Science.gov

Sample records for dimerization sequence influence

  1. Intermonomer hydrogen bonds enhance GxxxG-driven dimerization of the BNIP3 transmembrane domain: roles for sequence context in helix-helix association in membranes

    PubMed Central

    Lawrie, Charles M.; Sulistijo, Endah S.; MacKenzie, Kevin R.

    2009-01-01

    We determined the sequence dependence of human BNIP3 transmembrane domain dimerization using the biological assay TOXCAT. Mutants in which intermonomer hydrogen bonds between Ser 172 and His 173 are abolished show moderate interaction, indicating that side chain hydrogen bonds contribute to dimer stability but are not essential to dimerization. Mutants in which a GxxxG motif composed of Gly 180 and Gly 184 has been abolished show little or no interaction, demonstrating the critical nature of the GxxxG motif to BNIP3 dimerization. These findings show that side chain hydrogen bonds can enhance the intrinsic dimerization of a GxxxG motif and that sequence context can control how hydrogen bonds influence helix-helix interactions in membranes. The dimer interface mapped by TOXCAT mutagenesis agrees closely with the interfaces observed in the NMR structure and inferred from mutational analysis of dimerization on SDS-PAGE, showing that the native dimer structure is retained in detergents. We show that TOXCAT and SDS-PAGE give complementary and consistent information about BNIP3 TMD dimerization: TOXCAT is insensitive to mutations that have modest effects on self-association in detergents but readily discriminates among mutations that completely disrupt detergent-resistant dimerization. The close agreement between conclusions reached from TOXCAT and SDS-PAGE data for BNIP3 suggests that accurate estimates of the relative effects of mutations on native state protein-protein interactions can be obtained even when the detergent environment is strongly disruptive. PMID:20026130

  2. Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers.

    PubMed

    Rahman, Khondaker M; James, Colin H; Thurston, David E

    2011-07-01

    Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two electrophilic imine moieties (or their equivalent) capable of forming covalent aminal linkages with guanine C2-NH(2) functionalities. The PBD dimer SJG-136, which has a C8-O-(CH(2))(3)-O-C8'' central linker joining the two PBD moieties, is currently undergoing phase II clinical trials and current research is focused on developing analogues of SJG-136 with different linker lengths and substitution patterns. Using a reversed-phase ion pair HPLC/MS method to evaluate interaction with oligonucleotides of varying length and sequence, we recently reported (JACS, 2009, 131, 13 756) that SJG-136 can form three different types of adducts: inter- and intrastrand cross-linked adducts, and mono-alkylated adducts. These studies have now been extended to include PBD dimers with a longer central linker (C8-O-(CH(2))(5)-O-C8'), demonstrating that the type and distribution of adducts appear to depend on (i) the length of the C8/C8'-linker connecting the two PBD units, (ii) the positioning of the two reactive guanine bases on the same or opposite strands, and (iii) their separation (i.e. the number of base pairs, usually ATs, between them). Based on these data, a set of rules are emerging that can be used to predict the DNA-interaction behaviour of a PBD dimer of particular C8-C8' linker length towards a given DNA sequence. These observations suggest that it may be possible to design PBD dimers to target specific DNA sequences.

  3. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

    PubMed

    Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

    2016-01-01

    For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

  4. Influence of the C-terminus of the glycophorin A transmembrane fragment on the dimerization process.

    PubMed Central

    Orzáez, M.; Pérez-Payá, E.; Mingarro, I.

    2000-01-01

    The monomer-dimer equilibrium of the glycophorin A (GpA) transmembrane (TM) fragment has been used as a model system to investigate the amino acid sequence requirements that permit an appropriate helix-helix packing in a membrane-mimetic environment. In particular, we have focused on a region of the helix where no crucial residues for packing have been yet reported. Various deletion and replacement mutants in the C-terminal region of the TM fragment showed that the distance between the dimerization motif and the flanking charged residues from the cytoplasmic side of the protein is important for helix packing. Furthermore, selected GpA mutants have been used to illustrate the rearrangement of TM fragments that takes place when leucine repeats are introduced in such protein segments. We also show that secondary structure of GpA derivatives was independent from dimerization, in agreement with the two-stage model for membrane protein folding and oligomerization. PMID:10892817

  5. Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation

    PubMed Central

    Henderson, Jordana M.; Lebedev, Alexandre; Salcedo, Michelle P.; Zon, Gerald; McCaffrey, Anton P.; Paul, Natasha; Hogrefe, Richard I.

    2016-01-01

    For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol. PMID:27875576

  6. Accumulation of the Cyclobutane Thymine Dimer in Defined Sequences of Free and Nucleosomal DNA

    DTIC Science & Technology

    2013-08-01

    luteus , Nature, 1980, 285, 634–641. 15 F. Bourre, G. Renault, P. C. Seawell and A. Sarasin, Distri- bution of ultraviolet-induced lesions in Simian...40, 2495–2501. 54 L. K. Gordon and W. A. Haseltine, Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus UV

  7. Detergent properties influence the stability of the glycophorin A transmembrane helix dimer in lysophosphatidylcholine micelles.

    PubMed

    Stangl, Michael; Veerappan, Anbazhagan; Kroeger, Anja; Vogel, Peter; Schneider, Dirk

    2012-12-19

    Detergents might affect membrane protein structures by promoting intramolecular interactions that are different from those found in native membrane bilayers, and fine-tuning detergent properties can be crucial for obtaining structural information of intact and functional transmembrane proteins. To systematically investigate the influence of the detergent concentration and acyl-chain length on the stability of a transmembrane protein structure, the stability of the human glycophorin A transmembrane helix dimer has been analyzed in lyso-phosphatidylcholine micelles of different acyl-chain length. While our results indicate that the transmembrane protein is destabilized in detergents with increasing chain-length, the diameter of the hydrophobic micelle core was found to be less crucial. Thus, hydrophobic mismatch appears to be less important in detergent micelles than in lipid bilayers and individual detergent molecules appear to be able to stretch within a micelle to match the hydrophobic thickness of the peptide. However, the stability of the GpA TM helix dimer linearly depends on the aggregation number of the lyso-PC detergents, indicating that not only is the chemistry of the detergent headgroup and acyl-chain region central for classifying a detergent as harsh or mild, but the detergent aggregation number might also be important.

  8. A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication.

    PubMed

    van Bel, Nikki; Das, Atze T; Cornelissen, Marion; Abbink, Truus E M; Berkhout, Ben

    2014-12-19

    The 5' leader of the HIV-1 RNA genome encodes signals that control various steps in the replication cycle, including the dimerization initiation signal (DIS) that triggers RNA dimerization. The DIS folds a hairpin structure with a palindromic sequence in the loop that allows RNA dimerization via intermolecular kissing loop (KL) base pairing. The KL dimer can be stabilized by including the DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED). The role of the ED RNA dimer in HIV-1 replication has hardly been addressed because of technical challenges. We analyzed a set of leader mutants with a stabilized DIS hairpin for in vitro RNA dimerization and virus replication in T cells. In agreement with previous observations, DIS hairpin stability modulated KL and ED dimerization. An unexpected previous finding was that mutation of three nucleotides immediately upstream of the DIS hairpin significantly reduced in vitro ED formation. In this study, we tested such mutants in vivo for the importance of the ED in HIV-1 biology. Mutants with a stabilized DIS hairpin replicated less efficiently than WT HIV-1. This defect was most severe when the upstream sequence motif was altered. Virus evolution experiments with the defective mutants yielded fast replicating HIV-1 variants with second site mutations that (partially) restored the WT hairpin stability. Characterization of the mutant and revertant RNA molecules and the corresponding viruses confirmed the correlation between in vitro ED RNA dimer formation and efficient virus replication, thus indicating that the ED structure is important for HIV-1 replication.

  9. Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress

    PubMed Central

    Topolska-Woś, Agnieszka M.; Shell, Steven M.; Kilańczyk, Ewa; Szczepanowski, Roman H.; Chazin, Walter J.; Filipek, Anna

    2015-01-01

    CacyBP/SIP [calcyclin-binding protein/Siah-1 [seven in absentia homolog 1 (Siah E3 ubiquitin protein ligase 1)] interacting protein] is a multifunctional protein whose activity includes acting as an ERK1/2 phosphatase. We analyzed dimerization of mouse CacyBP/SIP in vitro and in mouse neuroblastoma cell line (NB2a) cells, as well as the structure of a full-length protein. Moreover, we searched for the CacyBP/SIP domain important for dimerization and dephosphorylation of ERK2, and we analyzed the role of dimerization in ERK1/2 signaling in NB2a cells. Cell-based assays showed that CacyBP/SIP forms a homodimer in NB2a cell lysate, and biophysical methods demonstrated that CacyBP/SIP forms a stable dimer in vitro. Data obtained using small-angle X-ray scattering supported a model in which CacyBP/SIP occupies an anti-parallel orientation mediated by the N-terminal dimerization domain. Site-directed mutagenesis established that the N-terminal domain is indispensable for full phosphatase activity of CacyBP/SIP. We also demonstrated that the oligomerization state of CacyBP/SIP as well as the level of post-translational modifications and subcellular distribution of CacyBP/SIP change after activation of the ERK1/2 pathway in NB2a cells due to oxidative stress. Together, our results suggest that dimerization is important for controlling phosphatase activity of CacyBP/SIP and for regulating the ERK1/2 signaling pathway.—Topolska-Woś, A. M., Shell, S. M., Kilańczyk, E., Szczepanowski, R. H., Chazin, W. J., Filipek, A. Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress. PMID:25609429

  10. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.

    PubMed

    Shaytan, Alexey K; Landsman, David; Panchenko, Anna R

    2015-06-01

    Nucleosome variability is essential for their functions in compacting the chromatin structure and regulation of transcription, replication and cell reprogramming. The DNA molecule in nucleosomes is wrapped around an octamer composed of four types of core histones (H3, H4, H2A, H2B). Nucleosomes represent dynamic entities and may change their conformation, stability and binding properties by employing different sets of histone variants or by becoming post-translationally modified. There are many variants of histones H2A and H2B. Specific H2A and H2B variants may preferentially associate with each other resulting in different combinations of variants and leading to the increased combinatorial complexity of nucleosomes. In addition, the H2A-H2B dimer can be recognized and substituted by chaperones/remodelers as a distinct unit, can assemble independently and is stable during nucleosome unwinding. In this review we discuss how sequence and structural variations in H2A-H2B dimers may provide necessary complexity and confer the nucleosome functional variability.

  11. Tumor-Specific D-Dimer Concentration Ranges and Influencing Factors: A Cross-Sectional Study

    PubMed Central

    Lei, Dansheng; Yuan, Feng; Pei, Feng; Zhang, Huifeng; Yu, Anming; Wang, Kun; Chen, Hu; Chen, Liang; Wu, Xianglei; Tong, Xianli; Wang, Yefu

    2016-01-01

    D-dimer level in cancer patients is associated with risk of venous thromboembolism and deep venous thrombosis. Most cancer patients have “abnormal” D-dimer levels based on the current normal reference range. To investigate tumor-specific D-dimer reference range, we compared D-dimer levels for nine different tumour types with healthy controls by using simultaneous quantile regression and constructing a median, 5th percentile, and 95th percentile model of normal tumour D-dimer concentration. Associations with tumour primary site, stage, pathological type, and treatment were also explored. Additionally, 190 patients were tracked to reveal the relevance of initial D-dimer levels to cancer prognosis. D-dimer ranges (median, 5th, 95th) in various cancers (mg/L) were: liver 1.12, 0.27, 5.25; pancreatic 0.96, 0.23, 4.81; breast 0.44, 0.2, 2.17; gastric 0.65, 0.22, 5.03; colorectal 0.73, 0.22, 4.45; lung 0.7, 0.25, 4.0; gynaecological 0.61, 0.22, 3.98; oesophageal 0.23, 0.7, 3.45; and head and neck 0.22, 0.44, 2.19. All were significantly higher than that of healthy controls (0.18, 0.07, 0.57). D-dimer peaked 1–2 days postoperatively but had decreased to the normal range by 1 week. Additionally, cancer patients with high initial D-dimer were shown a tendency of poor prognosis in survival rate. In conclusion, D-dimer levels in cancer depend on patient age, tumour primary site, and tumour stage. Thrombosis prevention is necessary if D-dimer has not decreased to the tumor-specific baseline a week after surgery. PMID:27835633

  12. Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding.

    PubMed

    Liko, Idlir; Degiacomi, Matteo T; Mohammed, Shabaz; Yoshikawa, Shinya; Schmidt, Carla; Robinson, Carol V

    2016-07-19

    Bovine cytochrome c oxidase is an integral membrane protein complex comprising 13 protein subunits and associated lipids. Dimerization of the complex has been proposed; however, definitive evidence for the dimer is lacking. We used advanced mass spectrometry methods to investigate the oligomeric state of cytochrome c oxidase and the potential role of lipids and posttranslational modifications in its subunit interfaces. Mass spectrometry of the intact protein complex revealed that both the monomer and the dimer are stabilized by large lipid entities. We identified these lipid species from the purified protein complex, thus implying that they interact specifically with the enzyme. We further identified phosphorylation and acetylation sites of cytochrome c oxidase, located in the peripheral subunits and in the dimer interface, respectively. Comparing our phosphorylation and acetylation sites with those found in previous studies of bovine, mouse, rat, and human cytochrome c oxidase, we found that whereas some acetylation sites within the dimer interface are conserved, suggesting a role for regulation and stabilization of the dimer, phosphorylation sites were less conserved and more transient. Our results therefore provide insights into the locations and interactions of lipids with acetylated residues within the dimer interface of this enzyme, and thereby contribute to a better understanding of its structure in the natural membrane. Moreover dimeric cytochrome c oxidase, comprising 20 transmembrane, six extramembrane subunits, and associated lipids, represents the largest integral membrane protein complex that has been transferred via electrospray intact into the gas phase of a mass spectrometer, representing a significant technological advance.

  13. RNA Dimerization Promotes PKR Dimerization and Activation

    PubMed Central

    Heinicke, Laurie A.; Wong, C. Jason; Lary, Jeffrey; Nallagatla, Subba Rao; Diegelman-Parente, Amy; Zheng, Xiaofeng; Cole, James L.; Bevilacqua, Philip C.

    2009-01-01

    The double-stranded RNA (dsRNA)-activated protein kinase (PKR) plays a major role in the innate immune response in humans. PKR binds dsRNA non-sequence specifically and requires a minimum of 15 bp dsRNA for one protein to bind and 30 bp dsRNA to induce protein dimerization and activation by autophosphorylation. PKR phosphorylates eIF2α, a translation initiation factor, resulting in the inhibition of protein synthesis. We investigated the mechanism of PKR activation by an RNA hairpin with a number of base pairs intermediate between these 15 to 30 bp limits: HIV-I TAR RNA, a 23 bp hairpin with three bulges that is known to dimerize. To test whether RNA dimerization affects PKR dimerization and activation, TAR monomers and dimers were isolated from native gels and assayed for RNA and protein dimerization. To modulate the extent of dimerization, we included TAR mutants with different secondary features. Native gel mixing experiments and analytical ultracentrifugation indicate that TAR monomers bind one PKR monomer and that TAR dimers bind two or three PKRs, demonstrating that RNA dimerization drives the binding of multiple PKR molecules. Consistent with functional dimerization of PKR, TAR dimers activated PKR while TAR monomers did not, and RNA dimers with fewer asymmetrical secondary structure defects, as determined by enzymatic structure mapping, were more potent activators. Thus, the secondary structure defects in the TAR RNA stem function as antideterminants to PKR binding and activation. Our studies support that dimerization of a 15–30 bp hairpin RNA, which effectively doubles its length, is a key step in driving activation of PKR and provide a model for how RNA folding can be related to human disease. PMID:19445956

  14. Influence of Linker Length and Composition on Enzymatic Activity and Ribosomal Binding of Neomycin Dimers

    PubMed Central

    Watkins, Derrick; Kumar, Sunil; Green, Keith D.

    2015-01-01

    The human and bacterial A site rRNA binding as well as the aminoglycoside-modifying enzyme (AME) activity against a series of neomycin B (NEO) dimers is presented. The data indicate that by simple modifications of linker length and composition, substantial differences in rRNA selectivity and AME activity can be obtained. We tested five different AMEs with dimeric NEO dimers that were tethered via triazole, urea, and thiourea linkages. We show that triazole-linked dimers were the worst substrates for most AMEs, with those containing the longer linkers showing the largest decrease in activity. Thiourea-linked dimers that showed a decrease in activity by AMEs also showed increased bacterial A site binding, with one compound (compound 14) even showing substantially reduced human A site binding. The urea-linked dimers showed a substantial decrease in activity by AMEs when a conformationally restrictive phenyl linker was introduced. The information learned herein advances our understanding of the importance of the linker length and composition for the generation of dimeric aminoglycoside antibiotics capable of avoiding the action of AMEs and selective binding to the bacterial rRNA over binding to the human rRNA. PMID:25896697

  15. Mass spectrometric identification, sequence evolution, and intraspecific variability of dimeric peptides encoded by cockroach akh genes.

    PubMed

    Sturm, Sebastian; Predel, Reinhard

    2015-02-01

    Neuropeptides are structurally the most diverse group of messenger molecules of the nervous system. Regarding neuropeptide identification, distribution, function, and evolution, insects are among the best studied invertebrates. Indeed, more than 100 neuropeptides are known from single species. Most of these peptides can easily be identified by direct tissue or cell profiling using MALDI-TOF MS. In these experiments, protein hormones with extensive post-translational modifications such as inter- and intramolecular disulfides are usually missed. It is evident that an exclusion of these bioactive molecules hinders the utilization of direct profiling methods in comprehensive peptidomic analyses. In the current study, we focus on the detection and structural elucidation of homo- and heterodimeric adipokinetic hormone precursor-related peptides (APRPs) of cockroaches. The physiological relevance of these molecules with highly conserved sequences in insects is still uncertain. Sequence similarities with vertebrate growth hormone-releasing factors have been reported, but remarkably, few data regarding APRP processing exist and these data are restricted to locusts. Here, we elucidated sequences of carbamidomethylated APRP monomers of different cockroaches by means of MALDI-TOF MS(2), and we were able to identify a surprisingly large number of APRP sequences, resulting either from intraspecific amino acid substitutions within the APRP sequences or C-terminal truncated APRPs.

  16. Influence of molecular interactions on the stability of hydrogen-bonded dimers of carboxylic acids

    NASA Astrophysics Data System (ADS)

    Kolbe, Alfred; Plass, Monika; Kresse, Horst; Kolbe, Adelheid; Drabowicz, Jozef; Zurawinski, Remiguisz

    1997-12-01

    Possibilities to change the molecular arrangement of hydrogen bonded dimers of carboxylic acids by offering other acceptor groups are investigated in different species of molecules, namely in amino acid conjugates, in sulfinyl- and phosphinyl-carboxylic acids and in some p- n-alkoxybenzoic acids. As a result it was found that the carboxylic dimers are rather easily broken by lattice forces, by forming other intra- and intermolecular hydrogen bonds to stronger acceptor groups, and by increasing the temperature.

  17. On the influence of microsolvation by argon atoms on the electron affinity properties of water dimer

    NASA Astrophysics Data System (ADS)

    Wielgus, Pawel; Gora, Robert W.; Szefczyk, Borys; Roszak, Szczepan; Leszczynski, Jerzy

    2006-03-01

    This work provides a comparison of neutral (H2O)2Arn and negatively charged (H2O)2-Arn complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n⩽4) the microsolvation of the dimer by argon atoms arises on the trans side with respect to the donor water molecule. The stabilization of an excess electron is enhanced by the delocalization of the electronic charge density due to microsolvation. The process of cis to trans rotation is induced by the electric field of the approaching negative charge. The interaction energy decomposition suggests a more ionic character of binding in the negatively charged complexes. The attachment of an electron is controlled by the correlation energy.

  18. On the influence of microsolvation by argon atoms on the electron affinity properties of water dimer.

    PubMed

    Wielgus, Pawel; Gora, Robert W; Szefczyk, Borys; Roszak, Szczepan; Leszczynski, Jerzy

    2006-03-07

    This work provides a comparison of neutral (H2O)2Ar(n) and negatively charged (H2O)(2-)Ar(n) complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n < or = 4) the microsolvation of the dimer by argon atoms arises on the trans side with respect to the donor water molecule. The stabilization of an excess electron is enhanced by the delocalization of the electronic charge density due to microsolvation. The process of cis to trans rotation is induced by the electric field of the approaching negative charge. The interaction energy decomposition suggests a more ionic character of binding in the negatively charged complexes. The attachment of an electron is controlled by the correlation energy.

  19. Response of Staphylococcus aureus to Subinhibitory Concentrations of a Sequence-Selective, DNA Minor Groove Cross-Linking Pyrrolobenzodiazepine Dimer

    PubMed Central

    Doyle, Marie; Feuerbaum, Eva-Anne; Fox, Keith R.; Hinds, Jason; Thurston, David E.; Taylor, Peter W.

    2009-01-01

    Synopsis Objectives ELB-21 is a pyrrolo[2,1-c][1,4]benzodiazepine dimer with potent anti-staphylococcal activity; it binds covalently to guanine residues on opposing strands of duplex DNA, interfering with regulatory proteins and transcription elongation in a sequence selective manner. Transcriptional and proteomic alterations induced by exposure of Staphylococcus aureus clinical isolate EMRSA-16 to ELB-21 were determined in order to define more precisely the bactericidal mechanism of the drug. Methods DNase I footprinting was used to identify high affinity DNA binding sites. Microarrays and gel electrophoresis were used to assess the ELB-21-induced phenotype. Results High affinity interstrand binding sites in which guanine residues were separated by four base pairs, and also some intrastrand cross-linking sites of variable length were identified. Exposure of EMRSA-16 to 0.015 mg/L ELB-21 elicited a twofold or greater up-regulation of 168 genes in logarithmic phase and 181 genes in stationary phase; the majority of genes affected were associated with resident prophages φSa2 and φSa3, pathogenicity island SaPI4 and DNA damage repair. ELB-21 induced a marked increase in the number of viable phage particles in culture supernatants. The expression of only a limited number of genes showed more than 50% reduction. Sixteen extracellular and four intracellular proteins were differentially expressed during logarithmic and stationary phases, including RecA, proteins associated with staphylococcal pathogenesis (IsaA, CspA), cell division and wall synthesis. Conclusions ELB-21 kills S. aureus by forming multiple interstand and intrastrand DNA cross-links, resulting in induction of the DNA damage response, derepression of resident prophages and modulation of a limited number of genes involved with cell wall synthesis. PMID:19744983

  20. Changes at the KinA PAS-A Dimerization Interface Influence Histidine Kinase Function

    SciTech Connect

    Lee, James; Tomchick, Diana R.; Brautigam, Chad A.; Machius, Mischa; Kort, Remco; Hellingwerf, Klaas J.; Gardner, Kevin H.

    2008-11-12

    The Bacillus subtilis KinA protein is a histidine protein kinase that controls the commitment of this organism to sporulate in response to nutrient deprivation and several other conditions. Prior studies indicated that the N-terminal Per-ARNT-Sim domain (PAS-A) plays a critical role in the catalytic activity of this enzyme, as demonstrated by the significant decrease of the autophosphorylation rate of a KinA protein lacking this domain. On the basis of the environmental sensing role played by PAS domains in a wide range of proteins, including other bacterial sensor kinases, it has been suggested that the PAS-A domain plays an important regulatory role in KinA function. We have investigated this potential by using a combination of biophysical and biochemical methods to examine PAS-A structure and function, both in isolation and within the intact protein. Here, we present the X-ray crystal structure of the KinA PAS-A domain, showing that it crystallizes as a homodimer using {beta}-sheet/{beta}-sheet packing interactions as observed for several other PAS domain complexes. Notably, we observed two dimers with tertiary and quaternary structure differences in the crystalline lattice, indicating significant structural flexibility in these domains. To confirm that KinA PAS-A also forms dimers in solution, we used a combination of NMR spectroscopy, gel filtration chromatography, and analytical ultracentrifugation, the results of which are all consistent with the crystallographic results. We experimentally tested the importance of several residues at the dimer interface using site-directed mutagenesis, finding changes in the PAS-A domain that significantly alter KinA enzymatic activity in vitro and in vivo. These results support the importance of PAS domains within KinA and other histidine kinases and suggest possible routes for natural or artificial regulation of kinase activity.

  1. Interactions at the Dimer Interface Influence the Relative Efficiencies for Purine Nucleotide Synthesis and Pyrophosphorolysis in a Phosphoribosyltransferase

    SciTech Connect

    Canyuk, Bhutorn; Medrano, Francisco J.; Wenck, MaryAnne; Focia, Pamela J.; Eakin, Ann E.; Craig III, Sydney P.

    2010-03-05

    Enzymes that salvage 6-oxopurines, including hypoxanthine phosphoribosyltransferases (HPRTs), are potential targets for drugs in the treatment of diseases caused by protozoan parasites. For this reason, a number of high-resolution X-ray crystal structures of the HPRTs from protozoa have been reported. Although these structures did not reveal why HPRTs need to form dimers for catalysis, they revealed the existence of potentially relevant interactions involving residues in a loop of amino acid residues adjacent to the dimer interface, but the contributions of these interactions to catalysis remained poorly understood. The loop, referred to as active-site loop I, contains an unusual non-proline cis-peptide and is composed of residues that are structurally analogous with Leu67, Lys68, and Gly69 in the human HPRT. Functional analyses of site-directed mutations (K68D, K68E, K68N, K68P, and K68R) in the HPRT from Trypanosoma cruzi, etiologic agent of Chagas disease, show that the side-chain at position 68 can differentially influence the K{sub m} values for all four substrates as well as the k{sub cat} values for both IMP formation and pyrophosphorolysis. Also, the results for the K68P mutant are inconsistent with a cis-trans peptide isomerization-assisted catalytic mechanism. These data, together with the results of structural studies of the K68R mutant, reveal that the side-chain of residue 68 does not participate directly in reaction chemistry, but it strongly influences the relative efficiencies for IMP formation and pyrophosphorolysis, and the prevalence of lysine at position 68 in the HPRT of the majority of eukaryotes is consistent with there being a biological role for nucleotide pyrophosphorolysis.

  2. Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence

    PubMed Central

    Heintz, Udo; Schlichting, Ilme

    2016-01-01

    The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics. DOI: http://dx.doi.org/10.7554/eLife.11860.001 PMID:26754770

  3. A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of β-Aryl Ether Linkages in Lignin β-Guaiacyl and β-Syringyl Ether Dimers

    PubMed Central

    2014-01-01

    Lignin biosynthesis occurs via radical coupling of guaiacyl and syringyl hydroxycinnamyl alcohol monomers (i.e., “monolignols”) through chemical condensation with the growing lignin polymer. With each chain-extension step, monolignols invariably couple at their β-positions, generating chiral centers. Here, we report on activities of bacterial glutathione-S-transferase (GST) enzymes that cleave β-aryl ether bonds in lignin dimers that are composed of different monomeric units. Our data reveal that these sequence-related enzymes from Novosphingobium sp. strain PP1Y, Novosphingobium aromaticivorans strain DSM12444, and Sphingobium sp. strain SYK-6 have conserved functions as β-etherases, catalyzing cleavage of each of the four dimeric α-keto-β-aryl ether-linked substrates (i.e., guaiacyl-β-guaiacyl, guaiacyl-β-syringyl, syringyl-β-guaiacyl, and syringyl-β-syringyl). Although each β-etherase cleaves β-guaiacyl and β-syringyl substrates, we have found that each is stereospecific for a given β-enantiomer in a racemic substrate; LigE and LigP β-etherase homologues exhibited stereospecificity toward β(R)-enantiomers whereas LigF and its homologues exhibited β(S)-stereospecificity. Given the diversity of lignin’s monomeric units and the racemic nature of lignin polymers, we propose that bacterial catabolic pathways have overcome the existence of diverse lignin-derived substrates in nature by evolving multiple enzymes with broad substrate specificities. Thus, each bacterial β-etherase is able to cleave β-guaiacyl and β-syringyl ether-linked compounds while retaining either β(R)- or β(S)-stereospecificity. PMID:25232892

  4. Binding of 12-s-12 dimeric surfactants to calf thymus DNA: Evaluation of the spacer length influence.

    PubMed

    Sarrión, Beatriz; Bernal, Eva; Martín, Victoria Isabel; López-López, Manuel; López-Cornejo, Pilar; García-Calderón, Margarita; Moyá, María Luisa

    2016-08-01

    Several cationic dimeric surfactants have shown high affinity towards DNA. Bis-quaternary ammonium salts (m-s-m) have been the most common type of dimeric surfactants investigated and it is generally admitted that those that posses a short spacer (s≤3) show better efficiency to bind or compact DNA. However, experimental results in this work show that 12-s-12 surfactants with long spacers make the surfactant/ctDNA complexation more favorable than those with short spacers. A larger contribution of the hydrophobic interactions, which control the binding Gibbs energy, as well as a higher average charge of the surfactant molecules bound to the nucleic acid, which favors the electrostatic attractions, could explain the experimental observations. Dimeric surfactants with intermediate spacer length seem to be the less efficient for DNA binding.

  5. Mitochondrial sequence variation suggests an African influence in Portuguese cattle.

    PubMed Central

    Cymbron, T; Loftus, R T; Malheiro, M I; Bradley, D G

    1999-01-01

    A total of 49 samples from indigenous Portuguese cattle breeds were analysed for sequence variation in the hypervariable region of the mitochondrial DNA D-loop. Sequence comparison and phylogenetic analyses revealed that haplotypes fell into two distinct groups. These corresponded with two separate haplotype clusters into which, respectively, all African, or alternatively all sequences of European origin, have previously been shown to fall. Here, the majority of sequences of African type were encountered in three southern, as compared to three northern breeds. This pattern of African influence may reflect an intercontinental admixture in the initial origins of Iberian breeds, or it is perhaps an introgression dating from the long and influential Moorish occupation of the south of the Iberian peninsula. PMID:10212450

  6. Influence of heparin on fibrinogen and D-dimer plasma levels in acute myocardial infarction treated with streptokinase.

    PubMed

    Salvioni, A; Marenzi, G C; Agostoni, P; Grazi, S; Guazzi, M D

    1994-05-01

    The purpose of this study was to investigate whether, to what extent, and through which mechanisms intravenous heparin, administered before and after streptokinase, affects the plasma levels of D-dimer and fibrinogen in myocardial infarction. Data concerning mortality and incidence of coronary recanalization in patients receiving heparin and thrombolytic therapy after acute myocardial infarction are controversial; furthermore, the mechanisms through which heparin acts in combination with thrombolytic therapy are unclear. Thirty-eight patients with acute myocardial infarction treated with streptokinase were considered. Nineteen of them received, immediately before the beginning of thrombolytic treatment, a bolus of heparin (100 U.kg-1 intravenously) and, 2 h later, intravenous heparin in doses raising the partial thromboplastin time to 2-2.5 times the normal value (Group 1); the remaining 19 did not receive anticoagulant treatment (Group 2). Multiple determinations of plasma D-dimer and fibrinogen levels were obtained in all patients before, and in the seven days following thrombolytic treatment. Six hours after streptokinase, fibrinogen decreased from 304 +/- 34 to 61 +/- 34 mg.dl-1 in Group 1 and from 312 +/- 29 to 38 +/- 21 mg.dl-1 in Group 2 (P < 0.02 versus Group 1). The same difference between groups persisted at the 12th and at the 18th hour. D-dimer values, from 0.5 +/- 0.1 microgram.dl-1 in Group 1 and 0.4 +/- 0.1 microgram.dl-1 in Group 2, increased at the 1st hour to 37.2 +/- 36.5 micrograms.dl-1 and 52.2 +/- 39.8 micrograms.dl-1, respectively. A peak value was reached in both groups at the 6th hour, which was followed by a slow decrease.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. The dimers of cyanamide

    NASA Astrophysics Data System (ADS)

    Moffat, J. B.

    Ab initio calculations have been performed on various dimeric forms of cyanamide. The "nondissociative" dimerization of cyanamide leads to cyclic molecules all of which are unstable with respect to cyanamide. However, the molecules produced by "dissociative" dimerization are stable relative to cyanamide. Dicyandiamide is found to be the most stable of nine dimeric configurations.

  8. The influence of lateral interactions on the critical behavior of a dimer-monomer surface reaction model

    NASA Astrophysics Data System (ADS)

    Satulovsky, J.; Albano, E. V.

    1992-12-01

    The ZGB model [Ziff et al., Phys. Rev. Lett. 56, 2553 (1986)] for a monomer-dimer surface reaction process of the type A+(1/2)B2→AB, exhibits two irreversible phase transitions (IPT) from a stationary regime with AB production for p1A≤pA≤p2A, to poisoned states with B (A)-species for pA≤p1A (pA≥p2A), respectively, where pA is the mole fraction of A-species in the gas phase and piA (i=1, 2) are critical points. A generalization of the ZGB model in order to account for both attractive and repulsive interactions between the reactants is presented and discussed. It is found that in most cases the first order IPT at p2A becomes of second order and the critical points are shifted. For some particular choices of the interactions energies it is found that the second order IPT at p1A becomes of first order. Also, a first order IPT from the reactive state to a effectively poisoned regime where A-species are adsorbed forming a c(2×2) metastable structure is obtained.

  9. Dimer crystallization of chiral proteoids.

    PubMed

    Wang, Po-Yuan; Mason, Thomas G

    2017-03-08

    Proteins can self-assemble into a variety of exquisitely organized structures through hierarchical reaction pathways. To examine how different core shapes of proteins and entropy combine to influence self-assembly, we create systems of lithographically fabricated proteomimetic colloids, or 'proteoids', and explore how Brownian monolayers of mobile proteoids, which have hard interactions, self-assemble as they are slowly crowded. Remarkably, chiral C-shaped proteoids having circular heads on only one side form enantiopure lock-and-key chiral dimers; these dimers have corrugated, shape-complementary perimeters, so they, in turn, form lock-and-key arrangements into chiral dimer crystals. Time-lapse video microscopy reveals the expulsion of monomers from the growing dimer crystals through tautomerization translocation reactions which expedite the crystallization kinetics. By lithographically mutating proteoids, we also tune the types and structures of the resulting dimer crystals. Thus, rational design of sub-particle features in hard-core colloidal shapes can be used to sterically select desired self-assembly pathways without introducing any site-specific attractions, thereby generating a striking degree of hierarchical self-ordering, reminiscent of protein crystallization.

  10. Influence of softening sequencing on electrocoagulation treatment of produced water.

    PubMed

    Esmaeilirad, Nasim; Carlson, Ken; Omur Ozbek, Pinar

    2015-01-01

    Electrocoagulation has been used to remove solids and some metals from both water and wastewater sources for decades. Additionally, chemical softening is commonly employed in water treatment systems to remove hardness. This paper assesses the combination and sequence of softening and EC methods to treat hydraulic fracturing flowback and produced water from shale oil and gas operations. EC is one of the available technologies to treat produced water for reuse in frac fluids, eliminating not only the need to transport more water but also the costs of providing fresh water. In this paper, the influence of chemical softening on EC was studied. In the softening process, pH was raised to 9.5 and 10.2 before and after EC, respectively. Softening, when practiced before EC was more effective for removing turbidity with samples from wells older than one month (99% versus 88%). However, neither method was successful in treating samples collected from early flowback (1-day and 2-day samples), likely due to the high concentration of organic matter. For total organic carbon, hardness, Ba, Sr, and B removal, application of softening before EC appeared to be the most efficient approach, likely due to the formation of solids before the coagulation process.

  11. An Analysis of Stimuli that Influence Compliance during the High-Probability Instruction Sequence

    ERIC Educational Resources Information Center

    Normand, Matthew P.; Kestner, Kathryn; Jessel, Joshua

    2010-01-01

    When we evaluated variables that influence the effectiveness of the high-probability (high-p) instruction sequence, the sequence was associated with a precipitous decrease in compliance with high-"p" instructions for 1 participant, thereby precluding continued use of the sequence. We investigated the reasons for this decrease. Stimuli associated…

  12. Influence of sequence heterochrony on hadrosaurid dinosaur postcranial development.

    PubMed

    Guenther, Merrilee F

    2009-09-01

    A goal of modern dinosaur paleobiology is to synthesize the understanding of dinosaurian development and phylogeny. This study explores the Iguanodontia, one clade that includes several taxa for which growth series are preserved. It is hypothesized that analysis of growth series of iguanodontian taxa will reveal important developmental differences at play during the evolution of the clade. Such differences can reflect the impact of sequence heterochrony on iguanodontian evolution. Data were collected on the growth stages of the postcranial skeleton of a basal iguanodontian, Tenontosaurus; a lambeosaurine hadrosaurid, Hypacrosaurus; and two hadrosaurine hadrosaurids, Brachylophosaurus and Maiasaura to test the hypothesis. The event-pairing method provides a framework for the comparison of ontogenetic sequences among related taxa to detect significant evolutionary changes in developmental sequence. Significant developmental events are identified for the group and then the relative timings of those events in the developmental sequence are compared among the different species. Synapomorphic characters of Hadrosauridae, including the development of a prominent biceps tubercle on the coracoid, appear to be the result of changes in the developmental sequences of hadrosaurid taxa compared to basal iguanodontian taxa. This analysis also recognizes the developmental sequence differences that result in the development of the robust appendicular elements that characterize Lambeosaurinae. This comparative methodology shows that the development of characters such as the well developed supraacetabular process of the ilium results from the early onset of the development of those characters in the lambeosaurine hadrosaurid Hypacrosaurus compared to the hadrosaurines Brachylophosaurus and Maiasaura.

  13. Evidence for involvement of the C-terminal domain in the dimerization of the CopY repressor protein from Enterococcus hirae

    SciTech Connect

    Pazehoski, Kristina O.; Cobine, Paul A.; Winzor, Donald J.; Dameron, Charles T.

    2011-03-11

    Research highlights: {yields} A metal-binding protein domain is directly involved in protein dimerization. {yields} Fusing the metal-binding domain to a monomeric protein induces dimerization. {yields} Frontal size-exclusion chromatography measures the strength of dimer interaction. {yields} Ultracentrifugation studies confirm the influence of metal binding on dimerization. -- Abstract: Metal binding to the C-terminal region of the copper-responsive repressor protein CopY is responsible for homodimerization and the regulation of the copper homeostasis pathway in Enterococcus hirae. Specific involvement of the 38 C-terminal residues of CopY in dimerization is indicated by zonal and frontal (large zone) size-exclusion chromatography studies. The studies demonstrate that the attachment of these CopY residues to the immunoglobulin-binding domain of streptococcal protein G (GB1) promotes dimerization of the monomeric protein. Although sensitivity of dimerization to removal of metal from the fusion protein is smaller than that found for CopY (as measured by ultracentrifugation studies), the demonstration that an unrelated protein (GB1) can be induced to dimerize by extending its sequence with the C-terminal portion of CopY confirms the involvement of this region in CopY homodimerization.

  14. Photochemical dimerization of organic compounds

    DOEpatents

    Crabtree, Robert H.; Brown, Stephen H.; Muedas, Cesar A.; Ferguson, Richard R.

    1992-01-01

    At least one of selectivity and reaction rate of photosensitized vapor phase dimerizations, including dehydrodimerizations, hydrodimerizations and cross-dimerizations of saturated and unsaturated organic compounds is improved by conducting the dimerization in the presence of hydrogen or nitrous oxide.

  15. Acoustic Markers of Prominence Influence Infants' and Adults' Segmentation of Speech Sequences

    ERIC Educational Resources Information Center

    Bion, Ricardo A. H.; Benavides-Varela, Silvia; Nespor, Marina

    2011-01-01

    Two experiments investigated the way acoustic markers of prominence influence the grouping of speech sequences by adults and 7-month-old infants. In the first experiment, adults were familiarized with and asked to memorize sequences of adjacent syllables that alternated in either pitch or duration. During the test phase, participants heard pairs…

  16. The influence of visual training on predicting complex action sequences.

    PubMed

    Cross, Emily S; Stadler, Waltraud; Parkinson, Jim; Schütz-Bosbach, Simone; Prinz, Wolfgang

    2013-02-01

    Linking observed and executable actions appears to be achieved by an action observation network (AON), comprising parietal, premotor, and occipitotemporal cortical regions of the human brain. AON engagement during action observation is thought to aid in effortless, efficient prediction of ongoing movements to support action understanding. Here, we investigate how the AON responds when observing and predicting actions we cannot readily reproduce before and after visual training. During pre- and posttraining neuroimaging sessions, participants watched gymnasts and wind-up toys moving behind an occluder and pressed a button when they expected each agent to reappear. Between scanning sessions, participants visually trained to predict when a subset of stimuli would reappear. Posttraining scanning revealed activation of inferior parietal, superior temporal, and cerebellar cortices when predicting occluded actions compared to perceiving them. Greater activity emerged when predicting untrained compared to trained sequences in occipitotemporal cortices and to a lesser degree, premotor cortices. The occipitotemporal responses when predicting untrained agents showed further specialization, with greater responses within body-processing regions when predicting gymnasts' movements and in object-selective cortex when predicting toys' movements. The results suggest that (1) select portions of the AON are recruited to predict the complex movements not easily mapped onto the observer's body and (2) greater recruitment of these AON regions supports prediction of less familiar sequences. We suggest that the findings inform both the premotor model of action prediction and the predictive coding account of AON function.

