed LSDA formulation can be systematically solved within the elegant graph embedding general dimensionality reduction framework. Our speaker clustering experiments on the GALE database clearly indicate that 1) our speaker clustering methods based on the GMM mean supervector representation and vector-based distance metrics outperform traditional speaker clustering methods based on the “bag of acoustic features” representation and statistical

  5. H-cluster stars

    NASA Astrophysics Data System (ADS)

    Lai, X. Y.; Gao, C. Y.; Xu, R. X.

    2013-06-01

    The study of dense matter at ultrahigh density has a very long history, which is meaningful for us to understand not only cosmic events in extreme circumstances but also fundamental laws of physics. It is well known that the state of cold matter at supranuclear density depends on the non-perturbative nature of quantum chromodynamics (QCD) and is essential for modelling pulsars. A so-called H-cluster matter is proposed in this paper as the nature of dense matter in reality. In compact stars at only a few nuclear densities but low temperature, quarks could be interacting strongly with each other there. That might render quarks grouped in clusters, although the hypothetical quark clusters in cold dense matter have not been confirmed due to the lack of both theoretical and experimental evidence. Motivated by recent lattice QCD simulations of the H-dibaryons (with structure uuddss), we therefore consider here a possible kind of quark clusters, H-clusters, that could emerge inside compact stars during their initial cooling as the dominant components inside (the degree of freedom could then be H-clusters there). Taking into account the in-medium stiffening effect, we find that at baryon densities of compact stars H-cluster matter could be more stable than nuclear matter. We also find that for the H-cluster matter with lattice structure, the equation of state could be so stiff that it would seem to be `superluminal' in the most dense region. However, the real sound speed for H-cluster matter is in fact difficult to calculate, so at this stage we do not put constraints on our model from the usual requirement of causality. We study the stars composed of H-clusters, i.e. H-cluster stars, and derive the dependence of their maximum mass on the in-medium stiffening effect, showing that the maximum mass could be well above 2 M⊙ as observed and that the resultant mass-radius relation fits the measurement of the rapid burster under reasonable parameters. Besides a general

  6. Organising Atoms, Clusters and Proteins on Surfaces

    NASA Astrophysics Data System (ADS)

    Palmer, Richard E.

    2008-10-01

    This talk will discuss new developments in the creation of nanoscale surface features and their applications in biomedicine. Electron-surface interactions and plasma methods play a crucial role in both the production and analysis of these ``atomic architectures.'' At the extreme limit, electron injection from the tip of a scanning tunnelling microscope (STM) enables bond-selective manipulation of individual polyatomic molecules [1]. On a more practical level, the controlled deposition of size-selected clusters [2], generated by magnetron sputtering and gas condensation followed by mass selection, represents a surprisingly efficient route to the fabrication of surface features of size 1-10 nm, the size scale of biological molecules such as proteins. STM and AFM measurements show the clusters can act as binding sites for individual protein molecules. For example, the pinning of size-selected AuN clusters (N = 1--2000) to the (hydrophobic) graphite surface presents bindings site for sulphur atoms and thus for the cysteine residues in protein molecules. Systematic studies of different proteins [3] provide ``ground rules'' for residue-specific protein immobilisation by clusters and have led to the development of a novel biochip for protein screening by a spin-off company. The 3D atomic structure of the clusters is highly relevant to such applications. We show that measurement of the scattered electron beam intensity - specifically, the high angle annular dark field (HAADF) signal - in the scanning transmission electron microscope (STEM) allows us (a) to count the number of atoms in a cluster on the surface and (b) to determine a 3D atom-density map of the cluster when an aberration-corrected STEM is used [4]. 1. P.A. Sloan and R.E. Palmer, Nature 434 367 (2005). 2. S. Pratontep, P. Preece, C. Xirouchaki, R.E. Palmer, C.F. Sanz-Navarro, S.D. Kenny and R. Smith, Phys. Rev. Lett. 90 055503 (2003). 3. R.E. Palmer, S. Pratontep and H.-G. Boyen, Nature Materials 2 443 (2003

  7. Combining cluster number counts and galaxy clustering

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Rosenfeld, Rogerio

    2016-08-01

    The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

  8. Trinuclear Metal Clusters in Catalysis by Terpenoid Synthases.

    PubMed

    Aaron, Julie A; Christianson, David W

    2010-01-01

    Terpenoid synthases are ubiquitous enzymes that catalyze the formation of structurally and stereochemically diverse isoprenoid natural products. Many isoprenoid coupling enzymes and terpenoid cyclases from bacteria, fungi, protists, plants, and animals share the class I terpenoid synthase fold. Despite generally low amino acid sequence identity among these examples, class I terpenoid synthases contain conserved metal binding motifs that coordinate to a trinuclear metal cluster. This cluster not only serves to bind and orient the flexible isoprenoid substrate in the precatalytic Michaelis complex, but it also triggers the departure of the diphosphate leaving group to generate a carbocation that initiates catalysis. Additional conserved hydrogen bond donors assist the metal cluster in this function. Crystal structure analysis reveals that the constellation of three metal ions required for terpenoid synthase catalysis is generally identical among all class I terpenoid synthases of known structure.

  9. Statistical properties of convex clustering

    PubMed Central

    Tan, Kean Ming; Witten, Daniela

    2016-01-01

    In this manuscript, we study the statistical properties of convex clustering. We establish that convex clustering is closely related to single linkage hierarchical clustering and k-means clustering. In addition, we derive the range of the tuning parameter for convex clustering that yields a non-trivial solution. We also provide an unbiased estimator of the degrees of freedom, and provide a finite sample bound for the prediction error for convex clustering. We compare convex clustering to some traditional clustering methods in simulation studies.

  10. Probing the Hierarchy in Stellar Clustering Morphology

    NASA Astrophysics Data System (ADS)

    Gouliermis, Dimitrios

    2015-08-01

    The formation of stars is a ``social'' process. It leads to the assembly of young stars at various length-scales into structures of diverse degrees of self-binding, from gravitationally-bound star clusters to unbound stellar associations, and beyond. These different young stellar systems are, however, not independent to each other. In nearby star-forming regions compact clusters appear at few 1-pc scales as the nested centers of star formation within loose stellar aggregations of few 10-pc sizes. Resolved populations across whole galaxies show that these structures are themselves components of larger stellar complexes with typical sizes of few 100-pc, and this structural behavior seems to extend to kpc scales in galactic super-structures and spiral arms. From the stellar clustering point-of-view, star formation behaves as a scale-free process, expressed by power-laws in size distributions and correlation functions. The origins of the self-similar stellar structural morphology, the scales where it changes behavior, and how these scales are determined, are fundamental questions to our understanding of star formation. Star-forming complexes in the Magellanic Clouds, imaged with the Hubble Space Telescope, provide a complete stellar sampling, necessary to address these questions across length-scales of typical molecular clouds. I will present the spatial distribution of newly-born stars and evidence of its origins, its correlation to molecular gas morphology, and the connection between star formation rate derived from star-counts and gas surface density, across the star-forming complex N66 in the Small Magellanic Cloud. I will discuss our findings in terms of stellar clustering at birth, its hierarchical behavior, and its relation to the ISM morphology in an attempt to disentangle the physical conditions between clustered and non-clustered star formation within a giant molecular cloud.

  11. Understanding ligand effects in gold clusters using mass spectrometry.

    PubMed

    Johnson, Grant E; Laskin, Julia

    2016-06-21

    This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because "each-atom-counts" toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well-defined surfaces may be explored using ion soft landing (SL) in a custom

  12. Iron-sulfur cluster exchange reactions mediated by the human Nfu protein.

    PubMed

    Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

    2016-10-01

    Human Nfu is an iron-sulfur cluster protein that has recently been implicated in multiple mitochondrial dysfunctional syndrome (MMDS1). The Nfu family of proteins shares a highly homologous domain that contains a conserved active site consisting of a CXXC motif. There is less functional conservation between bacterial and human Nfu proteins, particularly concerning their Iron-sulfur cluster binding and transfer roles. Herein, we characterize the cluster exchange chemistry of human Nfu and its capacity to bind and transfer a [2Fe-2S] cluster. The mechanism of cluster uptake from a physiologically relevant [2Fe-2S](GS)4 cluster complex, and extraction of the Nfu-bound iron-sulfur cluster by glutathione are described. Human holo Nfu shows a dimer-tetramer equilibrium with a protein to cluster ratio of 2:1, reflecting the Nfu-bridging [2Fe-2S] cluster. This cluster can be transferred to apo human ferredoxins at relatively fast rates, demonstrating a direct role for human Nfu in the process of [2Fe-2S] cluster trafficking and delivery. PMID:27538573

  13. Iron-sulfur cluster exchange reactions mediated by the human Nfu protein.

    PubMed

    Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

    2016-10-01

    Human Nfu is an iron-sulfur cluster protein that has recently been implicated in multiple mitochondrial dysfunctional syndrome (MMDS1). The Nfu family of proteins shares a highly homologous domain that contains a conserved active site consisting of a CXXC motif. There is less functional conservation between bacterial and human Nfu proteins, particularly concerning their Iron-sulfur cluster binding and transfer roles. Herein, we characterize the cluster exchange chemistry of human Nfu and its capacity to bind and transfer a [2Fe-2S] cluster. The mechanism of cluster uptake from a physiologically relevant [2Fe-2S](GS)4 cluster complex, and extraction of the Nfu-bound iron-sulfur cluster by glutathione are described. Human holo Nfu shows a dimer-tetramer equilibrium with a protein to cluster ratio of 2:1, reflecting the Nfu-bridging [2Fe-2S] cluster. This cluster can be transferred to apo human ferredoxins at relatively fast rates, demonstrating a direct role for human Nfu in the process of [2Fe-2S] cluster trafficking and delivery.

  14. [Treatment of cluster headache].

    PubMed

    Fabre, N

    2005-07-01

    Remarkable therapeutic improvements have come forward recently for trigemino-autonomic cephalalgias. Attack treatment in cluster headache is based on sumatriptan and oxygen. Non-vasoconstrictive treatments are opening a new post-triptan era but are not yet applicable. Prophylactic treatment of cluster headache is based on verapamil and lithium. The efficacy of anti-epileptic drugs in cluster headache remains to be demonstrated. Surgical treatment aimed at the parasympathetic pathways and at the trigeminal nerve demonstrates a high rate of recurrence and adverse events and questions about the relevance of a "peripheral" target in cluster headache. The efficacy of continuous hypothalamic stimulation in patients with intractable headache constitutes a breakthrough, but must be demonstrated at a larger scale and the benefice/risk ratio must be carefully evaluated. Indomethacin still remains the gold standard in paroxysmal hemicrania treatment. Until recently SUNCT was considered an intractable condition. However there are some reports of complete relief with lamotrigine, topiramate and gabapentin.

  15. Mantis BT Cluster Support

    SciTech Connect

    Riot, V.

    2009-06-05

    The software is a modidication to the Mantis BT V1.5 open source application provided by the mantis BT group to support cluster web servers. It also provides various cosmetic modifications used a LLNL.

  16. Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein.

    PubMed

    Poppe, Juliane; Warkentin, Eberhard; Demmer, Ulrike; Kowalewski, Björn; Dierks, Thomas; Schneider, Klaus; Ermler, Ulrich

    2014-09-01

    The molybdenum storage protein (MoSto) can store more than 100 Mo or W atoms as discrete polyoxometalate (POM) clusters. Here, we describe the three POM cluster sites along the threefold axis of the protein complex based on four X-ray structures with slightly different polyoxomolybdate compositions between 1.35 and 2 Å resolution. In contrast to the Moα-out binding site occupied by an Mo3 cluster, the Moα-in and Moβ binding sites contain rather weak and non-uniform electron density for the Mo atoms (but clearly identifiable by anomalous data), suggesting the presence of POM cluster ensembles and/or degradation products of larger aggregates. The "Moα-in cluster ensemble" was interpreted as an antiprism-like Mo6 species superimposed with an Mo7 pyramide and the "Moβ cluster ensemble" as an Mo13 cluster (present mostly in a degraded form) composed of a pyramidal Mo7 and a Mo3 building block linked by three spatially separated MoOx units. Inside the ball-shaped Mo13 cluster sits an occluded central atom, perhaps a metal ion. POM cluster formation at the Moα-in and Moβ sites appears to be driven by filtering out and binding/protecting self-assembled transient species complementary to the protein template.

  17. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria.

    PubMed Central

    Tam, R; Saier, M H

    1993-01-01

    Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence similarities, and their degrees of relatedness have been determined. Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater

  18. Spotlight on Cluster

    NASA Astrophysics Data System (ADS)

    1994-09-01

    For the first and only time during the development and construction of Cluster, all four satellites will be together in the space testing facilities of IABG in Munich. On this unique occasion, ESA invites you, and in particular the visual media, to a joint ESA/Industry briefing on the Cluster project at 10h30 on Tuesday, 11 October at IABG, Einsteinstrasse 20, OTTOBRUNN (Germany). After the meeting, ESA and Industry representatives as well as mission specialists will be available for interviews. A detailed agenda is enclosed. If you intend to participate please return the attached registration form by fax (33.1) 42.73.76.90 to ESA Public Relations Division. CLUSTER BRIEFING Tuesday 11 October 1994 - IABG (Munich) Agenda 09h30 Welcome and first photo opportunity 10h30-10h35 Welcome by IABG Director 10h35-10h40 Introduction by Kurt-Johann Gluitz, Dornier, Vice-President Satellite Systems 10h40-10h55 The ESA science programme by Roger Bonnet, Director of the ESA Science programme 10h55-11h10 The mission overview by Rudi Schmidt, ESA, Cluster Project Scientist 11h10-11h20 The Cluster project by John Credland, ESA Cluster Project Manager 11h20-11h30 Cluster and the European Industry by Gunther Lehn, Dornier Cluster Project Manager 11h30-12h00 Question and answer session 12h00-14h00 Interviews and buffet lunch 13h00-14h00 Second photo opportunity 14h00 End

  19. Wild Duck Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    On April 7, 2005, the Deep Impact spacecraft's Impactor Target Sensor camera recorded this image of M11, the Wild Duck cluster, a galactic open cluster located 6 thousand light years away. The camera is located on the impactor spacecraft, which will image comet Tempel 1 beginning 22 hours before impact until about 2 seconds before impact. Impact with comet Tempel 1 is planned for July 4, 2005.

  20. Crystal-Templated Colloidal Clusters Exhibit Directional DNA Interactions.

    PubMed

    McGinley, James T; Wang, Yifan; Jenkins, Ian C; Sinno, Talid; Crocker, John C

    2015-11-24

    Spherical colloids covered with grafted DNA have been used in the directed self-assembly of a number of distinct crystal and gel structures. Simulation suggests that the use of anisotropic building blocks greatly augments the variety of potential colloidal assemblies that can be formed. Here, we form five distinct symmetries of colloidal clusters from DNA-functionalized spheres using a single type of colloidal crystal as a template. The crystals are formed by simple sedimentation of a binary mixture containing a majority "host" species that forms close-packed crystals with the minority "impurity" species occupying substitutional or interstitial defect sites. After the DNA strands between the two species are hybridized and enzymatically ligated, the results are colloidal clusters, one for each impurity particle, with a symmetry determined by the nearest neighbors in the original crystal template. By adjusting the size ratio of the two spheres and the timing of the ligation, we are able to generate clusters having the symmetry of tetrahedra, octahedra, cuboctahedra, triangular orthobicupola, and icosahedra, which can be readily separated from defective clusters and leftover spheres by centrifugation. We further demonstrate that these clusters, which are uniformly covered in DNA strands, display directional binding with spheres bearing complementary DNA strands, acting in a manner similar to patchy particles or proteins having multiple binding sites. The scalable nature of the fabrication process, along with the reprogrammability and directional nature of their resulting DNA interactions, makes these clusters suitable building blocks for use in further rounds of directed self-assembly.

  1. Tidal disruption of open clusters in their parent molecular clouds

    NASA Technical Reports Server (NTRS)

    Long, Kevin

    1989-01-01

    A simple model of tidal encounters has been applied to the problem of an open cluster in a clumpy molecular cloud. The parameters of the clumps are taken from the Blitz, Stark, and Long (1988) catalog of clumps in the Rosette molecular cloud. Encounters are modeled as impulsive, rectilinear collisions between Plummer spheres, but the tidal approximation is not invoked. Mass and binding energy changes during an encounter are computed by considering the velocity impulses given to individual stars in a random realization of a Plummer sphere. Mean rates of mass and binding energy loss are then computed by integrating over many encounters. Self-similar evolutionary calculations using these rates indicate that the disruption process is most sensitive to the cluster radius and relatively insensitive to cluster mass. The calculations indicate that clusters which are born in a cloud similar to the Rosette with a cluster radius greater than about 2.5 pc will not survive long enough to leave the cloud. The majority of clusters, however, have smaller radii and will survive the passage through their parent cloud.

  2. Cluster functional renormalization group

    NASA Astrophysics Data System (ADS)

    Reuther, Johannes; Thomale, Ronny

    2014-01-01

    Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.

  3. Metallochaperones: bind and deliver

    SciTech Connect

    Rosenzweig, A.C.

    2010-03-08

    Metallochaperones deliver metal ions directly to target proteins via specific protein-protein interactions. Recent research has led to a molecular picture of how some metallochaperones bind metal ions, recognize their partner proteins, and accomplish metal ion transfer.

  4. Anthramycin binding to deoxyribonucleic acid-mitomycin C complexes. Evidence for drug-induced deoxyribonucleic acid conformational change and cooperativity in mitomycin C binding.

    PubMed

    Kaplan, D J; Hurley, L H

    1981-12-22

    Anthramycin and mitomycin C (MC) are two DNA reactive drugs, which bind covalently to GC pairs producing different effects on DNA: anthramycin stiffening and MC distorsion. This paper describes experiments in which we have used anthramycin as a probe to sense quantitatively the effects on DNA of MC binding. Saturation binding experiments show that both anthramycin and MC partially inhibit the binding of the other drug to DNA (maximum inhibition by MC and anthramycin, 22.4% and 19.7%, respectively) but by a mechanism other than direct site exclusion. This suggests that MC binds in the major groove of DNA, since anthramycin is known to bind in the minor groove. An abrupt reduction in the binding of anthramycin to DNA-MC complexes occurs between MC binding ratios of 0.030 and 0.035, which parallels and probably results from sudden intensification of a MC-induced DNA conformational change occurring between these binding ratios. Dialysis measurements indicate that anthramycin is very possibly binding at sites distant from MC sites and suggest a clustering of closely bound MC chromophores resulting from possible cooperative binding. S1 nuclease digest experiments demonstrate an initial enhancement of nuclease activity in DNA-MC complexes, the magnitude of which correlates well with the reduction of anthramycin binding, relative to the degree of MC binding. The enhanced nuclease activity in these complexes indicates regions of exposed DNA or helix base distortion which is related to or is the result of conformational change. PMID:6798992

  5. The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO2 photoreduction

    DOE PAGES

    Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.; Joseph, Babu

    2015-09-04

    In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO2 photoreduction reaction (bent CO2–), we find that flatter (2D-like) Pt clusters that “wet” the TiO2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO2 interfacial sites with geometries that can aid CO2 bond bending and charge transfer processes. Second, binding competitionmore » among each Pt–CO2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO2 surfaces for CO2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO2 on TiO2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.« less

  6. Ag(I)-binding to phytochelatins.

    PubMed

    Mehra, R K; Tran, K; Scott, G W; Mulchandani, P; Saini, S S

    1996-02-01

    Phytochelatins (PCs) are glutathione-derived peptides with the general structure (gamma-Glu-Cys)nGly, where n varies from 2 to 11. A variety of metal ions such as Cu(II), Cd(II), Pb(II), Zn(II), and Ag(I) induce PC synthesis in plants and some yeasts. It has generally been assumed that the inducer metals also bind PCs. However, very little information is available on the binding of metals other than Cu(I) and Cd(II) to PCs. In this paper, we describe the Ag(I)-binding characteristics of PCs with the structure (gamma-Glu-Cys)2Gly, (gamma-Glu-Cys)3Gly, and (gamma-Glu-Cys)4Gly. The Ag(I)-binding stoichiometries of these three peptides were determined by (i) UV/VIS spectrophotometry, (ii) luminescence spectroscopy at 77 K, and (iii) reverse-phase HPLC. The three techniques yielded similar results. ApoPCs exhibit featureless absorption in the 220-340 nm range. The binding of Ag(I) to PCs induced the appearance of specific absorption shoulders. The titration end point was indicated by the flattening of the characteristic absorption shoulders. Similarly, luminescence at 77 K due to Ag(I)-thiolate clusters increased with the addition of graded Ag(I) equivalents. The luminescence declined when Ag(I) equivalents in excess of the saturating amounts were added to the peptides. At neutral pH, (gamma-Glu-Cys)2Gly, (gamma-Glu-Cys)3Gly, and (gamma-Glu-Cys)4Gly bind 1.0, 1.5, and 4.0 equivalents of Ag(I), respectively. The Ag(I)-binding capacity of (gamma-Glu-Cys)2Gly and (gamma-Glu-Cys)3Gly was increased at pH 5.0 and below so that Ag(I)/-SH ratio approached 1.0. A similar pH-dependent binding of Ag(I) to glutathione was also observed. The increased Ag(I)-binding to PCs at lower pH is of physiological significance as these peptides accumulate in acidic vacuoles. We also report lifetime data on Ag(I)-PCs. The relatively long decay-times (approximately 0.1-0.3 msec) accompanied with a large Stokes shift in the emission band are indicative of spin-forbidden phosphorescence. PMID

  7. [Fe₄S₄]- and [Fe₃S₄]-cluster formation in synthetic peptides.