  17. A Sequence of the CIS Gene Promoter Interacts Preferentially with Two Associated STAT5A Dimers: a Distinct Biochemical Difference between STAT5A and STAT5B

    PubMed Central

    Verdier, Frédérique; Rabionet, Raquel; Gouilleux, Fabrice; Beisenherz-Huss, Christian; Varlet, Paule; Muller, Odile; Mayeux, Patrick; Lacombe, Catherine; Gisselbrecht, Sylvie; Chretien, Stany

    1998-01-01

    Two distinct genes encode the closely related signal transducer and activator of transcription proteins STAT5A and STAT5B. The molecular mechanisms of gene regulation by STAT5 and, particularly, the requirement for both STAT5 isoforms are still undetermined. Only a few STAT5 target genes, among them the CIS (cytokine-inducible SH2-containing protein) gene, have been identified. We cloned the human CIS gene and studied the human CIS gene promoter. This promoter contains four STAT binding elements organized in two pairs. By electrophoretic mobility shift assay studies using nuclear extracts of UT7 cells stimulated with erythropoietin, we showed that these four sequences bound to STAT5-containing complexes that exhibited different patterns and affinities: the three upstream STAT binding sequences bound to two distinct STAT5-containing complexes (C0 and C1) and the downstream STAT box bound only to the slower-migrating C1 band. Using nuclear extracts from COS-7 cells transfected with expression vectors for the prolactin receptor, STAT5A, and/or STAT5B, we showed that the C1 complex was composed of a STAT5 tetramer and was dependent on the presence of STAT5A. STAT5B lacked this property and bound with a stronger affinity than did STAT5A to the four STAT sequences as a homodimer (C0 complex). This distinct biochemical difference between STAT5A and STAT5B was confirmed with purified activated STAT5 recombinant proteins. Moreover, we showed that the presence on the same side of the DNA helix of a second STAT sequence increased STAT5 binding and that only half of the palindromic STAT binding sequence was sufficient for the formation of a STAT5 tetramer. Again, STAT5A was essential for this cooperative tetrameric association. This property distinguishes STAT5A from STAT5B and could be essential to explain the transcriptional regulation diversity of STAT5. PMID:9742102

  18. Clinical study on the influence of phloroglucinol on plasma angiotensin II and D-Dimer index in patients with severe pregnancy-induced hypertension.

    PubMed

    Ai, Liang; Lan, Xinzhi; Wang, Limin; Xu, Yanjie; Zhang, Bin

    2016-07-01

    To observe the effect of phloroglucinol on plasma angiotensin II and D-dimer index when it was applied to patients with severe pregnancy-induced hypertension. 212 cases of severe pregnancy-induced hypertension patients diagnosed clinically were selected to be randomly divided into the research group and the control group. The research groups were given phloroglucinol, while the control groups were given magnesium sulfate. The plasma angiotensin II and D-dimer index in patients were detected before treatment and after 7 days respectively with statistical analysis of results. The diffidence after treatment was statistically significant (P<0.05). Compared within the same group, the difference of each index before and after treatment in the research group was statistically significant (P<0.05), while the control group was not statistically significant (P>0.05). It showed that the research group could reduce the plasma D-dimer and angiotensin II index in severe pregnancy-induced hypertension patients, and its effect was significantly better than the control group according to the plasma D-dimer and angiotensin II index changes in patients, it indicated that it was effective of phloroglucinol treatment for patients with pregnancy-induced hypertension disease and superior to the western medicine conventional treatment, worth clinical promotion.

  19. Dimers in nucleating vapors

    NASA Astrophysics Data System (ADS)

    Lushnikov, A. A.; Kulmala, M.

    1998-09-01

    The dimer stage of nucleation may affect considerably the rate of the nucleation process at high supersaturation of the nucleating vapor. Assuming that the dimer formation limits the nucleation rate, the kinetics of the particle formation-growth process is studied starting with the definition of dimers as bound states of two associating molecules. The partition function of dimer states is calculated by summing the Boltzmann factor over all classical bound states, and the equilibrium population of dimers is found for two types of intermolecular forces: the Lennard-Jones (LJ) and rectangular well+hard core (RW) potentials. The principle of detailed balance is used for calculating the evaporation rate of dimers. The kinetics of the particle formation-growth process is then investigated under the assumption that the trimers are stable with respect to evaporation and that the condensation rate is a power function of the particle mass. If the power exponent λ=n/(n+1) (n is a non-negative integer), the kinetics of the process is described by a finite set of moments of particle mass distribution. When the characteristic time of the particle formation by nucleation is much shorter than that of the condensational growth, n+2 universal functions of a nondimensional time define the kinetic process. These functions are calculated for λ=2/3 (gas-to-particle conversion in the free molecular regime) and λ=1/2 (formation of islands on surfaces).

  20. Analysis of SecA Dimerization in Solution

    PubMed Central

    2015-01-01

    The Sec pathway mediates translocation of protein across the inner membrane of bacteria. SecA is a motor protein that drives translocation of preprotein through the SecYEG channel. SecA reversibly dimerizes under physiological conditions, but different dimer interfaces have been observed in SecA crystal structures. Here, we have used biophysical approaches to address the nature of the SecA dimer that exists in solution. We have taken advantage of the extreme salt sensitivity of SecA dimerization to compare the rates of hydrogen–deuterium exchange of the monomer and dimer and have analyzed the effects of single-alanine substitutions on dimerization affinity. Our results support the antiparallel dimer arrangement observed in one of the crystal structures of Bacillus subtilis SecA. Additional residues lying within the preprotein binding domain and the C-terminus are also protected from exchange upon dimerization, indicating linkage to a conformational transition of the preprotein binding domain from an open to a closed state. In agreement with this interpretation, normal mode analysis demonstrates that the SecA dimer interface influences the global dynamics of SecA such that dimerization stabilizes the closed conformation. PMID:24786965

  1. Collective motion of dimers.

    PubMed

    Penington, Catherine J; Korvasová, Karolína; Hughes, Barry D; Landman, Kerry A

    2012-11-01

    We consider a discrete agent-based model on a one-dimensional lattice and a two-dimensional square lattice, where each agent is a dimer occupying two sites. Agents move by vacating one occupied site in favor of a nearest-neighbor site and obey either a strict simple exclusion rule or a weaker constraint that permits partial overlaps between dimers. Using indicator variables and careful probability arguments, a discrete-time master equation for these processes is derived systematically within a mean-field approximation. In the continuum limit, nonlinear diffusion equations that describe the average agent occupancy of the dimer population are obtained. In addition, we show that multiple species of interacting subpopulations give rise to advection-diffusion equations. Averaged discrete simulation data compares very well with the solution to the continuum partial differential equation models. Since many cell types are elongated rather than circular, this work offers insight into population-level behavior of collective cellular motion.

  2. Specificity of DNA binding of the c-Myc/Max and ARNT/ARNT dimers at the CACGTG recognition site.

    PubMed Central

    Swanson, H I; Yang, J H

    1999-01-01

    Basic helix-loop-helix proteins that interact with the DNA recognition site CACGTG include the c-Myc/Max heterodimer and the ARNT (Ahreceptornucleartranslocator) homodimer. We have utilized a PCR-based protocol to identify high affinity binding sites of either the c-Myc/Max or ARNT/ARNT dimers and analyzed the ability of these dimers to interact with their derived consensus sequences and activate genes. chi(2)analysis of the selected DNA recognition sites revealed that DNA binding of the ARNT homodimer is symmetric, resulting in the consensus sequence RTCACGTGAY. Gel shift analysis demonstrated that the flanking nucleotides play an important role in dictating DNA binding affinity of the ARNT homodimer. These flanking sequences also regulate the ability of ARNT to competitively displace the c-Myc/Max heterodimer from a CACGTG-containing sequence. However, transient transfection analyses in CV-1 cells revealed that ARNT and c-Myc/Max exhibited similar abilities to activate transcription through each other's consensus sequences. Taken together, these results indicate that although binding affinity of these dimers for the CACGTG core sequences may be differentially influenced by flanking nucleotides, transcriptional activity may also be determined by other factors, such as cellular concentrations of these proteins and their co-activators. PMID:10454619

  3. Regional association analysis delineates a sequenced chromosome region influencing antinutritive seed meal compounds in oilseed rape.

    PubMed

    Snowdon, R J; Wittkop, B; Rezaidad, A; Hasan, M; Lipsa, F; Stein, A; Friedt, W

    2010-11-01

    This study describes the use of regional association analyses to delineate a sequenced region of a Brassica napus chromosome with a significant effect on antinutritive seed meal compounds in oilseed rape. A major quantitative trait locus (QTL) influencing seed colour, fibre content, and phenolic compounds was mapped to the same position on B. napus chromosome A9 in biparental mapping populations from two different yellow-seeded × black-seeded B. napus crosses. Sequences of markers spanning the QTL region identified synteny to a sequence contig from the corresponding chromosome A9 in Brassica rapa. Remapping of sequence-derived markers originating from the B. rapa sequence contig confirmed their position within the QTL. One of these markers also mapped to a seed colour and fibre QTL on the same chromosome in a black-seeded × black-seeded B. napus cross. Consequently, regional association analysis was performed in a genetically diverse panel of dark-seeded, winter-type oilseed rape accessions. For this we used closely spaced simple sequence repeat (SSR) markers spanning the sequence contig covering the QTL region. Correction for population structure was performed using a set of genome-wide SSR markers. The identification of QTL-derived markers with significant associations to seed colour, fibre content, and phenolic compounds in the association panel enabled the identification of positional and functional candidate genes for B. napus seed meal quality within a small segment of the B. rapa genome sequence.

  4. Sequence and Temperature Influence on Kinetics of DNA Strand Displacement at Gold Electrode Surfaces.

    PubMed

    Biala, Katarzyna; Sedova, Ada; Flechsig, Gerd-Uwe

    2015-09-16

    Understanding complex contributions of surface environment to tethered nucleic acid sensing experiments has proven challenging, yet it is important because it is essential for interpretation and calibration of indispensable methods, such as microarrays. We investigate the effects of DNA sequence and solution temperature gradients on the kinetics of strand displacement at heated gold wire electrodes, and at gold disc electrodes in a heated solution. Addition of a terminal double mismatch (toehold) provides a reduction in strand displacement energy barriers sufficient to probe the secondary mechanisms involved in the hybridization process. In four different DNA capture probe sequences (relevant for the identification of genetically modified maize MON810), all but one revealed a high activation energy up to 200 kJ/mol during hybridization, that we attribute to displacement of protective strands by capture probes. Protective strands contain 4 to 5 mismatches to ease their displacement by the surface-confined probes at the gold electrodes. A low activation energy (30 kJ/mol) was observed for the sequence whose protective strand contained a toehold and one central mismatch, its kinetic curves displayed significantly different shapes, and we observed a reduced maximum signal intensity as compared to other sequences. These findings point to potential sequence-related contributions to oligonucleotide diffusion influencing kinetics. Additionally, for all sequences studied with heated wire electrodes, we observed a 23 K lower optimal hybridization temperature in comparison with disc electrodes in heated solution, and greatly reduced voltammetric signals after taking into account electrode surface area. We propose that thermodiffusion due to temperature gradients may influence both hybridization and strand displacement kinetics at heated microelectrodes, an explanation supported by computational fluid dynamics. DNA assays with surface-confined capture probes and temperature

  5. Quantum Dimer Model: Phase Diagrams

    NASA Astrophysics Data System (ADS)

    Goldstein, Garry; Chamon, Claudio; Castelnovo, Claudio

    We present new theoretical analysis of the Quantum Dimer Model. We study dimer models on square, cubic and triangular lattices and we reproduce their phase diagrams (which were previously known only numerically). We show that there are several types of dimer liquids and solids. We present preliminary analysis of several other models including doped dimers and planar spin ice, and some results on the Kagome and hexagonal lattices.

  6. Evidence for dimerization of dimers in K+ channel assembly.

    PubMed Central

    Tu, L; Deutsch, C

    1999-01-01

    Voltage-gated K+ channels are tetrameric, but how the four subunits assemble is not known. We analyzed inactivation kinetics and peak current levels elicited for a variety of wild-type and mutant Kv1.3 subunits, expressed singly, in combination, and as tandem constructs, to show that 1) the dominant pathway involves a dimerization of dimers, and 2) dimer-dimer interaction may involve interaction sites that differ from those involved in monomer-monomer association. Moreover, using nondenaturing gel electrophoresis, we detected dimers and tetramers, but not trimers, in the translation reaction of Kv1.3 monomers. PMID:10096897

  7. Momentum sequence and environmental climate influence levels of perceived psychological momentum within a sport competition.

    PubMed

    Briki, Walid; Markman, Keith D; Coudevylle, Guillaume; Sinnapah, Stéphane; Hue, Olivier

    2016-01-01

    The present study examined the influence of momentum sequence (positive vs. negative) and environmental climate (hot-wet vs. neutral) on supporters' (i.e. virtual observers') reported levels of perceived psychological momentum (PM) during a simulated cycling competition. Participants supported one of two competing cyclists involved in a race that was displayed on a screen in a lecture hall. The race scenario was manipulated so that the supported cyclist appeared to undergo either a positive or negative momentum sequence. In addition, participants were either exposed to a hot-wet environmental climate or to a neutral environmental climate while observing the race scenario. According to the results, reported levels of PM were higher in the positive momentum sequence condition than in the negative momentum sequence condition, consistent with the notion that supporters' PM is influenced by a positivity bias, and reported levels of PM were also found to be higher in the hot-wet climate condition than in the neutral climate condition, consistent with the notion that environmental climate is a contextual factor that influences PM through the operation of a causal augmenting mechanism.

  8. Modulative influence of lysozyme dimer on defence mechanisms in the carp (Cyprinus carpio) and European sheatfish (Silurus glanis) after suppression induced by herbicide Roundup.

    PubMed

    Terech-Majewska, E; Siwicki, A K; Szweda, W

    2004-01-01

    Immunomodulation is a commonly used method of prophylaxis in humans and animals. Lysozyme dimer (KLP-602) was used at a dose of 50 ug/kg b.w. in order to correct the immunosuppression caused by the action of herbicide glyphosate (Roundup- Monsanto), which was used in a single bath for 10 minutes in a concentration of 100 mg/l of water. The investigations were carried out on 2 species of fish: the carp (Cyprinus carpio L.) and european catfish (Silurus glanis L.). Herbicide glyphosate caused a decrease in metabolic and phagocytic activity (RBA and PKA) and in proliferative response stimulated by Con A and LPS in carp and european catfish. The immunosuppression sustained for about 2 weeks. The results obtained indicate the possibility of correction of immunosuppression applying lysozyme dimmer (KLP-602) after use of which, the level of the studied indexes increased.

  9. Influence of 8 and 24-h storage of whole blood at ambient temperature on prothrombin time, activated partial thromboplastin time, fibrinogen, thrombin time, antithrombin and D-dimer.

    PubMed

    Kemkes-Matthes, Bettina; Fischer, Ronald; Peetz, Dirk

    2011-04-01

    This study evaluates the effect of whole blood storage on common coagulation parameters in order to confirm or revise acceptable storage limits as defined by current guidelines and diverse study reports. Aliquots were taken from the citrated whole blood of inpatients and outpatients (n = 147) within 4 h after blood withdrawal and after extended storage of whole blood for 8 and 24 h at ambient temperature. Aliquots were centrifuged and analyzed for prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen (Fbg), antithrombin (AT), thrombin time (TT) and D-dimer. For each parameter, samples from 33-56 patients were investigated covering a wide range of normal and pathological values. Samples from patients receiving heparin were excluded from analyses of APTT and TT. All assays were performed using reagents and an analyzer from Siemens Healthcare Diagnostics Products GmbH. The mean percentage change after 8 and 24-h storage was below 10% for all parameters. Considering the changes in individual samples, all parameters can be reliably tested after 8-h storage, since less than 15% of the samples demonstrated individual changes of above 10%. The acceptable storage time can be extended to 24 h for PT, TT and D-dimer. Clinically relevant changes were detected after 24-h storage for APTT: 41% of the investigated samples demonstrated changes of above 10%. After 24-h storage, changes for Fbg and AT values were more than 15% in five out of 49 and in three out of 45 samples, respectively. This sporadic increase of values is clinically acceptable except for borderline samples.

  10. The influence of movement segment difficulty on movements with two-stroke sequence.

    PubMed

    Rand, M K; Alberts, J L; Stelmach, G E; Bloedel, J R

    1997-06-01

    Arm movements in the horizontal plane consisting of two segments were examined to determine whether the difficulty of the second segment influenced the kinematic characteristics of the first segment. The direction of the first segment was an elbow extension movement away from the trunk and remained constant throughout the experiment. The direction of the second segment varied between forearm extension and flexion movements. Based on Fitts' law, two different indexes of difficulty (ID) of the second segment were utilized by changing target size and movement amplitude. The effects of changing ID were examined for two different movement amplitudes. All movements were single-joint movements employing elbow flexion/extension and were recorded by an x-y digitizer. Variations in the ID of the second segment produced context-dependent kinematic changes in the performance of the initial segment. Movement duration increased when the ID was increased by reducing target size for both extension-extension sequence and extension-flexion sequences. Peak velocity also decreased for higher ID targets in the extension-flexion sequence. However, there was an interaction between the ID and movement amplitude in the extension-flexion sequence. In this sequence the duration of movement for the high ID/large movement amplitude condition increased substantially compared with the low ID/small movement amplitude condition. In addition, changing ID of the second segment influenced the time between the two segments (intersegment interval) in the extension-flexion sequence. Collectively, these data suggest that the planning of complex movements is based in part on the accuracy demands of multiple segments of the sequence.

  11. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    SciTech Connect

    Sutherland, B.M.; Bennett, P.V.

    1995-10-10

    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  12. Programmed dissociation of dimer and trimer origami structures by aptamer-ligand complexes.

    PubMed

    Wu, Na; Willner, Itamar

    2017-01-26

    Dimer- and trimer-origami frames are bridged by duplexes that include caged, sequence-specific, anti-ATP and/or anti-cocaine aptamer sequences. The programmed dissociation of the origami dimers or trimers in the presence of ATP and/or cocaine ligands is demonstrated. The processes are followed by AFM imaging and by electrophoretic experiments.

  13. Trigger sequence can influence final morphology in the self-assembly of asymmetric telechelic polymers.

    PubMed

    Kumar, Aatish; Lowe, Christopher P; Cohen Stuart, Martien A; Bolhuis, Peter G

    2016-02-21

    We report on a numerical study of polymer network formation of asymmetric biomimetic telechelic polymers with two reactive ends based on a self-assembling collagen, elastin or silk-like polypeptide sequence. The two reactive ends of the polymer can be activated independently using physicochemical triggers such as temperature and pH. We show, using a simple coarse grained model that the order in which this triggering occurs influences the final morphology. For both of collagen-silk and elastin-silk topologies we find that for relatively short connector chains the morphology of the assembly is greatly influenced by the order of the trigger, whereas for longer chains the equilibrium situation is more easily achieved. Moreover, self-assembly is greatly enhanced at moderate collagen interaction strength, due to facilitated binding and unbinding of the peptides. This finding indicates that both the trigger sequence and strength can be used to steer self-assembly in these biomimetic polymer systems.

  14. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.

    PubMed

    Taylor, Jenny C; Martin, Hilary C; Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David; Bento, Celeste; Bignell, Patricia; Blair, Edward; Buckle, Veronica J; Bull, Katherine; Cais, Ondrej; Cario, Holger; Chapel, Helen; Copley, Richard R; Cornall, Richard; Craft, Jude; Dahan, Karin; Davenport, Emma E; Dendrou, Calliope; Devuyst, Olivier; Fenwick, Aimée L; Flint, Jonathan; Fugger, Lars; Gilbert, Rodney D; Goriely, Anne; Green, Angie; Greger, Ingo H; Grocock, Russell; Gruszczyk, Anja V; Hastings, Robert; Hatton, Edouard; Higgs, Doug; Hill, Adrian; Holmes, Chris; Howard, Malcolm; Hughes, Linda; Humburg, Peter; Johnson, David; Karpe, Fredrik; Kingsbury, Zoya; Kini, Usha; Knight, Julian C; Krohn, Jonathan; Lamble, Sarah; Langman, Craig; Lonie, Lorne; Luck, Joshua; McCarthy, Davis; McGowan, Simon J; McMullin, Mary Frances; Miller, Kerry A; Murray, Lisa; Németh, Andrea H; Nesbit, M Andrew; Nutt, David; Ormondroyd, Elizabeth; Oturai, Annette Bang; Pagnamenta, Alistair; Patel, Smita Y; Percy, Melanie; Petousi, Nayia; Piazza, Paolo; Piret, Sian E; Polanco-Echeverry, Guadalupe; Popitsch, Niko; Powrie, Fiona; Pugh, Chris; Quek, Lynn; Robbins, Peter A; Robson, Kathryn; Russo, Alexandra; Sahgal, Natasha; van Schouwenburg, Pauline A; Schuh, Anna; Silverman, Earl; Simmons, Alison; Sørensen, Per Soelberg; Sweeney, Elizabeth; Taylor, John; Thakker, Rajesh V; Tomlinson, Ian; Trebes, Amy; Twigg, Stephen R F; Uhlig, Holm H; Vyas, Paresh; Vyse, Tim; Wall, Steven A; Watkins, Hugh; Whyte, Michael P; Witty, Lorna; Wright, Ben; Yau, Chris; Buck, David; Humphray, Sean; Ratcliffe, Peter J; Bell, John I; Wilkie, Andrew O M; Bentley, David; Donnelly, Peter; McVean, Gilean

    2015-07-01

    To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

  15. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

    PubMed Central

    Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David; Bento, Celeste; Bignell, Patricia; Blair, Edward; Buckle, Veronica J; Bull, Katherine; Cais, Ondrej; Cario, Holger; Chapel, Helen; Copley, Richard R; Cornall, Richard; Craft, Jude; Dahan, Karin; Davenport, Emma E; Dendrou, Calliope; Devuyst, Olivier; Fenwick, Aimée L; Flint, Jonathan; Fugger, Lars; Gilbert, Rodney D; Goriely, Anne; Green, Angie; Greger, Ingo H.; Grocock, Russell; Gruszczyk, Anja V; Hastings, Robert; Hatton, Edouard; Higgs, Doug; Hill, Adrian; Holmes, Chris; Howard, Malcolm; Hughes, Linda; Humburg, Peter; Johnson, David; Karpe, Fredrik; Kingsbury, Zoya; Kini, Usha; Knight, Julian C; Krohn, Jonathan; Lamble, Sarah; Langman, Craig; Lonie, Lorne; Luck, Joshua; McCarthy, Davis; McGowan, Simon J; McMullin, Mary Frances; Miller, Kerry A; Murray, Lisa; Németh, Andrea H; Nesbit, M Andrew; Nutt, David; Ormondroyd, Elizabeth; Oturai, Annette Bang; Pagnamenta, Alistair; Patel, Smita Y; Percy, Melanie; Petousi, Nayia; Piazza, Paolo; Piret, Sian E; Polanco-Echeverry, Guadalupe; Popitsch, Niko; Powrie, Fiona; Pugh, Chris; Quek, Lynn; Robbins, Peter A; Robson, Kathryn; Russo, Alexandra; Sahgal, Natasha; van Schouwenburg, Pauline A; Schuh, Anna; Silverman, Earl; Simmons, Alison; Sørensen, Per Soelberg; Sweeney, Elizabeth; Taylor, John; Thakker, Rajesh V; Tomlinson, Ian; Trebes, Amy; Twigg, Stephen RF; Uhlig, Holm H; Vyas, Paresh; Vyse, Tim; Wall, Steven A; Watkins, Hugh; Whyte, Michael P; Witty, Lorna; Wright, Ben; Yau, Chris; Buck, David; Humphray, Sean; Ratcliffe, Peter J; Bell, John I; Wilkie, Andrew OM; Bentley, David; Donnelly, Peter; McVean, Gilean

    2015-01-01

    To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease causing variants in 21% of cases, rising to 34% (23/68) for Mendelian disorders and 57% (8/14) in trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, though only four were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis, but also highlight many outstanding challenges. PMID:25985138

  16. Calcium-dependent Dimerization of Human Soluble Calcium Activated Nucleotidase: Characterization of the Dimer Interface

    SciTech Connect

    Yang,M.; Horii, K.; Herr, A.; Kirley, T.

    2006-01-01

    Mammals express a protein homologous to soluble nucleotidases used by blood-sucking insects to inhibit host blood clotting. These vertebrate nucleotidases may play a role in protein glycosylation. The activity of this enzyme family is strictly dependent on calcium, which induces a conformational change in the secreted, soluble human nucleotidase. The crystal structure of this human enzyme was recently solved; however, the mechanism of calcium activation and the basis for the calcium-induced changes remain unclear. In this study, using analytical ultracentrifugation and chemical cross-linking, we show that calcium or strontium induce noncovalent dimerization of the soluble human enzyme. The location and nature of the dimer interface was elucidated using a combination of site-directed mutagenesis and chemical cross-linking, coupled with crystallographic analyses. Replacement of Ile{sup 170}, Ser{sup 172}, and Ser{sup 226} with cysteine residues resulted in calcium-dependent, sulfhydryl-specific intermolecular cross-linking, which was not observed after cysteine introduction at other surface locations. Analysis of a super-active mutant, E130Y, revealed that this mutant dimerized more readily than the wild-type enzyme. The crystal structure of the E130Y mutant revealed that the mutated residue is found in the dimer interface. In addition, expression of the full-length nucleotidase revealed that this membrane-bound form can also dimerize and that these dimers are stabilized by spontaneous oxidative cross-linking of Cys{sup 30}, located between the single transmembrane helix and the start of the soluble sequence. Thus, calcium-mediated dimerization may also represent a mechanism for regulation of the activity of this nucleotidase in the physiological setting of the endoplasmic reticulum or Golgi.

  17. Influence of Aqueous-Salt Conditions on the Structure and Dynamics of the Monomeric and Novel Dimeric forms of the Alzheimer s ABeta21-30 protein fragment

    NASA Astrophysics Data System (ADS)

    Smith, Micholas Dean

    The behavior of the Alzheimer's related peptide Abeta is the subject of much study. In typical computational studies the environment local to the peptide is assumed to be pure water; however, in vivo the peptide is found in the extracellular space near the plasma membrane which is rich in ionic species. In this thesis, the hypothesis that the presence of group I/IIA salts will result in increased sampling of disordered structures as well as modify the dynamics of meta-stable structural motifs in the small folding nucleus of the Abeta peptide (Abeta21-30) is examined under a variety of ionic environments and was shown that of the tested salts, CaCl2 (and MgCl2, to a much lesser degree) did increase the propensity for disordered states; while, the group IA salts, KCl and NaCl, had little effect on the secondary structure of the peptide. Further, study of three familial mutations of this peptide region is also performed under aqueous salt-environments to elucidate further mechanistic details of how aqueous salts modify the region's behavior. Finally, as experimental results have highlighted that aggregation rates of the full-length peptide are modified by the presence of CaCl2, this work examines novel dimers states of Abeta21-30 and their stabilities when exposed to CaCl2.

  18. Tracking Rh Atoms in Zeolite HY: First Steps of Metal Cluster Formation and Influence of Metal Nuclearity on Catalysis of Ethylene Hydrogenation and Ethylene Dimerization

    SciTech Connect

    Yang, Dong; Xu, Pinghong; Browning, Nigel D.; Gates, Bruce C.

    2016-07-07

    The initial steps of rhodium cluster formation from zeolite-supported mononuclear Rh(C2H4)2 complexes in H2 at 373 K and 1 bar were investigated by infrared and extended X-ray absorption fine structure spectroscopies and scanning transmission electron microscopy (STEM). The data show that ethylene ligands on the rhodium react with H2 to give supported rhodium hydrides and trigger the formation of rhodium clusters. STEM provided the first images of the smallest rhodium clusters (Rh2) and their further conversion into larger clusters. The samples were investigated in a plug-flow reactor as catalysts for the conversion of ethylene + H2 in a molar ratio of 4:1 at 1 bar and 298 K, with the results showing how the changes in catalyst structure affect the activity and selectivity; the rhodium clusters are more active for hydrogenation of ethylene than the single-site complexes, which are more selective for dimerization of ethylene to give butenes

  19. Dynamical dimer-dimer correlation functions from exact diagonalization

    SciTech Connect

    Werner, Ralph

    2001-05-01

    A regularization method is presented to deduce dynamic correlation functions from exact diagonalization calculations. It is applied to dimer-dimer correlation functions in quantum spin chains relevant for the description of spin-Peierls systems. Exact results for the XY model are presented. The analysis draws into doubt that the dimer-dimer correlation functions show the same scale invariance as spin-spin correlation functions. The results are applied to describe the quasielastic scattering in CuGeO{sub 3} and the hardening of the Peierls-active phonons.

  20. The influence of the local sequence environment on RNA loop structures.

    PubMed

    Schudoma, Christian; Larhlimi, Abdelhalim; Walther, Dirk

    2011-07-01

    RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized η/θ-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.

  1. Influence of processing sequence on the tribological properties of VGCF-X/PA6/SEBS composites

    NASA Astrophysics Data System (ADS)

    Osada, Yu; Nishitani, Yosuke; Kitano, Takeshi

    2016-03-01

    In order to develop the new tribomaterials for mechanical sliding parts with sufficient balance of mechanical and tribological properties, we investigated the influence of processing sequence on the tribological properties of the ternary nanocomposites: the polymer blends of polyamide 6 (PA6) and styrene-ethylene/butylene-styrene copolymer (SEBS) filled with vapor grown carbon fiber (VGCF-X), which is one of carbon nanofiber (CNF) and has 15nm diameter and 3μm length. Five different processing sequences: (1) VGCF-X, PA6 and SEBS were mixed simultaneously (Process A), (2) Re-mixing (Second compounding) of the materials prepared by Process A (Process AR),(3) SEBS was blended with PA6 (PA6/SEBS blends) and then these blends were mixed with VGCF-X (Process B), (4) VGCF-X was mixed with PA6 (VGCF-X/PA6 composites) and then these composites were blended with SEBS (Process C), and (5) VGCF-X were mixed with SEBS (VGCF-X/SEBS composites) and then these composites were blended with PA6 (Process D) were attempted for preparing of the ternary nanocomposites (VGCF-X/PA6/SEBS composites). These ternary polymer nanocomposites were extruded by a twin screw extruder and injection-molded. Their tribological properties were evaluated by using a ring-on-plate type sliding wear tester under dry condition. The tribological properties such as the frictional coefficient and the specific wear rate were influenced by the processing sequence. These results may be attributed to the change of internal structure formation, which is a dispersibility of SEBS particle and VGCF-X in ternary nanocomposites (VGCF-X/PA6/SEBS) by different processing sequences. In particular, the processing sequences of AR, B and D, which are those of re-mixing of VGCF-X, have a good dispersibility of VGCF-X for the improvement of tribological properties.

  2. Adsorption of dimeric surfactants in lamellar silicates

    NASA Astrophysics Data System (ADS)

    Balcerzak, Mateusz; Pietralik, Zuzanna; Domka, Ludwik; Skrzypczak, Andrzej; Kozak, Maciej

    2015-12-01

    The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay - hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1‧-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d001) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH2 and CH3 groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

  3. The acrylonitrile dimer ion

    NASA Astrophysics Data System (ADS)

    Ervasti, Henri K.; Jobst, Karl J.; Burgers, Peter C.; Ruttink, Paul J. Ae; Terlouw, Johan K.

    2007-04-01

    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH-CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical ionization experiments of acrylonitrile with an excess of carbon dioxide, undergo five dissociations in the [mu]s time frame, as witnessed by peaks at m/z 53, 54, 79, 80 and 105 in their metastable ion mass spectrum. Collision experiments on these product ions, deuterium labeling, and a detailed computational analysis using the CBS-QB3 model chemistry lead to the following conclusions: (i) the m/z 54 ions are ions CH2CHCNH+ generated by self-protonation in ion-dipole stabilized hydrogen-bridged dimer ions [CH2CHCN...H-C(CN)CH2]+ and [CH2CHCN...H-C(H)C(H)CN]+; the proton shifts in these ions are associated with a small reverse barrier; (ii) dissociation of the H-bridged ions into CH2CCNH+ or CHCH-CNH+ by self-catalysis is energetically feasible but kinetically improbable: experiment shows that the m/z 53 ions are CH2CHCN+ ions, generated by back dissociation; (iii) the peaks at m/z 79, 80 and 105 correspond with the losses of HCN, C2H2 and H, respectively. The calculations indicate that these ions are generated from dimer ions that have adopted the (much more stable) covalently bound "head-to-tail" structure [CH2CHCN-C(H2)C(H)CN]+; experiments indicate that the m/z 79 (C5H5N) and m/z 105 (C6H6N2) ions have linear structures but the m/z 80 (C4H4N2) ions consist of ionized pyrimidine in admixture with its stable pyrimidine-2-ylidene isomer. Acrylonitrile is a confirmed species in interstellar space and our study provides experimental and computational evidence that its dimer radical cation yields the ionized prebiotic pyrimidine molecule.

  4. Influence of sequence mismatches on the specificity of recombinase polymerase amplification technology.

    PubMed

    Daher, Rana K; Stewart, Gale; Boissinot, Maurice; Boudreau, Dominique K; Bergeron, Michel G

    2015-04-01

    Recombinase polymerase amplification (RPA) technology relies on three major proteins, recombinase proteins, single-strand binding proteins, and polymerases, to specifically amplify nucleic acid sequences in an isothermal format. The performance of RPA with respect to sequence mismatches of closely-related non-target molecules is not well documented and the influence of the number and distribution of mismatches in DNA sequences on RPA amplification reaction is not well understood. We investigated the specificity of RPA by testing closely-related species bearing naturally occurring mismatches for the tuf gene sequence of Pseudomonas aeruginosa and/or Mycobacterium tuberculosis and for the cfb gene sequence of Streptococcus agalactiae. In addition, the impact of the number and distribution of mismatches on RPA efficiency was assessed by synthetically generating 14 types of mismatched forward primers for detecting five bacterial species of high diagnostic relevance such as Clostridium difficile, Staphylococcus aureus, S. agalactiae, P. aeruginosa, and M. tuberculosis as well as Bacillus atropheus subsp. globigii for which we use the spores as internal control in diagnostic assays. A total of 87 mismatched primers were tested in this study. We observed that target specific RPA primers with mismatches (n > 1) at their 3'extrimity hampered RPA reaction. In addition, 3 mismatches covering both extremities and the center of the primer sequence negatively affected RPA yield. We demonstrated that the specificity of RPA was multifactorial. Therefore its application in clinical settings must be selected and validated a priori. We recommend that the selection of a target gene must consider the presence of closely-related non-target genes. It is advisable to choose target regions with a high number of mismatches (≥36%, relative to the size of amplicon) with respect to closely-related species and the best case scenario would be by choosing a unique target gene.

  5. D Dimer in acute care

    PubMed Central

    Sathe, Prachee M.; Patwa, Urvil D.

    2014-01-01

    Pulmonary embolism, Deep Vein Thrombosis (DVT) and Disseminated intravascular coagulation (DIC) are important sources of mortality and morbidity in intensive care unit (ICU). And every time D-dimer remains the the commonest investigation. Many times D-dimer is erroneously considered as a diagnostic test in above mentioned conditions. Its interpretation requires cautions. To circumvent this source of error it is necessary to understand D-dimer test and its significance in various disorder. This article review some basic details of D-dimer, condition associated with its increased level and some prognostic value in intracranial hemorrhage and gastrointestinal (GI) bleed. PMID:25337485

  6. Does the new rugby union scrum sequence positively influence the hooker's in situ spinal kinematics?

    PubMed Central

    Williams, Jonathan M; Jones, Michael D; Theobald, Peter S

    2016-01-01

    Background Scrummaging is unique to rugby union and involves 2 ‘packs’ of 8 players competing to regain ball possession. Intending to serve as a quick and safe method to restart the game, injury prevalence during scrummaging necessitates further evaluation of this environment. Aims The aim of this study was to determine the effect of scrummage engagement sequences on spinal kinematics of the hooker. The conditions investigated were: (1) live competitive scrummaging using the new ‘crouch, bind, set’ sequence; (2) live competitive scrummaging using the old ‘crouch touch pause engage’ sequence and (3) training scrummaging using a scrum machine. Methods Inertial sensors provided three-dimensional kinematic data across 5 spinal regions. Participants (n=29) were adult, male community club and university-level hookers. Results Engagement sequence had no effect on resultant kinematics of any spinal region. Machine scrummaging resulted in lesser magnitudes of motion in the upper spinal regions. Around two-thirds of the total available cervical motion was utilised during live scrummaging. Conclusions This study indicates that the most recent laws do not influence the spinal kinematics of the hooker during live scrummaging; however, there may be other benefits from these law changes that fall outside the scope of this investigation. PMID:27900153

  7. A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets

    PubMed Central

    Moon, Sunjin; Akey, Joshua M.

    2016-01-01

    A continuing challenge in the analysis of massively large sequencing data sets is quantifying and interpreting non-neutrally evolving mutations. Here, we describe a flexible and robust approach based on the site frequency spectrum to estimate the fraction of deleterious and adaptive variants from large-scale sequencing data sets. We applied our method to approximately 1 million single nucleotide variants (SNVs) identified in high-coverage exome sequences of 6515 individuals. We estimate that the fraction of deleterious nonsynonymous SNVs is higher than previously reported; quantify the effects of genomic context, codon bias, chromatin accessibility, and number of protein–protein interactions on deleterious protein-coding SNVs; and identify pathways and networks that have likely been influenced by positive selection. Furthermore, we show that the fraction of deleterious nonsynonymous SNVs is significantly higher for Mendelian versus complex disease loci and in exons harboring dominant versus recessive Mendelian mutations. In summary, as genome-scale sequencing data accumulate in progressively larger sample sizes, our method will enable increasingly high-resolution inferences into the characteristics and determinants of non-neutral variation. PMID:27197222

  8. Phase variable DNA repeats in Neisseria gonorrhoeae influence transcription, translation, and protein sequence variation

    PubMed Central

    Zelewska, Marta A.; Pulijala, Madhuri; Spencer-Smith, Russell; Mahmood, Hiba-Tun-Noor A.; Norman, Billie; Churchward, Colin P.; Calder, Alan

    2016-01-01

    There are many types of repeated DNA sequences in the genomes of the species of the genus Neisseria, from homopolymeric tracts to tandem repeats of hundreds of bases. Some of these have roles in the phase-variable expression of genes. When a repeat mediates phase variation, reversible switching between tract lengths occurs, which in the species of the genus Neisseria most often causes the gene to switch between on and off states through frame shifting of the open reading frame. Changes in repeat tract lengths may also influence the strength of transcription from a promoter. For phenotypes that can be readily observed, such as expression of the surface-expressed Opa proteins or pili, verification that repeats are mediating phase variation is relatively straightforward. For other genes, particularly those where the function has not been identified, gathering evidence of repeat tract changes can be more difficult. Here we present analysis of the repetitive sequences that could mediate phase variation in the Neisseria gonorrhoeae strain NCCP11945 genome sequence and compare these results with other gonococcal genome sequences. Evidence is presented for an updated phase-variable gene repertoire in this species, including a class of phase variation that causes amino acid changes at the C-terminus of the protein, not previously described in N. gonorrhoeae. PMID:28348872

  9. Information-Theoretic Properties of Auditory Sequences Dynamically Influence Expectation and Memory.

    PubMed

    Agres, Kat; Abdallah, Samer; Pearce, Marcus

    2017-01-25

    A basic function of cognition is to detect regularities in sensory input to facilitate the prediction and recognition of future events. It has been proposed that these implicit expectations arise from an internal predictive coding model, based on knowledge acquired through processes such as statistical learning, but it is unclear how different types of statistical information affect listeners' memory for auditory stimuli. We used a combination of behavioral and computational methods to investigate memory for non-linguistic auditory sequences. Participants repeatedly heard tone sequences varying systematically in their information-theoretic properties. Expectedness ratings of tones were collected during three listening sessions, and a recognition memory test was given after each session. Information-theoretic measures of sequential predictability significantly influenced listeners' expectedness ratings, and variations in these properties had a significant impact on memory performance. Predictable sequences yielded increasingly better memory performance with increasing exposure. Computational simulations using a probabilistic model of auditory expectation suggest that listeners dynamically formed a new, and increasingly accurate, implicit cognitive model of the information-theoretic structure of the sequences throughout the experimental session.