    PubMed

    Hoppe, Alessandra; Pandelia, Maria-Eirini; Gärtner, Wolfgang; Lubitz, Wolfgang

    2011-11-01

    [Fe₄S₄]- and [Fe₃S₄]-clusters are ubiquitous iron-sulfur motifs in biological systems. The [Fe₃S₄] composition is, however, of much lower natural abundance than the more typical [Fe₄S₄]-clusters. In the present study formation of [Fe₃S₄]-clusters has been examined using chemically synthesized model peptides consisting of 33 amino acids (maquettes). Maquettes are effective synthetic analogs for metal-ion binding sites, allowing for a facile modification of the primary coordination sphere of iron-sulfur clusters. Maquettes have been designed following the [FeS]-cluster-binding motif of dimethyl sulfoxide reductase subunit B (DmsB) from Escherichia coli that carries a [Fe₄S₄]-cluster, but incorporates a [Fe₃S₄]-cluster instead upon mutation of one of the coordinating cysteines. The time-dependent formation of iron-sulfur clusters and the effects of exchanging selected amino acids in the model peptides, known to regulate the [Fe₃S₄] to [Fe₄S₄] ratio in the DmsB protein, were monitored by UV/Vis- and EPR-spectroscopy. Exchange of cysteines within the conserved CxxCxxC motif has a much stronger effect on cluster formation and stoichiometry than the exchange of a coordinating external cysteine. Amino acid exchange in the binding motif shows a dependence of the cluster stoichiometry on the amino acid side chain. Formation of [Fe₃S₄]-clusters in maquettes is less favorable compared to native proteins. The [Fe₃S₄] moiety appears to be a rather transient species towards the more stable (final) incorporation of a [Fe₄S₄]-cluster. Results are best described by an assembly mechanism that considers a successive coordination of the iron atoms by the peptide, rather than incorporation of an already pre-formed mercaptoethanol-coordinated [Fe₄S₄]-cluster.

  8. The first intron of the human growth hormone gene contains a binding site for glucocorticoid receptor.

    PubMed Central

    Moore, D D; Marks, A R; Buckley, D I; Kapler, G; Payvar, F; Goodman, H M

    1985-01-01

    Glucocorticoid receptor (GCR) protein stimulates transcription from a variety of cellular genes. We show here that GCR partially purified from rat liver binds specifically to a site within the first intron of the human growth hormone (hGH) gene, approximately 100 base pairs downstream from the start of hGH transcription. GCR binding is selectively inhibited by methylation of two short, symmetrically arranged clusters of guanine residues within this site. A cloned synthetic 24-base-pair deoxyoligonucleotide containing the predicted GCR binding sequence interacts specifically with GCR. The hGH binding site shares sequence homology with a GCR binding site upstream from the human metallothionein II gene and a subset of GCR binding sites from mouse mammary tumor virus. All of these binding sites for this eukaryotic transcriptional regulatory protein show remarkable similarity in overall geometry to the binding sites for several prokaryotic transcriptional regulatory proteins. Images PMID:2983311

  9. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters.

    PubMed

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-08-18

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1-12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms.

  10. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    NASA Astrophysics Data System (ADS)

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-08-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms.

  11. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    PubMed Central

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-01-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms. PMID:27534599

  12. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters.

    PubMed

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-01-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1-12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms. PMID:27534599

  13. The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO2 photoreduction.

    PubMed

    Yang, Chi-Ta; Wood, Brandon C; Bhethanabotla, Venkat R; Joseph, Babu

    2015-10-14

    Using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO2 photoreduction reaction (bent CO2(-)), we find that flatter (2D-like) Pt clusters that "wet" the TiO2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt-TiO2 interfacial sites with geometries that can aid CO2 bond bending and charge transfer processes. Second, binding competition among each Pt-CO2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO2 surfaces for CO2 photocatalysis. Clusters of ∼6-8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO2 on TiO2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters. PMID:26360461

  14. Trends in methanol decomposition on transition metal alloy clusters from scaling and Brønsted–Evans–Polanyi relationships

    SciTech Connect

    Mehmood, Faisal; Rankin, Rees B.; Greeley, Jeffrey; Curtiss, Larry A.

    2012-05-15

    A combination of first principles Density Functional Theory calculations and thermochemical scaling relationships are employed to estimate the thermochemistry and kinetics of methanol decomposition on unsupported subnanometer metal clusters. The approach uses binding energies of various atomic and molecular species, determined on the pure metal clusters, to develop scaling relationships that are then further used to estimate the methanol decomposition thermodynamics for a series of pure and bimetallic clusters with four atoms per cluster. Additionally, activation energy barriers are estimated from Brønsted–Evans–Polanyi plots relating transition and final state energies on these clusters. The energetic results are combined with a simple, microkinetically-inspired rate expression to estimate reaction rates as a function of important catalytic descriptors, including the carbon and atomic oxygen binding energies to the clusters. Finally, based on these analyses, several alloy clusters are identified as promising candidates for the methanol decomposition reaction.

  15. Behavioral Clustering of School Children.

    ERIC Educational Resources Information Center

    Huberty, Carl J.; And Others

    This article illustrates how a cluster analysis can be conducted, validated, and interpreted. Data normed for a behavioral assessment instrument with 14 scales on a nationally representative sample of U.S. school children were utilized. The discussion explores the similarity index, cluster method, cluster typology, cluster validity, cluster…

  16. Electronic structure, stability, and oxidation of boron-magnesium clusters and cluster solids

    SciTech Connect

    Reber, Arthur C.; Khanna, Shiv N.

    2015-02-07

    Electronic structure studies on Mg{sub m}B{sub n}{sup −} (1 ≤ n ≤ 15, 0 ≤ m ≤ 3) clusters have been performed to identify the nature of bonding and the origin of stability in the mixed clusters. Boron clusters are found to have planar structures marked by tangential, radial, and π aromaticity. The maximum stability is achieved for when all three types of aromaticity are quenched. The ring like B{sub n}{sup −} clusters are shown to be electron deficient for n = 6-8, and the addition of Mg atoms is found to enhance the stability of the boron cluster through ionic bonding that quenches the aromaticity and produces umbrella-like structures. Several species including MgB{sub 6}{sup −}, MgB{sub 8}{sup −}, Mg{sub 2}B{sup −}, and Mg{sub 3}B{sub 7}{sup −} are found to have the largest Mg binding energies due to this mechanism. The transfer of a single electron from the Mg atom to the boron cluster results in a Mg atom with a half-filled 3s orbital that may serve as an ignition center for combustion. Studies on the MgB{sub 7} and MgB{sub 4} cluster solids indicate that they are constructed from icosahedral and umbrella-like motifs and are semiconductors with band gap energies of 1.46 eV and 0.41 eV, respectively.

  17. Creeping Motion of Self Interstitial Atom Clusters in Tungsten

    NASA Astrophysics Data System (ADS)

    Zhou, Wang Huai; Zhang, Chuan Guo; Li, Yong Gang; Zeng, Zhi

    2014-05-01

    The formation and motion features of self interstitial atom (SIA) clusters in tungsten are studied by molecular dynamics (MD) simulations. The static calculations show that the SIA clusters are stable with binding energy over 2 eV. The SIA clusters exhibit a fast one dimensional (1D) motion along <111>. Through analysis of the change of relative distance between SIAs, we find that SIAs jump in small displacements we call creeping motion, which is a new collective diffusion process different from that of iron. The potential energy surface of SIAs implicates that the creeping motion is due to the strong interaction between SIAs. These imply that several diffusion mechanism for SIA clusters can operate in BCC metals and could help us explore deep insight into the performance of materials under irradiation.

  18. Creeping Motion of Self Interstitial Atom Clusters in Tungsten

    PubMed Central

    Zhou, Wang Huai; Zhang, Chuan Guo; Li, Yong Gang; Zeng, Zhi

    2014-01-01

    The formation and motion features of self interstitial atom (SIA) clusters in tungsten are studied by molecular dynamics (MD) simulations. The static calculations show that the SIA clusters are stable with binding energy over 2 eV. The SIA clusters exhibit a fast one dimensional (1D) motion along 〈111〉. Through analysis of the change of relative distance between SIAs, we find that SIAs jump in small displacements we call creeping motion, which is a new collective diffusion process different from that of iron. The potential energy surface of SIAs implicates that the creeping motion is due to the strong interaction between SIAs. These imply that several diffusion mechanism for SIA clusters can operate in BCC metals and could help us explore deep insight into the performance of materials under irradiation. PMID:24865470

  19. Linked Supramolecular Building Blocks for Enhanced Cluster Formation

    PubMed Central

    McLellan, Ross; Palacios, Maria A; Beavers, Christine M; Teat, Simon J; Piligkos, Stergios; Brechin, Euan K; Dalgarno, Scott J

    2015-01-01

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures. PMID:25641542

  20. Linked supramolecular building blocks for enhanced cluster formation

    DOE PAGES

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; Teat, Simon J.; Piligkos, Stergios; Brechin, Euan K.; Dalgarno, Scott J.

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  1. Linked supramolecular building blocks for enhanced cluster formation

    SciTech Connect

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; Teat, Simon J.; Piligkos, Stergios; Brechin, Euan K.; Dalgarno, Scott J.

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  2. Electronic and magnetic properties of CrGen (15 ⩽ n ⩽ 29) clusters: A DFT study

    NASA Astrophysics Data System (ADS)

    Mahtout, Sofiane; Tariket, Yacine

    2016-06-01

    We report ab initio calculations of electronic and magnetic properties of medium-sized CrGen (15 ⩽ n ⩽ 29) clusters using density functional theory. The encapsulation of Cr atoms within Gen clusters leads to stable Cr encapsulated Gen clusters. The binding energies generally increase while the differences between the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) generally decrease with the increasing of cluster size. The clusters of CrGen at size 16, 17, 19, 22, 24 and 29 exhibit high stabilities when compared to their neighbors. This has been discussed in terms of their structures, energies and the effect of the position of doping atom. Doping of Gen clusters with one Cr atom leads to CrGen clusters with magnetic moment depending on the structure of the clusters and the position of Cr atom in the clusters. Moreover, vertical ionization potential, vertical electronic affinity, and chemical hardness are also analyzed.

  3. A DFT study on the adsorption of CO and CO{sub 2} molecules on Pt{sub 4} and Ir{sub 4} clusters

    SciTech Connect

    Munieswaran, P.; Seenithurai, S.; Pandyan, R. Kodi; Kumar, S. Vinodh; Saranya, C.; Mahendran, M.

    2015-06-24

    We analyze the electronic structure and adsorption binding energy of CO and CO{sub 2} molecules adsorbed on Ir{sub 4} and Pt{sub 4} clusters by using Density functional theory (DFT). It is found that the Ir{sub 4} cluster has more adsorption binding energy than Pt{sub 4} cluster. We show that the Ir and Ir - supported materials are good catalytic materials and could be useful for gas sensor applications.

  4. ROTATING GLOBULAR CLUSTERS

    SciTech Connect

    Bianchini, P.; Varri, A. L.; Bertin, G.; Zocchi, A.

    2013-07-20

    Internal rotation is thought to play a major role in the dynamics of some globular clusters. However, in only a few cases has internal rotation been studied by the quantitative application of realistic and physically justified global models. Here, we present a dynamical analysis of the photometry and three-dimensional kinematics of {omega} Cen, 47 Tuc, and M15, by means of a recently introduced family of self-consistent axisymmetric rotating models. The three clusters, characterized by different relaxation conditions, show evidence of differential rotation and deviations from sphericity. The combination of line-of-sight velocities and proper motions allows us to determine their internal dynamics, predict their morphology, and estimate their dynamical distance. The well-relaxed cluster 47 Tuc is interpreted very well by our model; internal rotation is found to explain the observed morphology. For M15, we provide a global model in good agreement with the data, including the central behavior of the rotation profile and the shape of the ellipticity profile. For the partially relaxed cluster {omega} Cen, the selected model reproduces the complex three-dimensional kinematics; in particular, the observed anisotropy profile, characterized by a transition from isotropy to weakly radial anisotropy and then to tangential anisotropy in the outer parts. The discrepancy found for the steep central gradient in the observed line-of-sight velocity dispersion profile and for the ellipticity profile is ascribed to the condition of only partial relaxation of this cluster and the interplay between rotation and radial anisotropy.

  5. Clustering in bubbly liquids

    NASA Astrophysics Data System (ADS)

    Figueroa, Bernardo; Zenit, Roberto

    2004-11-01

    We are conducting experiments to determine the amount of clustering that occurs when small gas bubbles ascend in clean water. In particular, we are interested in flows for which the liquid motion around the bubbles can be described, with a certain degree of accuracy, using potential flow theory. This model is applicable for the case of bubbly liquids in which the Reynolds number is large and the Weber number is small. To clearly observe the formation of bubble clusters we propose the use of a Hele-Shaw-type channel. In this thin channel the bubbles cannot overlap in the depth direction, therefore the identification of bubble clusters cannot be misinterpreted. Direct video image analysis is performed to calculate the velocity and size of the bubbles, as well as the formation of clusters. Although the walls do affect the motion of the bubbles, the clustering phenomena does occur and has the same qualitative behavior as in fully three-dimensional flows. A series of preliminary measurements are presented. A brief discussion of our plans to perform PIV measurements to obtain the liquid velocity fields is also presented.

  6. Supervised clustering of genes

    PubMed Central

    Dettling, Marcel; Bühlmann, Peter

    2002-01-01

    Background We focus on microarray data where experiments monitor gene expression in different tissues and where each experiment is equipped with an additional response variable such as a cancer type. Although the number of measured genes is in the thousands, it is assumed that only a few marker components of gene subsets determine the type of a tissue. Here we present a new method for finding such groups of genes by directly incorporating the response variables into the grouping process, yielding a supervised clustering algorithm for genes. Results An empirical study on eight publicly available microarray datasets shows that our algorithm identifies gene clusters with excellent predictive potential, often superior to classification with state-of-the-art methods based on single genes. Permutation tests and bootstrapping provide evidence that the output is reasonably stable and more than a noise artifact. Conclusions In contrast to other methods such as hierarchical clustering, our algorithm identifies several gene clusters whose expression levels clearly distinguish the different tissue types. The identification of such gene clusters is potentially useful for medical diagnostics and may at the same time reveal insights into functional genomics. PMID:12537558

  7. Cu(I) binding properties of a designed metalloprotein.

    PubMed

    Xie, Fei; Sutherland, Duncan E K; Stillman, Martin J; Ogawa, Michael Y

    2010-03-01

    The Cu(I) binding properties of the designed peptide C16C19-GGY are reported. This peptide was designed to form an alpha-helical coiled-coil but modified to incorporate a Cys-X-X-Cys metal-binding motif along its hydrophobic face. Absorption, emission, electrospray ionization mass spectrometry (ESI-MS), and circular dichroism (CD) experiments show that a 1:1 Cu-peptide complex is formed when Cu(I) is initially added to a solution of the monomeric peptide. This is consistent with our earlier study in which the emissive 1:1 complex was shown to exist as a peptide tetramer containing a tetranuclear copper cluster Kharenko et al. (2005) [11]. The presence of the tetranuclear copper center is now confirmed by ESI-MS which along with UV data show that this cluster is formed in a cooperative manner. However, spectroscopic titrations show that continued addition of Cu(I) results in the occupation of a second, lower affinity metal-binding site in the metallopeptide. This occupancy does not significantly affect the conformation of the metallopeptide but does result in a quenching of the 600nm emission. It was further found that the exogenous reductant tris(2-carboxyethyl)phosphine (TCEP) can competitively inhibit the binding of Cu(I) to the low affinity site of the peptide, but does not interact with Cu(I) clusters.

  8. The X-ray emitting gas in poor clusters with central dominant galaxies

    NASA Technical Reports Server (NTRS)

    Kriss, G. A.; Cioffi, D. F.; Canizares, C. R.

    1983-01-01

    The 12 clusters detected in the present study by the Einstein Observatory's X-ray imaging proportional counter show X-ray emission centered on the dominant galaxy in all cases. Comparison of the deduced distribution of binding mass with the light distribution of the central galaxies of four clusters indicates that the mass/luminosity ratio rises to over 200 solar masses/solar luminosity in the galaxy halos. These halos must therefore, like the clusters themselves, posses dark matter. The X-ray data clearly show that the dominant galaxies sit at the bottoms of the poor cluster gravitational potential wells, suggesting a similar origin for dominant galaxies in poor and rich clusters, perhaps through the merger and cannibalism of cluster galaxies. It is the luminosity of the distended cD envelope that reflects the relative wealth of the cluster environment.

  9. Density functional theory study of MgnNi2 (n = 1-6) clusters

    NASA Astrophysics Data System (ADS)

    Li, Jing; Liu, Xiao-Yong; Zhu, Zheng-He; Sheng, Yong

    2012-03-01

    The geometries of MgnNi2(n = 1-6) clusters are studied by using the hybrid density functional theory (B3LYP) with LANL2DZ basis sets. For the ground-state structures of MgnNi2 clusters, the stabilities and the electronic properties are investigated. The results show that the groundstate structures and symmetries of Mg clusters change greatly due to the Ni atoms. The average binding energies have a growing tendency while the energy gaps have a declining tendency. In addition, the ionization energies exhibit an odd—even oscillation feature. We also conclude that n = 3, 5 are the magic numbers of the MgnNi2 clusters. The Mg3Ni2 and Mg5Ni2 clusters are more stable than neighbouring clusters, and the Mg4Ni2 cluster exhibits a higher chemical activity.

  10. Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

    PubMed

    Manzoor, Dar; Pal, Sourav

    2015-06-18

    Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

  11. Multiferroic rhodium clusters.

    PubMed

    Ma, Lei; Moro, Ramiro; Bowlan, John; de Heer, Walt A; Kirilyuk, Andrei

    2014-10-10

    Simultaneous magnetic and electric deflection measurements of rhodium clusters (Rh(N), 6 ≤ N ≤ 40) reveal ferromagnetism and ferroelectricity at low temperatures, while neither property exists in the bulk metal. Temperature-independent magnetic moments (up to 1 μ(B) per atom) are observed, and superparamagnetic blocking temperatures up to 20 K. Ferroelectric dipole moments on the order of 1D with transition temperatures up to 30 K are observed. Ferromagnetism and ferroelectricity coexist in rhodium clusters in the measured size range, with size-dependent variations in the transition temperatures that tend to be anticorrelated in the range n = 6-25. Both effects diminish with size and essentially vanish at N = 40. The ferroelectric properties suggest a Jahn-Teller ground state. These experiments represent the first example of multiferroic behavior in pure metal clusters. PMID:25375737

  12. Squaring cooperative binding circles

    PubMed Central

    Deutman, Alexander B. C.; Monnereau, Cyrille; Moalin, Mohamed; Coumans, Ruud G. E.; Veling, Nico; Coenen, Michiel; Smits, Jan M. M.; de Gelder, René; Elemans, Johannes A. A. W.; Ercolani, Gianfranco; Nolte, Roeland J. M.; Rowan, Alan E.

    2009-01-01

    The cooperative binding effects of viologens and pyridines to a synthetic bivalent porphyrin receptor are used as a model system to study how the magnitudes of these effects relate to the experimentally obtained values. The full thermodynamic and kinetic circles concerning both activation and inhibition of the cage of the receptor for the binding of viologens were measured and evaluated. The results strongly emphasize the apparent character of measured binding and rate constants, in which the fractional saturation of receptors with other guests is linearly expressed in these constants. The presented method can be used as a simple tool to better analyze and comprehend the experimentally observed kinetics and thermodynamics of natural and artificial cooperative systems. PMID:19470643

  13. Mechanisms for optical binding

    NASA Astrophysics Data System (ADS)

    Andrews, David L.; Davila Romero, Luciana C.

    2009-08-01

    The phenomenon of optical binding is now experimentally very well established. With a recognition of the facility to collect and organize particles held in an optical trap, the related term 'optical matter' has also been gaining currency, highlighting possibilities for a significant interplay between optically induced inter-particle forces and other interactions such as chemical bonding and dispersion forces. Optical binding itself has a variety of interpretations. With some of these explanations being more prominent than others, and their applicability to some extent depending on the nature of the particles involved, a listing of these has to include the following: collective scattering, laser-dressed Casimir forces, virtual photon coupling, optically induced dipole resonance, and plasmon resonance coupling. It is the purpose of this paper to review and to establish the extent of fundamental linkages between these theoretical descriptions, recognizing the value that each has in relating the phenomenon of optical binding to the broader context of other, closely related physical measurements.

  14. STRUCTURAL PARAMETERS FOR 10 HALO GLOBULAR CLUSTERS IN M33

    SciTech Connect

    Ma, Jun

    2015-05-15

    In this paper, we present the properties of 10 halo globular clusters (GCs) with luminosities L ≃ 5–7 × 10{sup 5} L{sub ⊙} in the Local Group galaxy M33 using images from the Hubble Space Telescope WFPC2 in the F555W and F814W bands. We obtained the ellipticities, position angles, and surface brightness profiles for each GC. In general, the ellipticities of the M33 sample clusters are similar to those of the M31 clusters. The structural and dynamical parameters are derived by fitting the profiles to three different models combined with mass-to-light ratios (M/L values) from population-synthesis models. The structural parameters include core radii, concentration, half-light radii, and central surface brightness. The dynamical parameters include the integrated cluster mass, integrated binding energy, central surface mass density, and predicted line of sight velocity dispersion at the cluster center. The velocity dispersions of the four clusters predicted here agree well with the observed dispersions by Larsen et al. The results here showed that the majority of the sample halo GCs are better fitted by both the King model and the Wilson model than the Sérsic model. In general, the properties of the clusters in M33, M31, and the Milky Way fall in the same regions of parameter spaces. The tight correlations of cluster properties indicate a “fundamental plane” for clusters, which reflects some universal physical conditions and processes operating at the epoch of cluster formation.

  15. Physics of small metal clusters: Topology, magnetism, and electronic structure

    NASA Astrophysics Data System (ADS)

    Rao, B. K.; Jena, P.

    1985-08-01

    The electronic structure of small clusters of lithium atoms has been calculated using the self-consistent-field, molecular-orbital method. The exchange interaction is treated at the unrestricted Hartree-Fock level whereas the correlation is treated perturbatively up to second order by including pair excitations. This is done in two steps, one involving only the valence electrons and the other including all the electrons. A configuration-interaction calculation has also been done with all possible pair excitations. The equilibrium geometries of both the neutral and ionized clusters have been obtained by starting from random configurations and using the Hellmann-Feynman forces to follow the path of steepest descent to a minimum of the energy surface. The clusters of Li atoms each containing one to five atoms are found to be planar. The equilibrium geometry of a cluster is found to be intimately related to its electronic structure. The preferred spin configuration of a cluster has been found by minimizing the total energy of the cluster with respect to various spin assignments. The planar clusters are found to be less magnetic than expected by Hund's-rule coupling. For three-dimensional clusters, however, the magnetism is governed by Hund's rule. The effect of correlation has been found to have decisive influence on the equilibrium topology and magnetism of the clusters. The binding energy per atom, the energy of dissociation, and the ionization potential of the clusters are compared with experiment and with previous calculations. The physical origin of the magic numbers and the effect of the basis functions on the calculated properties have also been investigated.

  16. Silver cluster-biomolecule hybrids: from basics towards sensors.

    PubMed

    Bonačić-Koutecký, Vlasta; Kulesza, Alexander; Gell, Lars; Mitrić, Roland; Antoine, Rodolphe; Bertorelle, Franck; Hamouda, Ramzi; Rayane, Driss; Broyer, Michel; Tabarin, Thibault; Dugourd, Philippe

    2012-07-14

    We focus on the functional role of small silver clusters in model hybrid systems involving peptides in the context of a new generation of nanostructured materials for biosensing. The optical properties of hybrids in the gas phase and at support will be addressed with the aim to bridge fundamental and application aspects. We show that extension and enhancement of absorption of peptides can be achieved by small silver clusters due to the interaction of intense intracluster excitations with the π-π* excitations of chromophoric aminoacids. Moreover, we demonstrate that the binding of a peptide to a supported silver cluster can be detected by the optical fingerprint. This illustrates that supported silver clusters can serve as building blocks for biosensing materials. Moreover, the clusters can be used simultaneously to immobilize biomolecules and to increase the sensitivity of detection, thus replacing the standard use of organic dyes and providing label-free detection. Complementary to that, we show that protected silver clusters containing a cluster core and a shell liganded by thiolates exhibit absorption properties with intense transitions in the visible regime which are also suitable for biosensing applications.

  17. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    1999-01-01

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  18. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    2001-10-09

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  19. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Carolyn

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  20. Structure and energetics of small iron clusters.

    PubMed

    Cervantes-Salguero, Keitel; Seminario, Jorge M

    2012-09-01

    Electronic properties of Fe(2-10) clusters and their ions are described by an all-electron ab initio density functional theory computational analysis using the Handy's OPTX exchange and the gradient-corrected correlation functional of Perdew, Burke and Ernzerhof with a triple-zeta valence basis set plus polarization functions. Ground state structures, magnetic moments, dissociation energies, binding energies, IR vibrational spectra, vertical and adiabatic ionization energies, and electron affinities are reported. Two possible states for Fe(2) which are separated by 81.54 meV are described as possible Fe(2), while the septet (ground state) yields an accurate bond distance (error of 0.02 Å); the nonet yields a precise vibrational frequency (error of 10.1 cm(-1)). Fe(2) binding energy (0.05 eV/atom error) more closely resembles experimental data than any other previously reported computational methods. In addition, the Fe(6) is found to be the most stable cluster within our set being analyzed. PMID:22466530

  1. Carbon-vacancy complexes as traps for self-interstitial clusters in Fe-C alloys

    NASA Astrophysics Data System (ADS)

    Anento, N.; Serra, A.

    2013-09-01

    Self-interstitial loops in irradiated Fe-C alloys are formed by the growth of small self-interstitial atom clusters created directly in cascades. For these clusters to grow up to visible sizes they should be stopped by traps otherwise they would disappear in sinks due to their high one dimensional mobility. The well-known affinity of carbon with vacancies in α-Fe leads to the formation of carbon-vacancy (C-V) complexes that are potential candidates as traps for SIA loops. Applying molecular static simulations we have studied the interaction between the most abundant C-V complexes and SIA clusters using a metallic covalent interatomic model for the Fe-C system. The complexes studied, {Cn-Vm}, are C-V, C-V2 and C2-V. The maximum binding energies obtained for the interaction with a 1/2 <1 1 1> 61SIA cluster are 0.75 eV for the C-V, 1.4 eV for the C-V2 and 1.5 eV for C2-V. Finally, additional MD simulations were used to check the stability of the traps at high temperature. C-V} complexes have higher binding energies than single C atoms and their interaction depends strongly on their position relative to the SIA cluster. The vacancies of the complexes only recombine with the interstitials when they are at the edge of the cluster. The C-V2 complex located in the central region of the cluster has a binding energy of 1.4 eV which results in a good trap for the cluster. In this case the efficiency of a di-vacancy to stop the movement of the cluster is enhanced by the C atom that contributes to the binding energy and inhibits the vacancies to migrate to the cluster edge. C2-V extends to high temperatures the effectiveness of C-V2 as a trap at low temperatures. For this complex the higher interaction occurs at the periphery of the cluster when the vacancy recombination leaves two C atoms strongly tight with a binding energy up to 1.5 eV. Both linear and adjacent configurations are stable and should coexist. Since their binding energies with the cluster are comparable, the

  2. A sodium atom in a large water cluster: Electron delocalization and infrared spectra

    NASA Astrophysics Data System (ADS)

    Cwiklik, Lukasz; Buck, Udo; Kulig, Waldemar; Kubisiak, Piotr; Jungwirth, Pavel

    2008-04-01

    Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster. IR spectra of the sodium-water cluster are both computationally and experimentally obtained, with a good agreement between the two approaches.

  3. Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters.

    PubMed

    Bartolami, Eline; Bessin, Yannick; Gervais, Virginie; Dumy, Pascal; Ulrich, Sébastien

    2015-08-24

    We report herein the implementation of a dynamic covalent chemistry approach to the generation of multivalent clusters for DNA recognition. We show that biomolecular clusters can be expressed in situ by a programmed self-assembly process using chemoselective ligations. The cationic clusters are shown, by fluorescence displacement assay, gel electrophoresis and isothermal titration calorimetry, to effectively complex DNA through multivalent interactions. The reversibility of the ligation was exploited to demonstrate that template effects occur, whereby DNA imposes component selection in order to favor the most active DNA-binding clusters. Furthermore, we show that a chemical effector can be used to trigger DNA release through component exchange reactions. PMID:26177835

  4. Adaptive Tempering Monte Carlo Optimization of Calcium Clusters.

    NASA Astrophysics Data System (ADS)

    Dong, X.; Blaisten-Barojas, E.

    2006-03-01

    The global minimum energy structures of calcium clusters with 15 to 34 atoms were obtained by the Adaptive Tempering Monte Carlo (ATMC) method. The cluster binding energy was obtained within a tight binding approach with parameters reported in previous work[1]. The ATMC optimization process is fast and drives the system across configuration space very effectively reaching the global minimum within a small number of tempering events. The structure of six cluster sizes 15, 16, 18, 21, 23 and 25 corresponding to the global minimum has not been reported in the literature for any other metals. Three clusters Ca15, Ca21 and Ca23 are relatively more stable than the others in this size range. Melting of these clusters are further studied with the weighted histogram analysis method and the free energy profile is predicted. The melting transition is monitored with a novel structural order parameter that reflects the mobility of surface atoms, their bonding order and bonding directionality. [1] X. Dong, G. M. Wang, E. Blaisten-Barojas, Phys. Rev. B 70, 205409 (2004).

  5. Monomeric Yeast Frataxin is an Iron Binding Protein†

    SciTech Connect

    Cook, J.; Bencze, K; Jankovic, A; Crater, A; Busch, C; Bradley, P; Stemmler, A; Spaller, M; Stemmler, T

    2009-01-01

    Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.

  6. Monomeric Yeast Frataxin is an Iron-Binding Protein

    SciTech Connect

    Cook,J.; Bencze, K.; Jankovic, A.; Crater, A.; Busch, C.; Bradley, P.; Stemmler, A.; Spaller, M.; Stemmler, T.

    2006-01-01

    Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50 000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.

  7. Loss of p53 induces epidermal growth factor receptor promoter activity in normal human keratinocytes

    PubMed Central

    Bheda, A; Creek, KE; Pirisi, L

    2008-01-01

    Overexpression of the epidermal growth factor receptor (EGFR) in human papillomavirus type 16-immortalized human keratinocytes (HKc) is caused by the viral oncoprotein E6, which targets p53 for degradation. We have previously observed that expression of p53 RNAi in normal HKc is associated with an increase in EGFR mRNA and protein. We now report that p53 RNAi induces EGFR promoter activity up to approximately 10-fold in normal HKc, and this effect does not require intact p53 binding sites on the EGFR promoter. Exogenous wild-type p53 inhibits the EGFR promoter at low levels, and activates it at higher concentrations. Yin Yang 1 (YY1), which negatively regulates p53, induces EGFR promoter activity, and this effect is augmented by p53 RNAi. Intact p53 binding sites on the EGFR promoter are not required for activation by YY1. In addition, Sp1 and YY1 synergistically induce the EGFR promoter in normal HKc, indicating that Sp1 may recruit YY1 as a co-activator. Wild-type p53 suppressed Sp1- and YY1-mediated induction of the EGFR promoter. We conclude that acute loss of p53 in normal HKc induces EGFR expression bya mechanism that involves YY1 and Sp1 and does not require p53 binding to the EGFR promoter. PMID:18391986

  8. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application

    PubMed Central

    Hoinka, Jan; Berezhnoy, Alexey; Sauna, Zuben E.; Przytycka, Teresa M.

    2014-01-01

    Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a well established experimental procedure to identify aptamers - synthetic single-stranded (ribo)nucleic molecules that bind to a given molecular target. Recently, new sequencing technologies have revolutionized the SELEX protocol by allowing for deep sequencing of the selection pools after each cycle. The emergence of High Throughput SELEX (HT-SELEX) has opened the field to new computational opportunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selection process itself, we developed AptaCluster. This algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets. We performed HT-SELEX with Interleukin 10 receptor alpha chain (IL-10RA) as the target molecule and used AptaCluster to analyze the resulting sequences. AptaCluster allowed for the first survey of the relationships between sequences in different selection rounds and revealed previously not appreciated properties of the SELEX protocol. As the first tool of this kind, AptaCluster enables novel ways to analyze and to optimize the HT-SELEX procedure. Our AptaCluster algorithm is available as a very fast multiprocessor implementation upon request. PMID:25558474

  9. The ACS Survey of Galactic Globular Clusters. VIII. Effects of Environment on Globular Cluster Global Mass Functions

    NASA Astrophysics Data System (ADS)

    Paust, Nathaniel E. Q.; Reid, I. Neill; Piotto, Giampaolo; Aparicio, Antonio; Anderson, Jay; Sarajedini, Ata; Bedin, Luigi R.; Chaboyer, Brian; Dotter, Aaron; Hempel, Maren; Majewski, Steven; Marín-Franch, A.; Milone, Antonino; Rosenberg, Alfred; Siegel, Michael

    2010-02-01

    We have used observations obtained as part of the Hubble Space Telescope/ACS Survey of Galactic Globular Clusters to construct global present-day mass functions for 17 globular clusters utilizing multi-mass King models to extrapolate from our observations to the global cluster behavior. The global present-day mass functions for these clusters are well matched by power laws from the turnoff, ≈0.8 M sun, to 0.2-0.3 M sun on the lower main sequence. The slopes of those power-law fits, α, have been correlated with an extensive set of intrinsic and extrinsic cluster properties to investigate which parameters may influence the form of the present-day mass function. We do not confirm previous suggestions of correlations between α and either metallicity or Galactic location. However, we do find a strong statistical correlation with the related parameters central surface brightness, μ V , and inferred central density, ρ0. The correlation is such that clusters with denser cores (stronger binding energy) tend to have steeper mass functions (a higher proportion of low-mass stars), suggesting that dynamical evolution due to external interactions may have played a key role in determining α. Thus, the present-day mass function may owe more to nurture than to nature. Detailed modeling of external dynamical effects is therefore a requisite for determining the initial mass function for Galactic globular clusters.

  10. THE ACS SURVEY OF GALACTIC GLOBULAR CLUSTERS. VIII. EFFECTS OF ENVIRONMENT ON GLOBULAR CLUSTER GLOBAL MASS FUNCTIONS

    SciTech Connect

    Paust, Nathaniel E. Q.; Reid, I. Neill; Anderson, Jay E-mail: inr@stsci.edu

    2010-02-15

    We have used observations obtained as part of the Hubble Space Telescope/ACS Survey of Galactic Globular Clusters to construct global present-day mass functions for 17 globular clusters utilizing multi-mass King models to extrapolate from our observations to the global cluster behavior. The global present-day mass functions for these clusters are well matched by power laws from the turnoff, {approx}0.8 M {sub sun}, to 0.2-0.3 M {sub sun} on the lower main sequence. The slopes of those power-law fits, {alpha}, have been correlated with an extensive set of intrinsic and extrinsic cluster properties to investigate which parameters may influence the form of the present-day mass function. We do not confirm previous suggestions of correlations between {alpha} and either metallicity or Galactic location. However, we do find a strong statistical correlation with the related parameters central surface brightness, {mu} {sub V}, and inferred central density, {rho}{sub 0}. The correlation is such that clusters with denser cores (stronger binding energy) tend to have steeper mass functions (a higher proportion of low-mass stars), suggesting that dynamical evolution due to external interactions may have played a key role in determining {alpha}. Thus, the present-day mass function may owe more to nurture than to nature. Detailed modeling of external dynamical effects is therefore a requisite for determining the initial mass function for Galactic globular clusters.

  11. Health Occupations Cluster.

    ERIC Educational Resources Information Center

    Walraven, Catherine; And Others

    These instructional materials consist of a series of curriculum worksheets that cover tasks to be mastered by students in health occupations cluster programs. Covered in the curriculum worksheets are diagnostic procedures; observing/recording/reporting/planning; safety; nutrition/elimination; hygiene/personal care/comfort;…

  12. Nuclear Cluster Physics

    SciTech Connect

    Kamimura, Masayasu

    2011-05-06

    Predictive power of theory needs good models and accurate calculation methods to solve the Schroedinger equations of the systems concerned. We present some examples of successful predictions based on the nuclear cluster models of light nuclei and hypernuclei and on the calculation methods that have been developed by Kyushu group.

  13. Clustering in Bubble Suspensions

    NASA Astrophysics Data System (ADS)

    Zenit, Roberto

    2000-11-01

    A monidisperse bubble suspension is studied experimentally for the limit in which the Weber number is small and the Reynolds number is large. For this regime the suspension can be modeled using potential flow theory to describe the dynamics of the interstitial fluid. Complete theoretical descriptions have been composed (Spelt and Sangani, 1998) to model the behavior of these suspensions. Bubble clustering is a natural instability that arises from the potential flow considerations, in which bubbles tend to align in horizontal rafts as they move upwards. The appearance of bubble clusters was recently corroborated experimentally by Zenit et al. (2000), who found that although clusters did appear, their strength was not as strong as the predictions. Experiments involving gravity driven shear flows are used to explain the nature of the clustering observed in these type of flows. Balances of the bubble phase pressure (in terms of a calculated diffusion coefficient) and the Maxwell pressure (from the potential flow description) are presented to predict the stability of the bubble suspension. The predictions are compared with experimental results.

  14. Infrared Coronet Cluster

    NASA Technical Reports Server (NTRS)

    2007-01-01

    While perhaps not quite as well known as its star formation cousin of Orion, the Corona Australis region (containing, at its heart, the Coronet cluster) is one of the nearest and most active regions of ongoing star formation. The Spitzer image shows young stars plus diffuse emission from dust.

  15. Health Occupations Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Intended to assist the vocational teacher in designing and implementing a cluster program in health occupations, this guide suggests ideas for teaching the specific knowledge and skills that qualify students for entry-level employment in the health occupations field. The knowledge and skills are applicable to 12 occupations: dental assistant;…

  16. FUEL ROD CLUSTERS

    DOEpatents

    Schultz, A.B.

    1959-08-01

    A cluster of nuclear fuel rods and a tubular casing therefor through which a coolant flows in heat-exchange contact with the fuel rods is described. The fuel rcds are held in the casing by virtue of the compressive force exerted between longitudinal ribs of the fuel rcds and internal ribs of the casing or the internal surfaces thereof.

  17. Buckets, Clusters and Dienst

    NASA Technical Reports Server (NTRS)

    Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

    1997-01-01

    In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

  18. Detecting alternative graph clusterings.

    PubMed

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network.

  19. Construction Cluster Skills Standards.

    ERIC Educational Resources Information Center

    DePaul Univ., Chicago, IL. Built Environment Partnership.

    Twelve construction cluster skill standards and associated benchmarks were developed as part of a federally funded school-to-work initiative that included the following parties: the Chicago Public Schools; City Colleges of Chicago; and business, labor, and community organizations. The standards, which include core academic, generic workplace…

  20. PVM Support for Clusters

    NASA Technical Reports Server (NTRS)

    Springer, P.

    2000-01-01

    The latest version of PVM (3.4.3) now contains support for a PC cluster running Linux, also known as a Beowulf system. A PVM user of a computer outside the Beowulf system can add the Beowulf as a single machine.

  1. Curriculum Guide Construction Cluster.

    ERIC Educational Resources Information Center

    Kline, Ken

    As part of a model construction cluster curriculum development project, this guide was developed and implemented in the Beaverton (Oregon) School District. The curriculum guide contains 16 units covering the following topics: introduction to construction jobs; safety and first aid; blueprint readings; basic mathematics; site work; framing; roofing…

  2. The folate binding proteins.

    PubMed

    Corrocher, R; Olivieri, O; Pacor, M L

    1991-01-01

    Folates are essential molecules for cell life and, not surprisingly, their transport in biological fluids and their transfer to cells are finely regulated. Folate binding proteins play a major role in this regulation. This paper will review our knowledge on these proteins and examine the most recent advances in this field. PMID:1820987

  3. MD-2 binds cholesterol.

    PubMed

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  4. Sequential memory: Binding dynamics

    NASA Astrophysics Data System (ADS)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  5. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  6. Lectin binding in meningiomas.

    PubMed

    Kleinert, R; Radner, H

    1987-01-01

    Forty-two meningiomas of different morphological sub-type were examined to determine their pattern of binding to 11 different lectins which characterize cell surface components such as carbohydrate residues. Histiocytic and xanthoma cells within meningiomas could be demonstrated with six different lectins: wheat germ agglutinin (WGA), peanut agglutinin (PNA) Bauhinia purpurea agglutinin (BPA), Helix pomatia agglutinin (HPA), Vicia fava agglutinin (VFA) and Soyabean agglutinin (SBA). Vascular elements including endothelial cells and intimal cells, bound Ulex europaeus agglutinin type 1 (UEA 1), WGA and HPA. The fibrous stroma in fibrous and fibroblastic meningiomas bound PNA, Laburnum alpinum agglutinin (LAA) and SBA. Tumour cells in meningotheliomatous meningiomas and some areas of anaplastic meningiomas bound Concanavalin A, PNA, LAA and VFA whereas tumour cells in fibrous and fibroblastic meningiomas bound BPA, LAA and VFA. Lectin binding has proved to be of value in detecting histiocytic and xanthoma cells together with vascular elements within meningiomas. In addition, the different lectin binding patterns allow different histological sub-types of meningioma to be distinguished although the biological significance of the binding patterns is unclear. PMID:3658105

  7. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  8. Sequential memory: Binding dynamics.

    PubMed

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories-episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities. PMID:26520084

  9. Multiple sup 3 H-oxytocin binding sites in rat myometrial plasma membranes

    SciTech Connect

    Crankshaw, D.; Gaspar, V.; Pliska, V. )

    1990-01-01

    The affinity spectrum method has been used to analyse binding isotherms for {sup 3}H-oxytocin to rat myometrial plasma membranes. Three populations of binding sites with dissociation constants (Kd) of 0.6-1.5 x 10(-9), 0.4-1.0 x 10(-7) and 7 x 10(-6) mol/l were identified and their existence verified by cluster analysis based on similarities between Kd, binding capacity and Hill coefficient. When experimental values were compared to theoretical curves constructed using the estimated binding parameters, good fits were obtained. Binding parameters obtained by this method were not influenced by the presence of GTP gamma S (guanosine-5'-O-3-thiotriphosphate) in the incubation medium. The binding parameters agree reasonably well with those found in uterine cells, they support the existence of a medium affinity site and may allow for an explanation of some of the discrepancies between binding and response in this system.

  10. Structural properties of small rhodium clusters

    NASA Astrophysics Data System (ADS)

    Soon, Yee Yeen; Lim, Thong Leng; Yoon, Tiem Leong

    2015-04-01

    We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

  11. Structural properties of small rhodium clusters

    SciTech Connect

    Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

  12. Investigating Electronic Properties of Ionized PAH Clusters

    NASA Astrophysics Data System (ADS)

    Joblin, C.; Kokkin, D.; Bonnamy, A.; Toublanc, D.; Rapacioli, M.; Simon, A.; Dontot, L.; Gamboa, A.; Spiegelman, F.; Parneix, P.; Pino, T.; Pirali, O.; Feraud, G.; Friha, H.; Falvo, C.; Brechignac, P.; Garcia, G.; Nahon, L.; Mulas, G.