  10. Effect of stacking sequence on the coefficients of mutual influence of composite laminates

    NASA Astrophysics Data System (ADS)

    Dupir (Hudișteanu, I.; Țăranu, N.; Axinte, A.

    2016-11-01

    Fiber reinforced polymeric (FRP) composites are nowadays widely used in engineering applications due to their outstanding features, such as high specific strength and specific stiffness as well as good corrosion resistance. A major advantage of fibrous polymeric composites is that their anisotropy can be controlled through suitable choice of the influencing parameters. The unidirectional fiber reinforced composites provide much higher longitudinal mechanical properties compared to the transverse ones. Therefore, composite laminates are formed by stacking two or more laminas, with different fiber orientations, as to respond to complex states of stresses. These laminates experience the effect of axial-shear coupling, which is caused by applying normal or shear stresses, implying shear or normal strains, respectively. The normal-shear coupling is expressed by the coefficients of mutual influence. They are engineering constants of primary interest for composite laminates, since the mismatch of the material properties between adjacent layers can produce interlaminar stresses and/or plies delamination. The paper presents the variation of the in-plane and flexural coefficients of mutual influence for three types of multi-layered composites, with different stacking sequences. The results are obtained using the Classical Lamination Theory (CLT) and are illustrated graphically in terms of fiber orientations, for asymmetric, antisymmetric and symmetric laminates. Conclusions are formulated on the variation of these coefficients, caused by the stacking sequence.

  11. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast

    PubMed Central

    2017-01-01

    RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking. PMID:28301878

  12. The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif.

    PubMed

    Steinkruger, Jay D; Bartlett, Gail J; Hadley, Erik B; Fay, Lindsay; Woolfson, Derek N; Gellman, Samuel H

    2012-02-08

    Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.

  13. The d′--d--d′ Vertical Triad is Less Discriminating Than the a′--a--a′ Vertical Triad in the Antiparallel Coiled-coil Dimer Motif

    PubMed Central

    Steinkruger, Jay D.; Bartlett, Gail J.; Hadley, Erik B.; Fay, Lindsay; Woolfson, Derek N.; Gellman, Samuel H.

    2012-01-01

    Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called ‘knobs-into-holes’ (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exhibit significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral at a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pair-wise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well. PMID:22296518

  14. Final report on the amended safety assessment of diisopropyl dimer dilinoleate, dicetearyl dimer dilinoleate, diisostearyl dimer dilinoleate, dioctyl dimer dilinoleate, dioctyldodecyl dimer dilinoleate, and ditridecyl dimer dilinoleate.

    PubMed

    Fiume, Monice Zondlo

    2003-01-01

    Diisopropyl Dimer Dilinoleate, Dicetearyl Dimer Dilinoleate, Diisostearyl Dimer Dilinoleate, Dioctyl Dimer Dilinoleate, Dioctyldodecyl Dimer Dilinoleate, and Ditridecyl Dimer Dilinoleate are diesters of their respective alcohols and dilinoleic acid. They function as skin-conditioning agents in a variety of cosmetic products at concentrations around 10%, but may be used at concentrations up to 53% in lipsticks. These ingredients do not absorb radiation in the ultraviolet (UV) UVA or UVB range and the only impurities expected are <0.5% dilinoleic acid, <0.1% isopropyl alcohol or <1% isostearyl alcohol, and/or small amounts of dilinoleic acid and cetearyl alcohol or octyldodecanol, depending on which diester is used. The potential skin penetration of these ingredients was evaluated using an estimate of the octanol/water partition coefficient (logP of 17.7) based on the structure of Diisopropyl Dimer Dilinoleate. This is consistent with the insolubility of these ingredients in water. Safety test data on dilinoleic acid (no adverse effects) were considered relevant because dilinoleic acid is a component of these diesters and a likely breakdown product. The acute oral and dermal LD(50) values for rats of Diisopropyl, Diisostearyl, and Dioctyldodecyl Dimer Dilinoleate were >5.0 g/kg. In a subchronic feeding study, macrophage aggregation was seen in the mesenteric lymph node at the lowest dose level (0.1% in the diet). These ingredients did not produce skin or ocular irritation in animal tests, nor were they comedogenic. Ames testing, clastogenesis in human lymphocytes in culture, and L5178Y mouse lymphoma cell forward mutations were all negative, indicating no dilinoleic acid genotoxicity. No carcinogenicity or reproductive/developmental toxicity data were available; however, structural alerts that would suggest a mutagenic or carcinogenic risk are absent. Significant reproductive/developmental toxicity or other systemic toxicity is not expected with these ingredients

  15. Atomic force microscopy of crystalline insulins: the influence of sequence variation on crystallization and interfacial structure.

    PubMed Central

    Yip, C M; Brader, M L; DeFelippis, M R; Ward, M D

    1998-01-01

    The self-association of proteins is influenced by amino acid sequence, molecular conformation, and the presence of molecular additives. In the presence of phenolic additives, LysB28ProB29 insulin, in which the C-terminal prolyl and lysyl residues of wild-type human insulin have been inverted, can be crystallized into forms resembling those of wild-type insulins in which the protein exists as zinc-complexed hexamers organized into well-defined layers. We describe herein tapping-mode atomic force microscopy (TMAFM) studies of single crystals of rhombohedral (R3) LysB28ProB29 that reveal the influence of sequence variation on hexamer-hexamer association at the surface of actively growing crystals. Molecular scale lattice images of these crystals were acquired in situ under growth conditions, enabling simultaneous identification of the rhombohedral LysB28ProB29 crystal form, its orientation, and its dynamic growth characteristics. The ability to obtain crystallographic parameters on multiple crystal faces with TMAFM confirmed that bovine and porcine insulins grown under these conditions crystallized into the same space group as LysB28ProB29 (R3), enabling direct comparison of crystal growth behavior and the influence of sequence variation. Real-time TMAFM revealed hexamer vacancies on the (001) terraces of LysB28ProB29, and more rounded dislocation noses and larger terrace widths for actively growing screw dislocations compared to wild-type bovine and porcine insulin crystals under identical conditions. This behavior is consistent with weaker interhexamer attachment energies for LysB28ProB29 at active growth sites. Comparison of the single crystal x-ray structures of wild-type insulins and LysB28ProB29 suggests that differences in protein conformation at the hexamer-hexamer interface and accompanying changes in interhexamer bonding are responsible for this behavior. These studies demonstrate that subtle changes in molecular conformation due to a single sequence

  16. The influence of nucleotide sequence and temperature on the activity of thermostable DNA polymerases.

    PubMed

    Montgomery, Jesse L; Rejali, Nick; Wittwer, Carl T

    2014-05-01

    Extension rates of a thermostable, deletion-mutant polymerase were measured from 50°C to 90°C using a fluorescence activity assay adapted for real-time PCR instruments. Substrates with a common hairpin (6-base loop and a 14-bp stem) were synthesized with different 10-base homopolymer tails. Rates for A, C, G, T, and 7-deaza-G incorporation at 75°C were 81, 150, 214, 46, and 120 seconds(-1). Rates for U were half as fast as T and did not increase with increasing concentration. Hairpin substrates with 25-base tails from 0% to 100% GC content had maximal extension rates near 60% GC and were predicted from the template sequence and mononucleotide incorporation rates to within 30% for most sequences. Addition of dimethyl sulfoxide at 7.5% increased rates to within 1% to 17% of prediction for templates with 40% to 90% GC. When secondary structure was designed into the template region, extension rates decreased. Oligonucleotide probes reduced extension rates by 65% (5'-3' exo-) and 70% (5'-3' exo+). When using a separate primer and a linear template to form a polymerase substrate, rates were dependent on both the primer melting temperature (Tm) and the annealing/extension temperature. Maximum rates were observed from Tm to Tm - 5°C with little extension by Tm + 5°C. Defining the influence of sequence and temperature on polymerase extension will enable more rapid and efficient PCR.

  17. Sequence Context Influences the Structure and Aggregation Behavior of a PolyQ Tract

    PubMed Central

    Chiesa, G.; Mungianu, D.; García, J.; Pierattelli, R.; Felli, I. C.; Salvatella, X.

    2016-01-01

    Expansions of polyglutamine (polyQ) tracts in nine different proteins cause a family of neurodegenerative disorders called polyQ diseases. Since polyQ tracts are potential therapeutic targets for these pathologies there is great interest in characterizing the conformations that they adopt and in understanding how their aggregation behavior is influenced by the sequences flanking them. We used solution NMR to study at single-residue resolution a 156-residue proteolytic fragment of the androgen receptor that contains a polyQ tract associated with the disease called spinobulbar muscular atrophy, also known as Kennedy disease. Our findings indicate that a Leu-rich region preceding the polyQ tract causes it to become α-helical and appears to protect the protein against aggregation, which represents a new mechanism by which sequence context can minimize the deleterious properties of these repetitive regions. Our results have implications for drug discovery for polyQ diseases because they suggest that the residues flanking these repetitive sequences may represent viable therapeutic targets. PMID:27276254

  18. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula.

    PubMed

    Ingvarsson, Pär K

    2007-03-01

    Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.

  19. [Influence of the difference in start-up echo on signal intensity in the FIESTA sequence].

    PubMed

    Naka, Takanori; Takahashi, Mitsuyuki

    2008-11-20

    The FIESTA sequence is a fast imaging method used for various parts in recent years. A constant flip angle (CFA) or linear flip angle (LFA) are used as the start-up echo in many cases. It is reported from CFA, which is the conventional method, that the T1 value and T2 value influence the speed that reaches steady state. However, there is no such report in LFA. Therefore, we examined the influence of the difference of start-up echo method upon signal intensity. In phantoms other than vegetable oil, the difference was not accepted in the change of speed that reaches steady state and the signal intensity in steady-state transit. In LFA, signal intensity of vegetable oil was clearly lower than CFA. The same result was obtained regardless of on or off resonance. From the result, it was thought that it depended on T2/T1 for the speed that reaches steady state. Moreover, the difference in resonant frequency was considered to greatly influence LFA but not CFA. That is, it was suggested by the difference in start-up echo that the signal intensity of fat changes greatly.

  20. Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

    SciTech Connect

    Goffinont, S.; Davidkova, M.

    2009-08-21

    The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro {gamma}-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

  1. Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

    PubMed Central

    Pightling, Arthur W.; Petronella, Nicholas; Pagotto, Franco

    2014-01-01

    The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should

  2. Quantification of loading in biomechanical testing: the influence of dissection sequence.

    PubMed

    Funabashi, Martha; El-Rich, Marwan; Prasad, Narasimha; Kawchuk, Gregory N

    2015-09-18

    Sequential dissection is a technique used to investigate loads experienced by articular tissues. When the joint of interest is tested in an unconstrained manner, its kinematics change with each tissue removal. To address this limitation, sufficiently rigid robots are used to constrain joint kinematics. While this approach can quantify loads experienced by each tissue, it does not assure similar results when removal order is changed. Specifically, structure loading is assumed to be independent of removal order if the structure behaves linearly (i.e. principle of superposition applies), but dependent on removal order when response is affected by material and/or geometry nonlinearities and/or viscoelasticiy (e.g. biological tissues). Therefore, this experiment was conducted to evaluate if structure loading created through robotic testing is dependent on the order in which connectors are removed. Six identical models were 3D printed. Each model was composed of 2 rigid bodies and 3 connecting structures with nonlinear time-dependent behavior. To these models, pure rotations were applied about a predefined static center of rotation using a parallel robot. A unique dissection sequence was used for each of the six models and the same movements applied robotically after each dissection. When comparing the moments experienced by each structure between different removal sequences, a statistically significant difference (p<0.05) was observed. These results suggest that even in an optimized environment, the sequence in which nonlinear viscoelastic structures are removed influence model loading. These findings support prior work suggesting that tissue loads obtained from robotic testing are specific to removal order.

  3. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.

    PubMed

    Wu, Na; Willner, Itamar

    2016-04-13

    Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.

  4. Characterization of elements determining the dimerization properties of RelB and p50.

    PubMed Central

    Ryseck, R P; Novotny, J; Bravo, R

    1995-01-01

    Members of the Rel/NF-kappa B family of transcription factors share a region of approximately 300 amino acids which mediates dimerization and sequence-specific binding to DNA. Here we report a detailed characterization of the dimerization domain of RelB. The structural core sufficient to form stable Rel/NF-kappa B dimeric complexes consists of about 110 residues. The dimerization and DNA binding properties of more than 50 RelB mutants were analyzed by using p50 and p52 as partners. We present evidence that amino acids of a conserved element in the dimerization domain play a role in the recognition of a kappa B DNA target sequence. The analysis of hybrid molecules with dimerization domains containing different parts of p50 and RelB allowed us to identify some important structural elements determining homo- and heterodimerization properties. Furthermore, we were able to rescue the dimerization-defective mutant RelB-N287D by the introduction of a counteracting mutation intramolecularly (cis), and also intermolecularly (trans) by a mutation in the NF-kappa B dimerization partner p50. Correspondingly, a dimerization defective p50 mutant was effectively rescued by RelB-N287D. PMID:7760806

  5. Influence of biofilm density on anaerobic sequencing batch biofilm reactor treating mustard tuber wastewater.

    PubMed

    Chai, Hongxiang; Kang, Wei

    2012-11-01

    Considering the characteristics of high salinity, high concentration of organic matter, and high biodegradability, a new and efficient anaerobic sequencing batch biofilm reactor (ASBBR) was chosen as an anaerobic pretreatment unit to treat most organic compounds in mustard tuber wastewater. By changing the biofilm density of the reactor, the test was carried out to find out the influence of biofilm density on effluent COD, the content of the sludge dehydrogenase, and gas production rate. Results showed that under the condition of 30 °C, draining ratio of 1/3, and 2 days of hydraulic retention time, COD removal rate increased from 71.5 to 90.5 % when the biofilm density increased from 15 to 50 %; however, COD removal rate increased from 90.5 to 91.3 % when the biofilm density increased from 50 to 70 %. According to the influence of biofilm density on effluent COD, the content of the sludge dehydrogenase, and gas production rate, ASBBR should take 50 % biofilm density in mustard wastewater treatment. At the same time, these design parameters can be used to guide practical engineering.

  6. Influence of seasonal cycles in Martian atmosphere on entry, descent and landing sequence

    NASA Astrophysics Data System (ADS)

    Marčeta, Dušan; Šegan, Stevo; Rašuo, Boško

    2014-05-01

    The phenomena like high eccentricity of Martian orbit, obliquity of the orbital plane and close alignment of the winter solstice and the orbital perihelion, separately or together can significantly alter not only the level of some Martian atmospheric parameters but also the characteristics of its diurnal and seasonal cycle. Considering that entry, descent and landing (EDL) sequence is mainly driven by the density profile of the atmosphere and aerodynamic characteristic of the entry vehicle. We have performed the analysis of the influence of the seasonal cycles of the atmospheric parameters on EDL profiles by using Mars Global Reference Atmospheric Model (Mars-GRAM). Since the height of the deployment of the parachute and the time passed from the deployment to propulsion firing (descent time) are of crucial importance for safe landing and the achievable landing site elevation we paid special attention to the influence of the areocentric longitude of the Sun (Ls) on these variables. We have found that these variables have periodic variability with respect to Ls and can be very well approximated with a sine wave function whose mean value depends only on the landing site elevation while the amplitudes and phases depend only on the landing site latitude. The amplitudes exhibit behavior which is symmetric with respect to the latitude but the symmetry is shifted from the equator to the northern mid-tropics. We have also noticed that the strong temperature inversions which are usual for middle and higher northern latitudes while Mars is around its orbital perihelion significantly alter the descent time without influencing the height of the parachute deployment. At last, we applied our model to determine the dependence of the accessible landing region on Ls and found that this region reaches maximum when Mars is around the orbital perihelion and can vary 50° in latitude throughout the Martian year.

  7. Facile dimer synthesis for DNA-binding polyamide ligands.

    PubMed

    Wetzler, Modi; Wemmer, David E

    2010-08-06

    Pyrrole-imidazole polyamide ligands are highly sequence specific synthetic DNA-binding ligands that bind with high affinity. To counter the synthetic difficulties associated with coupling the electron-rich heterocyclic acids to the electron-deficient nucleophilic imidazole amine, a novel approach is described for synthesis of Fmoc-protected dimers for solid-phase peptide synthesis (SPPS). This method produces the dimers in high yields, is broadly applicable to other heterocyclic-containing polyamides, and results in improved ligand yields and synthesis times.

  8. Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviors

    PubMed Central

    Molodtsova, Daria; Harpur, Brock A.; Kent, Clement F.; Seevananthan, Kajendra; Zayed, Amro

    2014-01-01

    It is increasingly apparent that genes and networks that influence complex behavior are evolutionary conserved, which is paradoxical considering that behavior is labile over evolutionary timescales. How does adaptive change in behavior arise if behavior is controlled by conserved, pleiotropic, and likely evolutionary constrained genes? Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behavior, is fuelled by regulatory sequence evolution. However, we seldom have data on the strength of selection on mutations in coding and regulatory sequences, and this hinders our ability to study how pleiotropy influences coding and regulatory sequence evolution. Here we use population genomics to estimate the strength of selection on coding and regulatory mutations for a transcriptional regulatory network that influences complex behavior of honey bees. We found that replacement mutations in highly connected transcription factors and target genes experience significantly stronger negative selection relative to weakly connected transcription factors and targets. Adaptively evolving proteins were significantly more likely to reside at the periphery of the regulatory network, while proteins with signs of negative selection were near the core of the network. Interestingly, connectedness and network structure had minimal influence on the strength of selection on putative regulatory sequences for both transcription factors and their targets. Our study indicates that adaptive evolution of complex behavior can arise because of positive selection on protein-coding mutations in peripheral genes, and on regulatory sequence mutations in both transcription factors and their targets throughout the network. PMID:25566318

  9. Phenotypes of murine leukemia virus-induced tumors: influence of 3' viral coding sequences.

    PubMed Central

    Ott, D E; Keller, J; Sill, K; Rein, A

    1992-01-01

    Murine leukemia viruses (MuLVs) induce leukemias and lymphomas in mice. We have used fluorescence-activated cell sorter analysis to determine the hematopoietic phenotypes of tumor cells induced by a number of MuLVs. Tumor cells induced by ecotropic Moloney, amphotropic 4070A, and 10A1 MuLVs and by two chimeric MuLVs, Mo(4070A) and Mo(10A1), were examined with antibodies to 13 lineage-specific cell surface markers found on myeloid cell, T-cell, and B-cell lineages. The chimeric Mo(4070A) and Mo(10A1) MuLVs, consisting of Moloney MuLV with the carboxy half of the Pol region and nearly all of the Env region of 4070A and 10A1, respectively, were constructed to examine the possible influence of these sequences on Moloney MuLV-induced tumor cell phenotypes. In some instances, these phenotypic analyses were supplemented by Southern blot analysis for lymphoid cell-specific genomic DNA rearrangements at the immunoglobulin heavy-chain, the T-cell receptor gamma, and the T-cell receptor beta loci. The results of our analysis showed that Moloney MuLV, 4070A, Mo(4070A), and Mo(10A1) induced mostly T-cell tumors. Moloney MuLV and Mo(4070A) induced a wide variety of T-cell phenotypes, ranging from immature to mature phenotypes, while 4070A induced mostly prothymocyte and double-negative (CD4- CD8-) T-cell tumors. The tumor phenotypes obtained with 10A1 and Mo(10A1) were each less variable than those obtained with the other MuLVs tested. 10A1 uniformly induced a tumor consisting of lineage marker-negative cells that lack lymphoid cell-specific DNA rearrangements and histologically appear to be early undifferentiated erythroid cell-like precursors. The Mo(10A1) chimera consistently induced an intermediate T-cell tumor. The chimeric constructions demonstrated that while 4070A 3' pol and env sequences apparently did not influence the observed tumor cell phenotypes, the 10A1 half of pol and env had a strong effect on the phenotypes induced by Mo(10A1) that resulted in a phenotypic

  10. Bivalent Ligands Targeting Chemokine Receptor Dimerization: Molecular Design and Functional Studies

    PubMed Central

    Arnatt, Christopher Kent; Zhang, Yan

    2015-01-01

    Increasing evidence has shown that chemokine receptors may form functional dimers with unique pharmacological profiles. A common practice to characterize such G protein-coupled receptor dimerization processes is to apply bivalent ligands as chemical probes which can interact with both receptors simultaneously. Currently, two chemokine receptor dimers have been studied by applying bivalent compounds: the CXCR4-CXCR4 homodimer and the CCR5-MOR heterodimer. These bivalent compounds have revealed how dimerization influences receptor function and may lead to novel therapeutics. Future design of bivalent ligands for chemokine receptor dimers may be aided with the recently available CXCR4 homodimer, and CCR5 monomer crystal structures by more accurately simulating chemokine receptors and their dimers. PMID:25159160

  11. Haldane relation for interacting dimers

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Mastropietro, Vieri; Lucio Toninelli, Fabio

    2017-03-01

    We consider a model of weakly interacting close-packed dimers on the two-dimensional square lattice. In a previous paper, we computed both the multi-point dimer correlations, which display non-trivial critical exponents, continuously varying with the interaction strength; and the height fluctuations, which, after proper coarse graining and rescaling, converge to a massless Gaussian field with a suitable interaction-dependent pre-factor (‘amplitude’). In this paper, we prove the identity between the critical exponent of the two-point dimer correlation and the amplitude of this massless Gaussian field. This identity is the restatement, in the context of interacting dimers, of one of the Haldane universality relations, part of his Luttinger-liquid conjecture, originally formulated in the context of one-dimensional interacting Fermi systems. Its validity is a strong confirmation of the effective massless Gaussian field description of the interacting dimer model, which was proposed on the basis of formal bosonization arguments. We also conjecture that a certain discrete curve defined at the lattice level via the Temperley bijection converges in the scaling limit to an SLE κ process, with κ depending non-trivially on the interaction and related in a simple way to the amplitude of the limiting Gaussian field.

  12. Influence of laminate sequence and fabric type on the inherent acoustic nonlinearity in carbon fiber reinforced composites.

    PubMed

    Chakrapani, Sunil Kishore; Barnard, Daniel J; Dayal, Vinay

    2016-05-01

    This paper presents the study of influence of laminate sequence and fabric type on the baseline acoustic nonlinearity of fiber-reinforced composites. Nonlinear elastic wave techniques are increasingly becoming popular in detecting damage in composite materials. It was earlier observed by the authors that the non-classical nonlinear response of fiber-reinforced composite is influenced by the fiber orientation [Chakrapani, Barnard, and Dayal, J. Acoust. Soc. Am. 137(2), 617-624 (2015)]. The current study expands this effort to investigate the effect of laminate sequence and fabric type on the non-classical nonlinear response. Two hypotheses were developed using the previous results, and the theory of interlaminar stresses to investigate the influence of laminate sequence and fabric type. Each hypothesis was tested by capturing the nonlinear response by performing nonlinear resonance spectroscopy and measuring frequency shifts, loss factors, and higher harmonics. It was observed that the laminate sequence can either increase or decrease the nonlinear response based on the stacking sequence. Similarly, tests were performed to compare unidirectional fabric and woven fabric and it was observed that woven fabric exhibited a lower nonlinear response compared to the unidirectional fabric. Conjectures based on the matrix properties and interlaminar stresses were used in an attempt to explain the observed nonlinear responses for different configurations.

  13. Adventures in holographic dimer models

    NASA Astrophysics Data System (ADS)

    Kachru, Shamit; Karch, Andreas; Yaida, Sho

    2011-03-01

    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  14. Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis.

    PubMed

    Desmarais, Samantha M; Leitner, Thomas; Barron, Annelise E

    2012-02-01

    DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.

  15. Distinct DNA binding preferences for the c-Myc/Max and Max/Max dimers.

    PubMed Central

    Solomon, D L; Amati, B; Land, H

    1993-01-01

    The transcription factor c-Myc and its dimerisation partner Max are members of the basic/helix-loop-helix/leucine-zipper (bHLH-Z) family and bind to the DNA core sequence CACGTG. Using a site-selection protocol, we determined the complete 12 base pair consensus binding sites of c-Myc/Max (RACCACGTGGTY) and Max/Max (RANCACGTGNTY) dimers. We find that the c-Myc/Max dimer fails to bind the core when it is flanked by a 5'T or a 3'A, while the Max/Max dimer readily binds such sequences. Furthermore we show that inappropriate flanking sequences preclude transactivation by c-Myc in vivo. In conclusion, Max/Max dimers are less discriminatory than c-Myc/Max and may regulate other genes in addition to c-Myc/Max targets. PMID:8265351

  16. Theoretical studies on the dimerization of substituted paraphenylenediamine radical cations

    NASA Astrophysics Data System (ADS)

    Punyain, Kraiwan; Kelterer, Anne-Marie; Grampp, Günter

    2011-12-01

    Organic radical cations form dicationic dimers in solution, observed experimentally as diamagnetic species in temperature-dependent EPR and low temperature UV/Vis spectroscopy. Dimerization of paraphenylenediamine, N,N-dimethyl-paraphenylenediamine and 2,3,5,6-tetramethyl-paraphenylenediamine radical cation in ethanol/diethylether mixture was investigated theoretically according to geometry, energetics and UV/Vis spectroscopy. Density Functional Theory including dispersion correction describes stable dimers after geometry optimization with conductor-like screening model of solvation and inclusion of the counter-ion. Energy corrections were done on double-hybrid Density Functional Theory with perturbative second-order correlation (B2PLYP-D) including basis set superposition error (BSSE), and multireference Møller-Plesset second-order perturbation theory method (MRMP2) based on complete active space method (CASSCF(2,2)) single point calculation, respectively. All three dication π-dimers exhibit long multicenter π-bonds around 2.9 ± 0.1 Å with strongly interacting orbitals. Substitution with methyl groups does not influence the dimerization process substantially. Dispersion interaction and electrostatic attraction from counter-ion play an important role to stabilize the dication dimers in solution. Dispersion-corrected double hybrid functional B2PLYP-D and CASSCF(2,2) can describe the interaction energetics properly. Vertical excitations were computed with Tamm-Dancoff approximation for time-dependent Density Functional Theory (TDA-DFT) at the B3LYP level with the cc-pVTZ basis set including ethanol solvent molecules explicitly. A strong interaction of the counter-ion and the solvent ethanol with the monomeric species is observed, whereas in the dimers the strong interaction of both radical cation species is the dominating factor for the additional peak in UV/Vis spectra.

  17. Microwave Spectrum of the Isopropanol-Water Dimer

    NASA Astrophysics Data System (ADS)

    Mead, Griffin; Finneran, Ian A.; Carroll, Brandon; Blake, Geoffrey

    2016-06-01

    Microwave spectroscopy provides a unique opportunity to study model non-covalent interactions. Of particular interest is the hydrogen bonding of water, whose various molecular properties are influenced by both strong and weak intermolecular forces. More specifically, measuring the hydrogen bonded structures of water-alcohol dimers investigates both strong (OH ··· OH) and weak (CH ··· OH) hydrogen bond interactions. Recently, we have measured the pure rotational spectrum of the isopropanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) between 8-18 GHz. Here, we present the spectrum of this dimer and elaborate on the structure's strong and weak hydrogen bonding.

  18. Study of dissolution hydrodynamic conditions versus drug release from hypromellose matrices: the influence of agitation sequence.

    PubMed

    Asare-Addo, Kofi; Levina, Marina; Rajabi-Siahboomi, Ali R; Nokhodchi, Ali

    2010-12-01

    In this article, the influence of agitation in descending and ascending sequences as a systematic method development process for potentially discriminating fed and fasted states and evaluation of its effects on the drug release from swelling gel-forming hydrophilic matrix tablets were investigated. Theophylline extended release (ER) matrices containing hypromellose (hydroxypropyl methylcellulose (HPMC)) were evaluated in media with a pH range of 1.2-7.5, using an automated USP type III, Bio-Dis dissolution apparatus at 5, 10, 15, 20, 25 and 30 dips per minute (dpm). Agitation had a profound effect on the drug release from the HPMC K100LV matrices. Drug release in pH 1.2 changed from about 40% at 5 dpm to about 80% at 30 dpm over a 60 min period alone. The matrices containing HPMC K4M, K15M and K100M however were not significantly affected by the agitation rate. The similarity factor f2 was calculated using drug release at 10 dpm as a reference. The ascending agitations of 5-30 dpm and the descending order of agitation 30-5 dpm were also evaluated. Anomalous transport was the only kinetic of release for the K4M, K15M and K100M tablet matrices. The lower viscous polymer of K100LV had some matrices exhibiting Fickian diffusion as its kinetics of release. The use of systematic change of agitation method may indicate potential fed and fasted effects on drug release from hydrophilic matrices.

  19. Kinetics of DNA tile dimerization.

    PubMed

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  20. Kinetics of DNA Tile Dimerization

    PubMed Central

    2015-01-01

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile–tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency. PMID:24794259

  1. Diagnostic implication of fibrin degradation products and D-dimer in aortic dissection

    PubMed Central

    Dong, Jian; Duan, Xianli; Feng, Rui; Zhao, Zhiqing; Feng, Xiang; Lu, Qingsheng; Jing, Qing; Zhou, Jian; Bao, Junmin; Jing, Zaiping

    2017-01-01

    Fibrin degradation products (FDP) and D-dimer have been considered to be involved in many vascular diseases. In this study we aimed to explore the diagnostic implication of FDP and D-dimer in aortic dissection patients. 202 aortic dissection patients were collected as the case group, 150 patients with other cardiovascular diseases, including myocardial infarction (MI, n = 45), pulmonary infarction (n = 51) and abdominal aortic aneurysm (n = 54) were collected as non-dissection group, and 27 healthy people were in the blank control group. The FDP and D-dimer levels were detected with immune nephelometry. Logist regression analysis was performed to evaluate the influence of FDP and D-dimer for the aortic dissection patients. ROC curve was used to determine the diagnostic value of FDP and D-dimer. The FDP and D-dimer levels were significantly higher in aortic dissection patients than in non-dissection patients and the healthy controls. FDP and D-dimer were both the risk factors for patients with aortic dissection. From the ROC analysis, diagnostic value of FDP and D-dimer were not high to distinguish aortic dissection patients from the non-dissection patients. However FDP and D-dimer could be valuable diagnostic marker to differentiate aortic dissection patients and healthy controls with both AUC 0.863. PMID:28262748

  2. Diagnostic implication of fibrin degradation products and D-dimer in aortic dissection

    NASA Astrophysics Data System (ADS)

    Dong, Jian; Duan, Xianli; Feng, Rui; Zhao, Zhiqing; Feng, Xiang; Lu, Qingsheng; Jing, Qing; Zhou, Jian; Bao, Junmin; Jing, Zaiping

    2017-03-01

    Fibrin degradation products (FDP) and D-dimer have been considered to be involved in many vascular diseases. In this study we aimed to explore the diagnostic implication of FDP and D-dimer in aortic dissection patients. 202 aortic dissection patients were collected as the case group, 150 patients with other cardiovascular diseases, including myocardial infarction (MI, n = 45), pulmonary infarction (n = 51) and abdominal aortic aneurysm (n = 54) were collected as non-dissection group, and 27 healthy people were in the blank control group. The FDP and D-dimer levels were detected with immune nephelometry. Logist regression analysis was performed to evaluate the influence of FDP and D-dimer for the aortic dissection patients. ROC curve was used to determine the diagnostic value of FDP and D-dimer. The FDP and D-dimer levels were significantly higher in aortic dissection patients than in non-dissection patients and the healthy controls. FDP and D-dimer were both the risk factors for patients with aortic dissection. From the ROC analysis, diagnostic value of FDP and D-dimer were not high to distinguish aortic dissection patients from the non-dissection patients. However FDP and D-dimer could be valuable diagnostic marker to differentiate aortic dissection patients and healthy controls with both AUC 0.863.

  3. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs

    PubMed Central

    Plath, Friederike; Ringler, Philippe; Graff-Meyer, Alexandra; Stahlberg, Henning; Lauer, Matthias E.; Rufer, Arne C.; Graewert, Melissa A.; Svergun, Dmitri; Gellermann, Gerald; Finkler, Christof; Stracke, Jan O.; Koulov, Atanas; Schnaible, Volker

    2016-01-01

    ABSTRACT The formation of undesired high molecular weight species such as dimers is an important quality attribute for therapeutic monoclonal antibody formulations. Therefore, the thorough understanding of mAb dimerization and the detailed characterization mAb dimers is of great interest for future pharmaceutical development of therapeutic antibodies. In this work, we focused on the analyses of different mAb dimers regarding size, surface properties, chemical identity, overall structure and localization of possible dimerization sites. Dimer fractions of different mAbs were isolated to a satisfactory purity from bulk material and revealed 2 predominant overall structures, namely elongated and compact dimer forms. The elongated dimers displayed one dimerization site involving the tip of the Fab domain. Depending on the stress applied, these elongated dimers are connected either covalently or non-covalently. In contrast, the compact dimers exhibited non-covalent association. Several interaction points were detected for the compact dimers involving the hinge region or the base of the Fab domain. These results indicate that mAb dimer fractions are rather complex and may contain more than one kind of dimer. Nevertheless, the overall appearance of mAb dimers suggests the existence of 2 predominant dimeric structures, elongated and compact, which are commonly present in preparations of therapeutic mAbs. PMID:27031922

  4. Water dimer equilibrium constant of saturated vapor

    NASA Astrophysics Data System (ADS)

    Malomuzh, N. P.; Mahlaichuk, V. N.; Khrapatyi, S. V.

    2014-08-01

    The value and temperature dependence of the dimerization constant for saturated water vapor are determined. A general expression that links the second virial coefficient and the dimerization constant is obtained. It is shown that the attraction between water monomers and dimers is fundamental, especially at T > 350 K. The range of application for the obtained results is determined.

  5. Monitoring Retroviral RNA Dimerization In Vivo via Hammerhead Ribozyme Cleavage

    PubMed Central

    Pal, Bijay K.; Scherer, Lisa; Zelby, Laurie; Bertrand, Edouard; Rossi, John J.

    1998-01-01

    We have used a strategy for colocalization of Psi (Ψ)-tethered ribozymes and targets to demonstrate that Ψ sequences are capable of specific interaction in the cytoplasm of both packaging and nonpackaging cells. These results indicate that current in vitro dimerization models may have in vivo counterparts. The methodology used may be applied to further genetic analyses on Ψ domain interactions in vivo. PMID:9733882

  6. Structure- and conformation-activity studies of nociceptin/orphanin FQ receptor dimeric ligands

    PubMed Central

    Pacifico, Salvatore; Carotenuto, Alfonso; Brancaccio, Diego; Novellino, Ettore; Marzola, Erika; Ferrari, Federica; Cerlesi, Maria Camilla; Trapella, Claudio; Preti, Delia; Salvadori, Severo; Calò, Girolamo; Guerrini, Remo

    2017-01-01

    The peptide nociceptin/orphanin FQ (N/OFQ) and the N/OFQ receptor (NOP) constitute a neuropeptidergic system that modulates various biological functions and is currently targeted for the generation of innovative drugs. In the present study dimeric NOP receptor ligands with spacers of different lengths were generated using both peptide and non-peptide pharmacophores. The novel compounds (12 peptide and 7 nonpeptide ligands) were pharmacologically investigated in a calcium mobilization assay and in the mouse vas deferens bioassay. Both structure- and conformation-activity studies were performed. Results demonstrated that dimerization did not modify the pharmacological activity of both peptide and non-peptide pharmacophores. Moreover, when dimeric compounds were obtained with low potency peptide pharmacophores, dimerization recovered ligand potency. This effect depends on the doubling of the C-terminal address sequence rather than the presence of an additional N-terminal message sequence or modifications of peptide conformation. PMID:28383520

  7. A Strategy for Complex Dimer Formation When Biomimicry Fails: Total Synthesis of Ten Coccinellid Alkaloids

    PubMed Central

    2015-01-01

    Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature’s presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class. PMID:24959981

  8. A strategy for complex dimer formation when biomimicry fails: total synthesis of ten coccinellid alkaloids.

    PubMed

    Sherwood, Trevor C; Trotta, Adam H; Snyder, Scott A

    2014-07-09

    Although dimeric natural products can often be synthesized in the laboratory by directly merging advanced monomers, these approaches sometimes fail, leading instead to non-natural architectures via incorrect unions. Such a situation arose during our studies of the coccinellid alkaloids, when attempts to directly dimerize Nature's presumed monomeric precursors in a putative biomimetic sequence afforded only a non-natural analogue through improper regiocontrol. Herein, we outline a unique strategy for dimer formation that obviates these difficulties, one which rapidly constructs the coccinellid dimers psylloborine A and isopsylloborine A through a terminating sequence of two reaction cascades that generate five bonds, five rings, and four stereocenters. In addition, a common synthetic intermediate is identified which allows for the rapid, asymmetric formal or complete total syntheses of eight monomeric members of the class.

  9. Fiber optic D dimer biosensor

    DOEpatents

    Glass, R.S.; Grant, S.A.

    1999-08-17

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy. 4 figs.

  10. Fiber optic D dimer biosensor

    DOEpatents

    Glass, Robert S.; Grant, Sheila A.

    1999-01-01

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

  11. Mechanism of FGF receptor dimerization and activation

    NASA Astrophysics Data System (ADS)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise.

  12. Influence of severe vibrations on the visual perception of video sequences

    NASA Astrophysics Data System (ADS)

    Stern, Adrian; Fisher, E.; Rotman, Stanley R.; Kopeika, Norman S.

    2000-12-01

    There are two kinds of video image sequence distortions caused by vibration of the camera. The first is the vibration of the line-of-sight causing location changes of the scene in successive frames. The second effect is the blur of each frame of the sequence due to frame motion during its exposure. In this work, the relative effects of these two types of degradations on the ability of observers to recognize targets are investigated. This study is useful for evaluating the amount of effort required to compensate each effect. We found that the threshold contrast needed to recognize a target in a vibrating video sequence under certain conditions is more affected by the motion blur of each frame than the oscillation of the line-of-sight. For digital sequence restoration methods, this study determines the required precision of the deblurring and registration processes. It shows that the deblurring process should not be neglected as it often is.

  13. ERIS, an endoplasmic reticulum IFN stimulator, activates innate immune signaling through dimerization.

    PubMed

    Sun, Wenxiang; Li, Yang; Chen, Lu; Chen, Huihui; You, Fuping; Zhou, Xiang; Zhou, Yi; Zhai, Zhonghe; Chen, Danying; Jiang, Zhengfan

    2009-05-26

    We report here the identification and characterization of a protein, ERIS, an endoplasmic reticulum (ER) IFN stimulator, which is a strong type I IFN stimulator and plays a pivotal role in response to both non-self-cytosolic RNA and dsDNA. ERIS (also known as STING or MITA) resided exclusively on ER membrane. The ER retention/retrieval sequence RIR was found to be critical to retain the protein on ER membrane and to maintain its integrity. ERIS was dimerized on innate immune challenges. Coumermycin-induced ERIS dimerization led to strong and fast IFN induction, suggesting that dimerization of ERIS was critical for self-activation and subsequent downstream signaling.

  14. Application of sorting and next generation sequencing to study 5'-UTR influence on translation efficiency in Escherichia coli.

    PubMed

    Evfratov, Sergey A; Osterman, Ilya A; Komarova, Ekaterina S; Pogorelskaya, Alexandra M; Rubtsova, Maria P; Zatsepin, Timofei S; Semashko, Tatiana A; Kostryukova, Elena S; Mironov, Andrey A; Burnaev, Evgeny; Krymova, Ekaterina; Gelfand, Mikhail S; Govorun, Vadim M; Bogdanov, Alexey A; Sergiev, Petr V; Dontsova, Olga A

    2016-11-29

    Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid libraries encoding CER fluorescent protein preceded by randomized 5' untranslated regions (5'-UTR) and Red fluorescent protein (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated by efficiency of CER mRNA translation by a cell sorter and subjected to next generation sequencing. We tested efficiency of translation of the CER gene preceded by each of 48 natural 5'-UTR sequences and introduced random and designed mutations into natural and artificially selected 5'-UTRs. Several distinct properties could be ascribed to a group of 5'-UTRs most efficient in translation. In addition to known ones, several previously unrecognized features that contribute to the translation enhancement were found, such as low proportion of cytidine residues, multiple SD sequences and AG repeats. The latter could be identified as translation enhancer, albeit less efficient than SD sequence in several natural 5'-UTRs.

  15. Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database.