    2012-06-01

    Polycyclic aromatic hydrocarbon (PAH) clusters have been proposed as candidates for evaporating very small grains that are revealed by their mid-IR emission at the surface of UV-irradiated clouds in interstellar space. This motivates studies on the photostability and spectroscopic signatures of such species to validate their presence in interstellar environments and constrain their survival therein. We have used the molecular beam chamber SAPHIRS and the photoelectron-photoion coincidence spectrometer DELICIOUS II at the SOLEIL synchrotron facility to characterize the electronic properties of cationic coronene (C24H12) clusters up to the pentamer. These experimental results are analysed in the light of electronic structure calculations. In particular a Density Functional Tight Binding + Configuration Interaction scheme is developed to describe charge delocalization in these large systems and calculate the ionization potential, vibrational spectra, and charge transfer excited states. For the coronene dimer cation, complementary measurements are performed with the PIRENEA set-up to quantify some of the electronic transitions, in particular their oscillator strengths that cannot be extracted from the photoelectron spectroscopy. Emphasis will be put on the evolution of the spectra with cluster size. M. Rapacioli, C. Joblin and P. Boissel Astron. & Astrophys. 429, 193-204 (2005) G. Garcia, H. Soldi-Lose and L. Nahon Rev. Sci. Instrum. 80, 023102 (2009) Joint ANR project GASPARIM, ANR-10-BLAN-501 M. Rapacioli, A. Simon, L. Dontot and F. Spiegelman Phys. Status Solidi B 249 (2) 245-258 (2012)

  13. PDMS embedded Ag clusters: Coalescence and cluster-matrix interaction

    NASA Astrophysics Data System (ADS)

    Roese, S.; Engemann, D.; Hoffmann, S.; Latussek, K.; Sternemann, C.; Hövel, H.

    2016-05-01

    Polydimethylsiloxane (PDMS) has proven to be a suitable embedding medium for silver clusters to prevent aggregation. In order to investigate the influence of the PDMS on the electronic and local atomic structure of the clusters the measurement of x-ray absorption near edge structure (XANES) spectra for different coverages of silver clusters in PDMS and calculations of corresponding XANES spectra have been performed. The coalescence process and the cluster-PDMS interaction were investigated with XANES.

  14. Probing the Unique Size-Dependent Properties of Small Au Clusters, Au Alloy Clusters, and CO Chemisorbed Au Clusters in the Gas Phase

    SciTech Connect

    Zhai, Hua-jin; Li, Xi; Wang, Lai S.

    2007-04-01

    When materials are reduced in size to the nanometer scale, their physical and chemical properties undergo major changes and become size-dependent, forming the foundation for nanoscience and nanotechnology. Gold nanoparticles and small gold clusters have been the focus of intensive research activities lately. The modern “goldrush” is largely motivated by the recent discoveries that (i) nanogold shows unexpected catalytic properties for a wide spectrum of chemical reactions [1], (ii) nanogold enables selective binding to biomolecules such as DNA and thus can serve as biosensors [2], (iii) gold has important potential applications in nanoelectronics [3,4], and (iv) gold clusters and gold-containing compounds possess unique chemical properties [5]. All these golden discoveries have made gold a surprising and rewarding subject of investigation in nanoscience and cluster science. Indeed, some of our oldest notions regarding gold, such as its inertness, are being changed dramatically by the recent findings in nanogold.

  15. Femtosecond dynamics of cluster expansion

    NASA Astrophysics Data System (ADS)

    Gao, Xiaohui; Wang, Xiaoming; Shim, Bonggu; Arefiev, Alexey; Tushentsov, Mikhail; Breizman, Boris; Downer, Mike

    2010-03-01

    Noble gas clusters irradiated by intense ultrafast laser expand quickly and become typical plasma in picosecond time scale. During the expansion, the clustered plasma demonstrates unique optical properties such as strong absorption and positive contribution to the refractive index. Here we studied cluster expansion dynamics by fs-time-resolved refractive index and absorption measurements in cluster gas jets after ionization and heating by an intense pump pulse. The refractive index measured by frequency domain interferometry (FDI) shows the transient positive peak of refractive index due to clustered plasma. By separating it from the negative contribution of the monomer plasma, we are able to determine the cluster fraction. The absorption measured by a delayed probe shows the contribution from clusters of various sizes. The plasma resonances in the cluster explain the enhancement of the absorption in our isothermal expanding cluster model. The cluster size distribution can be determined. A complete understanding of the femtosecond dynamics of cluster expansion is essential in the accurate interpretation and control of laser-cluster experiments such as phase-matched harmonic generation in cluster medium.

  16. The Rotation of Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Tovmassian, H. M.

    2015-09-01

    The method for detection of the galaxy cluster rotation based on the study of distribution of member galaxies with velocities lower and higher than the cluster mean velocity over the cluster image is proposed. The search for rotation is made for flat clusters with a/b > 1.8 and BMI type clusters which are expected to be rotating. For comparison there were studied also round clusters and clusters of NBMI type, the second by brightness galaxy, which does not differ significantly from the cluster cD galaxy. Seventeen out of studied 65 clusters are found to be rotating. It was found that the detection rate is sufficiently high for flat clusters, over 60%, and clusters of BMI type with dominant cD galaxy, ≈ 35% . The obtained results show that clusters were formed from the huge primordial gas clouds and preserved the rotation of the primordial clouds, unless they did not experience mergings with other clusters and groups of galaxies, as a result of which the rotation was prevented.

  17. Theoretical study on the interaction of pristine, defective and strained graphene with Fen and Nin (n = 13, 38, 55) clusters

    NASA Astrophysics Data System (ADS)

    Song, Wei; Jiao, Menggai; Li, Kai; Wang, Ying; Wu, Zhijian

    2013-11-01

    The structural and electronic properties of Fen and Nin (n = 13, 38, 55) clusters interacting with pristine, defective and strained graphene are investigated by means of self-consistent charge density-functional tight binding (SCC-DFTB) method. The cluster size dependence, defect influence, and strain effect are discussed. We found that the defects play an important role in stabilizing metal clusters by forming metal-carbon σ bonds. Large charge redistribution of Fen compared to Nin lead to stronger interaction in Fen@graphene. The results suggested that tuning the morphological level of the substrate defect and cluster size could affect the catalytic activity of the metal cluster.

  18. Choosing the Number of Clusters in K-Means Clustering

    ERIC Educational Resources Information Center

    Steinley, Douglas; Brusco, Michael J.

    2011-01-01

    Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

  19. Enhanced binding strength between metal nanoclusters and carbon nanotubes with an atomic nickel defect.

    PubMed

    Sung, Dongchul; Park, Noejung; Kim, Gunn; Hong, Suklyun

    2012-05-25

    Using spin-polarized density functional theory calculations, we study binding properties of small metal nanoclusters (Cu(13) and Al(13)) onto carbon nanotubes (CNTs). On defect-free CNTs, the binding affinity with the Cu or Al cluster is very weak. When various defects such as vacancies, substitutional nickel defects, and nickel adatoms are introduced in CNTs to increase the binding strength, the binding energies of the metal nanoclusters increase substantially irrespective of types of defects. The effect of the Ni adatom is especially noticeable. Our results propose a method for improving the wettability of metal-CNT complex composites.

  20. DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry.

    PubMed

    Chen, Yao Chi; Wright, Jon D; Lim, Carmay

    2012-07-01

    DR_bind is a web server that automatically predicts DNA-binding residues, given the respective protein structure based on (i) electrostatics, (ii) evolution and (iii) geometry. In contrast to machine-learning methods, DR_bind does not require a training data set or any parameters. It predicts DNA-binding residues by detecting a cluster of conserved, solvent-accessible residues that are electrostatically stabilized upon mutation to Asp(-)/Glu(-). The server requires as input the DNA-binding protein structure in PDB format and outputs a downloadable text file of the predicted DNA-binding residues, a 3D visualization of the predicted residues highlighted in the given protein structure, and a downloadable PyMol script for visualization of the results. Calibration on 83 and 55 non-redundant DNA-bound and DNA-free protein structures yielded a DNA-binding residue prediction accuracy/precision of 90/47% and 88/42%, respectively. Since DR_bind does not require any training using protein-DNA complex structures, it may predict DNA-binding residues in novel structures of DNA-binding proteins resulting from structural genomics projects with no conservation data. The DR_bind server is freely available with no login requirement at http://dnasite.limlab.ibms.sinica.edu.tw.

  1. Generation of self-clusters of galectin-1 in the farnesyl-bound form

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Kazumi; Niwa, Yusuke; Nakabayashi, Takakazu; Hiramatsu, Hirotsugu

    2016-09-01

    Ras protein is involved in a signal transduction cascade in cell growth, and cluster formation of H-Ras and human galectin-1 (Gal-1) complex is considered to be crucial to achieve its physiological roles. It is considered that the complex is formed through interactions between Gal-1 and the farnesyl group (farnesyl-dependent model), post-translationally modified to the C-terminal Cys, of H-Ras. We investigated the role of farnesyl-bound Gal-1 in the cluster formation by analyzing the structure and properties of Gal-1 bound to farnesyl thiosalicylic acid (FTS), a competitive inhibitor of the binding of H-Ras to Gal-1. Gal-1 exhibited self-cluster formation upon interaction with FTS, and small- and large-size clusters were formed depending on FTS concentration. The galactoside-binding pocket of Gal-1 in the FTS-bound form was found to play an important role in small-size cluster formation. Large-size clusters were likely formed by the interaction among the hydrophobic sites of Gal-1 in the FTS-bound form. The present results indicate that Gal-1 in the FTS-bound form has the ability to form self-clusters as well as intrinsic lectin activity. Relevance of the self-clustering of FTS-bound Gal-1 to the cluster formation of the H-Ras–Gal-1complex was discussed by taking account of the farnesyl-dependent model and another (Raf-dependent) model.

  2. THEORETICAL STUDY ON THE INTERACTION BETWEEN XENON AND POSITIVE SILVER CLUSTERS IN GAS PHASE AND ON THE (001) CHABAZITE SURFACE

    SciTech Connect

    Hunter, D.

    2009-03-16

    A systematic study on the adsorption of xenon on silver clusters in the gas phase and on the (001) surface of silver-exchanged chabazite is reported. Density functional theory at the B3LYP level with the cluster model was employed. The results indicate that the dominant part of the binding is the {sigma} donation, which is the charge transfer from the 5p orbital of Xe to the 5s orbital of Ag and is not the previously suggested d{sub {pi}}-d{sub {pi}} back-donation. A correlation between the binding energy and the degree of {sigma} donation is found. Xenon was found to bind strongly to silver cluster cations and not to neutral ones. The binding strength decreases as the cluster size increases for both cases, clusters in the gas-phase and on the chabazite surface. The Ag{sup +} cation is the strongest binding site for xenon both in gas phase and on the chabazite surface with the binding energies of 73.9 and 14.5 kJ/mol, respectively. The results also suggest that the smaller silver clusters contribute to the negative chemical shifts observed in the {sup 129}Xe NMR spectra in experiments.

  3. Nuclear Cluster Aspects in Astrophysics

    SciTech Connect

    Kubono, Shigeru

    2010-03-01

    The role of nuclear clustering is discussed for nucleosynthesis in stellar evolution with Cluster Nucleosynthesis Diagram (CND) proposed before. Special emphasis is placed on alpha-induced stellar reactions together with molecular states for O and C burning.

  4. Animation of the Phoenix Cluster

    NASA Video Gallery

    This animation shows how large numbers of stars form in the Phoenix Cluster. It begins by showing several galaxies in the cluster and hot gas (in red). This hot gas contains more normal matter than...

  5. Observations of Distant Clusters

    NASA Technical Reports Server (NTRS)

    Donahue, Megan

    2004-01-01

    The is the proceedings and papers supported by the LTSA grant: Homer, D. J.\\& Donahue, M. 2003, in "The Emergence of Cosmic Structure": 13'h Astrophysics Conference Proceedings, Vol. 666,3 1 1-3 14, (AIP). Baumgartner, W. H., Loewenstein, M., Horner, D. J., Mushotzky, R. F. 2003, HEAD- AAS, 35.3503. Homer, D. J. , Donahue, M., Voit G. M. 2003, HEAD-AAS, 35.1309. Nowak, M. A., Smith, B., Donahue, M., Stocke, J. 2003, HEAD-AAS, 35.1316. Scott, D., Borys, C., Chapman, S. C., Donahue, M., Fahlman, G. G., Halpem, M. Newbury, P. 2002, AAS, 128.01. Jones, L. R. et al. 2002, A new era in cosmology, ASP Conference Proceedings, Vol. 283, p. 223 Donahue, M., Daly, R. A., Homer, D. J. 2003, ApJ, 584, 643, Constraints on the Cluster Environments and Hotspot magnetic field strengths for radio sources 3280 and 3254. Donahue, M., et al. 2003, ApJ, 598, 190. The mass, baryonic fraction, and x-ray temperature of the luminous, high-redshift cluster of galaxies MS045 1.6-0305 Perlman, E. S. et al. 2002, ApJS, 140, 256. Smith, B. J., Nowak, M., Donahue, M., Stocke, J. 2003, AJ, 126, 1763. Chandra Observations of the Interacting NGC44 10 Group of Galaxies. Postman, M., Lauer, T. R., Oegerle, W., Donahue, M. 2002, ApJ, 579, 93. The KPNO/deep-range cluster survey I. The catalog and space density of intermediate-redshift clusters. Molnar, S. M., Hughes, J. P., Donahue, M., Joy, M. 2002, ApJ, 573, L91, Chandra Observations of Unresolved X-Ray Sources around Two Clusters of Galaxies. Donahue, M., Mack, J., 2002 NewAR, 46, 155, HST NIcmos and WFPC2 observations of molecular hydrogen and dust around cooling flows. Koekemoer, A. M. et al. 2002 NewAR, 46, 149, Interactions between the A2597 central radio source and dense gas host galaxy. Donahue, M. et al. 2002 ApJ, 569,689, Distant cluster hunting II.

  6. Benzene-Water (BZWn (n = 1 - 10)) Clusters

    NASA Astrophysics Data System (ADS)

    Prakash, M.; Samy, K. Gopal; Subramanian, V.

    2009-11-01

    The gas-phase geometries, binding energies (BEs), infrared spectra and electron density parameters of benzene (BZ)-water (W) clusters (BZWn, where n = 1-10) have been calculated using Truhlar's meta hybrid functional, M05-2X, employing 6-31+G** basis set. Both basis set superposition error (BSSE) and zero point energy corrected BEs are in close agreement with the previously reported high level ab initio and experimental values. Among all of the BZWn clusters, the same with inverted book conformer of water hexamer has the highest BE when compared to all other water clusters. The Bader's theory of atoms in molecule (AIM) provides evidence for the presence of O-H···π interactions in all of these clusters. In addition, the roles of C-H···O and lone pair···π (lp···π) interactions in the stabilization of BZWn clusters are also evident from the AIM analysis. The trend in the electron density at the hydrogen bond critical points varies as O-H···π < lp···π < C-H···O. Spectral signatures of these clusters further reinforce the existence of weak H-bond between BZ and Wn clusters. The red shift in all of these clusters ranges from 13 to 95 cm-1. The results clearly show that the presence of π-cloud does not affect the H-bonded network of water clusters except in the case of W6 ring.

  7. Massive star clusters in galaxies.

    PubMed

    Harris, William E

    2010-02-28

    The ensemble of all star clusters in a galaxy constitutes its star cluster system. In this review, the focus of the discussion is on the ability of star clusters, particularly the systems of old massive globular clusters (GCs), to mark the early evolutionary history of galaxies. I review current themes and key findings in GC research, and highlight some of the outstanding questions that are emerging from recent work.

  8. The Assembly of Galaxy Clusters

    SciTech Connect

    Berrier, Joel C.; Stewart, Kyle R.; Bullock, James S.; Purcell, Chris W.; Barton, Elizabeth J.; Wechsler, Risa H.

    2008-05-16

    We study the formation of fifty-three galaxy cluster-size dark matter halos (M = 10{sup 14.0-14.76} M{sub {circle_dot}}) formed within a pair of cosmological {Lambda}CDM N-body simulations, and track the accretion histories of cluster subhalos with masses large enough to host {approx} 0.1L{sub *} galaxies. By associating subhalos with cluster galaxies, we find the majority of galaxies in clusters experience no 'pre-processing' in the group environment prior to their accretion into the cluster. On average, {approx} 70% of cluster galaxies fall into the cluster potential directly from the field, with no luminous companions in their host halos at the time of accretion; and less than {approx} 12% are accreted as members of groups with five or more galaxies. Moreover, we find that cluster galaxies are significantly less likely to have experienced a merger in the recent past ({approx}< 6 Gyr) than a field halo of the same mass. These results suggest that local, cluster processes like ram-pressure stripping, galaxy harassment, or strangulation play the dominant role in explaining the difference between cluster and field populations at a fixed stellar mass; and that pre-evolution or past merging in the group environment is of secondary importance for setting cluster galaxy properties for most clusters. The accretion times for z = 0 cluster members are quite extended, with {approx} 20% incorporated into the cluster halo more than 7 Gyr ago and {approx} 20% within the last 2 Gyr. By comparing the observed morphological fractions in cluster and field populations, we estimate an approximate time-scale for late-type to early-type transformation within the cluster environment to be {approx} 6 Gyr.

  9. [Cluster analysis in biomedical researches].

    PubMed

    Akopov, A S; Moskovtsev, A A; Dolenko, S A; Savina, G D

    2013-01-01

    Cluster analysis is one of the most popular methods for the analysis of multi-parameter data. The cluster analysis reveals the internal structure of the data, group the separate observations on the degree of their similarity. The review provides a definition of the basic concepts of cluster analysis, and discusses the most popular clustering algorithms: k-means, hierarchical algorithms, Kohonen networks algorithms. Examples are the use of these algorithms in biomedical research. PMID:24640781

  10. The Orion nebula star cluster

    NASA Technical Reports Server (NTRS)

    Panek, R. J.

    1982-01-01

    Photography through filters which suppress nebular light reveal a clustering of faint red stars centered on the Trapezium, this evidences a distinct cluster within the larger OB1 association. Stars within about 20 ft of trapezium comprise the Orion Nebula star cluster are considered. Topics discussed re: (1) extinction by dust grains; (2) photometric peculiarities; (3) spectroscopic peculiarities; (4) young variables; (5) the distribution and motion of gas within the cluster.

  11. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.; Furuya, F.R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

  12. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, James F.; Furuya, Frederic R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

  13. Adaptive Clustering of Hypermedia Documents.

    ERIC Educational Resources Information Center

    Johnson, Andrew; Fotouhi, Farshad

    1996-01-01

    Discussion of hypermedia systems focuses on a comparison of two types of adaptive algorithm (genetic algorithm and neural network) in clustering hypermedia documents. These clusters allow the user to index into the nodes to find needed information more quickly, since clustering is "personalized" based on the user's paths rather than representing…

  14. Connecting Remote Clusters with ATM

    SciTech Connect

    Hu, T.C.; Wyckoff, P.S.

    1998-10-01

    Sandia's entry into utilizing clusters of networked workstations is called Computational Plant or CPlant for short. The design of CPlant uses Ethernet to boot the individual nodes, Myrinet to communicate within a node cluster, and ATM to connect between remote clusters. This SAND document covers the work done to enable the use of ATM on the CPlant nodes in the Fall of 1997.

  15. Effects of edge dislocations on interstitial helium and helium cluster behavior in α-Fe

    NASA Astrophysics Data System (ADS)

    Wang, Y. X.; Xu, Q.; Yoshiie, T.; Pan, Z. Y.

    2008-05-01

    The properties of interstitial He in the vicinity of an edge dislocation were studied using molecular dynamics (MD) simulation. The distribution of the binding energy of a single interstitial He to the dislocation with and without a jog is calculated. The results show that the distribution of the binding energy is governed by the elastic interaction between the interstitial He and the dislocation. The interstitial He is strongly attracted to the dislocation in the tensile region of the dislocation. The jog acts as a stronger sink to absorb interstitial He. The binding energy to the jog is even larger than that of the dislocation. A small He cluster (composed of three interstitial He atoms) was trapped by the dislocation core in the form of a chain along the dislocation line. The dislocation changes the migration behavior of the He cluster, and provides a pipe for the small cluster to exhibit one-dimensional motion. The diffusion of the He cluster in the dislocation is faster than in the defect-free iron, where the He cluster migrates three-dimensionally (3D). If the dislocation is decorated by a jog, the small cluster sinks deep into the jog. The jog prevents the He cluster from escaping.

  16. Toward Parallel Document Clustering

    SciTech Connect

    Mogill, Jace A.; Haglin, David J.

    2011-09-01

    A key challenge to automated clustering of documents in large text corpora is the high cost of comparing documents in a multimillion dimensional document space. The Anchors Hierarchy is a fast data structure and algorithm for localizing data based on a triangle inequality obeying distance metric, the algorithm strives to minimize the number of distance calculations needed to cluster the documents into “anchors” around reference documents called “pivots”. We extend the original algorithm to increase the amount of available parallelism and consider two implementations: a complex data structure which affords efficient searching, and a simple data structure which requires repeated sorting. The sorting implementation is integrated with a text corpora “Bag of Words” program and initial performance results of end-to-end a document processing workflow are reported.

  17. Binaries in globular clusters

    NASA Technical Reports Server (NTRS)

    Hut, Piet; Mcmillan, Steve; Goodman, Jeremy; Mateo, Mario; Phinney, E. S.; Pryor, Carlton; Richer, Harvey B.; Verbunt, Frank; Weinberg, Martin

    1992-01-01

    Recent observations have shown that globular clusters contain a substantial number of binaries most of which are believed to be primordial. We discuss different successful optical search techniques, based on radial-velocity variables, photometric variables, and the positions of stars in the color-magnitude diagram. In addition, we review searches in other wavelengths, which have turned up low-mass X-ray binaries and more recently a variety of radio pulsars. On the theoretical side, we give an overview of the different physical mechanisms through which individual binaries evolve. We discuss the various simulation techniques which recently have been employed to study the effects of a primordial binary population, and the fascinating interplay between stellar evolution and stellar dynamics which drives globular-cluster evolution.

  18. Clusterization in Ternary Fission

    NASA Astrophysics Data System (ADS)

    Kamanin, D. V.; Pyatkov, Y. V.

    This lecture notes are devoted to the new kind of ternary decay of low excited heavy nuclei called by us "collinear cluster tri-partition" (CCT) due to the features of the effect observed, namely, decay partners fly away almost collinearly and at least one of them has magic nucleon composition. At the early stage of our work the process of "true ternary fission" (fission of the nucleus into three fragments of comparable masses) was considered to be undiscovered for low excited heavy nuclei. Another possible prototype—three body cluster radioactivity—was also unknown. The most close to the CCT phenomenon, at least cinematically, stands so called "polar emission", but only very light ions (up to isotopes of Be) were observed so far.

  19. Gravitational clustering: an overview

    NASA Astrophysics Data System (ADS)

    Labini, Francesco Sylos

    2008-01-01

    We discuss the differences and analogies of gravitational clustering in finite and infinite systems. The process of collective, or violent, relaxation leading to the formation of quasi-stationary states is one of the distinguished features in the dynamics of self-gravitating systems. This occurs, in different conditions, both in a finite than in an infinite system, the latter embedded in a static or in an expanding background. We then discuss, by considering some simple and paradigmatic examples, the problems related to the definition of a mean-field approach to gravitational clustering, focusing on role of discrete fluctuations. The effect of these fluctuations is a basic issue to be clarified to establish the range of scales and times in which a collision-less approximation may describe the evolution of a self-gravitating system and for the theoretical modeling of the non-linear phase.

  20. Processes involved in the formation of silver clusters on silicon surface

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, S. R.; Chini, T. K.; Datta, D.; Hippler, R.; Shyjumon, I.; Smirnov, B. M.

    2008-12-01

    We analyze scanning electron microscopy measurements for structures formed in the deposition of solid silver clusters onto a silicon(100) substrate and consider theoretical models of cluster evolution onto a surface as a result of diffusion and formation of aggregates of merged clusters. Scanning electron microscopy (SEM) data are presented in addition to energy dispersive X-ray spectrometry (EDX) measurements of the these films. Solid silver clusters are produced by a DC magnetron sputtering source with a quadrupole filter for selection of cluster sizes (4.1 and 5.6 nm or 1900 and 5000 atoms per cluster in this experiment); the energy of cluster deposition is 0.7 eV/atom. Rapid thermal annealing of the grown films allows analysis of their behavior at high temperatures. The results exhibit formation of cluster aggregates via the diffusion of deposited solid clusters along the surface; an aggregate consists of up to hundreds of individual clusters. This process is essentially described by the diffusion-limited aggregation (DLA) model, and thus a grown porous film consists of cluster aggregates joined by bridges. Subsequent annealing of this film leads to its melting at temperatures lower than to the melting point of bulk silver. Analysis of evaporation of this film at higher temperatures gives a binding energy in bulk silver of ɛ0= (2.74 ± 0.03) eV/atom.

  1. Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

    PubMed

    Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

    2016-02-18

    Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

  2. Tungsten Cluster Migration on Nanoparticles: Minimum Energy Pathway and Migration Mechanism

    SciTech Connect

    Chen, Dong; Hu, Wangyu; Gao, Fei; Deng, Huiqiu; Sun, Lixian

    2011-03-02

    Transition state searches have been employed to investigate the migration mechanisms of W clusters on W nanoparticles, and to determine the corresponding migration energies for the possible migration paths of these clusters. The tungsten clusters containing up to four adatoms are found to prefer 2D-compact structures with relatively low binding energies. The effect of interface and vertex regions on the migration behavior of the clusters is significantly strong, as compared to that of nanoparticle size. The migration mechanisms are quite different when the clusters are located at the center of the nanoparticle and near the interface or vertex areas. Near the interfaces and vertex areas, the substrate atoms tend to participate in the migration processes of the clusters, and can join the adatoms to form a larger cluster or lead to the dissociation of a cluster via the exchange mechanism, which results in the adatom crossing the facets. The lowest energy paths are used to be determined the energy barriers for W cluster migrations (from 1- to 4-atoms) on the facets, edges and vertex regions. The calculated energy barriers for the trimers suggest that the concerted migration is more probable than the successive jumping of a single adatom in the clusters. In addition, it of interest to note that the dimer shearing is a dominant migration mechanism for the tetramer, but needs to overcome a relatively higher migration energy than other clusters.

  3. Tailoring and Scaling Energetic Aluminum Clusters into Cluster Assembled Materials

    NASA Astrophysics Data System (ADS)

    Smith, Jordan Cesar

    As matter decreases in size the importance of a single atom increases exponentially. The properties of clusters, molecules with less than 100 atoms, will change drastically with the addition or removal of a single atom. Clusters have been shown to have properties that mimic other elements and properties that are completely unique. Cluster assemblies could enable the tailoring of precise properties in materials, providing cheap replacements for expensive elements, or novel materials for new applications. Aluminum clusters show great potential use in many applications including energy and catalysis. This work is focused on gaining a better understanding of how geometry and electronic structure affect aluminum cluster reactivity and how useful clusters might be successfully assembled into materials. The effects of doping aluminum cluster ions with boron atoms are reported and show that the addition of a single boron atom usually stabilizes the cluster while adding more boron atoms results in a breaking of symmetry and destabilization. A new analytical technique, matrix isolation cavity ring-down spectroscopy (MICRDS) was developed to help bridge the gap between gas phase cluster studies and condensed phase cluster materials. Molecules are trapped in an inert matrix and studied using cavity ring-down spectroscopy. MICRDS has the potential to also combine clusters into small stable units that would maintain their advantageous gas phase properties.

  4. Properties of the Brightest Cluster Galaxy and Its Host Cluster

    NASA Astrophysics Data System (ADS)

    Katayama, Haruyoshi; Hayashida, Kiyoshi; Takahara, Fumio; Fujita, Yutaka

    2003-03-01

    We investigate the relation between the properties of brightest cluster galaxies (BCGs) and those of their host clusters. To quantify the properties of cluster hot gas, we employ the parameter Z of the fundamental plane of X-ray clusters. It is found that the offset of the BCG from the peak of cluster X-ray emission is larger for smaller Z clusters. The parameter Z (not the redshift z), which depends mainly on virial density ρvir, is considered to represent the formation epoch of a cluster. We thus consider that the offset of the BCG is correlated with the dynamical equilibrium state of its host cluster. On the contrary, no significant correlation is found between the absolute optical magnitude of the BCG and the parameter Z. If the extreme brightness of the BCG is acquired mainly in the course of cluster evolution by environmental effect, BCGs are expected to be brighter in large Z clusters. Our result is not consistent with this simplified view. On the contrary, it is possible that the extreme brightness of the BCG is likely to be determined in the early history of cluster collapse.

  5. Basic cluster compression algorithm

    NASA Technical Reports Server (NTRS)

    Hilbert, E. E.; Lee, J.

    1980-01-01

    Feature extraction and data compression of LANDSAT data is accomplished by BCCA program which reduces costs associated with transmitting, storing, distributing, and interpreting multispectral image data. Algorithm uses spatially local clustering to extract features from image data to describe spectral characteristics of data set. Approach requires only simple repetitive computations, and parallel processing can be used for very high data rates. Program is written in FORTRAN IV for batch execution and has been implemented on SEL 32/55.

  6. Cosmology, Clusters and Calorimeters

    NASA Technical Reports Server (NTRS)

    Figueroa-Feliciano, Enectali

    2005-01-01

    I will review the current state of Cosmology with Clusters and discuss the application of microcalorimeter arrays to this field. With the launch of Astro-E2 this summer and a slew of new missions being developed, microcalorimeters are the next big thing in x-ray astronomy. I will cover the basics and not-so-basic concepts of microcalorimeter designs and look at the future to see where this technology will go.

  7. Astrophysics of galaxy clusters

    NASA Astrophysics Data System (ADS)

    Ettori, Stefano

    2016-07-01

    As the nodes of the cosmic web, clusters of galaxies trace the large-scale distribution of matter in the Universe. They are thus privileged sites in which to investigate the complex physics of structure formation. However, the complete story of how these structures grow, and how they dissipate the gravitational and non-thermal components of their energy budget over cosmic time, is still beyond our grasp. Most of the baryons gravitationally bound to the cluster's halo is in the form of a diffuse, hot, metal-enriched plasma that radiates primarily in the X-ray band. X-ray observations of the evolving cluster population provide a unique opportunity to address such fundamental open questions as: How do hot diffuse baryons accrete and dynamically evolve in dark matter potentials? How and when was the energy that we observe in the ICM generated and distributed? Where and when are heavy elements produced and how are they circulated? We will present the ongoing activities to define the strategy on how an X-ray observatory with large collecting area and an unprecedented combination of high spectral and angular resolution, such as Athena, can address these questions.

  8. First-principles studies on graphene-supported transition metal clusters.

    PubMed

    Sahoo, Sanjubala; Gruner, Markus E; Khanna, Shiv N; Entel, Peter

    2014-08-21

    Theoretical studies on the structure, stability, and magnetic properties of icosahedral TM13 (TM = Fe, Co, Ni) clusters, deposited on pristine (defect free) and defective graphene sheet as well as graphene flakes, have been carried out within a gradient corrected density functional framework. The defects considered in our study include a carbon vacancy for the graphene sheet and a five-membered and a seven-membered ring structures for graphene flakes (finite graphene chunks). It is observed that the presence of defect in the substrate has a profound influence on the electronic structure and magnetic properties of graphene-transition metal complexes, thereby increasing the binding strength of the TM cluster on to the graphene substrate. Among TM13 clusters, Co13 is absorbed relatively more strongly on pristine and defective graphene as compared to Fe13 and Ni13 clusters. The adsorbed clusters show reduced magnetic moment compared to the free clusters.

  9. Wade's rules and the stability of AunGem clusters

    NASA Astrophysics Data System (ADS)

    McDermott, Danielle; Newman, Kathie E.

    2015-03-01

    The properties of clusters formed from two connected Gem cage-like clusters, such as experimentally synthesized Au3Ge{18/5-}, are examined using first-principles DFT methods. We focus particularly on AunGe{12/q-} formed from a Wade-rules stable Ge6 cluster, where n = 0-3 and q = 0,2. The geometries, electronic structure, and thermal excitations of these clusters are examined using the SIESTA code. Cluster stability is tested using short molecular dynamics simulations. We find that intercluster bridges between Ge m cages, formed of either Ge-Ge or Au-Ge bonds, can either bind a cluster together or tear it apart depending on the orientation of the bridging atoms with respect to the cages. The properties of neutrally charged AuGe12 and Au2Ge12 are characterized, and we observe that radially directed molecular orbitals stabilize AuGe12 while a geometric asymmetry stabilizes Au2Ge12 and Au3Ge18. A two-dimensional {2/∞}[Au2Ge6] structure is examined and found to be more stable than other periodic [AunGe6] subunits. While no stable neutral isomers of Au3Ge12 are observed in our calculations, our work suggests additional charge stabilizes isomers of both Au2Ge12 and Au3Ge12.

  10. Optical Sensing by Transforming Chromophoric Silver Clusters in DNA Nanoreactors

    PubMed Central

    Story, Sandra P.; Juarez, Selina; Votto, Samuel S.; Herbst, Austin G.; Degtyareva, Natalya N.; Sengupta, Bidisha

    2014-01-01

    Bifunctional DNA oligonucleotides serve as templates for chromophoric silver clusters and as recognition sites for target DNA strands, and communication between these two components is the basis of an oligonucleotide sensor. Few-atom silver clusters exhibit distinct electronic spectra spanning the visible and near-infrared region, and they are selectively synthesized by varying the base sequence of the DNA template. In these studies, a 16-base cluster template is adjoined with a 12-base sequence complementary to the target analyte, and hybridization induces structural changes in the composite sensor that direct the conversion between two spectrally and stoichiometrically distinct clusters. Without its complement, the sensor strand selectively harbors ~7 silver atoms that absorb at 400 nm and that fold the DNA host. Upon association of the target with its recognition site, the sensor strand opens to expose the cluster template that has the binding site for ~11 silver atoms, and absorption at 720 nm with relatively strong emission develops in lieu of the violet absorption. Variations in the length and composition of the recognition site and the cluster template indicate that these types of dual component sensors provide a general platform for near infrared-based detection of oligonucleotides in challenging biological environments. PMID:22098274

  11. Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

    USGS Publications Warehouse

    Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

    1998-01-01

    Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that

  12. Cluster headache after orbital exenteration.

    PubMed

    Evers, S; Sörös, P; Brilla, R; Gerding, H; Husstedt, I W

    1997-10-01

    A 37-year-old man developed an ipsilateral headache which fulfilled the criteria for cluster headache after orbital extenteration because of a traumatic lesion of the bulb. The headache could be treated successfully by drugs usually applied in the therapy of cluster headache. Six similar cases of cluster headache after orbital exenteration could be identified in the literature suggesting that the eye itself is not necessarily part of the pathogenesis of cluster headache. We hypothesize that orbital exenteration can cause cluster headache by lesions of sympathetic structures. Possibly, these mechanisms are similar to those of sympathetic reflex dystrophy (Sudeck-Leriche syndrome) causing pain of the limbs. PMID:9350391

  13. Cluster AAR Campaign Summary Plots

    NASA Astrophysics Data System (ADS)

    Fazakerley, A. N.; Walsh, A. P.; Garza, K. J.; Christopher, I.; Sadeghi, S.; Lindqvist, P.; Mihaljcic, B.; Forsyth, C.; Pickett, J. S.; Marklund, G. T.; Lucek, E. A.; Dandouras, I. S.

    2010-12-01

    Since late 2008 the Cluster spacecraft have been making the first four-point measurements of the Auroral Acceleration Region, opening up an exciting new opportunity for the auroral science, Cluster and wider magnetospheric physics communities. In order to stimulate auroral research with Cluster and aid in event selection, we have produced a set of summary plots for those Cluster perigee passes best suited for addressing open questions in auroral physics. The plots incorporate data from WBD, FGM, EFW, PEACE and CIS and are available from the Cluster PEACE website.

  14. Stormy weather in galaxy clusters

    PubMed

    Burns

    1998-04-17

    Recent x-ray, optical, and radio observations coupled with particle and gas dynamics numerical simulations reveal an unexpectedly complex environment within clusters of galaxies, driven by ongoing accretion of matter from large-scale supercluster filaments. Mergers between clusters and continuous infall of dark matter and baryons from the cluster periphery produce long-lived "stormy weather" within the gaseous cluster atmosphere-shocks, turbulence, and winds of more than 1000 kilometers per second. This weather may be responsible for shaping a rich variety of extended radio sources, which in turn act as "barometers" and "anemometers" of cluster weather.

  15. Cluster energetics: Models and data

    NASA Astrophysics Data System (ADS)

    Ford, Ian; Vehkamäki, Hanna; Knott, Michael

    2000-08-01

    A wealth of information about the energies of clusters of several tens of molecules has been obtained recently through the analysis of nucleation rate data using the nucleation theorems. We describe here studies of n-pentanol and dibutylphthalate clusters, and using multicomponent nucleation theorems, we present data for binary clusters of water and ethanol, and n- and i-octane. We then attempt a synthesis of alkane cluster information obtained to date, and find that the cluster excess energies show a rough proportionality to the molecular size raised to the 2/3 power.

  16. Stormy weather in galaxy clusters

    PubMed

    Burns

    1998-04-17

    Recent x-ray, optical, and radio observations coupled with particle and gas dynamics numerical simulations reveal an unexpectedly complex environment within clusters of galaxies, driven by ongoing accretion of matter from large-scale supercluster filaments. Mergers between clusters and continuous infall of dark matter and baryons from the cluster periphery produce long-lived "stormy weather" within the gaseous cluster atmosphere-shocks, turbulence, and winds of more than 1000 kilometers per second. This weather may be responsible for shaping a rich variety of extended radio sources, which in turn act as "barometers" and "anemometers" of cluster weather. PMID:9545210

  17. Stellar Snowflake Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Figure 1 Stellar Snowflake Cluster Combined Image [figure removed for brevity, see original site] Figure 2 Infrared Array CameraFigure 3 Multiband Imaging Photometer

    Newborn stars, hidden behind thick dust, are revealed in this image of a section of the Christmas Tree cluster from NASA's Spitzer Space Telescope, created in joint effort between Spitzer's infrared array camera and multiband imaging photometer instruments.

    The newly revealed infant stars appear as pink and red specks toward the center of the combined image (fig. 1). The stars appear to have formed in regularly spaced intervals along linear structures in a configuration that resembles the spokes of a wheel or the pattern of a snowflake. Hence, astronomers have nicknamed this the 'Snowflake' cluster.

    Star-forming clouds like this one are dynamic and evolving structures. Since the stars trace the straight line pattern of spokes of a wheel, scientists believe that these are newborn stars, or 'protostars.' At a mere 100,000 years old, these infant structures have yet to 'crawl' away from their location of birth. Over time, the natural drifting motions of each star will break this order, and the snowflake design will be no more.

    While most of the visible-light stars that give the Christmas Tree cluster its name and triangular shape do not shine brightly in Spitzer's infrared eyes, all of the stars forming from this dusty cloud are considered part of the cluster.

    Like a dusty cosmic finger pointing up to the newborn clusters, Spitzer also illuminates the optically dark and dense Cone nebula, the tip of which can be seen towards the bottom left corner of each image.

    This combined image shows the presence of organic molecules mixed with dust as wisps of green, which have been illuminated by nearby star formation. The larger yellowish dots neighboring the baby red stars in the Snowflake Cluster are massive stellar infants forming

  18. Library Binding Manual. Revised Edition.

    ERIC Educational Resources Information Center

    Lakhanpal, S. K.

    This procedural manual is designed to be used in bindery sections in public, university and special libraries. It briefly discusses these general matters: administrative control; selection of a binder; when and what to bind; conventional binding; routines; missing issues; schedule for shipments; temporary binding; rare books, maps and newspapers;…

  19. Color segmentation using MDL clustering

    NASA Astrophysics Data System (ADS)

    Wallace, Richard S.; Suenaga, Yasuhito

    1991-02-01

    This paper describes a procedure for segmentation of color face images. A cluster analysis algorithm uses a subsample of the input image color pixels to detect clusters in color space. The clustering program consists of two parts. The first part searches for a hierarchical clustering using the NIHC algorithm. The second part searches the resultant cluster tree for a level clustering having minimum description length (MDL). One of the primary advantages of the MDL paradigm is that it enables writing robust vision algorithms that do not depend on user-specified threshold parameters or other " magic numbers. " This technical note describes an application of minimal length encoding in the analysis of digitized human face images at the NTT Human Interface Laboratories. We use MDL clustering to segment color images of human faces. For color segmentation we search for clusters in color space. Using only a subsample of points from the original face image our clustering program detects color clusters corresponding to the hair skin and background regions in the image. Then a maximum likelyhood classifier assigns the remaining pixels to each class. The clustering program tends to group small facial features such as the nostrils mouth and eyes together but they can be separated from the larger classes through connected components analysis.

  20. Scale free processes in stellar cluster formation

    NASA Astrophysics Data System (ADS)

    Bastian, Nate

    2015-08-01

    I will review what is known about stellar cluster formation, focussing on scale free processes, such as how lower mass open clusters related to their giant cousins, the young massive clusters, and potentially globular cluster as well.

  1. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    NASA Astrophysics Data System (ADS)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei

    2015-12-01

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  2. Controlled reactivity tuning of metal-functionalized vanadium oxide clusters.

    PubMed

    Kastner, Katharina; Forster, Johannes; Ida, Hiromichi; Newton, Graham N; Oshio, Hiroki; Streb, Carsten

    2015-05-18

    Controlling the assembly and functionalization of molecular metal oxides [Mx Oy ](n-) (M=Mo, W, V) allows the targeted design of functional molecular materials. While general methods exist that enable the predetermined functionalization of tungstates and molybdates, no such routes are available for molecular vanadium oxides. Controlled design of polyoxovanadates, however, would provide highly active materials for energy conversion, (photo-) catalysis, molecular magnetism, and materials science. To this end, a new approach has been developed that allows the reactivity tuning of vanadium oxide clusters by selective metal functionalization. Organic, hydrogen-bonding cations, for example, dimethylammonium are used as molecular placeholders to block metal binding sites within vanadate cluster shells. Stepwise replacement of the placeholder cations with reactive metal cations gives mono- and difunctionalized clusters. Initial reactivity studies illustrate the tunability of the magnetic, redox, and catalytic activity.

  3. The size of clusters in a neutrino-dominated universe

    NASA Technical Reports Server (NTRS)

    White, S. D. M.; Davis, M.; Frenk, C. S.

    1984-01-01

    Quite soon after the first collapse of structure, almost half the matter in a neutrino-dominated universe is expected to reside in clusters. The masses and binding energies of these neutrino clusters are too large for them to be identified with observed galaxy clusters. Even if such objects were able to suppress all galaxy formation, their X-ray emission would, however, make them highly visible if more than 2.5 percent of their mass was in ordinary matter. Such a low baryon density leads to insuffient cooling for galaxies to form in pancakes. A neutrino-dominated universe appears to conflict with observation irrespective of the details of the processes which govern galaxy formation.