    PubMed

    Unneberg, Per; Wennborg, Anders; Larsson, Magnus

    2003-04-15

    There exist a number of gene expression profiling techniques that utilize restriction enzymes for generation of short expressed sequence tags. We have studied how the choice of restriction enzyme influences various characteristics of tags generated in an experiment. We have also investigated various aspects of in silico transcript identification that these profiling methods rely on. First, analysis of 14 248 mRNA sequences derived from the RefSeq transcript database showed that 1-30% of the sequences lack a given restriction enzyme recognition site. Moreover, 1-5% of the transcripts have recognition sites located less than 10 bases from the poly(A) tail. The uniqueness of 10 bp tags lies in the range 90-95%, which increases only slightly with longer tags, due to the existence of closely related transcripts. Furthermore, 3-30% of upstream 10 bp tags are identical to 3' tags, introducing a risk of misclassification if upstream tags are present in a sample. Second, we found that a sequence length of 16-17 bp, including the recognition site, is sufficient for unique transcript identification by BLAST based sequence alignment to the UniGene Human non-redundant database. Third, we constructed a tag-to-gene mapping for UniGene and compared it to an existing mapping database. The mappings agreed to 79-83%, where the selection of representative sequences in the UniGene clusters is the main cause of the disagreement. The results of this study may serve to improve the interpretation of sequence-based expression studies and the design of hybridization arrays, by identifying short tags that have a high reliability and separating them from tags that carry an inherent ambiguity in their capacity to discriminate between genes. To this end, supplementary information in the form of a web companion to this paper is located at http:// biobase.biotech.kth.se/tagseq.

  16. trans-Acting Inhibition of Genomic RNA Dimerization by Rous Sarcoma Virus Matrix Mutants

    PubMed Central

    Garbitt, Rachel A.; Albert, Jessica A.; Kessler, Michelle D.; Parent, Leslie J.

    2001-01-01

    The genomic RNA of retroviruses exists within the virion as a noncovalently linked dimer. Previously, we identified a mutant of the viral matrix (MA) protein of Rous sarcoma virus that disrupts viral RNA dimerization. This mutant, Myr1E, is modified at the N terminus of MA by the addition of 10 amino acids from the Src protein, resulting in the production of particles containing monomeric RNA. Dimerization is reestablished by a single amino acid substitution that abolishes myristylation (Myr1E−). To distinguish between cis and trans effects involving Myr1E, additional mutations were generated. In Myr1E.cc and Myr1E−.cc, different nucleotides were utilized to encode the same protein as Myr1E and Myr1E−, respectively. The alterations in RNA sequence did not change the properties of the viral mutants. Myr1E.ATG− was constructed so that translation began at the gag AUG, resulting in synthesis of the wild-type Gag protein but maintenance of the src RNA sequence. This mutant had normal infectivity and dimeric RNA, indicating that the src sequence did not prevent dimer formation. All of the src-containing RNA sequences formed dimers in vitro. Examination of MA-green fluorescent protein fusion proteins revealed that the wild-type and mutant MA proteins Myr1E.ATG−, Myr1E−, and Myr1E−.cc had distinctly different patterns of subcellular localization compared with Myr1E and Myr1E.cc MA proteins. This finding suggests that proper localization of the MA protein may be required for RNA dimer formation and infectivity. Taken together, these results provide compelling evidence that the genomic RNA dimerization defect is due to a trans-acting effect of the mutant MA proteins. PMID:11119596

  17. Percolation of heteronuclear dimers irreversibly deposited on square lattices

    NASA Astrophysics Data System (ADS)

    Gimenez, M. C.; Ramirez-Pastor, A. J.

    2016-09-01

    The percolation problem of irreversibly deposited heteronuclear dimers on square lattices is studied. A dimer is composed of two segments, and it occupies two adjacent adsorption sites. Each segment can be either a conductive segment (segment type A ) or a nonconductive segment (segment type B ). Three types of dimers are considered: A A , B B , and A B . The connectivity analysis is carried out by accounting only for the conductive segments (segments type A ). The model offers a simplified representation of the problem of percolation of defective (nonideal) particles, where the presence of defects in the system is simulated by introducing a mixture of conductive and nonconductive segments. Different cases were investigated, according to the sequence of deposition of the particles, the types of dimers involved in the process, and the degree of alignment of the deposited objects. By means of numerical simulations and finite-size scaling analysis, the complete phase diagram separating a percolating from a nonpercolating region was determined for each case. Finally, the consistency of our results was examined by comparing with previous data in the literature for linear k -mers (particles occupying k adjacent sites) with defects.

  18. Percolation of heteronuclear dimers irreversibly deposited on square lattices.

    PubMed

    Gimenez, M C; Ramirez-Pastor, A J

    2016-09-01

    The percolation problem of irreversibly deposited heteronuclear dimers on square lattices is studied. A dimer is composed of two segments, and it occupies two adjacent adsorption sites. Each segment can be either a conductive segment (segment type A) or a nonconductive segment (segment type B). Three types of dimers are considered: AA, BB, and AB. The connectivity analysis is carried out by accounting only for the conductive segments (segments type A). The model offers a simplified representation of the problem of percolation of defective (nonideal) particles, where the presence of defects in the system is simulated by introducing a mixture of conductive and nonconductive segments. Different cases were investigated, according to the sequence of deposition of the particles, the types of dimers involved in the process, and the degree of alignment of the deposited objects. By means of numerical simulations and finite-size scaling analysis, the complete phase diagram separating a percolating from a nonpercolating region was determined for each case. Finally, the consistency of our results was examined by comparing with previous data in the literature for linear k-mers (particles occupying k adjacent sites) with defects.

  19. Influence of enhancer sequences on thymotropism and leukemogenicity of mink cell focus-forming viruses.

    PubMed Central

    Holland, C A; Thomas, C Y; Chattopadhyay, S K; Koehne, C; O'Donnell, P V

    1989-01-01

    Oncogenic mink cell focus-forming (MCF) viruses, such as MCF 247, show a positive correlation between the ability to replicate efficiently in the thymus and a leukemogenic phenotype. Other MCF viruses, such as MCF 30-2, replicate to high titers in thymocytes and do not accelerate the onset of leukemia. We used these two MCF viruses with different biological phenotypes to distinguish the effect of specific viral genes and genetic determinants on thymotropism and leukemogenicity. Our goal was to identify the viral sequences that distinguish thymotropic, nonleukemogenic viruses such as MCF 30-2 from thymotropic, leukemogenic viruses such as MCF 247. We cloned MCF 30-2, compared the genetic hallmarks of MCF 30-2 with those of MCF 247, constructed a series of recombinants, and tested the ability of recombinant viruses to replicate in the thymus and to induce leukemia. The results established that (i) MCF 30-2 and MCF 247 differ in the numbers of copies of the enhancer sequences in the long terminal repeats. (ii) The thymotropic phenotype of both viruses is independent of the number of copies of the enhancer sequences. (iii) The oncogenic phenotype of MCF 247 is correlated with the presence in the virus of duplicated enhancer sequences or with the presence of an enhancer with a specific sequence. These results show that the pathogenic phenotypes of MCF viruses are dissociable from the thymotropic phenotype and depend, at least in part, upon the enhancer sequences. On the basis of these results, we suggest that the molecular mechanisms by which the enhancer sequences determine thymotropism are different from those that determine oncogenicity. Images PMID:2536834

  20. Molecular epidemiology of betanodavirus-sequence analysis strategies and quasispecies influence outbreak source attribution.

    PubMed

    Hick, Paul; Gore, Kylie; Whittington, Richard

    2013-02-05

    The quasispecies structure of nervous necrosis virus (NNV) was determined to investigate an outbreak of viral nervous necrosis disease at a barramundi (Lates calcarifer) hatchery. A traditional epidemiological investigation indicated horizontal transmission of infection between two cohorts of fish. However, variation in the viral capsid protein gene sequence from cell culture-derived viral populations and from individual fish suggested that each cohort was infected with a different virus. Molecular support for the correct epidemiological conclusion was provided by determining the consensus NNV sequence directly from multiple fish, to show that each cohort was infected with the same quasispecies. Variation in the capsid gene of isolates obtained from this quasispecies was up to 3.3% compared with sequences determined directly from fish tissue, and ≤1.7% between individual fish within each cohort. Determination of the NNV quasispecies structure supported implementation of biosecurity measures to protect fish in the hatchery from environmental sources of infection.

  1. Influence of pH and sequence in peptide aggregation via molecular simulation

    SciTech Connect

    Enciso, Marta; Schütte, Christof; Delle Site, Luigi

    2015-12-28

    We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.

  2. Influence of Stacking Sequence and Notch Angle on the Charpy Impact Behavior of Hybrid Composites

    NASA Astrophysics Data System (ADS)

    Behnia, S.; Daghigh, V.; Nikbin, K.; Fereidoon, A.; Ghorbani, J.

    2016-09-01

    The low-velocity impact behavior of hybrid composite laminates was investigated. The epoxy matrix was reinforced with aramid, glass, basalt, and carbon fabrics using the hand lay-up technique. Different stacking sequences and notch angles were and notch angles considered and tested using a Charpy impact testing machine to study the hybridization and notch angle effects on the impact response of the hybrid composites. The energy absorption capability of specimens with different stacking sequences and notch angles is compared and discussed. It is shown that the hybridization can enhance the mechanical performance of composite materials.

  3. Functional Roles of the Dimer-Interface Residues in Human Ornithine Decarboxylase

    PubMed Central

    Lee, Chien-Yun; Liu, Yi-Liang; Lin, Chih-Li; Liu, Guang-Yaw; Hung, Hui-Chih

    2014-01-01

    Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389) are divergent, whereas 4 (134, 169, 294 and 322) are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT). In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis. PMID:25140796

  4. Formulaic Sequences and L2 Oral Proficiency: Does the Type of Target Language Influence the Association?

    ERIC Educational Resources Information Center

    Stengers, Helene; Boers, Frank; Housen, Alex; Eyckmans, June

    2011-01-01

    This paper investigates the extent to which productive use of formulaic sequences by intermediate students of two typologically different languages, i.e., English and Spanish, is associated with their oral proficiency in these languages. Previous research (e.g., Boers et al., "Language Teaching Research" 10: 245-261, 2006) has shown that…

  5. IgG dimers in multidonor-derived immunoglobulins: aspects of generation and function.

    PubMed

    Gronski, P

    2006-01-01

    Immunoglobulin G (IgG) concentrates for therapeutic purposes, like passive immunotherapy, supplementation in inherited or acquired deficiencies or immunomodulation, are prepared from multidonor-derived plasma pools. They usually contain varying amounts of dimeric IgG. The essential factor influencing dimer formation is the pool size; in addition, molecular properties of IgG and a variety of production process- and formulation-specific parameters are important. Numerous experimental findings suggest that dimers are predominantly generated by interactions of idiotypic and anti-idiotypic antibodies (Ids, anti-Ids). Ab-inherent crossreactivity, frequency distribution of both the affinities for particular Id-anti-Id interactions and the corresponding dimer concentrations still have to be elucidated. All these parameters influencing molecular features and functional activity of IgG dimers hamper the assay-dependent measurement of biological efficacy and correlation of total IgG content. A more detailed understanding may help to better control the dual nature of dimer-dependent biological activity comprising both undesirable (e.g., hypotension) and desirable effects of dimeric IgG (blockade of the reticuloendothelial system, RES, in immune thrombocytopenic purpura, ITP). These effects are detectable in in vitro and in vivo models and are thought to be of relevance for humans.

  6. G domain dimerization controls dynamin's assembly-stimulated GTPase activity

    SciTech Connect

    Chappie, Joshua S.; Acharya, Sharmistha; Leonard, Marilyn; Schmid, Sandra L.; Dyda, Fred

    2010-06-14

    Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 {angstrom} resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF{sub 4}{sup -}. The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.

  7. D-Dimer elevation and adverse outcomes.

    PubMed

    Halaby, Rim; Popma, Christopher J; Cohen, Ander; Chi, Gerald; Zacarkim, Marcelo Rodrigues; Romero, Gonzalo; Goldhaber, Samuel Z; Hull, Russell; Hernandez, Adrian; Mentz, Robert; Harrington, Robert; Lip, Gregory; Peacock, Frank; Welker, James; Martin-Loeches, Ignacio; Daaboul, Yazan; Korjian, Serge; Gibson, C Michael

    2015-01-01

    D-Dimer is a biomarker of fibrin formation and degradation. While a D-dimer within normal limits is used to rule out the diagnosis of deep venous thrombosis and pulmonary embolism among patients with a low clinical probability of venous thromboembolism (VTE), the prognostic association of an elevated D-dimer with adverse outcomes has received far less emphasis. An elevated D-dimer is independently associated with an increased risk for incident VTE, recurrent VTE, and mortality. An elevated D-dimer is an independent correlate of increased mortality and subsequent VTE across a broad variety of disease states. Therefore, medically ill subjects in whom the D-dimer is elevated constitute a high risk subgroup in which the prospective evaluation of the efficacy and safety of antithrombotic therapy is warranted.

  8. Solitary waves in dimer binary collision model

    NASA Astrophysics Data System (ADS)

    Ahsan, Zaid; Jayaprakash, K. R.

    2017-01-01

    Solitary wave propagation in nonlinear diatomic (dimer) chains is a very interesting topic of research in the study of nonlinear lattices. Such waves were recently found to be supported by the essentially nonlinear granular lattice and Toda lattice. An interesting aspect of this discovery is attributed to the realization of a spectrum of the mass ratio (the only system parameter governing the dynamics) that supports the propagation of such waves corresponding to the considered interaction potential. The objective of this exposition is to explore solitary wave propagation in the dimer binary collision (BC) model. Interestingly, the dimer BC model supports solitary wave propagation at a discrete spectrum of mass ratios similar to those observed in granular and Toda dimers. Further, we report a qualitative and one-to-one correspondence between the spectrum of the mass ratio corresponding to the dimer BC model and those corresponding to granular and Toda dimer chains.

  9. Dimerization of Human Growth Hormone by Zinc

    NASA Astrophysics Data System (ADS)

    Cunningham, Brian C.; Mulkerrin, Michael G.; Wells, James A.

    1991-08-01

    Size-exclusion chromatography and sedimentation equilibrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn2+-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn2+-hGH dimeric complex may be important for storage of hGH in secretory granules.

  10. Monomer-dimer problem on some networks

    NASA Astrophysics Data System (ADS)

    Wu, Ruijuan; Yan, Weigen

    2016-09-01

    Zhang et al. (2012) obtained the exact formula for the number of all possible monomer-dimer arrangements and the asymptotic growth constant on a scale-free small-world network. In this note, we generalize this result and obtain the exact solution on the monomer-dimer model on many networks. Particularly, we prove that these networks have the same asymptotic growth constant of the number of monomer-dimer arrangements.

  11. Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence

    NASA Astrophysics Data System (ADS)

    Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

    2014-06-01

    Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., 2,4AR, 2,4AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + 0,2X0-H]- and [peptide-NH3-H]-). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36]-, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

  12. Thermalization of a dimerized antiferromagnetic spin chain.

    PubMed

    Konstantinidis, N P

    2016-01-20

    Thermalization is investigated for the one-dimensional anisotropic antiferromagnetic Heisenberg model with dimerized nearest-neighbor interactions that break integrability. For this purpose the time evolution of local operator expectation values after an interacting quench is calculated directly with the Chebyshev polynomial expansion, and the deviation of the diagonal from the canonical thermal ensemble value is calculated for increasing system size for these operators. The spatial and spin symmetries of the Hamiltonian are taken into account to divide it into symmetry subsectors. The rate of thermalization is found to weaken with the dimerization parameter as the Hamiltonian evolves between two integrable limits, the non-dimerized and the fully dimerized where the chain breaks up into isolated dimers. This conclusion is supported by the distribution of the local operator off-diagonal elements between the eigenstates of the Hamiltonian with respect to their energy difference, which determines the strength of temporal fluctuations. The off-diagonal elements have a low-energy peak for small dimerization which facilitates thermalization, and originates in the reduction of spatial symmetry with respect to the non-dimerized limit. For increasing dimerization their distribution changes and develops a single low-energy maximum that relates to the fully dimerized limit and slows down thermalization.

  13. HLA class II sequence variants influence tuberculosis risk in populations of European ancestry

    PubMed Central

    Sveinbjornsson, Gardar; Gudbjartsson, Daniel F.; Halldorsson, Bjarni V.; Kristinsson, Karl G.; Gottfredsson, Magnus; Barrett, Jeffrey C.; Gudmundsson, Larus J.; Blondal, Kai; Gylfason, Arnaldur; Gudjonsson, Sigurjon Axel; Helgadottir, Hafdis T.; Jonasdottir, Adalbjorg; Jonasdottir, Aslaug; Karason, Ari; Kardum, Ljiljana Bulat; Knežević, Jelena; Kristjansson, Helgi; Kristjansson, Mar; Love, Arthur; Luo, Yang; Magnusson, Olafur T.; Sulem, Patrick; Kong, Augustine; Masson, Gisli; Thorsteinsdottir, Unnur; Dembic, Zlatko; Nejentsev, Sergey; Blondal, Thorsteinn; Jonsdottir, Ingileif; Stefansson, Kari

    2016-01-01

    Mycobacterium tuberculosis (M. tuberculosis) infections cause 9.0 million new tuberculosis (TB) cases and 1.5 million deaths annually1. To search for sequence variants that confer risk of TB we tested 28.3 million variants identified through whole-genome sequencing of 2,636 Icelanders for association with TB (8,162 cases and 277,643 controls), pulmonary TB (PTB), and M. tuberculosis infection. We found association of three sequence variants in the HLA class II region: rs557011[T] (MAF=40.2%) with M. tuberculosis infection (OR =1.14, P=3.1×10-13) and PTB (OR=1.25, P=5.8×10-12) and rs9271378[G] (MAF=32.5%) with PTB (OR=0.78, P=2.5×10-12), both located between HLA-DQA1 and HLA-DRB1. Finally, a missense variant p.Ala210Thr in HLA-DQA1, (MAF=19.1%, rs9272785) shows association with M. tuberculosis infection (P=9.3×10-9, OR=1.14). The association of these variants with PTB was replicated in large samples of European ancestry from Russia and Croatia (P< 5.9×10-4). These findings demonstrate that the HLA class II region contributes to the complex genetic risk of tuberculosis, possibly through reduced presentation of protective M. tuberculosis antigens to T cells. PMID:26829749

  14. The influence of the sequence of nanoparticles injection to solution on the rate of fibrinogen-thrombin reaction

    NASA Astrophysics Data System (ADS)

    Kirichenko, M. N.; Krivokhiza, S. V.; Chaikov, L. L.; Bulychev, N. A.

    2017-01-01

    The influence of Fe2O3 nanoparticles on the rate of fibrinogen-thrombin reaction is studied. The nanoparticles were obtained in acoustoplasma discharge with cavitation. The sequence of nanoparticles injection appeared to change dramatically the rate and result of enzymatic reaction. In case of nanoparticles injection to fibrinogen before thrombin addition, enzymatic reaction practically stopped at the first stage. The mixing of nanoparticles with thrombin before its addition to fibrinogen leads to acceleration of gel formation in comparison with reaction without nanoparticles. We believe that Fe2O3 nanoparticles can modify the rate of enzymatic reaction, in one case acting as inhibitors of the reaction and as activators in other.

  15. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization.

    PubMed

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-18

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  16. Single nucleotide polymorphism analysis using different colored dye dimer probes

    NASA Astrophysics Data System (ADS)

    Marmé, Nicole; Friedrich, Achim; Denapaite, Dalia; Hakenbeck, Regine; Knemeyer, Jens-Peter

    2006-09-01

    Fluorescence quenching by dye dimer formation has been utilized to develop hairpin-structured DNA probes for the detection of a single nucleotide polymorphism (SNP) in the penicillin target gene pbp2x, which is implicated in the penicillin resistance of Streptococcus pneumoniae. We designed two specific DNA probes for the identification of the pbp2x genes from a penicillin susceptible strain R6 and a resistant strain Streptococcus mitis 661 using green-fluorescent tetramethylrhodamine (TMR) and red-fluorescent DY-636, respectively. Hybridization of each of the probes to its respective target DNA sequence opened the DNA hairpin probes, consequently breaking the nonfluorescent dye dimers into fluorescent species. This hybridization of the target with the hairpin probe achieved single nucleotide specific detection at nanomolar concentrations via increased fluorescence.

  17. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    NASA Astrophysics Data System (ADS)

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  18. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    PubMed Central

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-01-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development. PMID:27752093

  19. HIV-2 genome dimerization is required for the correct processing of Gag: a second-site reversion in matrix can restore both processes in dimerization-impaired mutant viruses.

    PubMed

    L'Hernault, Anne; Weiss, Eva U; Greatorex, Jane S; Lever, Andrew M

    2012-05-01

    A unique feature of retroviruses is the packaging of two copies of their genome, noncovalently linked at their 5' ends. In vitro, dimerization of human immunodeficiency virus type 2 (HIV-2) RNA occurs by interaction of a self-complementary sequence exposed in the loop of stem-loop 1 (SL-1), also termed the dimer initiation site (DIS). However, in virions, HIV-2 genome dimerization does not depend on the DIS. Instead, a palindrome located within the packaging signal (Psi) is the essential motif for genome dimerization. We reported previously that a mutation within Psi decreasing genome dimerization and packaging also resulted in a reduced proportion of mature particles (A. L'Hernault, J. S. Greatorex, R. A. Crowther, and A. M. Lever, Retrovirology 4:90, 2007). In this study, we investigated further the relationship between HIV-2 genome dimerization, particle maturation, and infectivity by using a series of targeted mutations in SL-1. Our results show that disruption of a purine-rich ((392)-GGAG-(395)) motif within Psi causes a severe reduction in genome dimerization and a replication defect. Maintaining the extended SL-1 structure in combination with the (392)-GGAG-(395) motif enhanced packaging. Unlike that of HIV-1, which can replicate despite mutation of the DIS, HIV-2 replication depends critically on genome dimerization rather than just packaging efficiency. Gag processing was altered in the HIV-2 dimerization mutants, resulting in the accumulation of the MA-CA-p2 processing intermediate and suggesting a link between genome dimerization and particle assembly. Analysis of revertant SL-1 mutant viruses revealed that a compensatory mutation in matrix (70TI) could rescue viral replication and partially restore genome dimerization and Gag processing. Our results are consistent with interdependence between HIV-2 RNA dimerization and the correct proteolytic cleavage of the Gag polyprotein.

  20. Children's Preference for Sequenced Accompaniments: The Influence of Style and Perceived Tempo.

    ERIC Educational Resources Information Center

    Brittin, Ruth V.

    2000-01-01

    Explores the influence of tempo on musical preference for students in grades 2-6, focusing on the effects of various styles using a MIDI keyboard. Explains that the students listened to 10 musical selections identifying their preferences and perceptions of tempo. Reveals that the preferred styles were Hip-Hop, Heavy Rock Shuffle, Samba, and Funk2.…

  1. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

    PubMed Central

    Baird, Heather A; Gao, Yong; Galetto, Román; Lalonde, Matthew; Anthony, Reshma M; Giacomoni, Véronique; Abreha, Measho; Destefano, Jeffrey J; Negroni, Matteo; Arts, Eric J

    2006-01-01

    Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of intra- or intersubtype A

  2. Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds

    PubMed Central

    Rueda, Daniel; Sheen, Patricia; Gilman, Robert H.; Bueno, Carlos; Santos, Marco; Pando-Robles, Victoria; Batista, Cesar V.; Zimic, Mirko

    2014-01-01

    Recombinant wild-pyrazinamidase from H37Rv M. tuberculosis was analyzed by gel electrophoresis under differential reducing conditions to evaluate its quaternary structure. PZAse was fractionated by size exclusion chromatography under non-reducing conditions. PZAse activity was measured and mass spectrometry analysis was performed to determine the identity of proteins by de novo sequencing and to determine the presence of disulfide bonds. This study confirmed that M. tuberculosis wild type PZAse was able to form homo-dimers in vitro. Homo-dimers showed a slightly lower specific PZAse activity compared to monomeric PZAse. PZAse dimers were dissociated into monomers in response to reducing conditions. Mass spectrometry analysis confirmed the existence of disulfide bonds (C72-C138 and C138-C138) stabilizing the quaternary structure of the PZAse homo-dimer. PMID:25199451

  3. Recombination regulator PRDM9 influences the instability of its own coding sequence in humans.

    PubMed

    Jeffreys, Alec J; Cotton, Victoria E; Neumann, Rita; Lam, Kwan-Wood Gabriel

    2013-01-08

    PRDM9 plays a key role in specifying meiotic recombination hotspot locations in humans and mice via recognition of hotspot sequence motifs by a variable tandem-repeat zinc finger domain in the protein. We now explore germ-line instability of this domain in humans. We show that repeat turnover is driven by mitotic and meiotic mutation pathways, the latter frequently resulting in substantial remodeling of zinc fingers. Turnover dynamics predict frequent allele switches in populations with correspondingly fast changes of the recombination landscape, fully consistent with the known rapid evolution of hotspot locations. We found variation in meiotic instability between men that correlated with PRDM9 status. One particular "destabilizer" variant caused hyperinstability not only of itself but also of otherwise-stable alleles in heterozygotes. PRDM9 protein thus appears to regulate the instability of its own coding sequence. However, destabilizer variants are strongly self-limiting in populations and probably have little impact on the evolution of the recombination landscape.

  4. Egg laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs

    USGS Publications Warehouse

    Ackerman, Joshua T.; Eagles-Smith, Collin A.; Herzog, Mark P.; Yee, Julie L.; Hartman, C. Alex

    2016-01-01

    Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intra-clutch variation and sampling methodology could influence interpretability. We examined the influence of egg laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last egg laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg laying order were inconsistent among species and overall differences in egg volume, mass, length, and width were <3%. We summarized the literature and, among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75%-91%) rather than within clutches (9%-25%). Using simulations, we determined that to accurately estimate a population's mean egg mercury concentration using only a single random egg from a subset of nests, it would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy).

  5. Potassium Hexacyanoferrate (III)-Catalyzed Dimerization of Hydroxystilbene: Biomimetic Synthesis of Indane Stilbene Dimers.

    PubMed

    Xie, Jing-Shan; Wen, Jin; Wang, Xian-Fen; Zhang, Jian-Qiao; Zhang, Ji-Fa; Kang, Yu-Long; Hui, You-Wei; Zheng, Wen-Sheng; Yao, Chun-Suo

    2015-12-18

    Using potassium hexacyanoferrate (III)-sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products.

  6. Influence of Stacking Sequence on the Impact and Postimpact Bending Behavior of Hybrid Sandwich Composites

    NASA Astrophysics Data System (ADS)

    Özen, M.

    2017-01-01

    A new hybrid sandwich structure was developed by using carbon, e-glass, and s-glass fabrics as reinforcement materials, an epoxy resin as the matrix material for face sheets, and a PVC foam as the core material. Six different configurations were prepared. Sandwich composites plates with different stacking sequences were subjected to low-speed impacts will energies of 7.5, 15, and 22.5 J. Their impact response is analyzed and reported in terms of the peak load as a function of impact energy. After impact tests, 3-point bending tests were conducted to determine the bending behavior of the sandwich composites after impacts in terms of their flexural strength. The results obtained showed that the use of carbon fabrics in the face sheets increased the peak loads for all the impact energies considered. The presence of carbon fibers in skin regions increased the flexural strength of the composites, but e-glass fibers decreased this strength.

  7. Repair of oxidative DNA base damage in the host genome influences the HIV integration site sequence preference.

    PubMed

    Bennett, Geoffrey R; Peters, Ryan; Wang, Xiao-hong; Hanne, Jeungphill; Sobol, Robert W; Bundschuh, Ralf; Fishel, Richard; Yoder, Kristine E

    2014-01-01

    Host base excision repair (BER) proteins that repair oxidative damage enhance HIV infection. These proteins include the oxidative DNA damage glycosylases 8-oxo-guanine DNA glycosylase (OGG1) and mutY homolog (MYH) as well as DNA polymerase beta (Polβ). While deletion of oxidative BER genes leads to decreased HIV infection and integration efficiency, the mechanism remains unknown. One hypothesis is that BER proteins repair the DNA gapped integration intermediate. An alternative hypothesis considers that the most common oxidative DNA base damages occur on guanines. The subtle consensus sequence preference at HIV integration sites includes multiple G:C base pairs surrounding the points of joining. These observations suggest a role for oxidative BER during integration targeting at the nucleotide level. We examined the hypothesis that BER repairs a gapped integration intermediate by measuring HIV infection efficiency in Polβ null cell lines complemented with active site point mutants of Polβ. A DNA synthesis defective mutant, but not a 5'dRP lyase mutant, rescued HIV infection efficiency to wild type levels; this suggested Polβ DNA synthesis activity is not necessary while 5'dRP lyase activity is required for efficient HIV infection. An alternate hypothesis that BER events in the host genome influence HIV integration site selection was examined by sequencing integration sites in OGG1 and MYH null cells. In the absence of these 8-oxo-guanine specific glycosylases the chromatin elements of HIV integration site selection remain the same as in wild type cells. However, the HIV integration site sequence preference at G:C base pairs is altered at several positions in OGG1 and MYH null cells. Inefficient HIV infection in the absence of oxidative BER proteins does not appear related to repair of the gapped integration intermediate; instead oxidative damage repair may participate in HIV integration site preference at the sequence level.

  8. Electronic transitions of palladium dimer

    SciTech Connect

    Qian, Yue; Ng, Y. W.; Chen, Zhihua; Cheung, A. S.-C.

    2013-11-21

    The laser induced fluorescence spectrum of palladium dimer (Pd{sub 2}) in the visible region between 480 and 700 nm has been observed and analyzed. The gas-phase Pd{sub 2} molecule was produced by laser ablation of palladium metal rod. Eleven vibrational bands were observed and assigned to the [17.1] {sup 3}II{sub g} - X{sup 3}Σ{sub u}{sup +} transition system. The bond length (r{sub o}) and vibrational frequency (ΔG{sub 1/2}) of the ground X{sup 3}Σ{sub u}{sup +} state were determined to be 2.47(4) Å and 211.4(5) cm{sup −1}, respectively. A molecular orbital energy level diagram was used to understand the observed ground and excited electronic states. This is the first gas-phase experimental investigation of the electronic transitions of Pd{sub 2}.

  9. Comparison of different surface modification techniques for electrodes by means of electrochemistry and micro synchrotron radiation X-ray fluorescence. dimerization of cobalt(II) tetrasulfonated phthalocyanine and its influence on the electrodeposition on gold surfaces.

    PubMed

    Peeters, Karl; De Wael, Karolien; Vincze, Laszlo; Adriaens, Annemie

    2005-09-01

    This paper compares different electrochemical surface modification techniques with special attention to the immobilization of cobalt(II) tetrasulfonated phthalocyanine tetrasodium salt (Co(II)TSPc) on gold electrodes. Electrochemical and synchrotron radiation X-ray fluorescence (SR-XRF) microbeam analysis were performed in order to compare the amount of adsorbed CoTSPc onto the gold electrode and to determine the level of uniformity of the deposited layer. The nondestructive, quantitative characterization of CoTSPc deposition on gold electrodes by means of scanning SR-XRF on the microscopic scale has never been described before. The described methodology can be in general used for thin-film characterization. Depending on the degree of dimerization of the CoTSPc molecules, different electrochemical behavior is observed.

  10. Structural characterization of dimeric murine aminoacylase III.

    PubMed

    Ryazantsev, Sergey; Abuladze, Natalia; Newman, Debra; Bondar, Galyna; Kurtz, Ira; Pushkin, Alexander

    2007-05-01

    Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of approximately 9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16A resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

  11. Influence of ACE I/D Polymorphism on Circulating Levels of Plasminogen Activator Inhibitor 1, D-Dimer, Ultrasensitive C-Reactive Protein and Transforming Growth Factor β1 in Patients Undergoing Hemodialysis

    PubMed Central

    de Carvalho, Sara Santos; Simões e Silva, Ana Cristina; Sabino, Adriano de Paula; Evangelista, Fernanda Cristina Gontijo; Gomes, Karina Braga; Dusse, Luci Maria SantAna; Rios, Danyelle Romana Alves

    2016-01-01

    Background There is substantial evidence that chronic renal and cardiovascular diseases are associated with coagulation disorders, endothelial dysfunction, inflammation and fibrosis. Angiotensin-Converting Enzyme Insertion/Deletion polymorphism (ACE I/D polymorphism) has also be linked to cardiovascular diseases. Therefore, this study aimed to compare plasma levels of ultrassensible C-reactive protein (usCRP), PAI-1, D-dimer and TGF-β1 in patients undergoing HD with different ACE I/D polymorphisms. Methods The study was performed in 138 patients at ESRD under hemodialysis therapy for more than six months. The patients were divided into three groups according to the genotype. Genomic DNA was extracted from blood cells (leukocytes). ACE I/D polymorphism was investigated by single polymerase chain reaction (PCR). Plasma levels of D-dimer, PAI-1 and TGF-β1 were measured by enzyme-linked immunosorbent assay (ELISA), and the determination of plasma levels of usCRP was performed by immunonephelometry. Data were analyzed by the software SigmaStat 2.03. Results Clinical characteristics were similar in patients with these three ACE I/D polymorphisms, except for interdialytic weight gain. I allele could be associated with higher interdialytic weight gain (P = 0.017). Patients genotyped as DD and as ID had significantly higher levels of PAI-1 than those with II genotype. Other laboratory parameters did not significantly differ among the three subgroups (P = 0.033). Despite not reaching statistical significance, plasma levels of usCRP were higher in patients carrying the D allele. Conclusion ACE I/D polymorphisms could be associated with changes in the regulation of sodium, fibrinolytic system, and possibly, inflammation. Our data showed that high levels of PAI-1 are detected when D allele is present, whereas greater interdialytic gain is associated with the presence of I allele. However, further studies with different experimental designs are necessary to elucidate the

  12. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    PubMed

    D'Incao, J P; von Stecher, J; Greene, Chris H

    2009-07-17

    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

  13. Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers.

    PubMed

    Jang, Hyunbum; Muratcioglu, Serena; Gursoy, Attila; Keskin, Ozlem; Nussinov, Ruth

    2016-06-15

    Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms' dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.

  14. Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing.

    PubMed

    Xie, Yongchao; Wu, Bing; Zhang, Xu-Xiang; Yin, Jinbao; Mao, Liang; Hu, Maojie

    2016-02-01

    Graphene is a promising candidate as an antibacterial material owning to its bacterial toxicity. However, little information on influence of graphene on gut microbiota is available. In this study, mice were exposed to graphene for 4 weeks, and high-throughput sequencing was applied to characterize the changes in microbial community and antibiotic resistance genes (ARGs) in mouse gut. The results showed that graphene exposure increased biodiversity of gut microbiota, and changed their community. The 1 μg/d graphene exposure had higher influences on the gut microbiota than 10 μg/d and 100 μg/d graphene exposures, which might be due to higher aggregation of high-level graphene. The influence of graphene on gut microbiota might attribute to that graphene could induce oxidative stress and damage of cell membrane integrity. The results were verified by the increase of ratio of Gram-negative bacteria. Outer membrane of Gram-negative bacteria could reduce the membrane damage induced by graphene and make them more tolerance to graphene. Further, we found that graphene exposure significantly increased the abundance and types of ARGs, indicating a potential health risk of graphene. This study firstly provides new insight to the health effects of graphene on gut microbiota.

  15. Purification and characterization of dimeric dihydrodiol dehydrogenase from dog liver.

    PubMed

    Sato, K; Nakanishi, M; Deyashiki, Y; Hara, A; Matsuura, K; Ohya, I

    1994-09-01

    High NADP(+)-linked dihydrodiol dehydrogenase activity was detected in dog liver cytosol, from which a dimeric enzyme composed of M(r) 39,000 subunits was purified to homogeneity. The enzyme oxidized trans-cyclohexanediol, and trans-dihydrodiols of benzene and naphthalene, the [1R,2R]-isomers of which were selectively oxidized. In the reverse reaction in the presence of NADPH as a coenzyme, the enzyme reduced alpha-dicarbonyl compounds, such as methylglyoxal, 3-deoxyglucosone, and diacetyl, and some compounds with a carbonyl group, such as glyceraldehyde, lactaldehyde, and acetoin. 4-Hydroxyphenylketones and ascorbates inhibited the enzyme. The results of steady-state kinetic analyses indicated that the reaction proceeds through an ordered bi bi mechanism with the coenzyme binding to the free enzyme, and suggested that the inhibitors bind to the enzyme-NADP+ binary complex. The dimeric enzyme was detected in liver and kidney of dog, and was immunochemically similar to the dimeric enzymes from monkey kidney, rabbit lens, and pig liver. The sequences (total 127 amino acid residues) of eight peptides derived on enzymatic digestion of the dog liver enzyme did not show significant similarity with the primary structures of members of the aldo-keto reductase and short chain dehydrogenase superfamilies, which include monomeric dihydrodiol dehydrogenases and carbonyl reductase, respectively.

  16. Short-term Influence of Drilling Fluid on Ciliates from Activated Sludge in Sequencing Batch Reactors.

    PubMed

    Babko, Roman; Kuzmina, Tatiana; Łagód, Grzegorz; Jaromin-Gleń, Katarzyna; Danko, Yaroslav; Pawłowska, Małgorzata; Pawłowski, Artur

    2017-01-01

    Spent drilling muds are the liquid residues of rock drilling operations. Due to a high concentration of suspended solids and potentially detrimental chemical properties, they can negatively affect microorganisms participating in wastewater treatment processes. We evaluated the addition of a potassium-polymer drilling fluid (DF) to activated sludge in laboratory sequencing batch reactors (SBRs) for municipal wastewater treatment. Ciliate assemblage, the most dynamic component of eukaryotes in activated sludge, and which is highly sensitive to changes in the system, was evaluated. The average ciliate abundance dropped by about 51% (SBR 2; 1% DF added) and 33% (SBR 3; 3% DF added) in comparison to the control (SBR 1; wastewater only). A decrease in the total number of ciliate species during the experiment was observed, from 25 to 24 in SBR 2 and from 17 to 13 in SBR 3. Moreover, a drop in the number of dominant (>100 individuals mL) ciliate species was observed during the experiment-from eight in the control to five in SBR 2 and four in SBR 3-signaling noticeable changes in the quantitative structure of ciliate species. The species analyzed showed different responses to DF addition. The most sensitive was , which is bacteriovorus. In contrast, two predators, and , showed no reaction to DF addition. Our results indicate that addition of potassium-polymer DF, in doses of 1 to 3% of the treated wastewater volume, had no toxic effects on ciliates, but qualitative and quantitative changes in their community were observed.

  17. Influence of aeration intensity on mature aerobic granules in sequencing batch reactor.

    PubMed

    Gao, Da-Wen; Liu, Lin; Liang, Hong

    2013-05-01

    Aeration intensity is well known as an important factor in the formation of aerobic granules. In this research, two identical lab-scale sequencing batch reactors with aeration intensity of 0.8 (R1) and 0.2 m(3)/h (R2) were operated to investigate the characteristics and kinetics of matured aerobic granules. Results showed that both aeration intensity conditions induced granulation, but they showed different effects on the characteristics of aerobic granules. Compared with the low aeration intensity (R2), the aerobic granules under the higher aeration intensity (R1) had better physical characteristics and settling ability. However, the observed biomass yield (Y obs) in R1 [0.673 kg mixed liquor volatile suspended solids (MLVSS)/kg chemical oxygen demand (COD)] was lower than R2 (0.749 kg MLVSS/kg COD). In addition, the maximum specific COD removal rates (q max) and apparent half rate constant (K) of mature aerobic granular sludge under the two aeration intensities were at a similar level. Therefore, the matured aerobic granule system does not require to be operated in a higher aeration intensity, which will reduce the energy consumption.

  18. Influence of temperature on the partial nitritation of reject water in a granular sequencing batch reactor.

    PubMed

    López-Palau, Sílvia; Sancho, Irene; Pinto, Antonio; Dosta, Joan; Mata-Alvarez, Joan

    2013-01-01

    Two Granular Sequencing Batch Reactors were operated to perform partial nitrification of sludge reject water at different temperatures, from 25-41 degrees C. Every temperature was fixed for about a month in order to evaluate the nitritation rate, morphological features of aggregates and bacterial populations. The optimum temperature was found between 33 and 37 degrees C in terms of nitritation rate. Morphological features of granules did not show significant changes with temperature in the range between 28 and 37 degrees C; Feret diameter remained at 5.8 +/- 0.7mm and roundness was 0.76 +/- 0.02. Lower temperatures promoted the appearance of filamentous bacteria, leading to an increase of the sludge volume index (SVI) and a consequent reduction of biomass concentration. When the temperature was increased to 39 degrees C, more than the 80% of aggregates showed a diameter higher than 6mm but density decreased from 28 to 19 g VSS L(-1), resulting in an increase of the SVI from 33 to 80 mL g(-1). The establishment of 41 degrees C caused a rapid destabilization of the system and nitritation activity disappeared. Bacterial populations did not experience significant changes during the experimental period and Nitrosomonas was the dominant species at all the temperatures assayed.

  19. Influence of manure age and sunlight on the community structure of cattle fecal bacteria as revealed by Illumina sequencing

    NASA Astrophysics Data System (ADS)

    Wong, K.; Shaw, T. I.; Oladeinde, A.; Molina, M.

    2013-12-01

    Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. Stream and river impairment due to fecal pollution is largely the result of agricultural activities in the United States. In the last few years, numerous metagenomic studies utilized next generation sequencing to develop microbial community profiles by massively sequencing the 16sRNA hypervariable region. This technology supports the application of water quality assessment such as pathogen detection and fecal source tracking. The bacteria communities of samples in these studies were determined when they were freshly collected; therefore, little is known about how feces age or how environmental stress influences the microbial ecology of fecal materials. In this study we monitored bacteria community changes in cattle feces for 57 days after excretion (day 0, 2, 4 8, 15, 22, 29, 43, 57) by sequencing the 16s variable region 4, using Illumnia MiSeq. Twelve cattle feces were studied; half of the samples were directly exposed to sunlight (unshaded) and half were shaded. Results indicate that the relative abundance (RA) profile in both shaded and unshaded samples rapidly changed from day 0 to 15, but stabilized from day 22 to 57. Firmcutes were the most abundant phylum (~40%) at day 0, but were reduced to <10% by day 57. The RA of Proteobacteria was only 1% at day 0, but increased to ~50% by day 57in both shaded and unshaded samples. By the end of the study, shaded and unshaded samples had a similar RA of Firmcutes and Proteobacteria but the RA of Bacteroidetes and Actinobacteria was, respectively, about 7% lower and 10% higher for unshaded samples. UV intensity, moisture, and temperature were significantly different between shaded and unshaded plots, indicating that these environmental stresses could influence the structure of fecal bacteria community in the natural environment. According to the

  20. Did stresses from the Cerro Prieto Geothermal Field influence the El Mayor-Cucapah rupture sequence?

    NASA Astrophysics Data System (ADS)

    Trugman, Daniel T.; Borsa, Adrian A.; Sandwell, David T.

    2014-12-01

    The Mw 7.2 El Mayor-Cucapah (EMC) earthquake ruptured a complex fault system in northern Baja California that was previously considered inactive. The Cerro Prieto Geothermal Field (CPGF), site of the world's second largest geothermal power plant, is located approximately 15 km to the northeast of the EMC hypocenter. We investigate whether anthropogenic fluid extraction at the CPGF caused a significant perturbation to the stress field in the EMC rupture zone. We use Advanced Land Observing Satellite interferometric synthetic aperture radar data to develop a laterally heterogeneous model of fluid extraction at the CPGF and estimate that this extraction generates positive Coulomb stressing rates of order 15 kPa/yr near the EMC hypocenter, a value which exceeds the local tectonic stressing rate. Although we cannot definitively conclude that production at the CPGF triggered the EMC earthquake, its influence on the local stress field is substantial and should not be neglected in local seismic hazard assessments.

  1. Influence of the sequence-dependent flexure of DNA on transcription in E. coli.

    PubMed Central

    Collis, C M; Molloy, P L; Both, G W; Drew, H R

    1989-01-01

    In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA region of interest (e.g., promoter, operator or enhancer) close to certain kinds of DNA structure that may influence its ability to work in a living cell. In the present example, we have placed a promoter from T7 virus next to the special DNA structures; the T7 promoter is then linked to a gene for a marker protein (chloramphenicol acetyl transferase). When plasmids bearing the T7 promoter are grown in cells of E. coli that contain T7 RNA polymerase, the special DNA structures seem to have little or no influence over the activity of the T7 promoter, contrary to our expectations. Yet when the same plasmids are grown in cells of E. coli that do not contain T7 RNA polymerase, some of the DNA structures show a surprising promoter activity of their own. In particular, the favourable flexibility or curvature of DNA, in the close vicinity of potential -35 and -10 promoter regions, seems to be a significant factor in determining where E. coli RNA polymerase starts RNA chains. We show directly, in one example, that loss of curvature between -35 and -10 regions is associated with a nearly-complete loss of promoter activity. These results, and others of their kind, show that the structural and/or vibrational properties of DNA play a much more important role in determining E. coli promoter activity than has previously been supposed. Images PMID:2685760

  2. Sequence variations at the HLA-linked olfactory receptor cluster do not influence female preferences for male odors

    PubMed Central

    Thompson, Emma E; Haller, Gabe; Pinto, Jayant M; Sun, Ying; Zelano, Bethanne; Jacob, Suma; McClintock, Martha K.; Nicolae, Dan L.; Ober, Carole

    2013-01-01

    We previously reported that paternally-inherited human leukocyte antigen (HLA) alleles are a template for women's preference for male odors (P = 0.0007). However, it has been suggested that sequence variation in a nearby olfactory receptor (OR) cluster on chromosome 6p influences smell preference. To determine if the HLA-linked OR genes contribute to previously observed HLA-mediated behaviors, we use the odor preference data from our earlier study in combination with a new resequencing study of four functional HLA-linked OR genes in the same subjects. Our results indicate that OR alleles in the genes surveyed are not in linkage disequilibrium (LD) with HLA variation and do not explain the previous findings of HLA-associated odor preference. PMID:19833159

  3. Perception of musical tension in short chord sequences: the influence of harmonic function, sensory dissonance, horizontal motion, and musical training.

    PubMed

    Bigand, E; Parncutt, R; Lerdahl, F

    1996-01-01

    This study investigates the effect of four variables (tonal hierarchies, sensory chordal consonance, horizontal motion, and musical training) on perceived musical tension. Participants were asked to evaluate the tension created by a chord X in sequences of three chords [C major-->X-->C major] in a C major context key. The X chords could be major or minor triads major-minor seventh, or minor seventh chords built on the 12 notes of the chromatic scale. The data were compared with Krumhansl's (1990) harmonic hierarchy and with predictions of Lerdahl's (1988) cognitive theory, Hutchinson and Knopoff's (1978) and Parncutt's (1989) sensory-psychoacoustical theories, and the model of horizontal motion defined in the paper. As a main outcome, it appears that judgments of tension arose from a convergence of several cognitive and psychoacoustics influences, whose relative importance varies, depending on musical training.

  4. Helicobacter pylori cagA Promoter Region Sequences Influence CagA Expression and Interleukin 8 Secretion.

    PubMed

    Ferreira, Rui M; Pinto-Ribeiro, Ines; Wen, Xiaogang; Marcos-Pinto, Ricardo; Dinis-Ribeiro, Mário; Carneiro, Fátima; Figueiredo, Ceu

    2016-02-15

    Heterogeneity at the Helicobacter pylori cagA gene promoter region has been linked to variation in CagA expression and gastric histopathology. Here, we characterized the cagA promoter and expression in 46 H. pylori strains from Portugal. Our results confirm the relationship between cagA promoter region variation and protein expression originally observed in strains from Colombia. We observed that individuals with intestinal metaplasia were all infected with H. pylori strains containing a specific cagA motif. Additionally, we provided novel functional evidence that strain-specific sequences in the cagA promoter region and CagA expression levels influence interleukin 8 secretion by the host gastric epithelial cells.

  5. Assembly of Dimer-Based Photonic Crystals

    NASA Astrophysics Data System (ADS)

    Liddell Watson, Chekesha M.

    2011-03-01

    Recent advances in colloid synthesis to prepare monodisperse shape anisotropic particles provide the opportunity to address challenges related to structural diversity in ordered colloidal solids. In particular, computational simulations and mechanical models suggest that upon system densification nonspherical dimer colloids undergo disorder-order and order-order phase transitions to unconventional solid structures including, base-centered monoclinic crystals, degenerate aperiodic crystals, plastic crystal or rotator, etc. based on free energy minimization. The particle systems have notable analogy to molecular systems, where the shape of molecules and their packing density has been shown to critically influence structural phase behavior and lead to a rich variety of structures, both natural and synthetic. The materials engineering challenges have been in attaining sufficiently monodisperse (size uniformity) colloidal building blocks, as well as the lack of understanding and control of self-assembly processes for non-spherical colloids. This talk highlights our investigations of how particle shape programs the self-organization of colloidal structures. Methods including evaporation mediated assembly and confinement provide a platform to understand the formation of complex colloidal structures from non-spherical building blocks (silica-coated iron oxide, polystyrene, hollow silica shell). Optical property simulations for unconventional 2D and 3D structures with nonspherical particle bases will also be discussed.

  6. Egg-laying sequence influences egg mercury concentrations and egg size in three bird species: Implications for contaminant monitoring programs.

    PubMed

    Ackerman, Joshua T; Eagles-Smith, Collin A; Herzog, Mark P; Yee, Julie L; Hartman, C Alex

    2016-06-01

    Bird eggs are commonly used in contaminant monitoring programs and toxicological risk assessments, but intraclutch variation and sampling methodology could influence interpretability. The authors examined the influence of egg-laying sequence on egg mercury concentrations and burdens in American avocets, black-necked stilts, and Forster's terns. The average decline in mercury concentrations between the first and last eggs laid was 33% for stilts, 22% for terns, and 11% for avocets, and most of this decline occurred between the first and second eggs laid (24% for stilts, 18% for terns, and 9% for avocets). Trends in egg size with egg-laying order were inconsistent among species, and overall differences in egg volume, mass, length, and width were <3%. The authors summarized the literature, and among 17 species studied, mercury concentrations generally declined by 16% between the first and second eggs laid. Despite the strong effect of egg-laying sequence, most of the variance in egg mercury concentrations still occurred among clutches (75-91%) rather than within clutches (9%-25%). Using simulations, the authors determined that accurate estimation of a population's mean egg mercury concentration using only a single random egg from a subset of nests would require sampling >60 nests to represent a large population (10% accuracy) or ≥14 nests to represent a small colony that contained <100 nests (20% accuracy). Environ Toxicol Chem 2016;35:1458-1469. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

  7. Minding the gap: Frequency of indels in mtDNA control region sequence data and influence on population genetic analyses

    USGS Publications Warehouse

    Pearce, J.M.

    2006-01-01

    Insertions and deletions (indels) result in sequences of various lengths when homologous gene regions are compared among individuals or species. Although indels are typically phylogenetically informative, occurrence and incorporation of these characters as gaps in intraspecific population genetic data sets are rarely discussed. Moreover, the impact of gaps on estimates of fixation indices, such as FST, has not been reviewed. Here, I summarize the occurrence and population genetic signal of indels among 60 published studies that involved alignments of multiple sequences from the mitochondrial DNA (mtDNA) control region of vertebrate taxa. Among 30 studies observing indels, an average of 12% of both variable and parsimony-informative sites were composed of these sites. There was no consistent trend between levels of population differentiation and the number of gap characters in a data block. Across all studies, the average influence on estimates of ??ST was small, explaining only an additional 1.8% of among population variance (range 0.0-8.0%). Studies most likely to observe an increase in ??ST with the inclusion of gap characters were those with < 20 variable sites, but a near equal number of studies with few variable sites did not show an increase. In contrast to studies at interspecific levels, the influence of indels for intraspecific population genetic analyses of control region DNA appears small, dependent upon total number of variable sites in the data block, and related to species-specific characteristics and the spatial distribution of mtDNA lineages that contain indels. ?? 2006 Blackwell Publishing Ltd.

  8. NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.

    PubMed

    Keane, Sarah C; Van, Verna; Frank, Heather M; Sciandra, Carly A; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F

    2016-11-15

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a (2)H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a (2)H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.

  9. Vibrationally resolved emission of thiophosgene dimer

    NASA Astrophysics Data System (ADS)

    Berrios, Eduardo; Hui, Ho Yee; Gruebele, Martin

    2010-09-01

    During a study of thiophosgene electronic spectra, Fujiwara and co-workers observed a broad electronic transition peaked at 37 000 cm -1, attributed to thiophosgene dimer. Our dispersed fluorescence spectra of a thiophosgene molecular beam excited at 36 000 cm -1 reveal several vibrational modes too low in frequency for thiophosgene. We assign them to modes of thiophosgene dimer or their combination bands. MP2 calculations support the vibrational assignment. TD-DFT, CASSCF, and coupled cluster calculations suggest that the bright electronic state of thiophosgene dimer is the B 2u symmetry fifth excited singlet state. Two additional transitions are assigned to a thiophosgene synthesis impurity, trichloromethanesulfenyl chloride.

  10. Quantum dimer model for the pseudogap metal

    PubMed Central

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-01-01

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S=1/2, charge +e fermionic dimers. The model realizes a “fractionalized Fermi liquid” with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8×8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments. PMID:26195771

  11. Quantum dimer model for the pseudogap metal.

    PubMed

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-08-04

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  12. Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer.

    PubMed

    Cukier, Robert I

    2014-09-04

    Basic region leucine zipper (bZIP) transcription factors involved in DNA recognition are dimeric proteins. The monomers consist of two subdomains, a leucine zipper sequence responsible for dimerization and a highly basic DNA recognition sequence. Leucine zippers are strongly dimerized, and in a bZIP, the basic region can, in the absence of DNA, undergo extensive relative monomer-to-monomer fluctuations. In this work, LZ and bZIP potentials of mean force (PMFs), which provide free energies along reaction coordinates, are simulated with a distance replica exchange method. The method uses restraint potentials to provide sampling along a reaction coordinate and enhances configuration space exploration by exchanging information between neighboring restraint potential configurations. Restraint potentials that are constructed from sums over a number of atom distances are employed. Their use requires a modification of the Weighted Histogram Analysis Method (WHAM) procedure to combine and unbias the data from the different restraint-potential-biased window densities to provide a PMF. These methods are first used to obtain a PMF for separating a leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The PMF indicates a very strong binding free energy that only weakens when the monomers are separated by about 12 Å, which is about 6 Å beyond their bound, dimer equilibrium distance. PMFs are also obtained for separating the basic subdomain monomer parts of the GCN4 bZIP transcriptional factor, in the absence of DNA. In a monomer separation range spanning the open, crystal-based structure to closer configurations, the basic subdomain PMF is quite flat, implying essentially thermal sampling in this distance range. A PMF generated starting from a "collapsed" state, taken from a previous simulation ( J. Phys. Chem. B 2012 , 116 , 6071 ), where collapsed refers to the feature that the basic subdomain monomers are also effectively dimerized, shows that this state is

  13. Coiled-Coil–Mediated Dimerization Is Not Required for Myosin VI to Stabilize Actin during Spermatid Individualization in Drosophila melanogaster

    PubMed Central

    Noguchi, Tatsuhiko; Frank, Deborah J.; Isaji, Mamiko

    2009-01-01

    Myosin VI is a pointed-end–directed actin motor that is thought to function as both a transporter of cargoes and an anchor, capable of binding cellular components to actin for long periods. Dimerization via a predicted coiled coil was hypothesized to regulate activity and motor properties. However, the importance of the coiled-coil sequence has not been tested in vivo. We used myosin VI's well-defined role in actin stabilization during Drosophila spermatid individualization to test the importance in vivo of the predicted coiled coil. If myosin VI functions as a dimer, a forced dimer should fully rescue myosin VI loss of function defects, including actin stabilization, actin cone movement, and cytoplasmic exclusion by the cones. Conversely, a molecule lacking the coiled coil should not rescue at all. Surprisingly, neither prediction was correct, because each rescued partially and the molecule lacking the coiled coil functioned better than the forced dimer. In extracts, no cross-linking into higher molecular weight forms indicative of dimerization was observed. In addition, a sequence required for altering nucleotide kinetics to make myosin VI dimers processive is not required for myosin VI's actin stabilization function. We conclude that myosin VI does not need to dimerize via the predicted coiled coil to stabilize actin in vivo. PMID:19005209

  14. Mechanism of HIV-1 RNA dimerization in the central region of the genome and significance for viral evolution.

    PubMed

    Piekna-Przybylska, Dorota; Sharma, Gaurav; Bambara, Robert A

    2013-08-16

    The genome of HIV-1 consists of two identical or nearly identical RNA molecules. The RNA genomes are held in the same, parallel orientation by interactions at the dimer initiation site (DIS). Previous studies showed that in addition to interactions at DIS, sequences located 100 nucleotides downstream from the 5' splice site can dimerize in vitro through an intermolecular G-quartet structure. Here we report that the highly conserved G-rich sequence in the middle portion of the HIV-1 genome near the central polypurine tract (cPPT) dimerizes spontaneously under high ionic strength in the absence of protein. The antisense RNA does not dimerize, strongly indicating that RNA dimerization does not exclusively involve A:U and G:C base pairing. The cation-dependent reverse transcriptase pausing profile, CD spectra profile, and cation-dependent association and thermal dissociation characteristics indicate G-quartet structures. Different forms of G-quartets are formed including monomers and, significantly, intermolecular dimers. Our results indicate that RNA genome dimerization and parallel alignment initiated through interactions at DIS may be greatly expanded and stabilized by formation of an intermolecular G-quartet at a distant site near the cPPT. It is likely that formation of G-quartet structure near the cPPT in vivo keeps the RNA genomes in proximity over a long range, promoting genetic recombination in numerous hot spots.

  15. Influence of Exciplex formation on the electroluminescent properties of dimeric Zn (II) bis-2-(2'-hydroxyphenyl) benzoxazole complex and monomeric Zn (II) 2-(1'-hydroxynaphthyl) benzothiazole complex

    NASA Astrophysics Data System (ADS)

    Prakash, Sattey; Anand, R. S.; Manoharan, S. Sundar

    2011-10-01

    In this paper we present the factors affecting electroluminescent properties of Zinc complexes of oxazole & thiazole derivatives. Electroluminescent spectra of the Zinc (II) complex of bis-[2-(2'-hydroxyphenyl) benzoxazole], [Zn (HPBO)2]2 and 2-(1'-hydroxynaphthyl) benzothiazole [Zn (HNBT)2] show unusual broadening and shows structural and photophysical similarity with [Zn (HPBT)2]2, a dimeric complex. The [Zn (HPBO)2]2 complex as an emissive layer in the device structure ITO /PEDOT:PSS /TPD (30nm) /[Zn (HPBO)2]2 (60nm) /BCP (6nm) /Ca (3nm) /Al (200nm) shows a broad bluish green emission, with a full width at half maxima (FWHM1˜70nm). The EL spectra is much broader compared to the PL spectra because of exciplex formation at the interfacial region between the emissive layer (EML) & hole transport layer (HTL). We also show the device performance of Zinc 2-(1'-hydroxynaphthyl) benzothiazole [Zn (HNBT)2] complex as emissive layer. Distinctly this device shows a broad greenish yellow emission with a peak maxima at 535nm and 690nm, owing to the exciplex formation between electron transport layer (ETL) and emissive layer (EML), which is in sharp contrast to the exciplex formation across the HTL-EML interface observed for the [Zn (HPBO)2]2 complex.

  16. The influence of barley malt protein modification on beer foam stability and their relationship to the barley dimeric alpha-amylase inhibitor-I (BDAI-I) as a possible foam-promoting protein.

    PubMed

    Okada, Yoshihiro; Iimure, Takashi; Takoi, Kiyoshi; Kaneko, Takafumi; Kihara, Makoto; Hayashi, Katsuhiro; Ito, Kazutoshi; Sato, Kazuhiro; Takeda, Kazuyoshi

    2008-02-27

    The foam stability of beer is one of the important key factors in evaluating the quality of beer. The purpose of this study was to investigate the relationship between the level of malt modification (degradation of protein, starch, and so on) and the beer foam stability. This was achieved by examining foam-promoting proteins using two-dimensional gel electrophoresis (2DE). We found that the foam stability of beer samples brewed from the barley malts of cultivars B and C decreased as the level of malt modification increased; however, the foam stability of cultivar A did not change. To identify the property providing the increased foam stability of cultivar A, we analyzed beer proteins using 2DE. We analyzed three fractions that could contain beer foam-promoting proteins, namely, beer whole proteins, salt-precipitated proteins, and the proteins concentrated from beer foam. As a result, we found that in cultivar A, some protein spots did not change in any of these three protein fractions even when the level of malt modification increased, although the corresponding protein spots in cultivars B and C decreased. We analyzed these protein spots by peptide mass finger printing using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. As a result, all of these spots were identified as barley dimeric alpha-amylase inhibitor-I (BDAI-I). These results suggest that BDAI-I is an important contributor to beer foam stability.

  17. Saccades Influence the Visibility of Targets in Rapid Stimulus Sequences: The Roles of Mislocalization, Retinal Distance and Remapping

    PubMed Central

    Fracasso, Alessio; Melcher, David

    2016-01-01

    Briefly presented targets around the time of a saccade are mislocalized towards the saccadic landing point. This has been taken as evidence for a remapping mechanism that accompanies each eye movement, helping maintain visual stability across large retinal shifts. Previous studies have shown that spatial mislocalization is greatly diminished when trains of brief stimuli are presented at a high frequency rate, which might help to explain why mislocalization is rarely perceived in everyday viewing. Studies in the laboratory have shown that mislocalization can reduce metacontrast masking by causing target stimuli in a masking sequence to be perceived as shifted in space towards the saccadic target and thus more easily discriminated. We investigated the influence of saccades on target discrimination when target and masks were presented in a rapid serial visual presentation (RSVP), as well as with forward masking and with backward masking. In a series of experiments, we found that performance was influenced by the retinal displacement caused by the saccade itself but that an additional component of un-masking occurred even when the retinal location of target and mask was matched. These results speak in favor of a remapping mechanism that begins before the eyes start moving and continues well beyond saccadic termination. PMID:27445718

  18. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    2003-04-01

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  19. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  20. Epoxidation of alkenes catalyzed by phenyl group-modified, periodic mesoporous organosilica-entrapped, dimeric manganese-salen complexes.

    PubMed

    Hu, Jianglei; Wu, Qingyin; Li, Wei; Ma, Ling; Su, Fang; Guo, Yihang; Qiu, Yongqing

    2011-12-16

    A series of reusable, recoverable, diamine-bridged dimeric manganese-salen complexes were prepared by the encapsulation of homogeneous dimeric Mn(salen) complexes into nanocages of a 3D periodic mesoporous organosilica (PMO) support followed by silylation of the support with organosilane. The composition, structure, morphology, and textural properties of the prepared PMO-entrapped dimeric Mn(salen) complexes were characterized, and their catalytic performances were tested in the epoxidation of alkenes (styrene, cyclohexene, and 1-phenylcyclohexene), with NaClO as an oxygen source and 4-phenylpyridine-N-oxide as an axial ligand. Furthermore, the influences of the textural and morphological properties of the entrapped dimeric Mn(salen) complexes and the key reaction parameters on the catalytic activity and selectivity are discussed. Finally, the reusability of the supported dimeric Mn(salen) complexes was evaluated over three catalytic runs.

  1. Multiple-charge transfer and trapping in DNA dimers

    NASA Astrophysics Data System (ADS)

    Tornow, Sabine; Bulla, Ralf; Anders, Frithjof B.; Zwicknagl, Gertrud

    2010-11-01

    We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated hopping and the bond-bond interaction, which were recently calculated by Starikov [E. B. Starikov, Philos. Mag. Lett. 83, 699 (2003)10.1080/0950083031000151374] for different DNA dimers. The electronic degrees of freedom are coupled to an ohmic or a superohmic bath serving as dissipative environment. We employ the numerical renormalization group method in the nuclear tunneling regime and compare the results to Marcus theory for the thermal activation regime. For realistic parameters, the rate that at least one charge is transferred from the donor to the acceptor in the subspace of two excess electrons significantly exceeds the rate in the single charge sector. Moreover, the dynamics is strongly influenced by the Coulomb matrix elements. We find sequential and pair transfer as well as a regime where both charges remain self-trapped. The transfer rate reaches its maximum when the difference of the on-site and intersite Coulomb matrix element is equal to the reorganization energy which is the case in a guanine/cytosine (GC)-dimer. Charge transfer is completely suppressed for two excess electrons in adenine/thymine (AT)-dimer in an ohmic bath and replaced by damped coherent electron-pair oscillations in a superohmic bath. A finite bond-bond interaction W alters the transfer rate: it increases as function of W when the effective Coulomb repulsion exceeds the reorganization energy (inverted regime) and decreases for smaller Coulomb repulsion.

  2. Pfaffian Correlation Functions of Planar Dimer Covers

    NASA Astrophysics Data System (ADS)

    Aizenman, Michael; Valcázar, Manuel Laínz; Warzel, Simone

    2017-01-01

    The Pfaffian structure of the boundary monomer correlation functions in the dimer-covering planar graph models is rederived through a combinatorial/topological argument. These functions are then extended into a larger family of order-disorder correlation functions which are shown to exhibit Pfaffian structure throughout the bulk. Key tools involve combinatorial switching symmetries which are identified through the loop-gas representation of the double dimer model, and topological implications of planarity.

  3. The two-state dimer receptor model: a general model for receptor dimers.

    PubMed

    Franco, Rafael; Casadó, Vicent; Mallol, Josefa; Ferrada, Carla; Ferré, Sergi; Fuxe, Kjell; Cortés, Antoni; Ciruela, Francisco; Lluis, Carmen; Canela, Enric I

    2006-06-01

    Nonlinear Scatchard plots are often found for agonist binding to G-protein-coupled receptors. Because there is clear evidence of receptor dimerization, these nonlinear Scatchard plots can reflect cooperativity on agonist binding to the two binding sites in the dimer. According to this, the "two-state dimer receptor model" has been recently derived. In this article, the performance of the model has been analyzed in fitting data of agonist binding to A(1) adenosine receptors, which are an example of receptor displaying concave downward Scatchard plots. Analysis of agonist/antagonist competition data for dopamine D(1) receptors using the two-state dimer receptor model has also been performed. Although fitting to the two-state dimer receptor model was similar to the fitting to the "two-independent-site receptor model", the former is simpler, and a discrimination test selects the two-state dimer receptor model as the best. This model was also very robust in fitting data of estrogen binding to the estrogen receptor, for which Scatchard plots are concave upward. On the one hand, the model would predict the already demonstrated existence of estrogen receptor dimers. On the other hand, the model would predict that concave upward Scatchard plots reflect positive cooperativity, which can be neither predicted nor explained by assuming the existence of two different affinity states. In summary, the two-state dimer receptor model is good for fitting data of binding to dimeric receptors displaying either linear, concave upward, or concave downward Scatchard plots.

  4. Role of Rydberg states in the photostability of heterocyclic dimers: the case of pyrazole dimer.

    PubMed

    Zilberg, Shmuel; Haas, Yehuda

    2012-11-26

    A new route for the nonradiative decay of photoexcited, H-bonded, nitrogen-containing, heterocyclic dimers is offered and exemplified by a study of the pyrazole dimer. In some of these systems the N(3s) Rydberg state is the lowest excited singlet state. This state is formed by direct light absorption or by nonradiative transition from the allowed ππ* state. An isomer of this Rydberg state is formed by H atom transfer to the other component of the dimer. The newly formed H-bonded radical pair is composed of two radicals (a H-adduct of pyrazole, a heterocyclic analogue of the NH(4) radical) and the pyrazolium π-radical. It is calculated to have a shallow local minimum and is the lowest point on the PES of the H-pyrazole/pyrazolium radical pair. This species can cross back to the ground state of the original dimer through a relatively small energy gap and compete with the H-atom loss channel, known for the monomer. In both Rydberg dimers, an electron occupies a Rydberg orbital centered mostly on one of the two components of the dimer. This Rydberg Center Shift (RCS) mechanism, proposed earlier (Zilberg, S.; Kahan, A.; Haas, Y. Phys. Chem. Chem. Phys. 2012, 14, 8836), leads to deactivation of the electronically excited dimer while keeping it intact. It, thus, may explain the high photostability of the pyrazole dimer as well as other heterocyclic dimers.

  5. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Alkyl ketene dimers. 176.120 Section 176.120 Food... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl...

  6. 21 CFR 176.120 - Alkyl ketene dimers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Alkyl ketene dimers. 176.120 Section 176.120 Food... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl...

  7. Surface characterization and orientation interaction between diamond- like carbon layer structure and dimeric liquid crystals

    NASA Astrophysics Data System (ADS)

    Naradikian, H.; Petrov, M.; Katranchev, B.; Milenov, T.; Tinchev, S.

    2017-01-01

    Diamond-like carbon (DLC) and amorphous carbon films are very promising type of semiconductor materials. Depending on the hybridization sp2/sp3 ratio, the material’s band gap varies between 0.8 and 3 eV. Moreover carbon films possess different interesting for practice properties: comparable to the Silicon, Diamond like structure has 22-time better thermal conductivity etc. Here we present one type of implementation of such type nanostructure. That is one attempt for orientation of dimeric LC by using of pre-deposited DLC layer with different ratio of sp2/sp3 hybridized carbon content. It could be expected a pronounced π1-π2interaction between s and p orbital levels on the surface and the dimeric ring of LC. We present comparison of surface anchoring strengths of both orientation inter-surfaces DLC/dimeric LC and single wall carbon nanotubes (SWCNT)/dimeric LC. The mechanism of interaction of dimeric LC and activated surfaces with DLC or SWCNT will be discussed. In both cases we have π-π interaction, which in combination with hydrogen bonding, typical for the dimeric LCs, influence the LC alignment. The Raman spectroscopy data evidenced the presence of charge transfer between contacting hexagonal rings of DLC and the C = O groups of the LC molecules.

  8. Studies on the Dissociation and Urea-Induced Unfolding of FtsZ Support the Dimer Nucleus Polymerization Mechanism

    PubMed Central

    Montecinos-Franjola, Felipe; Ross, Justin A.; Sánchez, Susana A.; Brunet, Juan E.; Lagos, Rosalba; Jameson, David M.; Monasterio, Octavio

    2012-01-01

    FtsZ is a major protein in bacterial cytokinesis that polymerizes into single filaments. A dimer has been proposed to be the nucleating species in FtsZ polymerization. To investigate the influence of the self-assembly of FtsZ on its unfolding pathway, we characterized its oligomerization and unfolding thermodynamics. We studied the assembly using size-exclusion chromatography and fluorescence spectroscopy, and the unfolding using circular dichroism and two-photon fluorescence correlation spectroscopy. The chromatographic analysis demonstrated the presence of monomers, dimers, and tetramers with populations dependent on protein concentration. Dilution experiments using fluorescent conjugates revealed dimer-to-monomer and tetramer-to-dimer dissociation constants in the micromolar range. Measurements of fluorescence lifetimes and rotational correlation times of the conjugates supported the presence of tetramers at high protein concentrations and monomers at low protein concentrations. The unfolding study demonstrated that the three-state unfolding of FtsZ was due to the mainly dimeric state of the protein, and that the monomer unfolds through a two-state mechanism. The monomer-to-dimer equilibrium characterized here (Kd = 9 μM) indicates a significant fraction (∼10%) of stable dimers at the critical concentration for polymerization, supporting a role of the dimeric species in the first steps of FtsZ polymerization. PMID:22824282

  9. Functional Role of Dimerization of Human Peptidylarginine Deiminase 4 (PAD4)

    PubMed Central

    Liu, Yi-Liang; Chiang, Yu-Hsiu; Liu, Guang-Yaw; Hung, Hui-Chih

    2011-01-01

    Peptidylarginine deiminase 4 (PAD4) is a homodimeric enzyme that catalyzes Ca2+-dependent protein citrullination, which results in the conversion of arginine to citrulline. This paper demonstrates the functional role of dimerization in the regulation of PAD4 activity. To address this question, we created a series of dimer interface mutants of PAD4. The residues Arg8, Tyr237, Asp273, Glu281, Tyr435, Arg544 and Asp547, which are located at the dimer interface, were mutated to disturb the dimer organization of PAD4. Sedimentation velocity experiments were performed to investigate the changes in the quaternary structures and the dissociation constants (Kd) between wild-type and mutant PAD4 monomers and dimers. The kinetic data indicated that disrupting the dimer interface of the enzyme decreases its enzymatic activity and calcium-binding cooperativity. The Kd values of some PAD4 mutants were much higher than that of the wild-type (WT) protein (0.45 µM) and were concomitant with lower kcat values than that of WT (13.4 s−1). The Kd values of the monomeric PAD4 mutants ranged from 16.8 to 45.6 µM, and the kcat values of the monomeric mutants ranged from 3.3 to 7.3 s−1. The kcat values of these interface mutants decreased as the Kd values increased, which suggests that the dissociation of dimers to monomers considerably influences the activity of the enzyme. Although dissociation of the enzyme reduces the activity of the enzyme, monomeric PAD4 is still active but does not display cooperative calcium binding. The ionic interaction between Arg8 and Asp547 and the Tyr435-mediated hydrophobic interaction are determinants of PAD4 dimer formation. PMID:21731701

  10. Plasmonic Dimer-Like Nanoassemblies for Surface-Enhanced Raman Spectroscop

    NASA Astrophysics Data System (ADS)

    Rigo, Maria; Seo, Jaetae; Kim, Wan-Joong; Jung, Sungsoo; Hampton University Team; Etri Collaboration; Kriss Collaboration

    2011-05-01

    We report on the preparation of gold dimers in which the near-field coupling in their subwavelength gap is influenced by the individual gold nanoparticles size and the molecule's length used to assemble the dimers. The nano assemblies display plasmonic modes similar to those observed in rod-like nanoparticles. The longitudinal mode of the gold dimers shift as a function of gold nanoparticles size and concentration and it is influenced by the concentration of Rhodamine 6G (R6G), the molecule used as nanoparticle linker. We report large surface enhanced Raman scattering (SERS) enhancements for R6G when using linked-gold nano-assemblies as a SERS substrate. A discussion about the main origins for the large enhancement of molecular vibrational modes is presented. This work at Hampton University was supported by the National Science Foundation (HRD-0734635 and HRD-0630372).

  11. Structure of dimeric, recombinant Sulfolobus solfataricus phosphoribosyl diphosphate synthase: a bent dimer defining the adenine specificity of the substrate ATP.

    PubMed

    Andersen, Rune W; Leggio, Leila Lo; Hove-Jensen, Bjarne; Kadziola, Anders

    2015-03-01

    The enzyme 5-phosphoribosyl-1-α-diphosphate (PRPP) synthase (EC 2.7.6.1) catalyses the Mg(2+)-dependent transfer of a diphosphoryl group from ATP to the C1 hydroxyl group of ribose 5-phosphate resulting in the production of PRPP and AMP. A nucleotide sequence specifying Sulfolobus solfataricus PRPP synthase was synthesised in vitro with optimised codon usage for expression in Escherichia coli. Following expression of the gene in E. coli PRPP synthase was purified by heat treatment and ammonium sulphate precipitation and the structure of S. solfataricus PRPP synthase was determined at 2.8 Å resolution. A bent dimer oligomerisation was revealed, which seems to be an abundant feature among PRPP synthases for defining the adenine specificity of the substrate ATP. Molecular replacement was used to determine the S. solfataricus PRPP synthase structure with a monomer subunit of Methanocaldococcus jannaschii PRPP synthase as a search model. The two amino acid sequences share 35 % identity. The resulting asymmetric unit consists of three separated dimers. The protein was co-crystallised in the presence of AMP and ribose 5-phosphate, but in the electron density map of the active site only AMP and a sulphate ion were observed. Sulphate ion, reminiscent of the ammonium sulphate precipitation step of the purification, seems to bind tightly and, therefore, presumably occupies and blocks the ribose 5-phosphate binding site. The activity of S. solfataricus PRPP synthase is independent of phosphate ion.

  12. Groundwater influence on the aeolian sequence stratigraphy of the Mechertate-Chrita-Sidi El Hani system, Tunisian Sahel: Analogies to the wet-dry aeolian sequence stratigraphy at Meridiani Planum, Terby crater, and Gale crater, Mars

    NASA Astrophysics Data System (ADS)

    Essefi, Elhoucine; Komatsu, Goro; Fairén, Alberto G.; Chan, Marjorie A.; Yaich, Chokri

    2014-05-01

    A multidisciplinary study of the watershed and depressions of the Mechertate-Chrita-Sidi El Hani (MCSH) system in eastern Tunisia shows that groundwater upwelling and/or seepage toward the modern surface is important in the shaping of its geomorphologic features and sediment outcrops. Along the watershed of the system, groundwater is downward enriched with evaporitic minerals. These minerals precipitate as cement and protect the sediment outcrops from aeolian erosion. The water table is the limiting control on erosion and deposition, and also influences the succession of sediment along the system. The water table further determines the local base level, which controls the deposition within depressions. With increasing humidity at the limit of the capillary fringe, the landscape of the evaporative system is organized according to three sedimentary types: (1) unconsolidated sediment of aqueous and/or aeolian origin that is eroded and transported toward depressions (away from groundwater interactions), (2) consolidated sediment that is also aqueous and/or aeolian in origin and is protected from aeolian erosion by groundwater influence, and (3) sedimentary filling of depressions located within accumulation zones. These sediments are organized along a lateral, basinward profile. Here we show that during periods of relative water table fall, sediments from the watershed prograde to cover the sabkha basin fill. The rise and fall of the water table and the connected base level result in the deposition of genetically-related progradational and retrogradational sequences. We propose that these genetic sequences can be useful to interpret the sequence stratigraphy at three locations on Mars where sedimentary formations were probably controlled by direct groundwater influence: Meridiani Planum, Terby crater, and Gale crater. At Meridiani Planum, the exposed stratigraphic sequence of the Burns formation starts with deposition of dry aeolian sediment derived from a former

  13. Influence of recirculation on the performance of anaerobic sequencing batch biofilm reactor (AnSBBR) treating hypersaline composite chemical wastewater.

    PubMed

    Mohan, S Venkata; Lalit Babu, V; Vijaya Bhaskar, Y; Sarma, P N

    2007-05-01

    Influence of recirculation on the performance of anaerobic sequencing batch biofilm reactor (AnSBBR) was studied in the process of treating hypersaline (total dissolved inorganic solids (TDIS) approximately 26 g/l) and low biodegradable (BOD/COD approximately 0.3) composite chemical wastewater. Significant enhancement in the substrate removal efficiency and biogas yield was observed after introducing the recirculation to the system. Maximum efficiency (COD removal efficiency - 51%; SDR - 3.14 kg COD/cum-day) was observed at recirculation to feed (R/F) ratio of 2 (OLR - 6.15 kg C OD/cum-day; HLR - 2.30 cum (liquid)/cum day; UFV(A) - 0.023 m/h). Subsequent increase of R/F to 3 (OLR - 6.15 kg COD/cum-day; HLR - 3.07cum (liquid)/cum-day; UFV(A) - 0.035 m/h) resulted in reduction in COD removal efficiency (32%; SDR - 1.97 kg COD/cum-day). The enhanced performance of the system due to the introduction of recirculation was attributed to the improvement in the mass transfer between the substrate present in the bulk liquid and the attached biofilm. The hydrodynamic behavior due to recirculation mode of operation reduced the concentration gradient (substrate inhibition) of substrate and reaction by-products (VFA) resulting in mixed flow conditions.

  14. Efficiency influence of exogenous betaine on anaerobic sequencing batch biofilm reactor treating high salinity mustard tuber wastewater.

    PubMed

    He, Qiang; Kong, Xiang-Juan; Chai, Hong-Xiang; Fan, Ming-Yu; Du, Jun

    2012-01-01

    When treating a composite mustard tuber wastewater with high concentrations of salt (about 20 g Cl(-) L(-1)) and organics (about 8000 mg L(-1) COD) by an anaerobic sequencing batch biofilm reactor (ASBBR) in winter, both high salinity and low temperature will inhibit the activity of anaerobic microorganisms and lead to low treatment efficiency. To solve this problem, betaine was added to the influent to improve the activity of the anaerobic sludge, and an experimental study was carried to investigate the influence of betaine on treating high salinity mustard tuber wastewater by the ASBBR. The results show that, when using anaerobic acclimated sludge in the ASBBR, and controlling biofilm density at 50% and water temperature at 8-12 degrees C, the treatment efficiency of the reactor could be improved by adding the betaine at different concentrations. The efficiency reached the highest when the optimal dosage ofbetaine was 0.5 mmol L(-1). The average effluent COD, after stable acclimation, was 4461 mg L(-1). Relative to ASBBR without adding betaine, the activity of the sludge increased significantly. Meanwhile, the dehydrogenase activity of anaerobic microorganisms and the COD removal efficiency were increased by 18.6% and 18.1%, respectively.

  15. Influence of the C/N ratio on the performance of polyhydroxybutyrate (PHB) producing sequencing batch reactors at short SRTs.