  4. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    SciTech Connect

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei

    2015-12-31

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  5. Convex Clustering: An Attractive Alternative to Hierarchical Clustering

    PubMed Central

    Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

    2015-01-01

    The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

  6. Competition between supercluster and stuffed cage structures in medium-sized Gen (n=30-39) clusters

    NASA Astrophysics Data System (ADS)

    Wang, Lu; Zhao, Jijun

    2008-01-01

    We have performed an unbiased global search for the geometries of low-lying Gen clusters in the size range of 30⩽n⩽39 using genetic algorithm incorporated with a tight-binding model. Density functional theory calculations were carried out to further optimize the isomer structures. Gen (n=30-39) clusters prefer the motif of supercluster structures stacked by several stable subunits such as Ge10 and Ge6, connecting via a few bridging atoms. Size-dependent cluster properties such as binding energy, HOMO-LUMO gaps, and ionization potentials were discussed and compared with experiments.

  7. Comparative Density Functional Study of Methanol Decomposition on Cu4 and Co4 Clusters

    SciTech Connect

    Mehmood, Faisal; Greeley, Jeffrey P.; Zapol, Peter; Curtiss, Larry A.

    2010-11-18

    A density functional theory study of the decomposition of methanol on Cu4 and Co4 clusters is presented. The reaction intermediates and activation barriers have been determined for reaction steps to form H2 and CO. For both clusters, methanol decomposition initiated by C-H and O-H bond breaking was investigated. In the case of a Cu4 cluster, methanol dehydrogenation through hydroxymethyl (CH2OH), hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO) is found to be slightly more favorable. For a Co4 cluster, the dehydrogenation pathway through methoxy (CH3O) and formaldehyde (CH2O) is slightly more favorable. Each of these pathways results in formation of CO and H2. The Co cluster pathway is very favorable thermodynamically and kinetically for dehydrogenation. However, since CO binds strongly, it is likely to poison methanol decomposition to H2 and CO at low temperatures. In contrast, for the Cu cluster, CO poisoning is not likely to be a problem since it does not bind strongly, but the dehydrogenation steps are not energetically favorable. Pathways involving C-O bond cleavage are even less energetically favorable. The results are compared to our previous study of methanol decomposition on Pd4 and Pd8 clusters. Finally, all reaction energy changes and transition state energies, including those for the Pd clusters, are related in a linear, Broensted-Evans-Polanyi plot.

  8. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

    NASA Astrophysics Data System (ADS)

    Turi, László

    2016-04-01

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  9. Architectural repertoire of ligand-binding pockets on protein surfaces.

    PubMed

    Weisel, Martin; Kriegl, Jan M; Schneider, Gisbert

    2010-03-01

    Knowledge of the three-dimensional structure of ligand binding sites in proteins provides valuable information for computer-assisted drug design. We present a method for the automated extraction and classification of ligand binding site topologies, in which protein surface cavities are represented as branched frameworks. The procedure employs a growing neural gas approach for pocket topology assignment and pocket framework generation. We assessed the structural diversity of 623 known ligand binding site topologies based on framework cluster analysis. At a resolution of 5 A only 23 structurally distinct topology groups were formed; this suggests an overall limited structural diversity of ligand-accommodating protein cavities. Higher resolution allowed for identification of protein-family specific pocket features. Pocket frameworks highlight potentially preferred modes of ligand-receptor interactions and will help facilitate the identification of druggable subpockets suitable for ligand affinity and selectivity optimization. PMID:20069621

  10. Ab initio study of neutral (TiO2)n clusters and their interactions with water and transition metal atoms.

    PubMed

    Cakır, D; Gülseren, O

    2012-08-01

    We have systematically investigated the growth behavior and stability of small stoichiometric (TiO(2))(n) (n = 1-10) clusters as well as their structural, electronic and magnetic properties by using the first-principles plane wave pseudopotential method within density functional theory. In order to find out the ground state geometries, a large number of initial cluster structures for each n has been searched via total energy calculations. Generally, the ground state structures for the case of n = 1-9 clusters have at least one monovalent O atom, which only binds to a single Ti atom. However, the most stable structure of the n = 10 cluster does not have any monovalent O atom. On the other hand, Ti atoms are at least fourfold coordinated for the ground state structures for n ≥ 4 clusters. Our calculations have revealed that clusters prefer to form three-dimensional structures. Furthermore, all these stoichiometric clusters have nonmagnetic ground state. The formation energy and the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap for the most stable structure of (TiO(2))(n) clusters for each n have also been calculated. The formation energy and hence the stability increases as the cluster size grows. In addition, the interactions between the ground state structure of the (TiO(2))(n) cluster and a single water molecule have been studied. The binding energy (E(b)) of the H(2)O molecule exhibits an oscillatory behavior with the size of the clusters. A single water molecule preferably binds to the cluster Ti atom through its oxygen atom, resulting an average binding energy of 1.1 eV. We have also reported the interaction of the selected clusters (n = 3, 4, 10) with multiple water molecules. We have found that additional water molecules lead to a decrease in the binding energy of these molecules to the (TiO(2))(n) clusters. Finally, the adsorption of transition metal (TM) atoms (V, Co and Pt) on the n = 10 cluster has been

  11. Measuring Cluster Relaxedness

    SciTech Connect

    Moreland, Blythe; /Michigan U. /SLAC

    2012-08-24

    When is a dark matter halo 'relaxed'? In our efforts to understand the structure of the universe, dark matter simulations have provided essential grounds for theoretical predictions. These simulations provide a wealth of ways of parameterizing and measuring the features of astronomical objects. It is these measurements on which we base comparisons of our world and our attempts to re-create it. One of the essential questions dark matter simulations help address is how dark matter halos evolve. How does one characterize different states of that evolution? The focus of this project is identifying cluster relaxedness and how it relates to the internal structure of the halo. A dark matter simulation consists of an N-body simulation which takes an initial set of positions and velocities of the dark matter particles and evolves them under the influence of gravity [6]. Though scientists have so far not been able to detect dark matter particles, the information from these simulations is still valuable especially given the relationship between dark matter halos and galaxy clusters. Galaxies sit within dark matter halos and recent evidence points to filaments of dark matter forming the framework on which galaxy clusters grow [7]. A dark matter halo is a collapsed group of gravitationally bound dark matter particles. Subsets of bound particles form subhalos or substructures. The dark matter simulation is carried out over time - with decreasing redshift (z) or increasing scale factor (a = 1/1+z ). (Thus, z = 0 or a = 1.0 is present-day.) The merger history of a halo can be represented pictorally by a merger tree. A major merger event occurs when a structure joins the main halo with the mass ratio between it and the main halo being above a certain threshold. These events mark important points in the halo's evolution. And it is at these events that one hopes, and perhaps is more likely, to relate measures of relaxedness to this mass accretion. Cluster relaxedness is not a well

  12. Carboplatin binding to histidine

    SciTech Connect

    Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.; Levy, Colin; Schreurs, Antoine M. M.; Helliwell, John R.

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  13. Atomic and electronic properties of neutral and cationic metallic clusters

    NASA Astrophysics Data System (ADS)

    Kolchin, Andrew Marc

    2000-10-01

    We find optimal atomic and electronic structures for neutral and singly, positively charged clusters of beryllium and beryllium-lithium (of the form BeLik) using density functional theory in the local spin density approximation. Ions are moved with a steepest descent method, and the electronic wave functions optimized using a fictitious dynamics with simulated annealing, as conceived by Car and Parrinello. Shell-like orbitals, filling angular momentum states in the order: 1s 2p 2s 1d, are obtained for the beryllium clusters. The same ordering is found for the BeLik clusters which indicates a departure from the ordering found in pure alkali clusters by the lowering of the 2s level to below the 1d level due to the larger electron affinity of the Be impurity. We similarly calculate an atomic basis to which we relate these shell-like orbitals, and employ a Mulliken population analysis to visualize how the atomic orbitals might hybridize to create them. This analysis also allows us to observe an increasingly metallic behavior with cluster size, by associating the electron density distribution, and in the case of a charged cluster, the distribution of the hole, with atomic sites, and with regions of overlap between atom pairs. We quantitatively show the increase in density associated with bonding as cluster size increases, and the tendency of the hole to distribute itself near the most exterior atomic sites in clusters of high symmetry. Our results are compared with the predictions of the shell/jellium model in the context of our calculated binding energies and ionization potentials.

  14. The anion-binding polyanion: a molecular cobalt vanadium oxide with anion-sensitive visual response.

    PubMed

    Seliverstov, Andrey; Forster, Johannes; Heiland, Magdalena; Unfried, Johannes; Streb, Carsten

    2014-07-25

    An anionic molecular cobalt vanadium oxide cluster, (n-Bu4N)3[Co(AcO)V4O12] and its use as anion binding site is reported. Cluster formation is controlled by an anion-dependent dynamic solution equilibrium. Reversible anion binding in solution leads to significant spectral changes, allowing the ratiometric optical detection of the anion concentration in situ, even under harsh thermal conditions (T = 90 °C). Comparative studies showed that the spectral response is dependent on the type of anion so that carboxylates, weakly coordinating anions and halides can be distinguished.

  15. Are Earthquake Magnitudes Clustered?

    SciTech Connect

    Davidsen, Joern; Green, Adam

    2011-03-11

    The question of earthquake predictability is a long-standing and important challenge. Recent results [Phys. Rev. Lett. 98, 098501 (2007); ibid.100, 038501 (2008)] have suggested that earthquake magnitudes are clustered, thus indicating that they are not independent in contrast to what is typically assumed. Here, we present evidence that the observed magnitude correlations are to a large extent, if not entirely, an artifact due to the incompleteness of earthquake catalogs and the well-known modified Omori law. The latter leads to variations in the frequency-magnitude distribution if the distribution is constrained to those earthquakes that are close in space and time to the directly following event.

  16. The galactic globular cluster system

    NASA Technical Reports Server (NTRS)

    Djorgovski, S.; Meylan, G.

    1994-01-01

    We explore correlations between various properties of Galactic globular clusters, using a database on 143 objects. Our goal is identify correlations and trends which can be used to test and constrain theoretical models of cluster formation and evolution. We use a set of 13 cluster parameters, 9 of which are independently measured. Several arguments suggest that the number of clusters still missing in the obscured regions of the Galaxy is of the order of 10, and thus the selection effects are probably not severe for our sample. Known clusters follow a power-law density distribution with a slope approximately -3.5 to -4, and an apparent core with a core radius approximately 1 kpc. Clusters show a large dynamical range in many of their properties, more so for the core parameters (which are presumably more affected by dynamical evolution) than for the half-light parameters. There are no good correlations with luminosity, although more luminous clusters tend to be more concentrated. When data are binned in luminosity, several trends emerge: more luminous clusters tend to have smaller and denser cores. We interpret this as a differential survival effect, with more massive clusters surviving longer and reaching more evolved dynamical states. Cluster core parameters and concentrations also correlate with the position in the Galaxy, with clusters closer to the Galactic center or plane being more concentrated and having smaller and denser cores. These trends are more pronounced for the fainter (less massive) clusters. This is in agreement with a picture where tidal shocks form disk or bulge passages accelerate dynamical evolution of clusters. Cluster metallicities do not correlate with any other parameter, including luminosity and velocity dispersion; the only detectable trend is with the position in the Galaxy, probably reflecting Zinn's disk-halo dichotomy. This suggests that globular clusters were not self-enriched systems. Velocity dispersions show excellent correlations

  17. BINDING OF ANTIGEN BY IMMUNOCYTES

    PubMed Central

    Bystryn, Jean-Claude; Siskind, Gregory W.; Uhr, Jonathan W.

    1973-01-01

    The binding of antigen to cells with antibody on their surface has been studied in a model system consisting of murine myeloma cells (MOPC 315) and DNP conjugates. Specific binding occurred between the DNP groups of DNP conjugates and cell surface immunoglobulin. Using this model, the binding affinities of multivalent and univalent DNP conjugates were measured directly by equilibrium-binding techniques and indirectly by displacement of bound conjugate with univalent hapten. With both approaches the multivalent conjugate was shown to bind to cells with an avidity 100–300 fold greater than the univalent hapten. Nonspecific binding of unrelated protein and repeated washing of cells was found to markedly dedecrease the specific binding of univalent conjugates, presumably because the relatively weak bonds dissociate readily. PMID:4734402

  18. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin.

    PubMed

    Zhu, Yu; Ye, Xin-Hai; Liu, Yang; Yan, Zhi-Chao; Stanley, David; Ye, Gong-Yin; Fang, Qi

    2015-12-01

    Chitin-binding proteins (CBPs) are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP) from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs) of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton.

  19. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin

    PubMed Central

    Zhu, Yu; Ye, Xin-Hai; Liu, Yang; Yan, Zhi-Chao; Stanley, David; Ye, Gong-Yin; Fang, Qi

    2015-01-01

    Chitin-binding proteins (CBPs) are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP) from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs) of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton. PMID:26633500

  20. Density functional theory study on Ni-doped MgnNi (n = 1-7) clusters

    NASA Astrophysics Data System (ADS)

    Chen, Xue-Feng; Zhang, Yan; Qi, Kai-Tian; Li, Bing; Zhu, Zheng-He; Sheng, Yong

    2010-03-01

    The possible geometrical and the electronic structures of small MgnNi (n = 1-7) clusters are optimised by the density functional theory with a LANL2DZ basis set. The binding energy, the energy gap, the electron affinity, the dissociation energy and the second difference in energy are calculated and discussed. The properties of MgnNi clusters are also discussed when the number of Mg atom increases.

  1. 25. Steenbock symposium -- Biosynthesis and function of metal clusters for enzymes: Proceedings

    SciTech Connect

    1997-12-31

    This symposium was held June 10--14, 1997 in Madison, Wisconsin. The purpose of this conference was to provide a multidisciplinary forum for exchange of state-of-the-art information on biochemistry of enzymes that have an affinity for metal clusters. Attention is focused on the following: metal clusters involved in energy conservation and remediation; tungsten, molybdenum, and cobalt-containing enzymes; Fe proteins, and Mo-binding proteins; nickel enzymes; and nitrogenase.

  2. X-Ray Absorption Spectroscopy of Cuprous-Thiolate Clusters in Saccharomyces Cerevisiae Metallothionein

    SciTech Connect

    Zhang, L.; Pickering, I.J.; Winge, D.R.; George, G.N.

    2009-05-28

    Copper (Cu) metallothioneins are cuprous-thiolate proteins that contain multimetallic clusters, and are thought to have dual functions of Cu storage and Cu detoxification. We have used a combination of X-ray absorption spectroscopy (XAS) and density-functional theory (DFT) to investigate the nature of Cu binding to Saccharomyces cerevisiae metallothionein. We found that the XAS of metallothionein prepared, containing a full complement of Cu, was quantitatively consistent with the crystal structure, and that reconstitution of the apo-metallothionein with stoichiometric Cu results in the formation of a tetracopper cluster, indicating cooperative binding of the Cu ions by the metallothionein.

  3. Query Results Clustering by Extending SPARQL with CLUSTER BY

    NASA Astrophysics Data System (ADS)

    Ławrynowicz, Agnieszka

    The task of dynamic clustering of the search results proved to be useful in the Web context, where the user often does not know the granularity of the search results in advance. The goal of this paper is to provide a declarative way for invoking dynamic clustering of the results of queries submitted over Semantic Web data. To achieve this goal the paper proposes an approach that extends SPARQL by clustering abilities. The approach introduces a new statement, CLUSTER BY, into the SPARQL grammar and proposes semantics for such extension.

  4. Properties of The Brightest Cluster Galaxy and Its Host Cluster

    NASA Astrophysics Data System (ADS)

    Katayama, H.; Hayashida, K.; Takahara, F.

    2001-09-01

    We investigate the relation between the brightest cluster galaxy (BCG) and its host cluster. A BCG is a bright and massive elliptical galaxy in a cluster of galaxies. The luminosity of a BCG is 10 times larger than that of normal field galaxy and the mass of a BCG is about 1013Msolar which corresponds to that of galaxy group. In order to explain the origin of BCGs, the following three models are proposed: (1) star formation from cooling flow. In this model, intracluster gas gradually condenses at the center of the cluster and forms the BCG. (2) ``Galactic cannibalism'' or the accretion of smaller galaxies. In this model, dynamical friction accounts for the formation of the BCG. These two models predict the BCG evolves with the evolution of cluster. (3) Galaxy merging in the early history of the formation of the cluster. In this model, the property of BCGs is determined no later than cluster collapse. In any model, the formation of BCGs is related to the collapse and formation of its host cluster. The relation between the BCG and its host cluster was studied by Edge (1991). Edge (1991) found that the optical luminosity of the BCG is positively correlated with the X-ray luminosity and temperature of its host cluster. Edge (1991) concludes that these correlations indicate that the BCG responds to the overall cluster properties. In order to investigate the other relation between the BCG and its host cluster, we analyzed ROSAT archival data and compared the displacement between the X-ray peak and the BCG with the Z parameter of the fundamental relation found by Fujita and Takahara (1999). It is found that the displacement is larger with decreasing Z. Furthermore, the large Z clusters tend to have a regular X-ray profile, which implies a relaxed system. The fundamental parameter Z depends mainly on the virial density ρvir, and is considered to be related to the formation epoch of the cluster, i.e., large Z clusters are old clusters and small Z clusters are young

  5. How actin binds and assembles onto plasma membranes from Dictyostelium discoideum

    PubMed Central

    1988-01-01

    We have shown previously (Schwartz, M. A., and E. J. Luna. 1986. J. Cell Biol. 102: 2067-2075) that actin binds with positive cooperativity to plasma membranes from Dictyostelium discoideum. Actin is polymerized at the membrane surface even at concentrations well below the critical concentration for polymerization in solution. Low salt buffer that blocks actin polymerization in solution also prevents actin binding to membranes. To further explore the relationship between actin polymerization and binding to membranes, we prepared four chemically modified actins that appear to be incapable of polymerizing in solution. Three of these derivatives also lost their ability to bind to membranes. The fourth derivative (EF actin), in which histidine-40 is labeled with ethoxyformic anhydride, binds to membranes with reduced affinity. Binding curves exhibit positive cooperativity, and cross- linking experiments show that membrane-bound actin is multimeric. Thus, binding and polymerization are tightly coupled, and the ability of these membranes to polymerize actin is dramatically demonstrated. EF actin coassembles weakly with untreated actin in solution, but coassembles well on membranes. Binding by untreated actin and EF actin are mutually competitive, indicating that they bind to the same membrane sites. Hill plots indicate that an actin trimer is the minimum assembly state required for tight binding to membranes. The best explanation for our data is a model in which actin oligomers assemble by binding to clustered membrane sites with successive monomers on one side of the actin filament bound to the membrane. Individual binding affinities are expected to be low, but the overall actin-membrane avidity is high, due to multivalency. Our results imply that extracellular factors that cluster membrane proteins may create sites for the formation of actin nuclei and thus trigger actin polymerization in the cell. PMID:3392099

  6. Spectroscopic characterization of inductive binding in ions

    NASA Astrophysics Data System (ADS)

    Lessen, D.; Asher, R. L.; Brucat, P. J.

    1990-12-01

    Molecular ions without conventional covalent bonds have been synthesized via supersonic adiabatic expansion and studied in a tandem time-of-fligth mass spectrometer. Resonant laser photofragmentation of these ions reveal a wealth of vibrational and electronic structure previously unknown. The ground and excited state "bond" strengths of transition-metal rare-gas diatomic ions (MRg+) are determined spectroscopically. The vibrational structure of these diatomics has been analyzed using model metal rare-gas interatomic potential that incorporates only charge induced-dipole as the attractive force. This potential is used to predict the binding energy and structure of the MRg+n, n = 2-14, clusters. V+ is predicted to be four coordinate in its first "solvation shell" with Ar in accord with experimental observation. The dynamic of the MRg+n ions is probed by classical trajectory analysis of a model many-body potential. An example demonstrates that the lowest energy structure of a cluster can be less important to its dynamical structure at finite temperature than higher-lying, lower-symmetry isomers. Resonant photodissociation spectroscopy is used to show the existence of the charge dipole bound V(OH2)+ in both ground and excited states.

  7. A molecular placeholder strategy to access a family of transition-metal-functionalized vanadium oxide clusters.

    PubMed

    Kastner, Katharina; Margraf, Johannes T; Clark, Timothy; Streb, Carsten

    2014-09-15

    Systematic access to metal-functionalized polyoxometalates has thus far been limited to lacunary tungsten oxide and molybdenum oxide clusters. The first controlled, stepwise bottom-up assembly route to metal-functionalized molecular vanadium oxides is now presented. A di-vacant vanadate cluster with two metal binding sites, (DMA)2[V12O32Cl](3-) (DMA = dimethylammonium) is formed spontaneously in solution and characterized by single-crystal X-ray diffraction, ESI mass spectrometry, (51)V NMR spectroscopy, and elemental analyses. In the cluster, the metal binding sites are selectively blocked by hydrogen-bonded DMA placeholder cations. Reaction of the cluster with transition metals TM (Fe(3+), Co(2+), Cu(2+), Zn(2+)) gives access to mono-functionalized vanadate clusters (DMA)[{TM(L)}V12O32Cl](n-) (L = ligand). Metal binding is accomplished by significant distortions of the vanadium oxide framework reminiscent of a pincer movement. Cluster stability under technologically relevant conditions in the solid-state and solution is demonstrated.

  8. Clusters, molecular layers, and 3D crystals of water on Ni(111)

    SciTech Connect

    Thürmer, Konrad; Nie, Shu; Bartelt, Norman C.; Feibelman, Peter J.

    2014-11-14

    We examined the growth and stability of ice layers on Ni(111) up to ∼7 molecular layers (ML) thick using scanning tunneling microscopy. At low coverage, films were comprised of ∼1 nm wide two-dimensional (2D) clusters. Only above ∼0.5 ML did patches of continuous 2D layers emerge, coexisting with the clusters until the first ML was complete. The structure of the continuous layer is clearly different from that of the 2D clusters. Subsequently, a second molecular layer grew on top of the first. 3D crystallites started to form only after this 2nd ML was complete. 2D clusters re-appeared when thicker films were partially evaporated, implying that these clusters represent the equilibrium configuration at low coverage. Binding energies and image simulations computed with density functional theory suggest that the 2D clusters are partially dissociated and surrounded by H adatoms. The complete 2D layer contains only intact water molecules because of the lack of favorable binding sites for H atoms. We propose molecular structures for the 2D layer that are composed of the same pentagon-heptagon binding motif and water density observed on Pt(111). The similarity of the water structures on Pt and Ni suggests a general prescription for generating low-energy configurations on close-packed metal substrates.

  9. Cluster synchronization in oscillatory networks

    NASA Astrophysics Data System (ADS)

    Belykh, Vladimir N.; Osipov, Grigory V.; Petrov, Valentin S.; Suykens, Johan A. K.; Vandewalle, Joos

    2008-09-01

    Synchronous behavior in networks of coupled oscillators is a commonly observed phenomenon attracting a growing interest in physics, biology, communication, and other fields of science and technology. Besides global synchronization, one can also observe splitting of the full network into several clusters of mutually synchronized oscillators. In this paper, we study the conditions for such cluster partitioning into ensembles for the case of identical chaotic systems. We focus mainly on the existence and the stability of unique unconditional clusters whose rise does not depend on the origin of the other clusters. Also, conditional clusters in arrays of globally nonsymmetrically coupled identical chaotic oscillators are investigated. The design problem of organizing clusters into a given configuration is discussed.

  10. Rough Clustering for Cancer Datasets

    NASA Astrophysics Data System (ADS)

    Herawan, Tutut

    Cancer is becoming a leading cause of death among people in the whole world. It is confirmed that the early detection and accurate diagnosis of this disease can ensure a long survival of the patients. Expert systems and machine learning techniques are gaining popularity in this field because of the effective classification and high diagnostic capability. This paper presents the application of rough set theory for clustering two cancer datasets. These datasets are taken from UCI ML repository. The method is based on MDA technique proposed by [11]. To select a clustering attribute, the maximal degree of the rough attributes dependencies in categorical-valued information systems is used. Further, we use a divide-and-conquer method to partition/cluster the objects. The results show that MDA technique can be used to cluster to the data. Further, we present clusters visualization using two dimensional plot. The plot results provide user friendly navigation to understand the cluster obtained.

  11. Decaying neutrinos in galaxy clusters

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Splinter, Randall J.; Persic, Massimo; Salucci, Paolo

    1994-01-01

    Davidsen et al. (1991) have argued that the failure to detect UV photons from the dark matter (DM) in cluster A665 excludes the decaying neutrino hypothesis. Sciama et al. (1993) argued that because of high central concentration the DM in that cluster must be baryonic. We study the DM profile in clusters of galaxies simulated using the Harrison-Zel'dovich spectrum of density fluctuations, and an amplitude previously derived from numerical simulations (Melott 1984b; Anninos et al. 1991) and in agreement with microwave background fluctuations (Smoot et al. 1992). We find that with this amplitude normalization cluster neutrino DM densities are comparable to observed cluster DM values. We conclude that given this normalization, the cluster DM should be at least largely composed of neutrinos. The constraint of Davidsen et al. can be somewhat weakened by the presence of baryonic DM; but it cannot be eliminated given our assumptions.

  12. Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

    SciTech Connect

    Priyanka,; Dharamvir, Keya; Sharma, Hitesh

    2011-12-12

    The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding silicon doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.

  13. First-principles study on stability, and growth strategies of small AlnZr (n=1-9) clusters

    NASA Astrophysics Data System (ADS)

    Li, Zhi; Zhou, Zhonghao; Wang, Hongbin; Li, Shengli; Zhao, Zhen

    2016-09-01

    The geometries, relative stability as well as growth strategies of the AlnZr (n=1-9) clusters are investigated with spin polarized density functional theory: BLYP. The results reveal that the AlnZr clusters are more likely to form the dense accumulation structures than the AlN (N=1-10) clusters. The average binding energies of AlnZr are higher than those of AlN clusters. The AlnZr (n=3, 5, and 7) clusters are more stable than others by the differences of the total binding energies. Mülliken population analysis for the AlnZr clusters shows that the electron's adsorption ability of Zr is slightly lower than that of Al except for AlZr cluster. Local peaks of the HOMO-LUMO gap curve are found at n=3, 5, and 7. The reaction energies of AlnZr are higher, which means that AlnZr clusters are easier to react with Al clusters. Zr atom preferential reacts with Al2 cluster. Local peaks of the magnetic dipole moments are found at n=2, 5, and 8.

  14. Actin at receptor-rich domains of isolated acetylcholine receptor clusters.

    PubMed

    Bloch, R J

    1986-04-01

    Acetylcholine receptor (AChR) clusters of cultured rat myotubes, isolated by extraction with saponin (Bloch, R. J., 1984, J. Cell Biol. 99:984-993), contain a polypeptide that co-electrophoreses with purified muscle actins. A monoclonal antibody against actin reacts in immunoblots with this polypeptide and with purified actins. In indirect immunofluorescence, the antibody stains isolated AChR clusters only at AChR domains, strips of membrane within clusters that are rich in receptor. It also stains the postsynaptic region of the neuromuscular junction of adult rat skeletal muscle. Semiquantitative immunofluorescence analyses show that labeling by antiactin of isolated analyses show that labeling by antiactin of isolated AChR clusters is specific and saturable and that it varies linearly with the amount of AChR in the cluster. Filaments of purified gizzard myosin also bind preferentially at AChR-rich regions, and this binding is inhibited by MgATP. These experiments suggest that actin is associated with AChR-rich regions of receptor clusters. Depletion of actin by extraction of isolated clusters at low ionic strength selectively releases the actin-like polypeptide from the preparation. Simultaneously, AChRs redistribute within the plane of the membrane of the isolated clusters. Similarly, brief digestion with chymotrypsin reduces immunofluorescence staining and causes AChR redistribution. Treatments that deplete AChR from clusters in intact cells also reduce immunofluorescent staining for actin in isolated muscle membrane fragments. Upon reversal of these treatments, cluster reformation occurs in regions of the membrane that also stain for actin. I conclude that actin is associated with AChR domains and that changes in this association are accompanied by changes in the organization of isolated AChR clusters.

  15. Multipose binding in molecular docking.

    PubMed

    Atkovska, Kalina; Samsonov, Sergey A; Paszkowski-Rogacz, Maciej; Pisabarro, M Teresa

    2014-02-14

    Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

  16. Mass Determinations of Star Clusters

    NASA Astrophysics Data System (ADS)

    Meylan, Georges

    Mass determinations are difficult to obtain and still frequently characterised by deceptively large uncertainties. We review below the various mass estimators used for star clusters of all ages and luminosities. We highlight a few recent results related to (i) very massive old star clusters, (ii) the differences and similarities between star clusters and cores of dwarf elliptical galaxies, and (iii) the possible strong biases on mass determination induced by tidal effects.

  17. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  18. Brightest Cluster Galaxies and Core Gas Density in REXCESS Clusters

    NASA Astrophysics Data System (ADS)

    Haarsma, Deborah B.; Leisman, Luke; Donahue, Megan; Bruch, Seth; Böhringer, Hans; Croston, Judith H.; Pratt, Gabriel W.; Voit, G. Mark; Arnaud, Monique; Pierini, Daniele

    2010-04-01

    We investigate the relationship between brightest cluster galaxies (BCGs) and their host clusters using a sample of nearby galaxy clusters from the Representative XMM-Newton Cluster Structure Survey. The sample was imaged with the Southern Observatory for Astrophysical Research in R band to investigate the mass of the old stellar population. Using a metric radius of 12 h -1 kpc, we found that the BCG luminosity depends weakly on overall cluster mass as L BCG vprop M 0.18±0.07 cl, consistent with previous work. We found that 90% of the BCGs are located within 0.035 r 500 of the peak of the X-ray emission, including all of the cool core (CC) clusters. We also found an unexpected correlation between the BCG metric luminosity and the core gas density for non-cool-core (non-CC) clusters, following a power law of ne vprop L 2.7±0.4 BCG (where ne is measured at 0.008 r 500). The correlation is not easily explained by star formation (which is weak in non-CC clusters) or overall cluster mass (which is not correlated with core gas density). The trend persists even when the BCG is not located near the peak of the X-ray emission, so proximity is not necessary. We suggest that, for non-CC clusters, this correlation implies that the same process that sets the central entropy of the cluster gas also determines the central stellar density of the BCG, and that this underlying physical process is likely to be mergers.

  19. Bistability in Apoptosis by Receptor Clustering

    PubMed Central

    Ho, Kenneth L.; Harrington, Heather A.

    2010-01-01

    Apoptosis is a highly regulated cell death mechanism involved in many physiological processes. A key component of extrinsically activated apoptosis is the death receptor Fas which, on binding to its cognate ligand FasL, oligomerize to form the death-inducing signaling complex. Motivated by recent experimental data, we propose a mathematical model of death ligand-receptor dynamics where FasL acts as a clustering agent for Fas, which form locally stable signaling platforms through proximity-induced receptor interactions. Significantly, the model exhibits hysteresis, providing an upstream mechanism for bistability and robustness. At low receptor concentrations, the bistability is contingent on the trimerism of FasL. Moreover, irreversible bistability, representing a committed cell death decision, emerges at high concentrations which may be achieved through receptor pre-association or localization onto membrane lipid rafts. Thus, our model provides a novel theory for these observed biological phenomena within the unified context of bistability. Importantly, as Fas interactions initiate the extrinsic apoptotic pathway, our model also suggests a mechanism by which cells may function as bistable life/death switches independently of any such dynamics in their downstream components. Our results highlight the role of death receptors in deciding cell fate and add to the signal processing capabilities attributed to receptor clustering. PMID:20976242

  20. Independent variables in foam clusters

    NASA Astrophysics Data System (ADS)

    Fortes, M. A.; Teixeira, P. I. C.

    2001-11-01

    We find, by counting the degrees of freedom of two-dimensional bubble clusters (finite or periodic) of given topology and bubble areas, that the Plateau laws determine a unique configuration of a finite free cluster, but allow an infinite number of configurations of a periodic cluster. Each of these configurations is associated with a particular strain (stress) state of the cluster; there is in general one unstrained configuration, which corresponds to the minimum of the (surface) energy. Configurations of given topology that satisfy Plateau's laws may only exist in certain ranges of bubble area ratios and/or strains.

  1. Digging Deep in Pandora's Cluster

    NASA Astrophysics Data System (ADS)

    Blakeslee, John P.; Alamo-Martinez, Karla; Toloba, Elisa; Barro, Guillermo; Peng, Eric W.

    2015-01-01

    Abell 2744, the first and nearest (z=0.31) of the Hubble Frontier Fields, is extraordinarily rich in the number and variety of galaxies it contains. Nicknamed "Pandora's Cluster," it exhibits multiple peaks in the dark matter, X-ray, and galaxy density distributions, suggesting an ongoing collision of several massive clusters. The exceptional depth of the Hubble Frontier Field imaging now makes it possible to throw open Pandora's cluster and peer deep inside. To do this, we first model and remove the stellar light of the cluster galaxies; underneath we find not only distant background galaxies, but (like the Hope that lay at the bottom of Pandora's box) a large population of globular star clusters and compact cluster members within Abell 2744 itself. Our earlier work on the massive lensing cluster Abell 1689 (Alamo-Martinez et al. 2013) revealed the largest known population of globular clusters, with a spatial profile intermediate between the galaxy light and the dark matter. Abell 2744 is similarly massive, but far less regular in its density distribution; we examine what implications this has for the copious globular clusters coursing through its multiple cores.

  2. Active matter clusters at interfaces.

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    2016-03-01

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped) clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped), where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  3. Teaching In a Cluster College

    ERIC Educational Resources Information Center

    Lawler, Nancy

    1977-01-01

    Report on the advantages and disadvantages of the interdisciplinary cluster system at Oakton Community College (Illinois) after five years. Reviews effects on students, faculty, administrators, and curriculum. (RT)

  4. Evaporative attachment of slow electrons to free sodium clusters

    NASA Astrophysics Data System (ADS)

    Rabinovich, Roman Mikhailovich

    demonstrate that slow-electron capture offers a useful window into the statistical and binding properties of metal clusters. Conversely, they show that in interpreting electron capture and transfer reactions it is essential to account for the accompanying fragmentation effects.

  5. Adaptive cluster detection

    NASA Astrophysics Data System (ADS)

    Friedenberg, David

    2010-10-01

    the rate of falsely detected active regions. Additionally we examine the more general field of clustering and develop a framework for clustering algorithms based around diffusion maps. Diffusion maps can be used to project high-dimensional data into a lower dimensional space while preserving much of the structure in the data. We demonstrate how diffusion maps can be used to solve clustering problems and examine the influence of tuning parameters on the results. We introduce two novel methods, the self-tuning diffusion map which replaces the global scaling parameter in the typical diffusion map framework with a local scaling parameter and an algorithm for automatically selecting tuning parameters based on a cross-validation style score called prediction strength. The methods are tested on several example datasets.

  6. Nanoisland formation of small Agn-clusters on HOPG as determined by inner-shell photoionisation spectroscopy

    NASA Astrophysics Data System (ADS)

    Al-Hada, M.; Peters, S.; Peredkov, S.; Neeb, M.; Eberhardt, W.

    2015-09-01

    XPS (3d) and Auger spectra (MNN) of deposited Agn-clusters on a non-sputtered HOPG surface have been measured. Most of the XPS and Auger spectra appear very similar to the corresponding bulk spectrum, caused by a high mobility and agglomeration of the clusters on the inert carbon surface, independent of the initial cluster size. The metallic fingerprint of the cluster-agglomerated islands is sustained under UHV conditions for several days. Oxidised Ag-islands reveal a positive binding energy shift in distinct contrast to the negative XPS shift usually observed for silver oxide bulk compounds. The XPS binding energy shift has been used for estimation of the diameter of the cluster-assembled nanoislands (6-9 nm) using an electrostatic model.

  7. Characterization of Homogeneous, Cooperative Protein-DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy.

    PubMed

    Tessmer, Ingrid; Fried, Michael G

    2015-01-01

    Strong, positively cooperative binding can lead to the clustering of proteins on DNA. Here, we describe one approach to the analysis of such clusters. Our example is based on recent studies of the interactions of O(6)-alkylguanine DNA alkyltransferase (AGT) with high-molecular-weight DNAs (Adams et al., 2009; Tessmer, Melikishvili, & Fried, 2012). Cooperative cluster size distributions are predicted using the simplest homogeneous binding and cooperativity (HBC) model, together with data obtained by sedimentation equilibrium analysis. These predictions are tested using atomic force microscopy imaging; for AGT, measured cluster sizes are found to be significantly smaller than those predicted by the HBC model. A mechanism that may account for cluster size limitation is briefly discussed.

  8. Characterization of Homogeneous, Cooperative Protein-DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy.

    PubMed

    Tessmer, Ingrid; Fried, Michael G

    2015-01-01

    Strong, positively cooperative binding can lead to the clustering of proteins on DNA. Here, we describe one approach to the analysis of such clusters. Our example is based on recent studies of the interactions of O(6)-alkylguanine DNA alkyltransferase (AGT) with high-molecular-weight DNAs (Adams et al., 2009; Tessmer, Melikishvili, & Fried, 2012). Cooperative cluster size distributions are predicted using the simplest homogeneous binding and cooperativity (HBC) model, together with data obtained by sedimentation equilibrium analysis. These predictions are tested using atomic force microscopy imaging; for AGT, measured cluster sizes are found to be significantly smaller than those predicted by the HBC model. A mechanism that may account for cluster size limitation is briefly discussed. PMID:26412659

  9. Quantum chemical study of the interaction of elemental Hg with small neutral, anionic and cationic Au{sub n} (n = 1–6) clusters

    SciTech Connect

    Siddiqui, Shamoon Ahmad; Bouarissa, Nadir; Rasheed, Tabish; Al-Assiri, M.S.

    2013-03-15

    Graphical abstract: Binding energies as a function of cluster size for Au{sub n}Hg, Au{sub n}Hg{sup +} and Au{sub n}Hg{sup −} complexes. Highlights: ► Hg adsorption of neutral and charged Au{sub n} (n = 1–6) clusters has been discussed. ► Size and charged state of cluster significantly affect the Hg adsorption. ► Transfer of electron mainly found from s orbital of Hg to s orbital of Au. - Abstract: Adsorption of elemental mercury (Hg) on small neutral, cationic and anionic gold clusters (Au{sub n}, n = 1–6) has been studied by using the density functional theory (DFT). Results of this investigation show that frontier molecular orbital theory is a useful tool to predict the selectivity of Hg adsorption. It is found that adsorption of Hg on neutral, cationic and anionic Au{sub n} (n = 1–6) clusters are thermodynamically favorable. The binding energies of Hg on the cationic Au{sub n} clusters are greater than those on the neutral and anionic clusters. Natural bond orbital (NBO) analysis indicates that the flow of electrons in the neutral and charged clusters is mainly due to the s orbitals of Hg and Au. Results of NBO analysis also indicate that the binding energy of Hg with Au{sub n} clusters is directly proportional to the charge transfer, i.e. greater is the charge transfer, higher is the binding energy.

  10. Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species

    PubMed Central

    Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J.; Boonstra, Rudy

    2015-01-01

    Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, Kd) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in Kd (range 2.0–7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The Kd values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5–5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the Kd in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists. PMID:27293705

  11. Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species.

    PubMed

    Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J; Boonstra, Rudy

    2015-01-01

    Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, K d) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in K d (range 2.0-7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The K d values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5-5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the K d in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists.

  12. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

    PubMed

    Zhang, Shaoqiang; Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html. PMID:27487245

  13. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

    PubMed

    Zhang, Shaoqiang; Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html.

  14. Dynamic Clustering of the Bacterial Sensory Kinase BaeS.

    PubMed

    Koler, Moriah; Frank, Vered; Amartely, Hadar; Friedler, Assaf; Vaknin, Ady

    2016-01-01

    Several bacterial sensory-kinase receptors form clusters on the cell membrane. However, the dynamics of sensory-kinase clustering are largely unclear. Using measurements of fluorescence anisotropy and time-lapse imaging of Escherichia coli cells, we demonstrate that copper ions trigger self-association of BaeS receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. Copper ions did not trigger self-association of other fluorescently tagged sensory kinases, and other divalent metal ions could not elicit self-association of BaeS. The histidine residues in the BaeS periplasmic domain are essential for copper binding in vitro and are important for the copper-induced BaeS responses in vivo. BaeS clustering was triggered also under conditions that directly triggered BaeS-dependent transcriptional responses. Thus, clustering of sensory kinase receptors can be dynamic and context dependent and can be triggered by specific environmental cues. PMID:26950881

  15. Dynamic Clustering of the Bacterial Sensory Kinase BaeS

    PubMed Central

    Koler, Moriah; Frank, Vered; Amartely, Hadar; Friedler, Assaf; Vaknin, Ady

    2016-01-01

    Several bacterial sensory-kinase receptors form clusters on the cell membrane. However, the dynamics of sensory-kinase clustering are largely unclear. Using measurements of fluorescence anisotropy and time-lapse imaging of Escherichia coli cells, we demonstrate that copper ions trigger self-association of BaeS receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. Copper ions did not trigger self-association of other fluorescently tagged sensory kinases, and other divalent metal ions could not elicit self-association of BaeS. The histidine residues in the BaeS periplasmic domain are essential for copper binding in vitro and are important for the copper-induced BaeS responses in vivo. BaeS clustering was triggered also under conditions that directly triggered BaeS-dependent transcriptional responses. Thus, clustering of sensory kinase receptors can be dynamic and context dependent and can be triggered by specific environmental cues. PMID:26950881

  16. Proton transfer in gas-phase ammonium dinitramide clusters

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Thompson, Donald L.

    2003-02-01

    Proton transfer in gaseous ammonium dinitramide (ADN) clusters up to (ADN)2 is studied by using density-functional theory. Proton transfer between the hydrogen dinitramide and ammonia units does not occur in the ADN monomer, rather the ammonia-hydrogen dinitramide complex is stabilized by strong hydrogen bonding. However, proton transfer between hydrogen dinitramide and ammonia is observed in the ADN dimer [NH3HN(NO2)2]2, ADN solvated with a single ammonia molecule [NH3NH(NO2)2]NH3, and ADN solvated with a hydrogen dinitramide molecule [NH3HN(NO2)2]HN(NO2)2. Structural changes in the complexes relative to the free molecules and the binding energies of the clusters are given. Using population analysis, the total electrostatic interaction energy in each cluster is calculated. The electrostatic energy is a measure that distinguishes between the ionic or hydrogen-bonded nature of the clusters. Some implications of proton transfer in ADN clusters on the decomposition mechanism of ADN are discussed.