    PubMed

    Johnson, Katja; Kleerebezem, Robbert; van Loosdrecht, Mark C M

    2010-04-01

    Many waste streams that are suitable substrates for mixed culture bioplastic (polyhydroxyalkanoate, PHA) production are nutrient limited and may need to be supplemented to allow sufficient growth of PHA accumulating bacteria. The scope of this study was to investigate the necessity of nutrient supplementation for the enrichment of an efficient PHA producing mixed culture. We studied the influence of different degrees of carbon and nitrogen limitation on the performance of an acetate-fed feast-famine sequencing batch reactor (SBR) employed to enrich PHA storing bacteria. The microbial reaction rates in the SBR showed a shift with a change in the limiting substrate: high acetate uptake rates were found in carbon-limited SBRs (medium C/N ratios 6-13.2 Cmol/Nmol), while nitrogen-limited SBRs (medium C/N ratios 15-24 Cmol/Nmol) were characterized by high ammonia uptake rates. Biomass in strongly nitrogen-limited SBRs had higher baseline PHA contents in the SBR, but carbon-limited SBRs resulted usually in biomass with higher maximal PHA storage capacities. The PHA storage capacity in a nitrogen-limited SBR operated at 0.5 d SRT decreased significantly over less than 5 months operation. For the microbial selection and biomass production stage of a PHA production process carbon limitation seems thus favourable and nutrient deficient wastewaters may consequently require supplementation with nutrients for the selection of a stable PHA storing biomass with a high storage capacity.

  16. Solution-state Structure of a DNA Dodecamer Duplex Containing a Cis-syn Thymine Cyclobutane Dimer, the Major UV Photoproduct of DNA.

    SciTech Connect

    McAteer, Kathleen; Jing, Y; Kao, J; Taylor, J S.; Kennedy, Michael A.

    1998-10-09

    The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data.

  17. Multiply charged monopoles in cubic dimer model

    NASA Astrophysics Data System (ADS)

    Ganesh Jaya, Sreejith; Powell, Stephen

    2015-03-01

    The classical cubic dimer model is a 3D statistical mechanical system whose degrees of freedom are dimers that occupy the edges between nearest neighbour vertices of a cubic lattice. Dimer occupancies are subject to the local constraint that every vertex is associated with exactly one dimer. In the presence of an aligning interaction, it is known that the system exhibits an unconventional continuous thermal phase transition from a symmetry broken columnar phase to a Coulomb-phase. The transition is in the NCCP1 universality class, which also describes the Neel-VBS transition in the JQ model and the S =1/2 Heisenberg model with suppression of hedgehog defects. Using Monte-Carlo simulations of a pair of defects in a background of fluctuating dimers, we calculate the scaling exponents for fugacities of monopole defects of charge Q = 2 and 3 at this critical point. Our estimates suggest that Q = 3 monopoles are relevant and could therefore drive the JQ model away from the NCCP1 critical point on a hexagonal lattice.

  18. A dimeric state for PRC2

    PubMed Central

    Davidovich, Chen; Goodrich, Karen J.; Gooding, Anne R.; Cech, Thomas R.

    2014-01-01

    Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Long non-coding RNAs (lncRNAs) can recruit PRC2 to chromatin. Previous studies identified PRC2 subunits in a complex with the apparent molecular weight of a dimer, which might be accounted for by the incorporation of additional protein subunits or RNA rather than PRC2 dimerization. Here we show that reconstituted human PRC2 is in fact a dimer, using multiple independent approaches including analytical size exclusion chromatography (SEC), SEC combined with multi-angle light scattering and co-immunoprecipitation of differentially tagged subunits. Even though it contains at least two RNA-binding subunits, each PRC2 dimer binds only one RNA molecule. Yet, multiple PRC2 dimers bind a single RNA molecule cooperatively. These observations suggest a model in which the first RNA binding event promotes the recruitment of multiple PRC2 complexes to chromatin, thereby nucleating repression. PMID:24992961

  19. The diamagnetic susceptibility of the tubulin dimer.

    PubMed

    Bras, Wim; Torbet, James; Diakun, Gregory P; Rikken, Geert L J A; Diaz, J Fernando

    2014-01-01

    An approximate value of the diamagnetic anisotropy of the tubulin dimer, Δχ dimer, has been determined assuming axial symmetry and that only the α -helices and β -sheets contribute to the anisotropy. Two approaches have been utilized: (a) using the value for the Δχ α for an α -helical peptide bond given by Pauling (1979) and (b) using the previously determined anisotropy of fibrinogen as a calibration standard. The Δχ dimer ≈ 4 × 10(-27) JT(-2) obtained from these measurements are similar to within 20%. Although Cotton-Mouton measurements alone cannot be used to estimate Δχ directly, the value we measured, CMdimer = (1.41 ± 0.03) × 10(-8) T(-2)cm(2)mg(-1), is consistent with the above estimate for Δχ dimer. The method utilized for the determination of the tubulin dimer diamagnetic susceptibility is applicable to other proteins and macromolecular assemblies as well.

  20. Linking in domain-swapped protein dimers

    PubMed Central

    Baiesi, Marco; Orlandini, Enzo; Trovato, Antonio; Seno, Flavio

    2016-01-01

    The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G′, termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G′| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties. PMID:27659606

  1. Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

    PubMed Central

    Calgaro, Marcos R.; Neto, Mario de Oliveira; Figueira, Ana Carolina M.; Santos, Maria A.M.; Portugal, Rodrigo V.; Guzzi, Carolina A.; Saidemberg, Daniel M.; Bleicher, Lucas; Vernal, Javier; Fernandez, Pablo; Terenzi, Hernán; Palma, Mario Sergio; Polikarpov, Igor

    2007-01-01

    The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen–deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B–dependent transcription exercised by GR in cells. PMID:17600153

  2. Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.

    PubMed

    Ohnishi, Satoshi; Tochio, Naoya; Tomizawa, Tadashi; Akasaka, Ryogo; Harada, Takushi; Seki, Eiko; Sato, Manami; Watanabe, Satoru; Fujikura, Yukiko; Koshiba, Seizo; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

    2008-09-01

    The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain.

  3. LexA repressor forms stable dimers in solution. The role of specific dna in tightening protein-protein interactions.

    PubMed

    Mohana-Borges, R; Pacheco, A B; Sousa, F J; Foguel, D; Almeida, D F; Silva, J L

    2000-02-18

    Cooperativity in the interactions among proteins subunits and DNA is crucial for DNA recognition. LexA repressor was originally thought to bind DNA as a monomer, with cooperativity leading to tighter binding of the second monomer. The main support for this model was a high value of the dissociation constant for the LexA dimer (micromolar range). Here we show that the protein is a dimer at nanomolar concentrations under different conditions. The reversible dissociation of LexA dimer was investigated by the effects of hydrostatic pressure or urea, using fluorescence emission and polarization to monitor the dissociation process. The dissociation constant lies in the picomolar range (lower than 20 pM). LexA monomers associate with an unusual large volume change (340 ml/mol), indicating the burial of a large surface area upon dimerization. Whereas nonspecific DNA has no stabilizing effect, specific DNA induces tightening of the dimer and a 750-fold decrease in the K(d). In contrast to the previous model, a tight dimer rather than a monomer is the functional repressor. Accordingly, the LexA dimer only loses its ability to recognize a specific DNA sequence by RecA-induced autoproteolysis. Our work provides insights into the linkage between protein-protein interactions, DNA recognition, and DNA repair.

  4. Somatic homologous recombination in planta: the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects.

    PubMed

    Swoboda, P; Hohn, B; Gal, S

    1993-02-01

    We have previously described a non-selective method for scoring somatic recombination in the genome of whole plants. The recombination substrate consists of a defective partial dimer of Cauliflower Mosaic Virus (CaMV) sequences, which can code for production of viable virus only upon homologous recombination; this leads to disease symptoms on leaves. Brassica napus plants (rapeseed) harbouring the recombination substrate as a transgene were used to examine the time in plant development at which recombination takes place. The analysis of three transgene loci revealed recombination frequencies specific for each locus. Recombination frequencies were increased if more than one transgene locus was present per genome, either in allelic (homozygosity of the transgene locus) or in non-allelic positions. In both cases, the overall recombination frequency was found to be elevated to approximately the sum of the frequencies for the individual transgene loci or slightly higher, suggesting that the respective transgene loci behave largely independently of each other. For all plants tested (single locus, two or multiple loci) maximal recombination frequencies were of the order of 10(-6) events per cell division.

  5. Dimerization and DNA recognition rules of mithramycin and its analogues

    PubMed Central

    Weidenbach, Stevi; Hou, Caixia; Chen, Jhong-Min; Tsodikov, Oleg V.; Rohr, Jürgen

    2016-01-01

    The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me2+)-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM binds G/C-rich DNA, the exact DNA recognition rules that would allow one to map MTM binding sites remain incompletely understood. Towards this goal, we quantitatively investigated dimerization of MTM and several of its analogues, MTM SDK (for Short side chain, DiKeto), MTM SA-Trp (for Short side chain and Acid), MTM SA-Ala, and a biosynthetic precursor premithramycin B (PreMTM B), and measured the binding affinities of these molecules to DNA oligomers of different sequences and structural forms at physiological salt concentrations. We show that MTM and its analogues form stable dimers even in the absence of DNA. All molecules, except for PreMTM B, can bind DNA with the following rank order of affinities (strong to weak): MTM = MTM SDK > MTM SA-Trp > MTM SA-Ala. An X(G/C)(G/C)X motif, where X is any base, is necessary and sufficient for MTM binding to DNA, without a strong dependence on DNA conformation. These recognition rules will aid in mapping MTM sites across different promoters towards development of MTM analogues as useful anticancer agents. PMID:26760230

  6. TMDOCK: An Energy-Based Method for Modeling α-Helical Dimers in Membranes.

    PubMed

    Lomize, Andrei L; Pogozheva, Irina D

    2017-02-03

    TMDOCK is a novel computational method for the modeling of parallel homodimers formed by transmembrane (TM) α-helices. Three-dimensional (3D) models of dimers are generated by threading a target amino acid sequence through several structural templates, followed by local energy minimization. This is the first method that identifies helix dimerization modes and ranks them based on the calculated free energy of α-helix association. Free energy components include van der Waals, hydrogen bonding, and dipole interactions; side-chain conformational entropy; and solvation energy in the anisotropic lipid environment. TMDOCK reproduced 26 experimental dimeric structures formed by TM α-helices of 21 single-pass membrane proteins (including 4 mutants) with Cα atom rmsd from 1.0 to 3.3Å. Assessment of dimerization heterogeneity of these TM domains demonstrated that 7 of them have a unique dimer structure, 12 have at least 2 alternative conformations, and 2 have a large number of different association modes. All unique experimental structures of proteins from the first group and eight structures from the second group were reproduced in computations as top-ranked models. A fast version of the method is available through the web server (http://membranome.org/tm_server.php).

  7. A deoxyribozyme that harnesses light to repair thymine dimers in DNA.

    PubMed

    Chinnapen, Daniel J-F; Sen, Dipankar

    2004-01-06

    In vitro selection was used to investigate whether nucleic acid enzymes are capable of catalyzing photochemical reactions. The reaction chosen was photoreactivation of thymine cyclobutane dimers in DNA by using serotonin as cofactor and light of wavelengths longer than the absorption spectrum of DNA. Curiously, the dominant single-stranded DNA sequence selected, UV1A, was found to repair its internal thymine dimer substrate efficiently even in the absence of serotonin or any other cofactor. UV1C, a 42-nucleotide fragment of UV1A, repaired the thymine dimer substrate in trans (k(cat)/k(uncat) = 2.5 x 10(4)), showing optimal activity with 305 nm light and thus resembling naturally occurring photolyase enzymes. Mechanistic investigation of UV1C indicated that its catalytic role likely exceeded the mere positioning of the substrate in a conformation favorable for photoreactivation. A higher-order structure, likely a quadruplex, formed by specific guanine bases within the deoxyribozyme, was implicated as serving as a light-harvesting antenna, with photoreactivation of the thymine dimer proceeding possibly via electron donation from an excited guanine base. In a primordial "RNA world," self-replicating nucleic acid populations may have been vulnerable to deactivation via UV light-mediated pyrimidine dimer formation. Photolyase nucleic acid enzymes such as the one described here could thus have played a role in preserving the integrity of such an RNA world.

  8. Partition-DFT on the water dimer.

    PubMed

    Gómez, Sara; Nafziger, Jonathan; Restrepo, Albeiro; Wasserman, Adam

    2017-02-21

    As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium Cs-character to C2h-character as the distance between the two oxygen atoms of the dimer decreases below RO-O∼2.5 Å. For a range of RO-O between 1 and 5 Å, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the Cs geometry for all RO-O. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.

  9. Slab photonic crystals with dimer colloid bases

    SciTech Connect

    Riley, Erin K.; Liddell Watson, Chekesha M.

    2014-06-14

    The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd, even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.

  10. Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9

    PubMed Central

    Geraldo, Marcos Tadeu; Valente, Guilherme Targino; Nakajima, Rafael Takahiro; Martins, Cesar

    2016-01-01

    Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts. PMID:27196604

  11. Integrable oscillator type and Schrödinger type dimers

    NASA Astrophysics Data System (ADS)

    Khare, Avinash; Saxena, Avadh

    2017-02-01

    A PT-symmetric dimer is a two-site nonlinear oscillator dimer or a two-site nonlinear Schrödinger dimer where one site loses and the other site gains energy at the same rate. We present a wide class of integrable oscillator type dimers whose Hamiltonian is of arbitrary even order. Further, we also present a wide class of integrable nonlinear Schrödinger type dimers where again the Hamiltonian is of arbitrary even order. Finally, we consider a recently discussed complex dimer model and point out a few integrable cases in that model.

  12. Graded-index optical dimer formed by optical force.

    PubMed

    Akbarzadeh, Alireza; Koschny, Thomas; Kafesaki, Maria; Economou, Eleftherios N; Soukoulis, Costas M

    2016-05-30

    We propose an optical dimer formed from two spherical lenses bound by the pressure that light exerts on matter. With the help of the method of force tracing, we find the required graded-index profiles of the lenses for the existence of the dimer. We study the dynamics of the opto-mechanical interaction of lenses under the illumination of collimated light beams and quantitatively validate the performance of proposed dimer. We also examine the stability of dimer due to the lateral misalignments and we show how restoring forces bring the dimer into lateral equilibrium. The dimer can be employed in various practical applications such as optical manipulation, sensing and imaging.

  13. Rubidium dimer destruction by a diode laser

    SciTech Connect

    Ban, T.; Aumiler, D.; Pichler, G.

    2005-02-01

    We observed rubidium dimer destruction by excitation of rubidium vapor with diode laser light tuned across the Rb D{sub 2} resonance line in a 2400 GHz tuning interval. The destruction was measured for rubidium atom concentrations in the (1-9)x10{sup 16} cm{sup -3} range, pump beam power up to 43 mW, and with a 5 Torr of the helium buffer gas. We discuss the physical mechanisms involved and specify the molecular pathways which may effectively lead to the observed dimer destruction.

  14. Properties of the two-dimensional heterogeneous Lennard-Jones dimers: An integral equation study

    NASA Astrophysics Data System (ADS)

    Urbic, Tomaz

    2016-11-01

    Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions and the thermodynamic properties. Obtained results are compared to Monte Carlo simulation data. The critical parameters for selected types of dimers were also estimated and the influence of the Lennard-Jones parameters was studied. We have also tested the correctness of the site-site integral equation theory using different closures.

  15. Properties of the two-dimensional heterogeneous Lennard-Jones dimers: An integral equation study.

    PubMed

    Urbic, Tomaz

    2016-11-21

    Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions and the thermodynamic properties. Obtained results are compared to Monte Carlo simulation data. The critical parameters for selected types of dimers were also estimated and the influence of the Lennard-Jones parameters was studied. We have also tested the correctness of the site-site integral equation theory using different closures.

  16. Regulation of UVR8 photoreceptor dimer/monomer photo-equilibrium in Arabidopsis plants grown under photoperiodic conditions.

    PubMed

    Findlay, Kirsten M W; Jenkins, Gareth I

    2016-08-01

    The UV RESISTANCE LOCUS 8 (UVR8) photoreceptor specifically mediates photomorphogenic responses to UV-B. Photoreception induces dissociation of dimeric UVR8 into monomers to initiate responses. However, the regulation of dimer/monomer status in plants growing under photoperiodic conditions has not been examined. Here we show that UVR8 establishes a dimer/monomer photo-equilibrium in plants growing in diurnal photoperiods in both controlled environments and natural daylight. The photo-equilibrium is determined by the relative rates of photoreception and dark-reversion to the dimer. Experiments with mutants in REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 (RUP1) and RUP2 show that these proteins are crucial in regulating the photo-equilibrium because they promote reversion to the dimer. In plants growing in daylight, the UVR8 photo-equilibrium is most strongly correlated with low ambient fluence rates of UV-B (up to 1.5 μmol m(-2) s(-1) ), rather than higher fluence rates or the amount of photosynthetically active radiation. In addition, the rate of reversion of monomer to dimer is reduced at lower temperatures, promoting an increase in the relative level of monomer at approximately 8-10 °C. Thus, UVR8 does not behave like a simple UV-B switch under photoperiodic growth conditions but establishes a dimer/monomer photo-equilibrium that is regulated by UV-B and also influenced by temperature.

  17. Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase.

    PubMed

    Urulangodi, Madhusoodanan; Dhanaraju, Rajkumar; Gupta, Kanchan; Roy, Rajendra P; Bujnicki, Janusz M; Rao, Desirazu N

    2016-01-01

    EcoP15I DNA methyltransferase (M.EcoP15I) recognizes short asymmetric sequence, 5'-CAGCAG-3', and methylates the second adenine only on one strand of the double-stranded DNA (dsDNA). In vivo, this methylation is sufficient to protect the host DNA from cleavage by the cognate restriction endonuclease, R.EcoP15I, because of the stringent cleavage specificity requirements. Biochemical and structural characterization support the notion that purified M.EcoP15I exists and functions as dimer. However, the exact role of dimerization in M.EcoP15I reaction mechanism remains elusive. Here we engineered M.EcoP15I to a stable monomeric form and studied the role of dimerization in enzyme catalyzed methylation reaction. While the monomeric form binds single-stranded DNA (ssDNA) containing the recognition sequence it is unable to methylate it. Further we show that, while the monomeric form has AdoMet binding and Mg(2+) binding motifs intact, optimal dsDNA binding required for methylation is dependent on dimerization. Together, our biochemical data supports a unique subunit organization for M.EcoP15I to catalyze the methylation reaction.

  18. RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus.

    PubMed

    Ishimaru, Daniella; Plant, Ewan P; Sims, Amy C; Yount, Boyd L; Roth, Braden M; Eldho, Nadukkudy V; Pérez-Alvarado, Gabriela C; Armbruster, David W; Baric, Ralph S; Dinman, Jonathan D; Taylor, Deborah R; Hennig, Mirko

    2013-02-01

    Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem-loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through 'kissing' loop-loop interactions. We also show that loop-loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop-loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.

  19. Properties of the Lennard-Jones dimeric fluid in two dimensions: an integral equation study.

    PubMed

    Urbic, Tomaz; Dias, Cristiano L

    2014-03-07

    The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

  20. Formation of covalent di-tyrosine dimers in recombinant α-synuclein

    PubMed Central

    van Maarschalkerweerd, A; Pedersen, MN; Peterson, H; Nilsson, M; Nguyen, TTT; Skamris, T; Rand, K; Vetri, V; Langkilde, AE; Vestergaard, B

    2015-01-01

    Parkinson's disease is associated with fibril deposition in the diseased brain. Misfolding events of the intrinsically disordered synaptic protein α-synuclein are suggested to lead to the formation of transient oligomeric and cytotoxic species. The etiology of Parkinson's disease is further associated with mitochondrial dysfunction and formation of reactive oxygen species. Oxidative stress causes chemical modification of native α-synuclein, plausibly further influencing misfolding events. Here, we present evidence for the spontaneous formation of covalent di-tyrosine α-synuclein dimers in standard recombinant protein preparations, induced without extrinsic oxidative or nitrative agents. The dimers exhibit no secondary structure but advanced SAXS studies reveal an increased structural definition, resulting in a more hydrophobic micro-environment than the highly disordered monomer. Accordingly, monomers and dimers follow distinct fibrillation pathways. PMID:28232892

  1. Properties of the Lennard-Jones dimeric fluid in two dimensions: An integral equation study

    SciTech Connect

    Urbic, Tomaz; Dias, Cristiano L.

    2014-03-07

    The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

  2. A new lignan dimer from Mallotus philippensis.

    PubMed

    Mai, Nguyen Thi; Cuong, Nguyen Xuan; Thao, Nguyen Phuong; Nam, Nguyen Hoai; Khoi, Nguyen Huu; Minh, Chau Van; Heyden, Yvan Vander; Thuan, Ngo Thi; Tuyen, Nguyen Van; Quetin-Leclercq, Joëlle; Kiem, Phan Van

    2010-03-01

    A new lignan dimer, bilariciresinol (1), was isolated from the leaves of Mallotus philippensis, along with platanoside (2), isovitexin (3), dihydromyricetin (4), bergenin (5), 4-O-galloylbergenin (6), and pachysandiol A (7). Their structures were elucidated by spectroscopic experiments including 1D and 2D NMR and FTICR-MS.

  3. Functional Asymmetry in Kinesin and Dynein Dimers

    PubMed Central

    Rank, Katherine C.; Rayment, Ivan

    2012-01-01

    Active transport along the microtubule lattice is a complex process that involves both the Kinesin and Dynein superfamily of motors. Transportation requires sophisticated regulation much of which occurs through the motor’s tail domain. However, a significant portion of this regulation also occurs through structural changes that arise in the motor and the microtubule upon binding. The most obvious structural change being the manifestation of asymmetry. To a first approximation in solution, kinesin dimers exhibit two-fold symmetry, and microtubules, helical symmetry. The higher symmetries of both the kinesin dimers and microtubule lattice are lost on formation of the kinesin-microtubule complex. Loss of symmetry has functional consequences such as an asymmetric hand-over-hand mechanism in plus-end directed kinesins, asymmetric microtubule binding in the Kinesin-14 family, spatially biased stepping in dynein, and cooperative binding of additional motors to the microtubule. This review focuses on how the consequences of asymmetry affect regulation of motor heads within a dimer, dimers within an ensemble of motors, and suggests how these asymmetries may affect regulation of active transport within the cell. PMID:23066835

  4. Amplitude enhancement by a gold dimer

    NASA Astrophysics Data System (ADS)

    Hong, Xin; Wang, Jingxin; Jin, Zheng

    2016-10-01

    The unique optical properties such as brightness, non-bleaching, good bio-compatibility make gold particles ideal label candidates for molecular probes. Due to the strongly enhanced field, aggregation of gold nanoparticles finds themselves plenty of applications in bio-imaging. But limited by its small cross-section associated with nanometer sized particle, it is a big challenge to employ it in a single molecular detection. The field enhancement results from the effect of plasmonic coupling between two closely attached gold nanoparticle under the right excitation condition. With the aim to apply the gold dimer probe to find the molecules in our recently established optical detection method, we compared of the amplitude enhancement by the dimer relative to a single particle. The amplitude distribution under a highly focused illumination objective was calculated, whose results suggest that at the optimized excitation condition, the local field can be enhanced 190 fold. In consequence, experimental detection was carried out. Gold dimers were linked together by the hybridization of two single chain DNAs. Dimer and single particle probes were mixed together in one detection. Overwhelming contrast between these two kinds of probes were clearly exhibited in the experimental detection image. This method can provide a way to a high specific detection in early diagnosis.

  5. On the intermolecular Coulombic decay of singly and doubly ionized states of water dimer.

    PubMed

    Stoychev, Spas D; Kuleff, Alexander I; Cederbaum, Lorenz S

    2010-10-21

    A semiquantitative study of the intermolecular Coulombic decay (ICD) of singly and doubly ionized water dimer has been carried out with the help of ab initio computed ionization spectra and potential energy curves (PECs). These PECs are particular cuts through the (H(2)O)(2), (H(2)O)(2) (+), and (H(2)O)(2) (++) hypersurfaces along the distance between the two oxygen atoms. A comparison with the recently published experimental data for the ICD in singly ionized water dimers [T. Jahnke, H. Sann, T. Havermeier et al., Nat. Phys. 6, 139 (2010)] and in large water clusters [M. Mucke, M. Braune, S. Barth et al., Nat. Phys. 6, 143 (2010)] shows that such a simplified description in which the internal degrees of freedom of the water molecules are frozen gives surprisingly useful results. Other possible decay channels of the singly ionized water dimer are also investigated and the influence of the H-atom participating in the hydrogen bond on the spectra of the proton-donor and proton-acceptor molecules in the dimer is discussed. Importantly, the decay processes of one-site dicationic states of water dimer are discussed and an estimate of the ICD-electron spectra is made. More than 33% of the dications produced by Auger decay are found to undergo ICD. The qualitative results show that the ICD following Auger decay in water is also expected to be an additional source of low-energy electrons proven to be extremely important for causing damages to living tissues.

  6. DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection

    PubMed Central

    Seow, Nianjia; Tan, Yen Nee; Yung, Lin-Yue Lanry; Su, Xiaodi

    2015-01-01

    We have developed a unique DNA-assembled gold nanoparticles (AuNPs) dimer for dynamic light scattering (DLS) sensing of transcription factors, exemplified by estrogen receptor (ER) that binds specifically to a double-stranded (ds) DNA sequence containing estrogen response element (ERE). Here, ERE sequence is incorporated into the DNA linkers to bridge the AuNPs dimer for ER binding. Coupled with DLS, this AuNP dimer-based DLS detection system gave distinct readout of a single ‘complex peak’ in the presence of the target molecule (i.e., ER). This unique signature marked the first time that such nanostructures can be used to study transcription factor-DNA interactions, which DLS alone cannot do. This was also unlike previously reported AuNP-DLS assays that gave random and broad distribution of particles size upon target binding. In addition, the ERE-containing AuNP dimers could also suppress the light-scattering signal from the unbound proteins and other interfering factors (e.g., buffer background), and has potential for sensitive detection of target proteins in complex biological samples such as cell lysates. In short, the as-developed AuNP dimer probe coupled with DLS is a simple (mix and test), rapid (readout in ~5 min) and sensitive (low nM levels of ER) platform to detect sequence-specific protein-DNA binding event. PMID:26678946

  7. DNA-Directed Assembly of Nanogold Dimers: A Unique Dynamic Light Scattering Sensing Probe for Transcription Factor Detection

    NASA Astrophysics Data System (ADS)

    Seow, Nianjia; Tan, Yen Nee; Yung, Lin-Yue Lanry; Su, Xiaodi

    2015-12-01

    We have developed a unique DNA-assembled gold nanoparticles (AuNPs) dimer for dynamic light scattering (DLS) sensing of transcription factors, exemplified by estrogen receptor (ER) that binds specifically to a double-stranded (ds) DNA sequence containing estrogen response element (ERE). Here, ERE sequence is incorporated into the DNA linkers to bridge the AuNPs dimer for ER binding. Coupled with DLS, this AuNP dimer-based DLS detection system gave distinct readout of a single ‘complex peak’ in the presence of the target molecule (i.e., ER). This unique signature marked the first time that such nanostructures can be used to study transcription factor-DNA interactions, which DLS alone cannot do. This was also unlike previously reported AuNP-DLS assays that gave random and broad distribution of particles size upon target binding. In addition, the ERE-containing AuNP dimers could also suppress the light-scattering signal from the unbound proteins and other interfering factors (e.g., buffer background), and has potential for sensitive detection of target proteins in complex biological samples such as cell lysates. In short, the as-developed AuNP dimer probe coupled with DLS is a simple (mix and test), rapid (readout in ~5 min) and sensitive (low nM levels of ER) platform to detect sequence-specific protein-DNA binding event.

  8. Magnetic anisotropy of heteronuclear dimers in the gas phase and supported on graphene: relativistic density-functional calculations.

    PubMed

    Błoński, Piotr; Hafner, Jürgen

    2014-04-09

    The structural and magnetic properties of mixed PtCo, PtFe, and IrCo dimers in the gas phase and supported on a free-standing graphene layer have been calculated using density-functional theory, both in the scalar-relativistic limit and self-consistently including spin-orbit coupling. The influence of the strong magnetic moments of the 3d atoms on the spin and orbital moments of the 5d atoms, and the influence of the strong spin-orbit coupling contributed by the 5d atom on the orbital moments of the 3d atoms have been studied in detail. The magnetic anisotropy energy is found to depend very sensitively on the nature of the eigenstates in the vicinity of the Fermi level, as determined by band filling, exchange splitting and spin-orbit coupling. The large magnetic anisotropy energy of free PtCo and IrCo dimers relative to the easy direction parallel to the dimer axis is coupled to a strong anisotropy of the orbital magnetic moments of the Co atom for both dimers, and also on the Ir atom in IrCo. In contrast the PtFe dimer shows a weak perpendicular anisotropy and only small spin and orbital anisotropies of opposite sign on the two atoms. For dimers supported on graphene, the strong binding within the dimer and the stronger interaction of the 3d atom with the substrate stabilizes an upright geometry. Spin and orbital moments on the 3d atom are strongly quenched, but due to the weaker binding within the dimer the properties of the 5d atom are more free-atom-like with increased spin and orbital moments. The changes in the magnetic moment are reflected in the structure of the electronic eigenstates near the Fermi level, for all three dimers the easy magnetic direction is now parallel to the dimer axis and perpendicular to the graphene layer. The already very large magnetic anisotropy energy (MAE) of IrCo is further enhanced by the interaction with the support, the MAE of PtFe changes sign, and that of the PtCo dimer is reduced. These changes are discussed in relation to

  9. Localized light-induced protein dimerization in living cells using a photocaged dimerizer

    PubMed Central

    Ballister, Edward R.; Aonbangkhen, Chanat; Mayo, Alyssa M.; Lampson, Michael A.; Chenoweth, David M.

    2015-01-01

    Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein–protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations. PMID:25400104

  10. Analysis of motion tracking in echocardiographic image sequences: influence of system geometry and point-spread function.

    PubMed

    Touil, Basma; Basarab, Adrian; Delachartre, Philippe; Bernard, Olivier; Friboulet, Denis

    2010-03-01

    This paper focuses on motion tracking in echocardiographic ultrasound images. The difficulty of this task is related to the fact that echographic image formation induces decorrelation between the underlying motion of tissue and the observed speckle motion. Since Meunier's seminal work, this phenomenon has been investigated in many simulation studies as part of speckle tracking or optical flow-based motion estimation techniques. Most of these studies modeled image formation using a linear convolution approach, where the system point-spread function (PSF) was spatially invariant and the probe geometry was linear. While these assumptions are valid over a small spatial area, they constitute an oversimplification when a complete image is considered. Indeed, echocardiographic acquisition geometry relies on sectorial probes and the system PSF is not perfectly invariant, even if dynamic focusing is performed. This study investigated the influence of sectorial geometry and spatially varying PSF on speckle tracking. This was done by simulating a typical 64 elements, cardiac probe operating at 3.5 MHz frequency, using the simulation software Field II. This simulation first allowed quantification of the decorrelation induced by the system between two images when simple motion such as translation or incompressible deformation was applied. We then quantified the influence of decorrelation on speckle tracking accuracy using a conventional block matching (BM) algorithm and a bilinear deformable block matching (BDBM) algorithm. In echocardiography, motion estimation is usually performed on reconstructed images where the initial sectorial (i.e., polar) data are interpolated on a cartesian grid. We therefore studied the influence of sectorial acquisition geometry, by performing block matching on cartesian and polar data. Simulation results show that decorrelation is spatially variant and depends on the position of the region where motion takes place relative to the probe. Previous

  11. Dimerization of visual pigments in vivo

    PubMed Central

    Zhang, Tao; Cao, Li-Hui; Kumar, Sandeep; Enemchukwu, Nduka O.; Zhang, Ning; Lambert, Alyssia; Zhao, Xuchen; Jones, Alex; Wang, Shixian; Dennis, Emily M.; Fnu, Amrita; Ham, Sam; Rainier, Jon; Yau, King-Wai; Fu, Yingbin

    2016-01-01

    It is a deeply engrained notion that the visual pigment rhodopsin signals light as a monomer, even though many G protein-coupled receptors are now known to exist and function as dimers. Nonetheless, recent studies (albeit all in vitro) have suggested that rhodopsin and its chromophore-free apoprotein, R-opsin, may indeed exist as a homodimer in rod disk membranes. Given the overwhelmingly strong historical context, the crucial remaining question, therefore, is whether pigment dimerization truly exists naturally and what function this dimerization may serve. We addressed this question in vivo with a unique mouse line (S-opsin+Lrat−/−) expressing, transgenically, short-wavelength–sensitive cone opsin (S-opsin) in rods and also lacking chromophore to exploit the fact that cone opsins, but not R-opsin, require chromophore for proper folding and trafficking to the photoreceptor’s outer segment. In R-opsin’s absence, S-opsin in these transgenic rods without chromophore was mislocalized; in R-opsin’s presence, however, S-opsin trafficked normally to the rod outer segment and produced functional S-pigment upon subsequent chromophore restoration. Introducing a competing R-opsin transmembrane helix H1 or helix H8 peptide, but not helix H4 or helix H5 peptide, into these transgenic rods caused mislocalization of R-opsin and S-opsin to the perinuclear endoplasmic reticulum. Importantly, a similar peptide-competition effect was observed even in WT rods. Our work provides convincing evidence for visual pigment dimerization in vivo under physiological conditions and for its role in pigment maturation and targeting. Our work raises new questions regarding a potential mechanistic role of dimerization in rhodopsin signaling. PMID:27462111

  12. Dimer site-bond percolation on a triangular lattice

    NASA Astrophysics Data System (ADS)

    Ramirez, L. S.; De la Cruz Félix, N.; Centres, P. M.; Ramirez-Pastor, A. J.

    2017-02-01

    A generalization of the site-percolation problem, in which pairs of neighbor sites (site dimers) and bonds are independently and randomly occupied on a triangular lattice, has been studied by means of numerical simulations. Motivated by considerations of cluster connectivity, two distinct schemes (denoted as S{\\cap}B and S{\\cup}B ) have been considered. In S{\\cap}B (S{\\cup}B ), two points are said to be connected if a sequence of occupied sites and (or) bonds joins them. Numerical data, supplemented by analysis using finite-size scaling theory, were used to determine (i) the complete phase diagram of the system (phase boundary between the percolating and nonpercolating regions), and (ii) the values of the critical exponents (and universality) characterizing the phase transition occurring in the system.

  13. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair.

    PubMed

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  14. Tetramer-dimer equilibrium of oxyhemoglobin mutants determined from auto-oxidation rates.

    PubMed Central

    Griffon, N.; Baudin, V.; Dieryck, W.; Dumoulin, A.; Pagnier, J.; Poyart, C.; Marden, M. C.

    1998-01-01

    fraction dimer will influence the observed oxidation rate. PMID:9541399

  15. Effects of Dosage Sequence on the Efficacy of Nonfumigant Nematicides, Plantain Yields, and Nematode Seasonal Fluctuations as influenced by Rainfall.

    PubMed

    Badra, T; Caveness, F E

    1983-10-01

    Four nonfumigant nematicides applied three times during the wet season were used to study dosage sequence and nematicide effectiveness. Control of Helicotylenchus multicinctus (Cobb) Thorne and Meloidogyne javanica (Treub) Chitwood increased plantain (Musa AAB) yields. The nematicide (aldicarb, carbofuran, oxamyl, and miral) performance and yield response varied with dosage sequences. Applications of 2, 3, and 2 g ai/tree in March, July, and October (sequence I), respectively, gave greater control of M. javanica than did applications of 3, 2, and 2 g ai/tree in March, June, and September (sequence II), respectively. However, the high initial dose sequence was effective against H. multicinctus. Persistence of the different nematicides differed over the 14-month experimental period. Miral, aldicarb, and carbofuran were the most effective treatments against either species by the end of the wet and dry seasons. Dry season residual nematode populations were significantly lower in nematicide treated than in control plots. Yield increases over controls were 96.9, 90.1, 78.4, and 70.1% for carbofuran applied by sequence II, aldicarb by II and I, and oxantyl by II, respectively. Nematode populations directly fluctuated with rainfall and dropped to low (H. multicinctus) or to undetectable (M. javanica juveniles) levels during the dry season. Of the two nematodes studied, the more serious pest to plantain was H. multicinctus; it was tolerant to drought and survived the dry season in untreated soils.

  16. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    SciTech Connect

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N.

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  17. NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome

    PubMed Central

    Keane, Sarah C.; Van, Verna; Frank, Heather M.; Sciandra, Carly A.; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F.

    2016-01-01

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5′-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5′-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5′ (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones. PMID:27791166

  18. On the Pyrazine and Pyrazine-Pyrimidine Dimers.

    DTIC Science & Technology

    1986-06-01

    Lennard - Jones -hydrogen-bonding (LJ-HB) potential energy calculations. The pyrazine isotopic hetero- and homo-dimers possess nearly identical spectra with the exception that the perpendicular dimer features are displaced to the red by approx. 11 cm. Exchange or exciton interactions in this system are vanishingly small (less than 1/cm). The geometrics suggested by the isotopically substituted pyrazine dimer spectra are the same as those found for the pyrazine-h sub 4 homo-dimer: a parallel planar hydrogen bonded and a perpendicular dimer. The pyrazine-h sub 4 and pyrazine-h

  19. Pyrimidine dimer formation and repair in human skin

    SciTech Connect

    Sutherland, B.M.; Harber, L.C.; Kochevar, I.E.

    1980-09-01

    Cyclobutyl pyrimidine dimers have been detected in the DNA of human skin following in vivo irradiation with suberythermal doses of ultraviolet (UV) radiation from FS-20 sun lamp fluorescent tubes. Dimers were assayed by treatment of extracted DNA with Micrococus luteus UV-specific endonuclease, alkaline agarose electrophoresis, and ethidum bromide staining. This technique, in contrast to conventional dimer assays, can be used with nonradioactive DNA and is optimal at low UV light doses. These data suggest that some dimer disappearance by excision repair occurs within 20 min of UV irradiation and that photoreactivation of dimers can make a contribution to the total repair process.

  20. Biomimetic Total Syntheses of (-)-Leucoridines A and C through the Dimerization of (-)-Dihydrovalparicine.

    PubMed

    Kokkonda, Praveen; Brown, Keaon R; Seguin, Trevor J; Wheeler, Steven E; Vaddypally, Shivaiah; Zdilla, Michael J; Andrade, Rodrigo B

    2015-10-19

    Concise biomimetic syntheses of the Strychnos-Strychnos-type bis-indole alkaloids (-)-leucoridine A (1) and C (2) were accomplished through the biomimetic dimerization of (-)-dihydrovalparicine (3). En route to 3, the known alkaloids (+)-geissoschizoline (8) and (-)-dehydrogeissoschizoline (10) were also prepared. DFT calculations were employed to elucidate the mechanism, which favors a stepwise aza-Michael/spirocyclization sequence over the alternate hetero-Diels-Alder cycloaddition reaction.

  1. Dimerization and enzymatic activity of fungal 17β-hydroxysteroid dehydrogenase from the short-chain dehydrogenase/reductase superfamily

    PubMed Central

    Kristan, Katja; Deluca, Dominga; Adamski, Jerzy; Stojan, Jure; Rižner, Tea Lanišnik

    2005-01-01

    Background 17β-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17β-HSDcl) is a member of the short-chain dehydrogenase/reductase (SDR) superfamily. SDR proteins usually function as dimers or tetramers and 17β-HSDcl is also a homodimer under native conditions. Results We have investigated here which secondary structure elements are involved in the dimerization of 17β-HSDcl and examined the importance of dimerization for the enzyme activity. Sequence similarity with trihydroxynaphthalene reductase from Magnaporthe grisea indicated that Arg129 and His111 from the αE-helices interact with the Asp121, Glu117 and Asp187 residues from the αE and αF-helices of the neighbouring subunit. The Arg129Asp and His111Leu mutations both rendered 17β-HSDcl monomeric, while the mutant 17β-HSDcl-His111Ala was dimeric. Circular dichroism spectroscopy analysis confirmed the conservation of the secondary structure in both monomers. The three mutant proteins all bound coenzyme, as shown by fluorescence quenching in the presence of NADP+, but both monomers showed no enzymatic activity. Conclusion We have shown by site-directed mutagenesis and structure/function analysis that 17β-HSDcl dimerization involves the αE and αF helices of both subunits. Neighbouring subunits are connected through hydrophobic interactions, H-bonds and salt bridges involving amino acid residues His111 and Arg129. Since the substitutions of these two amino acid residues lead to inactive monomers with conserved secondary structure, we suggest dimerization is a prerequisite for catalysis. A detailed understanding of this dimerization could lead to the development of compounds that will specifically prevent dimerization, thereby serving as a new type of inhibitor. PMID:16359545

  2. Excitonic interaction in the fluorene dimer

    NASA Astrophysics Data System (ADS)

    Wessel, John; Beck, Steven; Highstrete, Clark

    1994-12-01

    The fluorene van der Waals dimer exhibits a complex origin spectrum. This region has been studied by resonance two-photon ionization and by fluorescence excitation spectroscopies. The spectra can be interpreted on the basis of intermediate strength exciton coupling, in which the electronic interaction is comparable to the van der Waals vibrational energies. The spectra are reasonably well described by two distorted adiabatic potential surfaces, which correspond to the two excitonic components of the origin system. A single Franck-Condon active intermolecular mode provides a reasonable description of the system, however the potentials have significant cubic and quartic contributions. Non-Born-Oppenheimer nuclear momentum coupling is present and intermodal (IVR) interactions are observed, even for intermolecular modes as low as v=1. The results are remarkably different from prior observations of excitonic structure in other systems, providing a detailed picture of coupling between electronic and intermolecular motion in a van der Waals dimer.

  3. Electronic Transitions of Palladium and Vanadium Dimer

    NASA Astrophysics Data System (ADS)

    Qian, Yue; Ng, Y. W.; Cheung, A. S.-C.

    2013-06-01

    The laser induced fluorescence (LIF) spectrum of palladium dimer (Pd_{2}) in the visible region between 480 and 700 nm has been studied. Five vibrational bands were recorded and analyzed; they are assigned to a ^{3} Π _{g} - X^{3} Σ _{u} ^{+} system. The vibrational frequency of the ground X^{3} Σ _{u} ^{+} state has been determined to be 211.4 cm^{-1}. This is the first experimental observation of the LIF spectrum of Pd_{2}. In addition, the LIF spectrum of vanadium dimer (V_{2}) has also been studied; several new transition band systems were observed in the wavelength between 480 and 530 nm. The analysis of the spectra recorded for these two molecules will be presented.

  4. Minimization of a Protein–DNA Dimerizer

    PubMed Central

    Stafford, Ryan L.; Arndt, Hans-Dieter; Brezinski, Mary L.; Ansari, Aseem Z.; Dervan, Peter B.

    2011-01-01

    A protein–DNA dimerizer constructed from a DNA-binding polyamide and the peptide FYPWMKG facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. The Exd binding domain can be reduced to a dipeptide WM attached to the polyamide through an ε-aminohexanoic acid linker with retention of protein–DNA dimerizer activity. Screening a library of analogues indicated that the tryptophan indole moiety is more important than methionine’s side chain or the N-terminal acetamide. Remarkably, switching the stereochemistry of the tryptophan residue (l to d) stabilizes the dimerizer•Exd•DNA ternary complex at 37 °C. These observations provide design principles for artificial transcription factors that may function in concert with the cellular regulatory circuitry. PMID:17290996

  5. Fibrillar dimer formation of islet amyloid polypeptides

    NASA Astrophysics Data System (ADS)

    Chiu, Chi-cheng; de Pablo, Juan J.

    2015-09-01

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 - 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 - 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  6. Fibrillar dimer formation of islet amyloid polypeptides

    SciTech Connect

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  7. Theoretical studies of transition metal dimers

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Bauschlicher, Charles W., Jr.

    1985-01-01

    The CASSCF approach was used to perform the MCSCF calculations for a number of transition metal dimers, including the Sc2, Ti2, Cr2, Cu2, TiV, Y2, Nb2, and Mo2 molecules; in addition, CASSCF/CI calculations were carried out for Sc2, Ti2, Cu2, and Y2. The CASSCF procedure is shown to provide a consistent set of calculations for these molecules, from which trends and a simple qualitative picture of the electronic structure may be derived. In particular, the calculations confirmed the ground states of the Sc2 and the TiV, and led to predictions for other molecules in this series. In addition to specific predictions, the study provides a simple qualitative picture of the bonding in these dimers.

  8. Snake venom disintegrins: novel dimeric disintegrins and structural diversification by disulphide bond engineering.

    PubMed Central

    Calvete, Juan J; Moreno-Murciano, M Paz; Theakston, R David G; Kisiel, Dariusz G; Marcinkiewicz, Cezary

    2003-01-01

    We report the isolation and amino acid sequences of six novel dimeric disintegrins from the venoms of Vipera lebetina obtusa (VLO), V. berus (VB), V. ammodytes (VA), Echis ocellatus (EO) and Echis multisquamatus (EMS). Disintegrins VLO4, VB7, VA6 and EO4 displayed the RGD motif and inhibited the adhesion of K562 cells, expressing the integrin alpha5beta1 to immobilized fibronectin. A second group of dimeric disintegrins (VLO5 and EO5) had MLD and VGD motifs in their subunits and blocked the adhesion of the alpha4beta1 integrin to vascular cell adhesion molecule 1 with high selectivity. On the other hand, disintegrin EMS11 inhibited both alpha5beta1 and alpha4beta1 integrins with almost the same degree of specificity. Comparison of the amino acid sequences of the dimeric disintegrins with those of other disintegrins by multiple-sequence alignment and phylogenetic analysis, in conjunction with current biochemical and genetic data, supports the view that the different disintegrin subfamilies evolved from a common ADAM (a disintegrin and metalloproteinase-like) scaffold and that structural diversification occurred through disulphide bond engineering. PMID:12667142

  9. High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.

    PubMed

    Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J; Burnett, John C; Zhou, Jiehua

    2016-09-22

    The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.

  10. Palmitoylated APP Forms Dimers, Cleaved by BACE1.

    PubMed

    Bhattacharyya, Raja; Fenn, Rebecca H; Barren, Cory; Tanzi, Rudolph E; Kovacs, Dora M

    2016-01-01

    A major rate-limiting step for Aβ generation and deposition in Alzheimer's disease brains is BACE1-mediated cleavage (β-cleavage) of the amyloid precursor protein (APP). We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187) in the E1-ectodomain. 8-10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP) shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs), when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors.

  11. Palmitoylated APP Forms Dimers, Cleaved by BACE1

    PubMed Central

    Fenn, Rebecca H.; Barren, Cory; Tanzi, Rudolph E.; Kovacs, Dora M.

    2016-01-01

    A major rate-limiting step for Aβ generation and deposition in Alzheimer’s disease brains is BACE1-mediated cleavage (β-cleavage) of the amyloid precursor protein (APP). We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187) in the E1-ectodomain. 8–10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP) shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs), when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors. PMID:27875558

  12. Small molecule and peptide-mediated inhibition of Epstein-Barr virus nuclear antigen 1 dimerization

    SciTech Connect

    Kim, Sun Young; Song, Kyung-A; Kieff, Elliott; Kang, Myung-Soo

    2012-07-27

    Highlights: Black-Right-Pointing-Pointer Evidence that targeting EBNA1 dimer, an EBV onco-antigen, can be achievable. Black-Right-Pointing-Pointer A small molecule and a peptide as EBNA1 dimerization inhibitors identified. Black-Right-Pointing-Pointer Both inhibitors associated with EBNA1 and blocked EBNA1 DNA binding activity. Black-Right-Pointing-Pointer Also, prevented its dimerization, and repressed viral gene transcription. -- Abstract: Latent Epstein-Barr virus (EBV) infection is associated with human B cell lymphomas and certain carcinomas. EBV episome persistence, replication, and gene expression are dependent on EBV-encoded nuclear antigen 1 (EBNA1)'s DNA binding domain (DBD)/dimerization domain (DD)-mediated sequence-specific DNA binding activity. Homodimerization of EBNA1 is essential for EBNA1 DNA binding and transactivation. In this study, we characterized a novel small molecule EBNA1 inhibitor EiK1, screened from the previous high throughput screening (HTS). The EiK1 compound specifically inhibited the EBNA1-dependent, OriP-enhanced transcription, but not EBNA1-independent transcription. A Surface Plasmon Resonance Biacore assay revealed that EiK1 associates with EBNA1 amino acid 459-607 DBD/DD. Consistent with the SPR data, in vitro gel shift assays showed that EiK1 suppressed the activity of EBNA1 binding to the cognate familial repeats (FR) sequence, but not control RBP-J{kappa} binding to the J{kappa} site. Subsequently, a cross-linker-mediated in vitro multimerization assay and EBNA1 homodimerization-dependent yeast two-hybrid assay showed that EiK1 significantly inhibited EBNA1 dimerization. In an attempt to identify more highly specific peptide inhibitors, small peptides encompassing the EBNA1 DBD/DD were screened for inhibition of EBNA1 DBD-mediated DNA binding function. The small peptide P85, covering EBNA1 a.a. 560-574, significantly blocked EBNA1 DNA binding activity in vitro, prevented dimerization in vitro and in vivo, associated with

  13. Influence of the sequence on the ab initio band structures of single and double stranded DNA models

    NASA Astrophysics Data System (ADS)

    Bogár, Ferenc; Bende, Attila; Ladik, János

    2014-06-01

    The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree-Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine-cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.

  14. Synthesis, NMR and crystal characterization of dimeric terephthalates derived from epimeric 4,5-seco-cholest-3-yn-5-ols.

    PubMed

    Alarcón-Manjarrez, Carlos; Arcos-Ramos, Rafael; Álamo, Marcos Flores; Iglesias-Arteaga, Martín A

    2016-05-01

    Two dimeric steroidal terephthalates derived from epimeric 4,5-seco-cholest-3-yn-5-ols were prepared starting from cholesterol in a five-step synthetic sequence. X-ray crystallography shows that the obtained compounds display novel supramolecular networks in the solid state in which the facial hydrophobicity of the steroidal skeletons plays an important role. Unambiguous NMR characterization of the obtained dimers is also provided.

  15. The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers

    SciTech Connect

    Olek, Anna T.; Rayon, Catherine; Makowski, Lee; Kim, Hyung Rae; Ciesielski, Peter; Badger, John; Paul, Lake N.; Ghosh, Subhangi; Kihara, Daisuke; Crowley, Michael; Himmel, Michael E.; Bolin, Jeffrey T.; Carpita, Nicholas C.

    2014-07-10

    Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice (Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain, elongated structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. As a result, the arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize.

  16. The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers

    DOE PAGES

    Olek, Anna T.; Rayon, Catherine; Makowski, Lee; ...

    2014-07-10

    Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice (Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain, elongatedmore » structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. As a result, the arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize.« less

  17. The chemokine monocyte chemoattractant protein-1 induces functional responses through dimerization of its receptor CCR2

    PubMed Central

    Rodríguez-Frade, José Miguel; Vila-Coro, Antonio J.; Martín de Ana, Ana; Albar, Juan Pablo; Martínez-A., Carlos; Mellado, Mario

    1999-01-01

    Cytokines interact with hematopoietin superfamily receptors and stimulate receptor dimerization. We demonstrate that chemoattractant cytokines (chemokines) also trigger biological responses through receptor dimerization. Functional responses are induced after pairwise crosslinking of chemokine receptors by bivalent agonistic antichemokine receptor mAb, but not by their Fab fragments. Monocyte chemoattractant protein (MCP)-1-triggered receptor dimerization was studied in human embryonic kidney (HEK)-293 cells cotransfected with genes coding for the CCR2b receptor tagged with YSK or Myc sequences. After MCP-1 stimulation, immunoprecipitation with Myc-specific antibodies revealed YSK-tagged receptors in immunoblotting. Receptor dimerization also was validated by chemical crosslinking in both HEK-293 cells and the human monocytic cell line Mono Mac 1. Finally, we constructed a loss-of-function CCR2bY139F mutant that acted as a dominant negative, blocking signaling through the CCR2 wild-type receptor. This study provides functional support for a model in which the MCP-1 receptor is activated by ligand-induced homodimerization, allowing discussion of the similarities between bacterial and leukocyte chemotaxis. PMID:10097088

  18. The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers.

    PubMed

    Olek, Anna T; Rayon, Catherine; Makowski, Lee; Kim, Hyung Rae; Ciesielski, Peter; Badger, John; Paul, Lake N; Ghosh, Subhangi; Kihara, Daisuke; Crowley, Michael; Himmel, Michael E; Bolin, Jeffrey T; Carpita, Nicholas C

    2014-07-01

    Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice (Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain, elongated structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. The arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize.

  19. Effective binding force calculation in a dimeric protein by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Sergi, Alessandro; Ciccotti, Giovanni; Falconi, Mattia; Desideri, Alessandro; Ferrario, Mauro

    2002-04-01

    A good example of macromolecular recognition is found in the interaction of the two monomers of the dimeric superoxide dismutase protein found in Photobacterium leiognathi. We have produced, by molecular dynamics simulation techniques, a specific path for the rupture of the dimer and calculated the effective force involved in the process by extending a well established free energy calculation scheme, the molecular dynamics blue moon approach to rare events. Within this picture we have generalized the approach to a vectorial reaction coordinate and performed a number of different simulations in function of the monomer-momomer separation, at fixed relative orientation. We find a deep minimum and we compute the height of the free energy barrier to break the dimer. As for the system characterization we have found that, when the separation distance increases, the protein structure is stable and the monomer-monomer interface is uniformly hydrated. Moreover, identifying the crucial contacts for the stabilization of the dimer, we have found the sequence of the different microscopic events in the monomer-monomer recognition and we have developed a view of the process which requires a merging of standard explanations, in agreement with the recent picture of recognition as a dynamical process mixing the various mechanisms previously considered [Kimura et al., Biophys. J. 80 635 (2001)].

  20. Selective and asymmetric action of trypsin on the dimeric forms of seminal RNase.

    PubMed Central

    De Lorenzo, C.; Dal Piaz, F.; Piccoli, R.; Di Maro, A.; Pucci, P.; D'Alessio, G.

    1998-01-01

    Dimeric seminal RNase (BS-RNase) is an equilibrium mixture of conformationally different quaternary structures, one characterized by the interchange between subunits of their N-terminal ends (the MXM form); the other with no interchange (the M=M form). Controlled tryptic digestion of each isolated quaternary form generates, as limit digest products, folded and enzymatically active molecules, very resistant to further tryptic degradation. Electrospray mass spectrometric analyses and N-terminal sequence determinations indicate that trypsin can discriminate between the conformationally different quaternary structures of seminal RNase, and exerts a differential and asymmetric action on the two dimeric forms, depending on the original quaternary conformation of each form. The two digestion products from the MXM and the M=M dimeric forms have different structures, which are reminiscent of the original quaternary conformation of the dimers: one with interchange, the other with no interchange, of the N-terminal ends. The surprising resistance of these tryptic products to further tryptic action is explained by the persistence in each digestion product of the original intersubunit interface. PMID:9865960

  1. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    SciTech Connect

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  2. Detrimental effect of the 6 His C-terminal tag on YedY enzymatic activity and influence of the TAT signal sequence on YedY synthesis

    PubMed Central

    2013-01-01

    Background YedY, a molybdoenzyme belonging to the sulfite oxidase family, is found in most Gram-negative bacteria. It contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. Despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine N-oxide, its natural substrate and its role in the cell remain unknown. Although sequence conservation of the YedY family displays a strictly conserved hydrophobic C-terminal residue, all known studies on Escherichia coli YedY have been performed with an enzyme containing a 6 histidine-tag at the C-terminus which could hamper enzyme activity. Results In this study, we demonstrate that the tag fused to the C-terminus of Rhodobacter sphaeroides YedY is detrimental to the enzyme’s reductase activity and results in an eight-fold decrease in catalytic efficiency. Nonetheless this C-terminal tag does not influence the properties of the molybdenum active site, as assayed by EPR spectroscopy. When a cleavable His-tag was fused to the N-terminus of the mature enzyme in the absence of the signal sequence, YedY was expressed and folded with its cofactor. However, when the signal sequence was added upstream of the N-ter tag, the amount of enzyme produced was approximately ten-fold higher. Conclusion Our study thus underscores the risk of using a C-terminus tagged enzyme while studying YedY, and presents an alternative strategy to express signal sequence-containing enzymes with an N-terminal tag. It brings new insights into molybdoenzyme maturation in R. sphaeroides showing that for some enzymes, maturation can occur in the absence of the signal sequence but that its presence is required for high expression of active enzyme. PMID:24180491

  3. Dryland Crop Yields and Soil Organic Matter as Influenced by Long-Term Tillage and Cropping Sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Novel management practices are needed to improve the declining dryland crop yields and soil organic matter using conventional farming practices in the northern Great Plains. We evaluated the 21-yr effect of tillage and cropping sequence on dryland grain and biomass (stems + leaves) yields of spring ...

  4. Targeted next-generation sequencing in steroid-resistant nephrotic syndrome: mutations in multiple glomerular genes may influence disease severity

    PubMed Central

    Bullich, Gemma; Trujillano, Daniel; Santín, Sheila; Ossowski, Stephan; Mendizábal, Santiago; Fraga, Gloria; Madrid, Álvaro; Ariceta, Gema; Ballarín, José; Torra, Roser; Estivill, Xavier; Ars, Elisabet

    2015-01-01

    Genetic diagnosis of steroid-resistant nephrotic syndrome (SRNS) using Sanger sequencing is complicated by the high genetic heterogeneity and phenotypic variability of this disease. We aimed to improve the genetic diagnosis of SRNS by simultaneously sequencing 26 glomerular genes using massive parallel sequencing and to study whether mutations in multiple genes increase disease severity. High-throughput mutation analysis was performed in 50 SRNS and/or focal segmental glomerulosclerosis (FSGS) patients, a validation cohort of 25 patients with known pathogenic mutations, and a discovery cohort of 25 uncharacterized patients with probable genetic etiology. In the validation cohort, we identified the 42 previously known pathogenic mutations across NPHS1, NPHS2, WT1, TRPC6, and INF2 genes. In the discovery cohort, disease-causing mutations in SRNS/FSGS genes were found in nine patients. We detected three patients with mutations in an SRNS/FSGS gene and COL4A3. Two of them were familial cases and presented a more severe phenotype than family members with mutation in only one gene. In conclusion, our results show that massive parallel sequencing is feasible and robust for genetic diagnosis of SRNS/FSGS. Our results indicate that patients carrying mutations in an SRNS/FSGS gene and also in COL4A3 gene have increased disease severity. PMID:25407002

  5. Effects of plasma D-dimer levels on early mortality and long-term functional outcome after spontaneous intracerebral hemorrhage.

    PubMed

    Hu, Xin; Fang, Yuan; Ye, Feng; Lin, Sen; Li, Hao; You, Chao; Liu, Ming

    2014-08-01

    The activation of hemostatic systems has been detected in spontaneous intracerebral hemorrhage (ICH) patients. The influence of plasma D-dimer levels on clinical outcome remains unclear. This study aimed to investigate the impact of elevated plasma D-dimer levels on early mortality and long-term functional outcome in spontaneous ICH. A total of 259 spontaneous ICH patients (<24hours from ictus) between November 2010 and October 2011 were included. Clinical information and radiological findings were collected at admission. Spearman correlation analyses revealed that D-dimer concentrations were correlated with midline shift, hematoma volume, intraventricular hemorrhage (IVH) score and Glasgow Coma Scale score. Patients with subarachnoid extension had significantly higher D-dimer levels than those without SAH extension. Comparison of patients with IVH and those without yielded a similar result. Multivariate stepwise backward logistic analysis identified plasma D-dimer levels as an independent risk factor for 7 day mortality (adjusted odds ratio [OR]=1.237, 95% confidence interval [CI] 1.017-1.504, p=0.033) and 3 month poor functional outcome (modified Rankin Scale score ≥ 3) (adjusted OR=2.279, 95% CI 1.130-6.595, p=0.026). The mechanisms by which elevated D-dimer affects the prognoses of spontaneous ICH patients remain unclear and require clarification in future studies.

  6. Evidence of Alternative Cystatin C Signal Sequence Cleavage Which Is Influenced by the A25T Polymorphism

    PubMed Central

    Nguyen, Annie; Hulleman, John D.

    2016-01-01

    Cystatin C (Cys C) is a small, potent, cysteine protease inhibitor. An Ala25Thr (A25T) polymorphism in Cys C has been associated with both macular degeneration and late-onset Alzheimer’s disease. Previously, studies have suggested that this polymorphism may compromise the secretion of Cys C. Interestingly, we found that untagged A25T, A25T tagged C-terminally with FLAG, or A25T FLAG followed by green fluorescent protein (GFP), were all secreted as efficiently from immortalized human cells as their wild-type (WT) counterparts (e.g., 112%, 100%, and 88% of WT levels from HEK-293T cells, respectively). Supporting these observations, WT and A25T Cys C variants also showed similar intracellular steady state levels. Furthermore, A25T Cys C did not activate the unfolded protein response and followed the same canonical endoplasmic reticulum (ER)-Golgi trafficking pathway as WT Cys C. WT Cys C has been shown to undergo signal sequence cleavage between residues Gly26 and Ser27. While the A25T polymorphism did not affect Cys C secretion, we hypothesized that it may alter where the Cys C signal sequence is preferentially cleaved. Under normal conditions, WT and A25T Cys C have the same signal sequence cleavage site after Gly26 (referred to as ‘site 2’ cleavage). However, in particular circumstances when the residues around site 2 are modified (such as by the presence of an N-terminal FLAG tag immediately after Gly26, or by a Gly26Lys (G26K) mutation), A25T has a significantly higher likelihood than WT Cys C of alternative signal sequence cleavage after Ala20 (‘site 1’) or even earlier in the Cys C sequence. Overall, our results indicate that the A25T polymorphism does not cause a significant reduction in Cys C secretion, but instead predisposes the protein to be cleaved at an alternative signal sequence cleavage site if site 2 is hindered. Additional N-terminal amino acids resulting from alternative signal sequence cleavage may, in turn, affect the protease

  7. Surface-subsurface model for a dimer-dimer catalytic reaction: a Monte Carlo simulation study

    NASA Astrophysics Data System (ADS)

    Khan, K. M.; Albano, E. V.

    2002-02-01

    The surface-subsurface model for a dimer-dimer reaction of the type A2 + 2B2→2AB2 has been studied through Monte Carlo simulation via a model based on the lattice gas non-thermal Langmuir-Hinshelwood mechanism, which involves the precursor motion of the B2 molecule. The motion of precursors is considered on the surface as well as in the subsurface. The most interesting feature of this model is that it yields a steady reactive window, which is separated by continuous and discontinuous irreversible phase transitions. The phase diagram is qualitatively similar to the well known Ziff, Gulari and Barshad (ZGB) model. The width of the window depends upon the mobility of precursors. The continuous transition disappears when the mobility of the surface precursors is extended to the third-nearest neighbourhood. The dependence of production rate on partial pressure of B2 dimer is predicted by simple mathematical equations in our model.

  8. Cation templating and electronic structure effects in uranyl cage clusters probed by the isolation of peroxide-bridged uranyl dimers.

    PubMed

    Qiu, Jie; Vlaisavljevich, Bess; Jouffret, Laurent; Nguyen, Kevin; Szymanowski, Jennifer E S; Gagliardi, Laura; Burns, Peter C

    2015-05-04

    The self-assembly of uranyl peroxide polyhedra into a rich family of nanoscale cage clusters is thought to be favored by cation templating effects and the pliability of the intrinsically bent U-O2-U dihedral angle. Herein, the importance of ligand and cationic effects on the U-O2-U dihedral angle were explored by studying a family of peroxide-bridged dimers of uranyl polyhedra. Four chemically distinct peroxide-bridged uranyl dimers were isolated that contain combinations of pyridine-2,6-dicarboxylate, picolinate, acetate, and oxalate as coordinating ligands. These dimers were synthesized with a variety of counterions, resulting in the crystallographic characterization of 15 different uranyl dimer compounds containing 17 symmetrically distinct dimers. Eleven of the dimers have U-O2-U dihedral angles in the expected range from 134.0 to 156.3°; however, six have 180° U-O2-U dihedral angles, the first time this has been observed for peroxide-bridged uranyl dimers. The influence of crystal packing, countercation linkages, and π-π stacking impact the dihedral angle. Density functional theory calculations indicate that the ligand does not alter the electronic structure of these systems and that the U-O2-U bridge is highly pliable. Less than 3 kcal·mol(-1) is required to bend the U-O2-U bridge from its minimum energy configuration to a dihedral angle of 180°. These results suggest that the energetic advantage of bending the U-O2-U dihedral angle of a peroxide-bridged uranyl dimer is at most a modest factor in favor of cage cluster formation. The role of counterions in stabilizing the formation of rings of uranyl ions, and ultimately their assembly into clusters, is at least as important as the energetic advantage of a bent U-O2-U interaction.

  9. Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus uv-specific endonucleases

    SciTech Connect

    Gordon, L.K.; Haseltine, W.A.

    1980-12-25

    A comparison was made of the activity of the uv-specific endonucleases of bacteriophage T4 (T4 endonuclease V) and of Micrococcus luteus on ultraviolet light-irradiated DNA substrates of defined sequence. The two enzyms cleave DNA at the site of pyrimidine dimers with the same frequency. The products of the cleavage reaction are the same. The pyrimidine dimer DNA-glycosylase activity of both enzymes is more active on double-stranded DNA than it is on single-stranded DNA.

  10. Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales--influences of gene partitions and taxon sampling.

    PubMed

    Liu, Juan; Qi, Zhe-Chen; Zhao, Yun-Peng; Fu, Cheng-Xin; Jenny Xiang, Qiu-Yun

    2012-09-01

    The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales. Genomic analyses were conducted to examine the rate and pattern of cpDNA genome evolution in Smilax relative to other major lineages of monocots. The cpDNA genomic sequences were combined with those available for Lilium to evaluate the phylogenetic position of Liliales and to investigate the influence of taxon sampling, gene sampling, gene function, natural selection, and substitution rate on phylogenetic inference in monocots. Phylogenetic analyses using sequence data of gene groups partitioned according to gene function, selection force, and total substitution rate demonstrated evident impacts of these factors on phylogenetic inference of monocots and the placement of Liliales, suggesting potential evolutionary convergence or adaptation of some cpDNA genes in monocots. Our study also demonstrated that reduced taxon sampling reduced the bootstrap support for the placement of Liliales in the cpDNA phylogenomic analysis. Analyses of sequences of 77 protein genes with some missing data and sequences of 81 genes (all protein genes plus the rRNA genes) support a sister relationship of Liliales to the commelinids-Asparagales clade, consistent with the APG III system. Analyses of 63 cpDNA protein genes for 32 taxa with few missing data, however, support a sister relationship of Liliales (represented by Smilax and Lilium) to Dioscoreales-Pandanales. Topology tests indicated that these two alignments do not significantly differ given any of these three cpDNA genomic sequence data sets. Furthermore, we found no saturation effect of the data, suggesting that the cpDNA genomic sequence data used in the study are appropriate for monocot phylogenetic study and long-branch attraction is unlikely to be the cause to explain the result of two well-supported, conflict placements of Liliales. Further analyses using

  11. Children's Representation and Imitation of Events: How Goal Organization Influences 3-Year-Old Children's Memory for Action Sequences.

    PubMed

    Loucks, Jeff; Mutschler, Christina; Meltzoff, Andrew N

    2016-11-24

    Children's imitation of adults plays a prominent role in human cognitive development. However, few studies have investigated how children represent the complex structure of observed actions which underlies their imitation. We integrate theories of action segmentation, memory, and imitation to investigate whether children's event representation is organized according to veridical serial order or a higher level goal structure. Children were randomly assigned to learn novel event sequences either through interactive hands-on experience (Study 1) or via storybook (Study 2). Results demonstrate that children's representation of observed actions is organized according to higher level goals, even at the cost of representing the veridical temporal ordering of the sequence. We argue that prioritizing goal structure enhances event memory, and that this mental organization is a key mechanism of social-cognitive development in real-world, dynamic environments. It supports cultural learning and imitation in ecologically valid settings when social agents are multitasking and not demonstrating one isolated goal at a time.

  12. Onion-like glycodendrimersomes from sequence-defined Janus glycodendrimers and influence of architecture on reactivity to a lectin

    PubMed Central

    Xiao, Qi; Zhang, Shaodong; Wang, Zhichun; Sherman, Samuel E.; Moussodia, Ralph-Olivier; Peterca, Mihai; Muncan, Adam; Williams, Dewight R.; Hammer, Daniel A.; Vértesy, Sabine; André, Sabine; Gabius, Hans-Joachim; Klein, Michael L.; Percec, Virgil

    2016-01-01

    A library of eight amphiphilic Janus glycodendrimers (GDs) with d-mannose (Man) headgroups, a known routing signal for lectin-mediated transport processes, was constructed via an iterative modular methodology. Sequence-defined variations of the Janus GD modulate the surface density and sequence of Man after self-assembly into multilamellar glycodendrimersomes (GDSs). The spatial mode of Man presentation is decisive for formation of either unilamellar or onion-like GDS vesicles. Man presentation and Janus GD concentration determine GDS size and number of bilayers. Beyond vesicle architecture, Man topological display affects kinetics and plateau level of GDS aggregation by a tetravalent model lectin: the leguminous agglutinin Con A, which is structurally related to endogenous cargo transporters. The agglutination process was rapid, efficient, and readily reversible for onion-like GDSs, demonstrating their value as versatile tools to explore the nature of physiologically relevant glycan/lectin pairing. PMID:26787853

  13. The nucleotide sequence, DNA damage location, and protein stoichiometry influence the base excision repair outcome at CAG/CTG repeats.

    PubMed

    Goula, Agathi-Vasiliki; Pearson, Christopher E; Della Maria, Julie; Trottier, Yvon; Tomkinson, Alan E; Wilson, David M; Merienne, Karine

    2012-05-08

    Expansion of CAG/CTG repeats is the underlying cause of >14 genetic disorders, including Huntington's disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases, the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. We provide molecular insights into how base excision repair (BER) protein stoichiometry may contribute to the tissue-selective instability of CAG/CTG repeats by using specific repair assays. Oligonucleotide substrates with an abasic site were mixed with either reconstituted BER protein stoichiometries mimicking the levels present in HD mouse striatum or cerebellum, or with protein extracts prepared from HD mouse striatum or cerebellum. In both cases, the repair efficiency at CAG/CTG repeats and at control DNA sequences was markedly reduced under the striatal conditions, likely because of the lower level of APE1, FEN1, and LIG1. Damage located toward the 5' end of the repeat tract was poorly repaired, with the accumulation of incompletely processed intermediates as compared to an AP lesion in the center or at the 3' end of the repeats or within control sequences. Moreover, repair of lesions at the 5' end of CAG or CTG repeats involved multinucleotide synthesis, particularly at the cerebellar stoichiometry, suggesting that long-patch BER processes lesions at sequences susceptible to hairpin formation. Our results show that the BER stoichiometry, nucleotide sequence, and DNA damage position modulate repair outcome and suggest that a suboptimal long-patch BER activity promotes CAG/CTG repeat instability.

  14. Targeting of the activation-induced cytosine deaminase is strongly influenced by the sequence and structure of the targeted DNA.

    PubMed

    Shen, Hong Ming; Ratnam, Sarayu; Storb, Ursula

    2005-12-01

    Activation-induced deaminase (AID) initiates immunoglobulin somatic hypermutation (SHM). Since in vitro AID was shown to deaminate cytosines on single-stranded DNA or the nontranscribed strand, it remained a puzzle how in vivo AID targets both DNA strands equally. Here we investigate the roles of transcription and DNA sequence in cytosine deamination. Strikingly different results are found with different substrates. Depending on the target sequence, the transcribed DNA strand is targeted as well as or better than the nontranscribed strand. The preferential targeting is not related to the frequency of AID hot spots. Comparison of cytosine deamination by AID and bisulfite shows different targeting patterns suggesting that AID may locally unwind the DNA. We conclude that somatic hypermutation on both DNA strands is the natural outcome of AID action on a transcribed gene; furthermore, the DNA sequence or structure and topology play major roles in targeting AID in vitro and in vivo. On the other hand, the lack of mutations in the first approximately 100 nucleotides and beyond about 1 to 2 kb from the promoter of immunoglobulin genes during SHM must be due to special conditions of transcription and chromatin in vivo.

  15. Mapping structurally defined guanine oxidation products along DNA duplexes: influence of local sequence context and endogenous cytosine methylation.

    PubMed

    Ming, Xun; Matter, Brock; Song, Matthew; Veliath, Elizabeth; Shanley, Ryan; Jones, Roger; Tretyakova, Natalia

    2014-03-19

    DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated (Me)CG dinucleotides and at 5' Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of (Me)CG sequences may be caused by a lowered ionization potential of guanine bases paired with (Me)C and the preferential intercalation of riboflavin photosensitizer adjacent to (Me)C:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational "hotspots" at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer.

  16. High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency

    PubMed Central

    Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J.; Burnett, John C.; Zhou, Jiehua

    2016-01-01

    The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy. PMID:27652575

  17. Synthesis and pharmacological evaluation of dimer derivatives of the bradykinin receptor antagonist HOE-140.

    PubMed

    Daffix, I; Amblard, M; Bergé, G; Dodey, P; Pruneau, D; Paquet, J L; Fouchet, C; Franck, R M; Defrêne, E; Luccarini, J M; Bélichard, P; Martinez, J

    1998-07-01

    The synthesis and pharmacological evaluation of dimer derivatives of the C-terminal fragments of the potent bradykinin antagonist HOE-140, linked through their N-termini, were performed. The influence of peptide moiety length was studied using the succinyl moiety as a linker. Our attention focused on the dimer of the C-terminal tetrapeptide of HOE-140 (compound JMV 980), which displayed some inhibiting activity (IC50 = 247 nM) for bradykinin B2 receptors. Unexpectedly, it was orally active in inhibiting bradykinin-induced hypotension in the rat. Based on this tetrapeptide dimer model, we synthesized pseudotetrapeptide dimer bradykinin antagonists 29 and 33, which exhibited high affinity (Ki = 76 and 61 nM, respectively) for the human cloned B2 receptor. In addition, compound 29 inhibited bradykinin-induced contraction of the human umbilical vein giving a pKB value of 6.45. Compounds 29 and 33 were selective toward B2 receptors because they did not bind to the cloned human B1 receptor up to 10 microM.

  18. First-principles study on electron transport through BN-dimer embedded zigzag carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Egami, Yoshiyuki; Akera, Hiroshi

    2017-04-01

    First-principles calculations are performed for electron transmission through a metallic zigzag carbon nanotube with substitutional BN dimers parallel to the nanotube axis. The transmission coefficient is calculated in the energy range (around the charge neutrality point) in which there exist two degenerate subbands for each spin. Wave functions in the circumferential direction of one of the degenerate subbands can be chosen so as to have nodes at the position of a carbon dimer parallel to the nanotube axis. It is shown that the transmission probability of an incident wave with such wave-function nodes depends crucially on positions of BN dimers relative to the nodes. By placing each of dimers at one of the nodes, the transmission probability is substantially enhanced and is well described by the Born approximation in spite of spatially extended scattering potential due to ionized B and N. This suggests that the arrangement in the circumferential direction of various impurities influences transport through metallic zigzag carbon nanotubes.

  19. Activation and inhibition of erythropoietin receptor function: role of receptor dimerization.

    PubMed Central

    Watowich, S S; Hilton, D J; Lodish, H F

    1994-01-01

    Members of the cytokine receptor superfamily have structurally similar extracellular ligand-binding domains yet diverse cytoplasmic regions lacking any obvious catalytic domains. Many of these receptors form ligand-induced oligomers which are likely to participate in transmembrane signaling. A constitutively active (factor-independent) mutant of the erythropoietin receptor (EPO-R), R129C in the exoplasmic domain, forms disulfide-linked homodimers, suggesting that the wild-type EPO-R is activated by ligand-induced homodimerization. Here, we have taken two approaches to probe the role EPO-R dimerization plays in signal transduction. First, on the basis of the crystal structure of the ligand-bound, homodimeric growth hormone receptor (GH-R) and sequence alignment between the GH-R and EPO-R, we identified residues of the EPO-R which may be involved in intersubunit contacts in an EPO-R homodimer. Residue 129 of the EPO-R corresponds to a residue localized to the GH-R dimer interface region. Alanine or cysteine substitutions were introduced at four other residues of the EPO-R predicted to be in the dimer interface region. Substitution of residue E-132 or E-133 with cysteine renders the EPO-R constitutively active. Like the arginine-to-cysteine mutation at position 129 in the exoplasmic domain (R129C), E132C and E133C form disulfide-linked homodimers, suggesting that constitutive activity is due to covalent dimerization. In the second approach, we have coexpressed the wild-type EPO-R with inactive mutants of the receptor missing all or part of the cytosolic domain. These truncated receptors have a dominant inhibitory effect on the proliferative action of the wild-type receptor. Taken together, these results strengthen the hypothesis that an initial step in EPO- and EPO-R-mediated signal transduction is ligand-induced receptor dimerization. Images PMID:8196600

  20. UV light-induced cyclobutane pyrimidine dimers are mutagenic in mammalian cells

    SciTech Connect

    Protic-Sabljic, M.; Tuteja, N.; Munson, P.J.; Hauser, J.; Kraemer, K.H.; Dixon, K.

    1986-10-01

    We used a simian virus 40-based shuttle vector plasmid, pZ189, to determine the role of pyrimidine cyclobutane dimers in UV light-induced mutagenesis in monkey cells. The vector DNA was UV irradiated and then introduced into monkey cells by transfection. After replication, vector DNA was recovered from the cells and tested for mutations in its supF suppressor tRNA marker gene by transformation of Escherichia coli carrying a nonsense mutation in the beta-galactosidase gene. When the irradiated vector was treated with E. coli photolyase prior to transfection, pyrimidine cyclobutane dimers were removed selectively. Removal of approximately 90% of the pyrimidine cyclobutane dimers increased the biological activity of the vector by 75% and reduced its mutation frequency by 80%. Sequence analysis of 72 mutants recovered indicated that there were significantly fewer tandem double-base changes and G X C----A X T transitions (particularly at CC sites) after photoreactivation of the DNA. UV-induced photoproducts remained (although at greatly reduced levels) at all pyr-pyr sites after photoreactivation, but there was a relative increase in photoproducts at CC and TC sites and a relative decrease at TT and CT sites, presumably due to a persistence of (6-4) photoproducts at some CC and TC sites. These observations are consistent with the fact that mutations were found after photoreactivation at many sites at which only cyclobutane dimers would be expected to occur. From these results we conclude that UV-induced pyrimidine cyclobutane dimers are mutagenic in DNA replicated in monkey cells.

  1. Modulation of ceramide synthase activity via dimerization.

    PubMed

    Laviad, Elad L; Kelly, Samuel; Merrill, Alfred H; Futerman, Anthony H

    2012-06-15

    Ceramide, the backbone of all sphingolipids, is synthesized by a family of ceramide synthases (CerS) that each use acyl-CoAs of defined chain length for N-acylation of the sphingoid long chain base. CerS mRNA expression and enzymatic activity do not always correlate with the sphingolipid acyl chain composition of a particular tissue, suggesting post-translational mechanism(s) of regulation of CerS activity. We now demonstrate that CerS activity can be modulated by dimer formation. Under suitable conditions, high M(r) CerS complexes can be detected by Western blotting, and various CerS co-immunoprecipitate. CerS5 activity is inhibited in a dominant-negative fashion by co-expression with catalytically inactive CerS5, and CerS2 activity is enhanced by co-expression with a catalytically active form of CerS5 or CerS6. In a constitutive heterodimer comprising CerS5 and CerS2, the activity of CerS2 depends on the catalytic activity of CerS5. Finally, CerS dimers are formed upon rapid stimulation of ceramide synthesis by curcumin. Together, these data demonstrate that ceramide synthesis can be regulated by the formation of CerS dimers and suggest a novel way to generate the acyl chain composition of ceramide (and downstream sphingolipids), which may depend on the interaction of CerS with each other.

  2. Caffeine dimerization: effects of sugar, salts, and water structure.

    PubMed

    Shimizu, Seishi

    2015-10-01

    Sugars and salts strongly affect the dimerization of caffeine in water. Such a change of dimerization, considered to be crucial for bitter taste suppression, has long been rationalized by the change of "water structure" induced by the additives; "kosmotropic" (water structure enhancing) salts and sugars promote dimerization, whereas "chaotropic" (water structure breaking) salts suppress dimerization. Based on statistical thermodynamics, here we challenge this consensus; we combine the rigorous Kirkwood-Buff theory of solution with the classical isodesmic model of caffeine association. Instead of the change of water structure, we show that the enhancement of caffeine dimerization is due to the exclusion of additives from caffeine, and that the weakening of dimerization is due to the binding of additives on caffeine.

  3. Metal enhanced fluorescence of Ag-nanoshell dimer

    NASA Astrophysics Data System (ADS)

    Liaw, Jiunn-Woei; Chen, Huang-Chih; Chen, Bae-Renn; Kuo, Mao-Kuen

    2014-04-01

    The plasmon modes of Ag-nanoshell dimer on metal enhanced fluorescence (MEF) are studied theoretically. The amplified excitation rate of a dimer (two identical Ag nanoshells) illuminated by a plane wave for exciting a molecule located at the gap center is calculated. Subsequently, the apparent quantum yield of the emission of the excited molecule affected by the dimer is investigated. The multiple multipole method is used for the both simulations. Finally, the enhancement factor of the dimer on the overall photoluminescence of the molecule in terms of the two parameters is evaluated. Our results show that Ag-nanoshell dimer is a dual-band photoluminescence enhancer for MEF at the bonding dipole and quadrupole modes. The former is broadband, and the latter narrowband. Both bands depend on the gap size. Moreover, the average enhancement factor of Ag-nanoshell dimer for MEF with a Stokes shift is discussed.