  17. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design

    PubMed Central

    Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html. PMID:27487245

  18. Carboplatin binding to histidine.

    PubMed

    Tanley, Simon W M; Diederichs, Kay; Kroon-Batenburg, Loes M J; Levy, Colin; Schreurs, Antoine M M; Helliwell, John R

    2014-09-01

    Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  19. Characterization of Pt-Au and Ni-Au Clusters on TiO(2)(110)

    SciTech Connect

    Chen, D. A.; Mullins, David R; Ratliff, J. S.; He, Wei; Tenney, Samuel

    2011-01-01

    The surface composition and properties of Pt-Au and Ni-Au clusters on TiO{sub 2}(110) have been studied by scanning tunneling microscopy (STM), low energy ion scattering (LEIS) and soft X-ray photoelectron spectroscopy (sXPS). STM studies show that bimetallic clusters are formed during sequential deposition of the two metals, regardless of the order of deposition. At the 2 ML of Au/2 ML of Pt or Ni coverages studied here, the second metal contributes to the growth of existing clusters rather than forming new pure metal clusters. LEIS experiments demonstrate that the surfaces of the bimetallic clusters are almost 100% Au when 2 ML of Au is deposited on top of 2 ML of Pt or Ni. However, a much larger fraction of Pt or Ni (50 and 20%, respectively) remains at the surface when 2 ML of Pt or Ni is deposited on 2 ML of Au, most likely due to limited diffusion of atoms within the clusters at room temperature. According to sXPS investigations, the binding energies of the metals in the bimetallic clusters are shifted from those observed for pure metal clusters; the Pt(4f{sub 7/2}) and Ni(3p{sub 3/2}) peaks are shifted to lower binding energies while the position of the Au(4f{sub 7/2}) peak is dominated by surface core level shifts. Pure Pt clusters as well as 0.4 ML of Au on 2 ML of Pt clusters reduce the titania support upon encapsulation after annealing to 800 K, whereas 2 ML of Au on 2 ML of Pt clusters do not reduce titania, presumably because there is no Pt at the surface of the clusters. Pure Ni clusters are also known to become encapsulated upon heating, but the reduction of titania is much less extensive compared to that of pure Pt clusters.

  20. Characterization of Pt-Au and Ni-Au Clusters on TiO2(110)

    SciTech Connect

    S Tenney; W He; J Ratliff; D Mullins; D Chen

    2011-12-31

    The surface composition and properties of Pt-Au and Ni-Au clusters on TiO{sub 2}(110) have been studied by scanning tunneling microscopy (STM), low energy ion scattering (LEIS) and soft X-ray photoelectron spectroscopy (sXPS). STM studies show that bimetallic clusters are formed during sequential deposition of the two metals, regardless of the order of deposition. At the 2 ML of Au/2 ML of Pt or Ni coverages studied here, the second metal contributes to the growth of existing clusters rather than forming new pure metal clusters. LEIS experiments demonstrate that the surfaces of the bimetallic clusters are almost 100% Au when 2 ML of Au is deposited on top of 2 ML of Pt or Ni. However, a much larger fraction of Pt or Ni (50 and 20%, respectively) remains at the surface when 2 ML of Pt or Ni is deposited on 2 ML of Au, most likely due to limited diffusion of atoms within the clusters at room temperature. According to sXPS investigations, the binding energies of the metals in the bimetallic clusters are shifted from those observed for pure metal clusters; the Pt(4f{sub 7/2}) and Ni(3p{sub 3/2}) peaks are shifted to lower binding energies while the position of the Au(4f{sub 7/2}) peak is dominated by surface core level shifts. Pure Pt clusters as well as 0.4 ML of Au on 2 ML of Pt clusters reduce the titania support upon encapsulation after annealing to 800 K, whereas 2 ML of Au on 2 ML of Pt clusters do not reduce titania, presumably because there is no Pt at the surface of the clusters. Pure Ni clusters are also known to become encapsulated upon heating, but the reduction of titania is much less extensive compared to that of pure Pt clusters.

  1. Analyzing geographic clustered response

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  2. Clustered engine study

    NASA Technical Reports Server (NTRS)

    Shepard, Kyle; Sager, Paul; Kusunoki, Sid; Porter, John; Campion, AL; Mouritzan, Gunnar; Glunt, George; Vegter, George; Koontz, Rob

    1993-01-01

    Several topics are presented in viewgraph form which together encompass the preliminary assessment of nuclear thermal rocket engine clustering. The study objectives, schedule, flow, and groundrules are covered. This is followed by the NASA groundrules mission and our interpretation of the associated operational scenario. The NASA reference vehicle is illustrated, then the four propulsion system options are examined. Each propulsion system's preliminary design, fluid systems, operating characteristics, thrust structure, dimensions, and mass properties are detailed as well as the associated key propulsion system/vehicle interfaces. A brief series of systems analysis is also covered including: thrust vector control requirements, engine out possibilities, propulsion system failure modes, surviving system requirements, and technology requirements. An assessment of vehicle/propulsion system impacts due to the lessons learned are presented.

  3. Ionized cluster beam deposition

    NASA Astrophysics Data System (ADS)

    Kirkpatrick, A. R.

    1983-11-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  4. Ionized cluster beam deposition

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, A. R.

    1983-01-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  5. DFT investigation on structure, electronic and magnetic properties of Crn (n=2-8) clusters

    NASA Astrophysics Data System (ADS)

    Shah, Esha V.; Kumar, Vipin; Roy, Debesh R.

    2016-05-01

    A density functional investigation on the series of chromium clusters, i.e., Crn (n=2-8) is performed for finding their lowest energy structures and various electronic and magnetic properties. For electronic properties, we have predicted binding energy, HOMO-LUMO (HLG), chemical hardness (η) etc., and also for magnetic behavior, we have predicted the magnetic moments of the lowest energy cluster isomers. A systematic search imposing all possible initial magnetic configurations of the clusters is considered for finding lowest energy structures. All the calculations is carried out using a very popular GGA functional Perdew, Burke and Ernzerhof (PBE), as implemented in the VASP code.

  6. Selenate reductase activity in Escherichia coli requires Isc iron-sulfur cluster biosynthesis genes.

    PubMed

    Yee, Nathan; Choi, Jessica; Porter, Abigail W; Carey, Sean; Rauschenbach, Ines; Harel, Arye

    2014-12-01

    The selenate reductase in Escherichia coli is a multi-subunit enzyme predicted to bind Fe-S clusters. In this study, we examined the iron-sulfur cluster biosynthesis genes that are required for selenate reductase activity. Mutants devoid of either the iscU or hscB gene in the Isc iron-sulfur cluster biosynthesis pathway lost the ability to reduce selenate. Genetic complementation by the wild-type sequences restored selenate reductase activity. The results indicate the Isc biosynthetic system plays a key role in selenate reductase Fe-S cofactor assembly and is essential for enzyme activity.

  7. Trifluoperazine binding to mutant calmodulins.

    PubMed

    Massom, L R; Lukas, T J; Persechini, A; Kretsinger, R H; Watterson, D M; Jarrett, H W

    1991-01-22

    Trifluoperazine (TFP) binding by 14 calmodulins, including 12 produced by site-directed mutagenesis, was determined. While vertebrate calmodulin binds 4.2 +/- 0.2 equiv of TFP, Escherichia coli expressed but unmutated calmodulins bind about 5.0 +/- 0.5 equiv of TFP. The cause for this difference is not known. The E. coli expressed proteins consist of two different series expressed from different calmodulin genes, CaMI and SYNCAM. The wild-type genes code for proteins that differ by nine conservative amino acid substitutions. Both these calmodulins bind 5 equiv of TFP with similar affinities, thus none of these conservative substitutions has any additional effect on TFP binding. Some altered calmodulins (deletion of EE83-84 or SEEE81-84, changing DEE118-120----KKK, M124----I,E120----K, or E82----K) have no appreciable effect on TFP binding. Other mutations affect either the binding of one TFP (deletion of E84) or about two TFP (changing E84----K, EEE82-84----KKK, E67----A, DEQ6-8----KKK, or E11----K). The mutations that affect TFP binding are localized to three regions of calmodulin: The amino-terminal alpha-helix, the central helix between the two globular ends of calmodulin, and a calcium-binding site in the second calcium-binding domain. The results are consistent with each of these regions either directly participating in drug binding or involved structurally in maintaining or inducing the correct conformation for TFP binding in the amino-terminal half of calmodulin.

  8. The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO2 photoreduction

    SciTech Connect

    Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.; Joseph, Babu

    2015-09-04

    In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO2 photoreduction reaction (bent CO2), we find that flatter (2D-like) Pt clusters that “wet” the TiO2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO2 interfacial sites with geometries that can aid CO2 bond bending and charge transfer processes. Second, binding competition among each Pt–CO2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO2 surfaces for CO2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO2 on TiO2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.

  9. Effect of Graphene with Nanopores on Metal Clusters

    SciTech Connect

    Zhou, Hu; Chen, Xianlang; Wang, Lei; Zhong, Xing; Zhuang, Guilin; Li, Xiaonian; Mei, Donghai; Wang, Jianguo

    2015-10-07

    Porous graphene, which is a novel type of defective graphene, shows excellent potential as a support material for metal clusters. In this work, the stability and electronic structures of metal clusters (Pd, Ir, Rh) supported on pristine graphene and graphene with different sizes of nanopore were investigated by first-principle density functional theory (DFT) calculations. Thereafter, CO adsorption and oxidation reaction on the Pd-graphene system were chosen to evaluate its catalytic performance. Graphene with nanopore can strongly stabilize the metal clusters and cause a substantial downshift of the d-band center of the metal clusters, thus decreasing CO adsorption. All binding energies, d-band centers, and adsorption energies show a linear change with the size of the nanopore: a bigger size of nanopore corresponds to a stronger metal clusters bond to the graphene, lower downshift of the d-band center, and weaker CO adsorption. By using a suitable size nanopore, supported Pd clusters on the graphene will have similar CO and O2 adsorption ability, thus leading to superior CO tolerance. The DFT calculated reaction energy barriers show that graphene with nanopore is a superior catalyst for CO oxidation reaction. These properties can play an important role in instructing graphene-supported metal catalyst preparation to prevent the diffusion or agglomeration of metal clusters and enhance catalytic performance. This work was supported by National Basic Research Program of China (973Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21176221, 21136001, 21101137, 21306169, and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational

  10. Ambient preparation and reactions of gas phase silver cluster cations and anions.

    PubMed

    Wleklinski, Michael; Sarkar, Depanjan; Hollerbach, Adam; Pradeep, Thalappil; Cooks, R Graham

    2015-07-28

    Electrospray ionization of metal salt solutions followed by ambient heating transforms the resulting salt clusters into new species, primarily naked ionic metal clusters. The experiment is done by passing the clusters through a heated coiled loop outside the mass spectrometer which releases the counter-anion while generating the anionic or cationic naked metal cluster. The nature of the anion in the starting salt determines the type of metal cluster observed. For example, silver acetate upon heating generates only positive silver clusters, Ag(n)(+), but silver fluoride generates both positive and negative silver clusters, Ag(n)(+/-) (3 < n < 20). Both unheated and heated metal salt sprays yield ions with characteristic geometric and electronic magic numbers. There is also a strong odd/even effect in the cationic and anionic silver clusters. Thermochemical control is suggested as the basis for favored formation of the observed clusters, with anhydride elimination occurring from the acetates and fluorine elimination from the fluorides to give cationic and anionic clusters, respectively. Data on the intermediates observed as the temperature is ramped support this. The naked metal clusters react with gaseous reagents in the open air, including methyl substituted pyridines, hydrocarbons, common organic solvents, ozone, ethylene, and propylene. Argentation of hydrocarbons, including saturated hydrocarbons, is shown to occur and serves as a useful analytical ionization method. The new cluster formation methodology allows investigation of ligand-metal binding including in reactions of industrial importance, such as olefin epoxidation. These reactions provide insight into the physicochemical properties of silver cluster anions and cations. The potential use of the ion source in ion soft landing is demonstrated by reproducing the mass spectra of salts heated in air using a custom surface science instrument. PMID:26105831

  11. Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters

    PubMed Central

    Tellaroli, Paola; Bazzi, Marco; Donato, Michele; Brazzale, Alessandra R.; Drăghici, Sorin

    2016-01-01

    Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward’s minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward’s and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository. PMID:27015427

  12. Single-particle selection and alignment with heavy atom cluster-antibody conjugates.

    PubMed

    Jensen, G J; Kornberg, R D

    1998-08-01

    A method is proposed for selecting and aligning images of single biological particles to obtain high-resolution structural information by cryoelectron microscopy. The particles will be labeled with multiple heavy atom clusters to permit the precise determination of particle locations and relative orientations even when imaged close to focus with a low electron dose, conditions optimal for recording high-resolution detail. Heavy atom clusters should also allow selection of images free from many kinds of defects, including specimen movement and particle inhomogeneity. Heavy atom clusters may be introduced in a general way by the construction of "adaptor" molecules based on single-chain Fv antibody fragments, consisting of a constant framework region engineered for optimal cluster binding and a variable antigen binding region selected for a specific target. The success of the method depends on the mobility of the heavy atom cluster on the particle, on the precision to which clusters can be located in an image, and on the sufficiency of cluster projections alone to orient and select particles for averaging. The necessary computational algorithms were developed and implemented in simulations that address the feasibility of the method.

  13. Charge separation promoted activation of molecular oxygen by neutral gold clusters.

    PubMed

    Woodham, Alex P; Meijer, Gerard; Fielicke, André

    2013-02-01

    Gold nanoparticles and sub-nanoparticles famously act as highly efficient and selective low-temperature oxidation catalysts with molecular oxygen, in stark contrast to the nobility of the bulk phase. The origins of this activity and the nature of the active species remain open questions. Gas-phase studies of isolated gold clusters hold promise for disentangling these problems. Here we address the interaction of neutral gold clusters (Au(n); 4 ≤ n ≤ 21) with molecular oxygen by probing the highly characteristic O-O vibrational stretch frequencies. This reveals that for selected cluster sizes the oxygen is highly activated with respect to the free moiety. Complementary quantum chemical calculations provide evidence for substantial electron transfer to the O(2) unit and concomitant rearrangement of the parent gold cluster structure upon binding and activation. This gives evidence for a model of the interaction between neutral gold clusters and molecular oxygen.

  14. Structural and electronic properties of stable Lin (n=2-10) clusters: A density functional study

    NASA Astrophysics Data System (ADS)

    Chetri, Pawan; Deka, Ramesh Ch.; Choudhury, Amarjyoti

    2013-12-01

    Structure and relative stability of Lin clusters for n=1-10 were investigated using density functional methods based DMol3 program. The structures of Li clusters were determined in terms of Li-Li bond length and the results are in very good agreement with experimental values. Stability of the clusters was determined from their relative energy values binding energies and second difference energy. We also determined fragmentation energy of each size of cluster. We arrived at some interesting result like the transition of Lin from 2-dimension to 3-dimension for a particular value of n and also the variation of HOMO-LUMO gap with cluster size. Many structures are characterized for the first time in this work.

  15. Actin Mediates the Nanoscale Membrane Organization of the Clustered Membrane Protein Influenza Hemagglutinin

    PubMed Central

    Gudheti, Manasa V.; Curthoys, Nikki M.; Gould, Travis J.; Kim, Dahan; Gunewardene, Mudalige S.; Gabor, Kristin A.; Gosse, Julie A.; Kim, Carol H.; Zimmerberg, Joshua; Hess, Samuel T.

    2013-01-01

    The influenza viral membrane protein hemagglutinin (HA) is required at high concentrations on virion and host-cell membranes for infectivity. Because the role of actin in membrane organization is not completely understood, we quantified the relationship between HA and host-cell actin at the nanoscale. Results obtained using superresolution fluorescence photoactivation localization microscopy (FPALM) in nonpolarized cells show that HA clusters colocalize with actin-rich membrane regions (ARMRs). Individual molecular trajectories in live cells indicate restricted HA mobility in ARMRs, and actin disruption caused specific changes to HA clustering. Surprisingly, the actin-binding protein cofilin was excluded from some regions within several hundred nanometers of HA clusters, suggesting that HA clusters or adjacent proteins within the same clusters influence local actin structure. Thus, with the use of imaging, we demonstrate a dynamic relationship between glycoprotein membrane organization and the actin cytoskeleton at the nanoscale. PMID:23708358

  16. Structure and dynamics of ion clusters in linear octupole traps: Phase diagrams, chirality, and melting mechanisms

    SciTech Connect

    Yurtsever, E.; Onal, E. D.; Calvo, F.

    2011-05-15

    The stable structures and melting dynamics of clusters of identical ions bound by linear octupole radiofrequency traps are theoretically investigated by global optimization methods and molecular dynamics simulations. By varying the cluster sizes in the range of 10-1000 ions and the extent of trap anisotropy by more than one order of magnitude, we find a broad variety of stable structures based on multiple rings at small sizes evolving into tubular geometries at large sizes. The binding energy of these clusters is well represented by two contributions arising from isotropic linear and octupolar traps. The structures generally exhibit strong size effects, and chiral arrangements spontaneously emerge in many crystals. Sufficiently large clusters form nested, coaxial tubes with different thermal stabilities. As in isotropic octupolar clusters, the inner tubes melt at temperatures that are lower than the overall melting point.

  17. Analysis of xylosyltransferase II binding to the anticoagulant heparin

    SciTech Connect

    Casanova, Javier Carrera; Ambrosius, Michael; Kuhn, Joachim; Kleesiek, Knut; Goetting, Christian

    2009-05-22

    The key enzymes in the biosynthetic pathway of glycosaminoglycan production are represented by the human xylosyltransferase I and its isoform II (XylT-I and XylT-II). The glycosaminoglycan heparin interacts with a variety of proteins, thereby regulating their activities, also those of xylosyltransferases. The identification of unknown amino acids responsible for heparin-binding of XylT-II was addressed in this study. Thus, six XylT-II fragments were designed as fusion proteins with MBP and we received soluble and purified MBP/XylT-II from Escherichia coli. Heparin-binding studies showed that all fragments bound with low affinity to heparin. Prolonging of XylT-II fragments did not account for a cooperative effect of multiple heparin-binding motifs and in turn for a stronger heparin-binding. Sequence alignment and surface polarity plot led to the identification of two highly positively charged Cardin-Weintraub motifs with surface accessibility, resulting in combination with short clusters of basic amino acids for strong heparin-binding of native xylosyltransferases.

  18. A single native ganglioside GM1-binding site is sufficient for cholera toxin to bind to cells and complete the intoxication pathway.

    PubMed

    Jobling, Michael G; Yang, Zhijie; Kam, Wendy R; Lencer, Wayne I; Holmes, Randall K

    2012-01-01

    Cholera toxin (CT) from Vibrio cholerae is responsible for the majority of the symptoms of the diarrheal disease cholera. CT is a heterohexameric protein complex with a 240-residue A subunit and a pentameric B subunit of identical 103-residue B polypeptides. The A subunit is proteolytically cleaved within a disulfide-linked loop to generate the A1 and A2 fragments. The B subunit of wild-type (wt) CT binds 5 cell surface ganglioside GM(1) (GM(1)) molecules, and the toxin-GM(1) complex traffics from the plasma membrane (PM) retrograde through endosomes and the Golgi apparatus to the endoplasmic reticulum (ER). From the ER, the enzymatic A1 fragment retrotranslocates to the cytosol to cause disease. Clustering of GM(1) by multivalent toxin binding can structurally remodel cell membranes in ways that may assist toxin uptake and retrograde trafficking. We have recently found, however, that CT may traffic from the PM to the ER by exploiting an endogenous glycosphingolipid pathway (A. A. Wolf et al., Infect. Immun. 76:1476-1484, 2008, and D. J. F. Chinnapen et al., Dev. Cell 23:573-586, 2012), suggesting that multivalent binding to GM(1) is dispensable. Here we formally tested this idea by creating homogenous chimeric holotoxins with defined numbers of native GM(1) binding sites from zero (nonbinding) to five (wild type). We found that a single GM(1) binding site is sufficient for activity of the holotoxin. Therefore, remodeling of cell membranes by mechanisms that involve multivalent binding of toxin to GM(1) receptors is not essential for toxicity of CT. Through multivalent binding to its lipid receptor, cholera toxin (CT) can remodel cell membranes in ways that may assist host cell invasion. We recently found that CT variants which bind no more than 2 receptor molecules do exhibit toxicity, suggesting that CT may be able to enter cells by coopting an endogenous lipid sorting pathway without clustering receptors. We tested this idea directly by using purified variants

  19. Three-center tight-binding potential model for C and Si

    NASA Astrophysics Data System (ADS)

    Lu, Wen-Cai; Wang, C. Z.; Zhao, Li-Zhen; Qin, Wei; Ho, K. M.

    2015-07-01

    A tight-binding potential model which goes beyond the Slater-Koster two-center approximation and includes explicit three-center and crystal field expressions is presented. Using carbon and silicon as examples, we show that various bulk structures, surface reconstructions, and the structures of clusters and liquids of C and Si can be well described by the present three-center tight-binding model. These results demonstrate that three-center interaction and crystal field effect are very important for improving the transferability of tight-binding models in describing the structures and properties of materials over a broad range of bonding configurations.

  20. Steroid hormones in cluster headaches.

    PubMed

    Stillman, Mark

    2006-04-01

    For decades, glucocorticoid therapy has been a well-recognized abortive treatment for cluster headaches. However, the role of steroid hormones, including both glucocorticoids and sex steroids, in the pathophysiology and therapy of cluster headaches has been a topic of much debate and speculation. Current research now points to the importance of cortisol and testosterone in the pathogenesis of cluster headaches, and they appear to be linked mechanistically to another hormone, melatonin. Melatonin, unlike cortisol or testosterone, is not a product of the hypothalamic pituitary axis but of the retinohypothalamic pineal axis, and is the major biomarker of circadian rhythms. The regulation of steroids and melatonin in the pathogenesis of cluster headaches in turn depends on the sympathetic nervous system. Accumulated evidence suggests sympathetic dysfunction--embodied in the Horner sign so commonly seen in the cluster headache--as a necessary ingredient in the inception of the cluster headache. Sympathetic dysfunction now is thought to be associated with the hypercortisolism, hypotestosteronism, and lower-than-normal melatonin levels in the active cluster patient. Future research may hold the key to a fuller explanation of the complex interaction of hormonal systems in the cluster headache.