  4. Morphinane alkaloid dimers from Sinomenium acutum.

    PubMed

    Jin, Hui-Zi; Wang, Xiao-Ling; Wang, Hong-Bing; Wang, Yu-Bo; Lin, Li-Ping; Ding, Jian; Qin, Guo-Wei

    2008-01-01

    Two new morphinane alkaloid dimers, 2,2'-disinomenine (1) and 7',8'-dihydro-1,1'-disinomenine (2), and known 1, 1'-disinomenine (3), were isolated from ethanol extracts of stems of Sinomenium acutum. Their structures were elucidated on the basis of spectroscopic methods. The absolute configuration of alkaloids 1-3 was determined by direct comparison of their CD spectra with the known alkaloid sinomenine. The isolated alkaloids were tested for cytotoxicity against A549, P388, and HeLa cell lines, and 1 and 3 showed weak inhibition against A549 and Hela cells.

  5. Thermodynamic properties for the sodium dimer

    NASA Astrophysics Data System (ADS)

    Song, Xiao-Qin; Wang, Chao-Wen; Jia, Chun-Sheng

    2017-04-01

    We present a closed-form expression of the classical vibrational partition function for the improved Rosen-Morse potential energy model. We give explicit expressions for the vibrational mean energy, vibrational specific heat, vibrational free energy, and vibrational entropy for diatomic molecule systems. The properties of these thermodynamic functions for the Na2 dimer are discussed in detail. We find that the improved Rosen-Morse potential model is superior to the harmonic oscillator in calculating the heat capacity for the Na2 molecules.

  6. Thermodynamics of acetylene van der Waals dimerization

    NASA Technical Reports Server (NTRS)

    Colussi, A. J.; Sander, S. P.; Friedl, R. R.

    1991-01-01

    Integrated band intensities of the 620/cm absorption in (C2H2)2 are measured by FTIR spectroscopy at constant acetylene pressure between 198 and 273 K. These data, in conjunction with ab initio results for (C2H2)2, are used for the statistical evaluation of the equilibrium constant Kp(T) for acetylene-cluster dimerization. The present results are used to clarify the role of molecular clusters in chemical systems at or near equilibrium, in particular in Titan's stratosphere.

  7. Dimerization of thymol blue in solution: Theoretical evidence.

    PubMed

    Balderas-Hernández, Patricia; Vargas, Rubicelia; Rojas-Hernández, Alberto; Ramírez-Silva, Ma Teresa; Galván, Marcelo

    2007-02-28

    The possibility of dimerization of thymol blue was addressed by ab initio and force field calculations. In agreement with experimental information, a dimer forming symmetrical chemical environments for hydrogen bond formation was determined. This dimer is stable in vacuum and aqueous media and corresponds to the same protonated state proposed by the experiment. A comparison of the CVFF and MM3 force fields and ab initio results shows the suitability of CVFF to qualitatively describe this system.

  8. VIDAS D-dimer: fast quantitative ELISA for measuring D-dimer in plasma.

    PubMed

    Pittet, J L; de Moerloose, P; Reber, G; Durand, C; Villard, C; Piga, N; Rolland, D; Comby, S; Dupuy, G

    1996-03-01

    VIDAS D-dimer (bioMérieux) is a new quantitative ELISA for D-dimer determination designed for the VIDAS automated system. The test contains single-dose, ready-to-use reagents and is completed within 35 min. Quantitative results are obtained from a calibration curve stored in the software of the system and expressed as fibrinogen equivalent units. The two-step capture/tag test relies on two complementary monoclonal anti-D-dimer antibodies, the second one being labeled with alkaline phosphatase. The upper limit of the measuring range is 1000 micrograms/L and the lower detection limit is <50 micrograms/L, which is below the lower limit of the reference interval (68-494 micrograms/L). Reproducibility (CV) within and between runs ranges from 5% to 7%. There is no interference from heparin, bilirubin, hemoglobin, fibrinogen degradation products, or plasma turbidity. Comparison with a conventional ELISA (y) gave good correlation (r= 0.91, n= 579) and comparable results (y= 1.35x - 148, S(y/x)= 750), especially for D-dimer concentrations ranging from 0 to 1000 micrograms/L (y= 1.09x - 10.6, r= 0.88, S(y/x)= 170).

  9. Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

    SciTech Connect

    Mani, Devendra; Arunan, E.

    2014-10-28

    Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

  10. Functional connectivity in the resting-state motor networks influences the kinematic processes during motor sequence learning.

    PubMed

    Bonzano, Laura; Palmaro, Eleonora; Teodorescu, Roxana; Fleysher, Lazar; Inglese, Matilde; Bove, Marco

    2015-01-01

    Neuroimaging studies support the involvement of the cerebello-cortical and striato-cortical motor loops in motor sequence learning. Here, we investigated whether the gain of motor sequence learning could depend on a-priori resting-state functional connectivity (rsFC) between motor areas and structures belonging to these circuits. Fourteen healthy subjects underwent a resting-state functional magnetic resonance imaging session. Afterward, they were asked to reproduce a verbally-learned sequence of finger opposition movements as fast and as accurately as possible. All subjects increased their movement rate with practice, by reducing the touch duration and/or intertapping interval. The rsFC analysis showed that, at rest, the left and right primary motor cortex (M1) and left and right supplementary motor area (SMA) were mainly connected with other motor areas. The covariate analysis taking into account the different kinematic parameters indicated that the subjects achieving greater movement rate increase were those showing stronger rsFC of the left M1 and SMA with the right lobule VIII of the cerebellum. Notably, the subjects with greater intertapping interval reduction showed stronger rsFC of the left M1 and SMA with the association nuclei of the thalamus. Conversely, the regression analysis with the right M1 and SMA seeds showed only a few significant clusters for the different covariates not located in the cerebellum and thalamus. No common clusters were found between the right M1 and SMA. All of these findings indicated important functional connections at rest of those neural circuits responsible for motor learning improvement, involving the motor areas related to the hemisphere directly controlling the finger movements, the thalamus and cerebellum.

  11. Diagnosing Lung Nodules on Oncologic MR/PET Imaging: Comparison of Fast T1-Weighted Sequences and Influence of Image Acquisition in Inspiration and Expiration Breath-Hold

    PubMed Central

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios; Brendle, Cornelia; Schmidt, Holger; Pfannenberg, Christina A.; laFougère, Christian; Nikolaou, Konstantin

    2016-01-01

    Objective First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. Materials and Methods The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Results Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Conclusion Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR

  12. Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

    SciTech Connect

    Stogios, Peter J.; Cuesta-Seijo, Jose Antonio; Chen, Lu; Pomroy, Neil C.; Privé, Gilbert G.

    2010-09-22

    The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel {beta}-sheet with a strand from the other chain. We have solved the crystal structures of the BTB domains from Fanconi anemia zinc finger (FAZF) and Miz1 (Myc-interacting zinc finger 1) to resolutions of 2.0 {angstrom} and 2.6 {angstrom}, respectively. Unlike previous examples of BTB domain structures, the FAZF BTB domain is a nonswapped dimer, with each N-terminal {beta}-strand associated with its own chain. As a result, the dimerization interface in the FAZF BTB domain is about half as large as in the domain-swapped dimers. The Miz1 BTB domain resembles a typical swapped BTB dimer, although it has a shorter N-terminus that is not able to form the interchain sheet. Using cysteine cross-linking, we confirmed that the promyelocytic leukemia zinc finger (PLZF) BTB dimer is strand exchanged in solution, while the FAZF BTB dimer is not. A phylogenic tree of the BTB fold based on both sequence and structural features shows that the common ancestor of the BTB domain in BTB-ZF (bric a brac, tramtrack, broad-complex zinc finger) proteins was a domain-swapped dimer. The differences in the N-termini seen in the FAZF and Miz1 BTB domains appear to be more recent developments in the structural evolution of the domain.

  13. Influence of potential pulses amplitude sequence in a voltammetric electronic tongue (VET) applied to assess antioxidant capacity in aliso.

    PubMed

    Fuentes, Esteban; Alcañiz, Miguel; Contat, Laura; Baldeón, Edwin O; Barat, José M; Grau, Raúl

    2017-06-01

    Four signals configurations were studied, two of them built by small increases of potential and two with bigger increments. The highest current values were obtained when pulses with bigger change of potential were used although the best results were shown by the pulse sequence which included an intermediate pulse before the relevant pulse. A mathematical model based on trolox pattern was developed to predict antioxidant capacity of aliso, employing information obtained from all the electrodes, although model validation could be done only employing the information from gold electrode.

  14. Disordered clusters of Bak dimers rupture mitochondria during apoptosis

    PubMed Central

    Uren, Rachel T; O’Hely, Martin; Iyer, Sweta; Bartolo, Ray; Shi, Melissa X; Brouwer, Jason M; Alsop, Amber E; Dewson, Grant; Kluck, Ruth M

    2017-01-01

    During apoptosis, Bak and Bax undergo major conformational change and form symmetric dimers that coalesce to perforate the mitochondrial outer membrane via an unknown mechanism. We have employed cysteine labelling and linkage analysis to the full length of Bak in mitochondria. This comprehensive survey showed that in each Bak dimer the N-termini are fully solvent-exposed and mobile, the core is highly structured, and the C-termini are flexible but restrained by their contact with the membrane. Dimer-dimer interactions were more labile than the BH3:groove interaction within dimers, suggesting there is no extensive protein interface between dimers. In addition, linkage in the mobile Bak N-terminus (V61C) specifically quantified association between dimers, allowing mathematical simulations of dimer arrangement. Together, our data show that Bak dimers form disordered clusters to generate lipidic pores. These findings provide a molecular explanation for the observed structural heterogeneity of the apoptotic pore. DOI: http://dx.doi.org/10.7554/eLife.19944.001 PMID:28182867

  15. Assembly of Drosophila centromeric nucleosomes requires CID dimerization.

    PubMed

    Zhang, Weiguo; Colmenares, Serafin U; Karpen, Gary H

    2012-01-27

    Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.

  16. Assembly of Drosophila Centromeric Nucleosomes Requires CID Dimerization

    PubMed Central

    Zhang, Weiguo; Colmenares, Serafin U.; Karpen, Gary H.

    2012-01-01

    SUMMARY Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four helix bundle, which mediates intra-nucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly. PMID:22209075

  17. Excited state two photon absorption of a charge transfer radical dimer in the near infrared.

    PubMed

    Schiccheri, Nicola; Meneghetti, Moreno

    2005-06-02

    Nonlinear transmission measurements of a solution of radical dimers of tetramethyl-tetrathiafulvalene, (TMTTF+)2, recorded with 9 ns laser pulses at 1064 nm are reported and interpreted on the basis of a multiphoton absorption process. One finds that the process can be interpreted with a sequence of three photon absorption, the first being a one photon absorption related to the intermolecular charge transfer process characteristic of the dimers and the second a two photon absorption from the excited state created with the first process. A model calculation allows one to obtain the value of the two photon absorption cross section which is found to be several orders of magnitude larger than those usually found for two photon absorbing systems excited from the ground state. These results show the importance of an excited-state population for obtaining large nonlinear optical responses.

  18. Pathogenic Cysteine Removal Mutations in FGFR Extracellular Domains Stabilize Receptor Dimers and Perturb the TM Dimer Structure.

    PubMed

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-10-09

    Missense mutations that introduce or remove cysteine residues in receptor tyrosine kinases are believed to cause pathologies by stabilizing the active receptor tyrosine kinase dimers. However, the magnitude of this stabilizing effect has not been measured for full-length receptors. Here, we characterize the dimer stabilities of three full-length fibroblast growth factor receptor (FGFR) mutants harboring pathogenic cysteine substitutions: the C178S FGFR1 mutant, the C342R FGFR2 mutant, and the C228R FGFR3 mutant. We find that the three mutations stabilize the FGFR dimers. We further see that the mutations alter the configuration of the FGFR transmembrane dimers. Thus, both aberrant dimerization and perturbed dimer structure likely contribute to the pathological phenotypes arising due to these mutations.

  19. The influence of sequence of precursor films on CZTSe thin films prepared by ion-beam sputtering deposition

    NASA Astrophysics Data System (ADS)

    Zhao, Jun; Liang, Guangxing; Zeng, Yang; Fan, Ping; Hu, Juguang; Luo, Jingting; Zhang, Dongping

    2017-02-01

    The CuZnSn (CZT) precursor thin films are grown by ion-beam sputtering Cu, Zn, Sn targets with different orders and then sputtering Se target to fabricate Cu2ZnSnSe4 (CZTSe) absorber thin films on molybdenum substrates. They are annealed in the same vacuum chamber at 400 °C. The characterization methods of CZTSe thin films include X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and X-ray photoelectron spectra (XPS) in order to study the crystallographic properties, composition, surface morphology, electrical properties and so on. The results display that the CZTSe thin films got the strongest diffraction peak intensity and were with good crystalline quality and its morphology appeared smooth and compact with a sequence of Cu/Zn/Sn/Se, which reveals that the expected states for CZTSe are Cu1+, Zn2+, Sn4+, Se2+. With the good crystalline quality and close to ideal stoichiometric ratio the resistivity of the CZTSe film with the sequence of Cu/Zn/Sn/Se is lower, whose optical band gap is about 1.50 eV. Project supported by the National Natural Science Foundation of China (No. 61404086), the Basical Research Program of Shenzhen (Nos. JCYJ20150324140036866, JCYJ20150324141711581), and the Natural Science Foundation of SZU (No. 2014017).

  20. Influence of fiber lay-up sequence on mechanical properties of SiC(f)/SiC composites

    SciTech Connect

    Singh, D.; Singh, J.P.; Sutaria, M.

    1996-03-01

    Mechanical properties of Nicalon-fiber-reinforced silicon carbide matrix composites with two different fiber lay-up sequences (0{degree}/40{degree}/60{degree} and 0{degree}/45{degree}) were evaluated at various temperatures ranging from ambient to 1300{degree}C. Composites with 0{degree}/40{degree}/60{degree} fiber lay-up sequence showed a higher average first matrix cracking stress than that of 0{degree}/45{degree} composites. The measured room-temperature ultimate strength of the 0{degree}/40{degree}/60{degree} composites was 300 MPa compared to 180 MPa for the 0{degree}/45{degree} composites. These measured ultimate strengths were correlated to the predictions made with an analytical model and to in-situ fiber strength characteristics. The large difference in room-temperature ultimate strengths between the two sets of composites is attributed to the relative contributions of the off-axis fibers to the load-bearing capacity of each composite. Up to 1200{degree}C, ultimate strength and work-of-fracture in each set of composites increased, but then declined above 1300{degree}C. The decreases were correlated to in-situ Nicalon fiber strength and fiber/matrix interface degradation.

  1. Influence of dosing sequence and film thickness on structure and resistivity of Al-ZnO films grown by atomic layer deposition

    SciTech Connect

    Pollock, Evan B. Lad, Robert J.

    2014-07-01

    Aluminum-doped zinc oxide (AZO) films were deposited onto amorphous silica substrates using an atomic layer deposition process with diethyl zinc (DEZ), trimethyl aluminum (TMA), and deionized water at 200 °C. Three different Al doping sequences were used at a ZnO:Al ratio of 11:1 within the films. A minimum film resistivity of 1.6 × 10{sup −3} Ω cm was produced using sequential dosing of DEZ, TMA, DEZ, followed by H{sub 2}O for the Al doping step. This “ZAZW” sequence yielded an AZO film resistivity that is independent of film thickness, crystallographic texture, and grain size, as determined by high resolution x-ray diffraction (XRD). A pseudo-Voigt analysis method yields values for grain sizes that are smaller than those calculated using other XRD methods. Anisotropic grain sizes or variations in crystallographic texture have minimal influence on film resistivity, which suggests that factors other than film texture, such as intragrain scattering, may be important in influencing film resistivity.

  2. Rotational Spectrum of Propargyl Alcohol Dimer

    NASA Astrophysics Data System (ADS)

    Mani, Devendra; Arunan, E.

    2013-06-01

    Propargyl alcohol is a molecule of interest to astrophysics as well as combustion studies. Rotational-tunneling spectra of propargyl alcohol monomer is well known and shows that the molecule exists in gauche form. Recently we reported microwave spectra of Ar...propargyl alcohol complex. Propargyl alcochol exists in gauche form in the complex as well. In this study we have recorded pure rotational spectra of propargyl alcohol dimer between 4-13 GHz range.A total of 47 transitions, 24 a-type, 16 b-type and 7 c-type, have been observed and fitted with semi rigid rotor asymmetric top hamiltonian. The fitted rotational constants are: A = 2321.83323(47) MHz, B = 1150.47726(24) MHz and C = 1124.89000(20) MHz. The standard deviation for the fit is 2.5 kHz. The experimental rotational constants are very close to the structure predicted by ab-initio calculations in which two gauche-propargyl alcohol moieties are in three point contact stabilized by O-H...O, O-H...pi and C-H...pi interactions. Few transitions for duterated isotopologues of the dimer have also been observed and search for the remaining transitions is in progress. Details will be presented in the talk. E. Hirota,J. Mol. Spectrosc. 26 (1968) 335-350. J.C. Pearson, B.J. Drouin, J. Mol. Spectrosc. 234 (2005) 149-156. D. Mani, E. Arunan, ChemPhysChem 14 (2013) 754-763.

  3. The role of dimerization in prion replication.

    PubMed Central

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István

    2002-01-01

    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication. PMID:11916832

  4. Fibrillar dimer formation of islet amyloid polypeptides

    DOE PAGES

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimentalmore » and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.« less

  5. Structure of the Response Regulator PhoP from Mycobacterium tuberculosis Reveals a Dimer Through the Receiver Domain

    SciTech Connect

    S Menon; S Wang

    2011-12-31

    The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosphorylation of the receiver domain remains unclear due to a lack of structural information on the full-length proteins. Here we report the crystal structure of the full-length PhoP of M. tuberculosis. Unlike other known structures of full-length proteins of the same subfamily, PhoP forms a dimer through its receiver domain with the dimer interface involving {alpha}4-{beta}5-{alpha}5, a common interface for activated receiver domain dimers. However, the switch residues, Thr99 and Tyr118, are in a conformation resembling those of nonactivated receiver domains. The Tyr118 side chain is involved in the dimer interface interactions. The receiver domain is tethered to the DNA-binding domain through a flexible linker and does not impose structural constraints on the DNA-binding domain. This structure suggests that phosphorylation likely facilitates/stabilizes receiver domain dimerization, bringing the DNA-binding domains to close proximity, thereby increasing their binding affinity for direct repeat DNA sequences.

  6. Amyloidogenic Processing but not AICD Production Requires a Precisely Oriented APP Dimer Assembled by Transmembrane GXXXG Motifs

    PubMed Central

    Kienlen-Campard, Pascal; Tasiaux, Bernadette; Van Hees, Joanne; Li, Mingli; Huysseune, Sandra; Sato, Takeshi; Fei, Jeffrey Z.; Aimoto, Saburo; Courtoy, Pierre J.; Smith, Steven O.; Constantinescu, Stefan N.; Octave, Jean-Noël

    2009-01-01

    The β-amyloid peptide (Aβ) is the major constituent of the amyloid core of senile plaques found in the brain of patients with Alzheimer's disease (AD). Aβ is produced by the sequential cleavage of the Amyloid Precursor Protein (APP) by β- and γ-secretases. Cleavage of APP by γ-secretase also generates the APP Intracellular C-terminal Domain (AICD) peptide, which might be involved in regulation of gene transcription. APP contains three glycine-xxx-glycine (GxxxG) motifs in its juxtamembrane and transmembrane (TM) regions. Such motifs are known to promote dimerization via close apposition of TM sequences. We demonstrate that pairwise replacement of glycines by leucines or isoleucines, but not alanines, in a GxxxG motif led to a drastic reduction of Aβ40 and Aβ42 secretion. β-Cleavage of mutant APP was not inhibited, and reduction of Aβ secretion resulted from inhibition of γ-cleavage. It was anticipated that decreased γ-cleavage of mutant APP would result from inhibition of its dimerization. Surprisingly, mutations of the GxxxG motif actually enhanced dimerization of the APP C-terminal fragments, possibly via a different TM α-helical interface. Increased dimerization of the TM APP C-terminal domain did not affect AICD production. These results clearly demonstrate that both orientation and dimerization of the APP TM domain differently affect Aβ and AICD production. PMID:18201969

  7. Synthesis and biochemical evaluation of the CBI-PDE-I-dimer, a benzannelated analog of (+)-CC-1065 that also produces delayed toxicity in mice.

    PubMed

    Aristoff, P A; Johnson, P D; Sun, D; Hurley, L H

    1993-07-09

    A practical synthesis of CBI (2) was developed and applied to the synthesis of benzannelated analogs of CC-1065, including CBI-PDE-I-dimer (13) and CBI-bis-indole [(+)-A'BC]. The CBI-PDE-I-dimer was shown to have similar DNA sequence selectivity and structural effects on DNA as (+)-CC-1065. Of particular importance was the observed duplex winding effect that has been associated with the pyrrolidine ring of the nonalkylated subunits of (+)-CC-1065 and possibly correlated with its delayed toxicity effects. The effect of CBI-PDE-I-dimer was also compared to (+)-CC-1065 in the inhibition of duplex unwinding by helicase II and nick sealing by T4 ligase and found to be quantitatively similar. The in vitro and in vivo potencies of the CBI compounds corresponded very closely to the corresponding CPI derivatives. Finally, CBI-PDE-I-dimer was like (+)-CC-1065 in causing delayed toxicity in mice.

  8. Influence of the germline sequence on the thermodynamic stability and fibrillogenicity of human lambda 6 light chains.

    PubMed

    del Pozo Yauner, Luis; Ortiz, Ernesto; Sánchez, Rosalba; Sánchez-López, Rosana; Güereca, Leopoldo; Murphy, Charles L; Allen, Amy; Wall, Jonathan S; Fernández-Velasco, D Alejandro; Solomon, Alan; Becerril, Baltazar

    2008-08-01

    Light chain-associated amyloidosis is a fatal disease characterized by the aggregation and pathologic deposition of monoclonal light chain-related fragments as amyloid fibrils in organs or tissues throughout the body. Notably, it has been observed that proteins encoded by the lambda variable light chain (V(L)) gene segment 6a are invariably associated with amyloid deposition; however, the contribution of the gene to this phenomenon has not been established. In this regard, we have determined the thermodynamic stability and kinetics of in vitro fibrillogenesis of a recombinant (r) V(L) protein, designated 6aJL2, which contains the predicted sequences encoded by the 6a and JL2 germline genes. Additionally, we studied a 6a mutant (6aJL2-Arg25Gly), that is present in approximately 25% of all amyloid-associated lambda6 light chains. Remarkably, the wild-type 6aJL2 protein was more stable than were all known amyloidogenic kappa and lambda light chains for which stability parameters are available; more importantly, it was even more so (and less fibrillogenic) than the only clinically proven nonamyloidogenic lambda6 protein, Jto. Conversely, the mutated 6aJL2-R25G molecule was considerably less stable and more fibrillogenic than was the native 6aJL2. Our data indicate that the propensity of lambda6 light chains to form amyloid can not be attributed to thermodynamic instability of the germline-encoded Vlambda6 domain, but rather, is dependent on sequence alterations that render such proteins amyloidogenic.

  9. Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

    PubMed Central

    Urbaniak, Katarzyna; Heimgartner, Heinz

    2017-01-01

    An intriguing stepwise diradical mechanism of the dimerization of the reactive intermediate (thiocarbonyl S-methanide) appearing in the reaction of phenyl selenophen-2-yl thioketone with diazomethane was studied by means of computational methods. The preferred formation of the unusual macroheterocycle, competitive with the 1,3-ring closure leading to a thiirane and the head-to-head dimerization yielding a 1,4-dithiane derivative, respectively, was explained based on the analysis of the structure of the favored conformer of the intermediate, delocalized diradical species. The influence of selenium as a ‘heavy atom’ for stabilization of this intermediate has been emphasized.

  10. Salt bridge residues between I-Ak dimer of dimers alpha-chains modulate antigen presentation.

    PubMed

    Yadati, S; Nydam, T; Demian, D; Wade, T K; Gabriel, J L; Barisas, B G; Wade, W F

    1999-03-15

    Class II dimers of dimers are predicted to have functional significance in antigen presentation. The putative contact amino acids of the I-Ak class II dimer of dimers have been identified by molecular modeling based on the DR1 crystal structure (Nydam et al., Int. Immunol. 10, 1237,1998). We have previously reported the role in antigen presentation of dimer of dimers contact amino acids located in the C-terminal domains of the alpha- and beta-chains of class II. Our calculations show that residues Ealpha89 and Ralpha145 in the alpha2-domain form an inter alpha-chain salt bridge between pairs of alphabeta-heterodimers. Other residues, Qalpha92 and Nalpha115, may be involved in close association in that part of the alpha-chain. We investigated the role of these amino acids on class II expression and antigen presentation. Class II composed of an Ealpha89K substituted alpha-chain paired with a wt beta-chain exhibited inhibited antigen presentation and expression of alpha-chain serologic epitopes. In contrast, mutation of Ralpha145E had less affect on antigen presentation and did not affect I-Ak serologic epitopes. Interchanging charges of the salt bridge residues by expressing both Ralpha145E and Ealpha89K on the same chain obviated the large negative effect of the Ealpha89K mutation on antigen presentation but not on the serologic epitopes. Our results are similar for those reported for mutation of DR3's inter-chain salt bridge with the exception that double mutants did not moderate the DR3 defect. Interestingly, the amino acids differences between I-A and DR change the location of the inter-chain salt bridges. In DR1 these residues are located at positions Ealpha88 and Kalpha111; in I-Ak these residues are located at position Ealpha89 and Ralpha145. Inter alpha-chain salt bridges are thus maintained in various class II molecules by amino acids located in different parts of the alpha2-domain. This conservation of structure suggests that considerable functional

  11. Structure, Aggregation, and Activity of a Covalent Insulin Dimer Formed During Storage of Neutral Formulation of Human Insulin.

    PubMed

    Hjorth, Christian Fogt; Norrman, Mathias; Wahlund, Per-Olof; Benie, Andrew J; Petersen, Bent O; Jessen, Christian M; Pedersen, Thomas Å; Vestergaard, Kirsten; Steensgaard, Dorte B; Pedersen, Jan Skov; Naver, Helle; Hubálek, František; Poulsen, Christian; Otzen, Daniel

    2016-04-01

    A specific covalently linked dimeric species of insulin high molecular weight products (HMWPs), formed during prolonged incubation of a neutral pharmaceutical formulation of human insulin, were characterized in terms of tertiary structure, self-association, biological activity, and fibrillation properties. The dimer was formed by a covalent link between A21Asn and B29Lys. It was analyzed using static and dynamic light scattering and small-angle X-ray scattering to evaluate its self-association behavior. The tertiary structure was obtained using nuclear magnetic resonance and X-ray crystallography. The biological activity of HMWP was determined using 2 in vitro assays, and its influence on fibrillation was investigated using Thioflavin T assays. The dimer's tertiary structure was nearly identical to that of the noncovalent insulin dimer, and it was able to form hexamers in the presence of zinc. The dimer exhibited reduced propensity for self-association in the absence of zinc but significantly postponed the onset of fibrillation in insulin formulations. Consistent with its dimeric state, the tested species of HMWP showed little to no biological activity in the used assays. This study is the first detailed characterization of a specific type of human insulin HMWP formed during storage of a marketed pharmaceutical formulation. These results indicate that this specific type of HMWP is unlikely to antagonize the physical stability of the formulation, as HMWP retained a tertiary structure similar to the noncovalent dimer and participated in hexamer assembly in the presence of zinc. In addition, increasing amounts of HMWP reduce the rate of insulin fibrillation.

  12. A Wacky Bridge to mTORC1 Dimerization.

    PubMed

    Montagne, Jacques

    2016-01-25

    The activity of the mTORC1 protein complex depends on multiple metabolic inputs that regulate dimerization, recruitment to the lysosome, and activation. In this issue of Developmental Cell, David-Morrison et al. (2016) show that the Drosophila protein Wacky and its mammalian counterpart WAC act as adaptors in the process of mTORC1 dimerization.

  13. Influence of application sequence and timing of eugenol and lauric arginate (LAE) on survival of spoilage organisms.

    PubMed

    Manrique, Yudith; Gibis, Monika; Schmidt, Herbert; Weiss, Jochen

    2017-06-01

    The effectiveness of sequential applications of the antimicrobials eugenol and lauric arginate (LAE) was investigated against Staphylococcus carnosus, Listeria innocua, Escherichia coli K12, and Pseudomonas fluorescens. The antimicrobials were applied simultaneously at half of their minimum lethal concentrations (MLC) or sequentially at t = 0 h and t = 3, 4, 6 or 8 h. Bacterial survival was determined by direct plate counts. Survivals kinetic were fitted to a growth and mortality model to obtain characteristic parameters that described time-dependent changes from growth to mortality or vice versa. The most effective was a simultaneous exposure of both antimicrobials to the spoilage organisms at the beginning of the incubation period. Efficiency decreases depending on order and timing of the two antimicrobials were observed upon sequential treatments. These were most effective when antimicrobials where applied within a short time period (3-4 h) and when eugenol was first applied against S. carnosus and P. fluorescens. No sequence effects were observed for L. innocua, and sequential treatments proved to be ineffective against E. coli K12. These results were attributed to cells adapting to the first applied antimicrobial. In some cases, this provided protection against the second antimicrobial rendering the overall treatment less effective.

  14. Sequence Variation in Amplification Target Genes and Standards Influences Interlaboratory Comparison of BK Virus DNA Load Measurement

    PubMed Central

    Solis, Morgane; Meddeb, Mariam; Sueur, Charlotte; Domingo-Calap, Pilar; Soulier, Eric; Chabaud, Angeline; Perrin, Peggy; Moulin, Bruno; Bahram, Seiamak; Stoll-Keller, Françoise; Caillard, Sophie; Barth, Heidi

    2015-01-01

    International guidelines define a BK virus (BKV) load of ≥4 log10 copies/ml as presumptive of BKV-associated nephropathy (BKVN) and a cutoff for therapeutic intervention. To investigate whether BKV DNA loads (BKVL) are comparable between laboratories, 2 panels of 15 and 8 clinical specimens (urine, whole blood, and plasma) harboring different BKV genotypes were distributed to 20 and 27 French hospital centers in 2013 and 2014, respectively. Although 68% of the reported results fell within the acceptable range of the expected result ±0.5 log10, the interlaboratory variation ranged from 1.32 to 5.55 log10. Polymorphisms specific to BKV genotypes II and IV, namely, the number and position of mutations in amplification target genes and/or deletion in standards, arose as major sources of interlaboratory disagreements. The diversity of DNA purification methods also contributed to the interlaboratory variability, in particular for urine samples. Our data strongly suggest that (i) commercial external quality controls for BKVL assessment should include all major BKV genotypes to allow a correct evaluation of BKV assays, and (ii) the BKV sequence of commercial standards should be provided to users to verify the absence of mismatches with the primers and probes of their BKV assays. Finally, the optimization of primer and probe design and standardization of DNA extraction methods may substantially decrease interlaboratory variability and allow interinstitutional studies to define a universal cutoff for presumptive BKVN and, ultimately, ensure adequate patient care. PMID:26468499

  15. Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa).

    PubMed

    Struck, Torsten H; Nesnidal, Maximilian P; Purschke, Günter; Halanych, Kenneth M

    2008-08-01

    Phylogenetic reconstructions may be hampered by multiple substitutions in nucleotide positions obliterating signal, a phenomenon called saturation. Traditionally, plotting ti/tv ratios against genetic distances has been used to reveal saturation by assessing when ti/tv stabilizes at 1. However, interpretation of results and assessment of comparability between different data sets or partitions are rather subjective. Herein, we present the new C factor, which quantifies convergence of ti/tv ratios, thus allowing comparability. Furthermore, we introduce a comparative value for homoplasy, the O/E ratio, based on alterations of tree length. Simulation studies and an empirical example, based on annelid rRNA-gene sequences, show that the C factor correlates with noise, tree length and genetic distance and therefore is a proxy for saturation. The O/E ratio correlates with the C factor, which does not provide an intrinsic threshold of exclusion, and thus both together can objectively guide decisions to exclude saturated nucleotide positions. However, analyses also showed that, for reconstructing annelid phylogeny using Maximum Likelihood, an increase in numbers of positions improves tree reconstruction more than does the exclusion of saturated positions.

  16. Integrability of PT-symmetric dimers

    NASA Astrophysics Data System (ADS)

    Pickton, J.; Susanto, H.

    2013-12-01

    The coupled discrete linear and Kerr nonlinear Schrödinger equations with gain and loss describing transport on dimers with parity-time (PT)-symmetric potentials are considered. The model is relevant among others to experiments in optical couplers and proposals on Bose-Einstein condensates in PT-symmetric double-well potentials. It is known that the models are integrable. Here, the integrability is exploited further to construct the phase portraits of the system. A pendulum equation with a linear potential and a constant force for the phase difference between the fields is obtained, which explains the presence of unbounded solutions above a critical threshold parameter. The behavior of all solutions of the system, including changes in the topological structure of the phase plane, is then discussed.

  17. Photodissociable dimer reduction products of 2-thiopyrimidine derivatives.

    PubMed

    Wrona, M; Giziewicz, J; Shugar, D

    1975-12-01

    Both 4,6-dimethyl-2-thipyrimidine and its 1-methyl derivative undergo polarographic reduction in aqueous medium, via a 1e/1H+ reduction to a free radical which rapidly dimerizes to products isolates and identified as 4,4'-bis-(4,6-dimethyl-3,4-dihydropyrimidin-2-thione) and the corresponding 1-methyl dimer. The dimers may be oxidized electrolytically to regenerate the parent monomers. Both dimers also undergo photodissociation to quantitatively regenerate the parent monomers, in high quantum yield, 0.23 and 0.35 M/Einstein. The correlation between electrochemical and photochemical reductions of 2-thiopyrimidines are discussed, as well as the significance of the dimer photodissociation reactions in relation to nucleic acid photochemistry.

  18. Palladium dimers adsorbed on graphene: A DFT study

    NASA Astrophysics Data System (ADS)

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-05-01

    The 2D structure of graphene shows a great promise for enhanced catalytic activity when adsorbed with palladium. We performed a systematic density functional theory (DFT) study of the adsorption of palladium dimer (Pd2) on graphene using SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Pd2-graphene system are calculated. Both horizontal and vertical orientations of Pd2 on graphene are studied. Our calculations revealed that the minimum energy configuration for Pd dimer is parallel to the graphene sheet with its two atoms occupying centre of adjacent hexagonal rings of graphene sheet. Magnetic moment is induced for Pd dimer adsorbed on graphene in vertical orientation while horizontal orientation of Pd dimer on graphene do not exhibit magnetism. Insignificant energy differences among adsorption sites means that dimer mobility on the graphene sheet is high. There is imperceptible distortion of graphene sheet perpendicular to its plane. However, some lateral displacements are seen.

  19. Internal structure of nanoparticle dimers linked by DNA.

    PubMed

    Chi, Cheng; Vargas-Lara, Fernando; Tkachenko, Alexei V; Starr, Francis W; Gang, Oleg

    2012-08-28

    We construct nanoparticle dimers linked by DNA. These dimers are basic units in a possible multiscale, hierarchical assembly and serve as a model system to understand DNA-mediated interactions, especially in the nontrivial regime when the nanoparticle and DNA are comparable in their sizes. We examine the structure of nanoparticle dimers in detail by a combination of scattering experiments and molecular simulations. We find that, for a given DNA length, the interparticle separation within the dimer is controlled primarily by the number of linking DNA. We summarize our findings in a simple model that captures the interplay of the number of DNA bridges, their length, the particle's curvature, and the excluded volume effects. We demonstrate the applicability of the model to our results, without any free parameters. As a consequence, the increase of dimer separation with increasing temperature can be understood as a result of changing the number of connecting DNA.

  20. Structures of dimeric hydrolysis products of thorium.

    PubMed

    Wilson, Richard E; Skanthakumar, S; Sigmon, Ginger; Burns, Peter C; Soderholm, L

    2007-04-02

    Three unique thorium dimeric compounds have been crystallized from either direct hydrolysis of Th4+(aq)/HCl or titration of Th(OH)4(am) with Th(NO3)4(aq) and their structures determined using single-crystal X-ray diffraction. The compound [Th2(micro2-OH)2(NO3)6(H2O)6]H2O (1) is identical to that identified previously by Johansson. Two additional unreported compounds have been identified, [Th2(micro2-OH)2(NO3)4(H2O)8](NO3)2 (2) and [Th2(micro2-OH)2Cl2(H2O)12]Cl4.2H2O (3). 1 crystallizes in the monoclinic space group P21/c, with a = 6.792(2) A, b = 11.710(4) A, c = 13.778(5) A, and beta = 102.714(5) degrees and 2 crystallizes in the monoclinic space group P21/n, with a = 6.926(5) A, b = 7.207(1) A, c = 21.502(1) A, and beta = 96.380(1) degrees . The chloride-containing dimer, 3, crystallizes in triclinic P, with a = 8.080(2) A, b = 8.880(2) A, c = 9.013(2) A, alpha = 97.41(3) degrees , beta = 91.00(3), and gamma = 116.54(3) degrees . We also present high-energy X-ray scattering data demonstrating the presence of the hydroxo-bridged moiety in solution and discuss our findings in the context of known solid-state structures. The three structures demonstrate 11-, 10-, and 9-coordinate thorium, respectively, and coupled with the scattering experiments provide additional structural and chemical insight into tetravalent actinide hydrolysis.

  1. Retention of nucleic acids in ion-pair reversed-phase high-performance liquid chromatography depends not only on base composition but also on base sequence.

    PubMed

    Qiao, Jun-Qin; Liang, Chao; Wei, Lan-Chun; Cao, Zhao-Ming; Lian, Hong-Zhen

    2016-12-01

    The study on nucleic acid retention in ion-pair reversed-phase high-performance liquid chromatography mainly focuses on size-dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double-stranded DNAs were investigated on silica-based C18 stationary phase by ion-pair reversed-phase high-performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self-dimerization have weaker retention than those not prone to self-dimerization but with the same base composition. However, homo-oligonucleotides are suitable for the size-dependent separation as a special case of oligonucleotides. For double-stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double-stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion-pair reversed-phase high-performance liquid chromatography.

  2. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: excision of dimers in cell extracts

    SciTech Connect

    Reynolds, R.J.; Love, J.D.; Friedberg, E.C.

    1981-08-01

    Cell-free extracts prepared from rad1-19, rad2-2, rad3-1, rad4-3, rad7-1, rad10-1, rad14-1, rad16-1, and cycl-1 (rad7) mutants of Saccharomyces cerevisiae all catalyze the preferential excision of thymine-containing pyrimidine dimers from ultraviolet-irradiated DNA specifically incised with M. luteus ultraviolet deoxyribonucleic acid incising activity.

  3. Imaging the impulsive alignment of noble-gas dimers via Coulomb explosion

    NASA Astrophysics Data System (ADS)

    Veltheim, A. von; Borchers, B.; Steinmeyer, G.; Rottke, H.

    2014-02-01

    The impulsive alignment of the noble-gas dimers Ne2, Ar2, Kr2, and Xe2 is experimentally investigated by determining the alignment through Coulomb explosion imaging after their double ionization. This approach yields a favorably detailed insight into the temporal evolution of the alignment succeeding the aligning laser pulse. Particular emphasis is put on analyzing higher order coherences induced in the density matrix as these coherences determine the details of the temporal evolution of the aligned molecular ensemble. The recorded data enable an extraction of polarizability anisotropies for the dimers and of their rotational constants in the vibrational ground state. At the elevated level of rotational excitation obtained, centrifugal distortion starts influencing the temporal evolution of the alignment.

  4. Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility

    PubMed Central

    Meyer, Febé E.; Shuey, Louise S.; Naidoo, Sitha; Mamni, Thandekile; Berger, Dave K.; Myburg, Alexander A.; van den Berg, Noëlani; Naidoo, Sanushka

    2016-01-01

    Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction. PMID:26973660

  5. Isolation site influences virulence phenotype of serotype 14 Streptococcus pneumoniae strains belonging to multilocus sequence type 15.

    PubMed

    Amin, Zarina; Harvey, Richard M; Wang, Hui; Hughes, Catherine E; Paton, Adrienne W; Paton, James C; Trappetti, Claudia

    2015-12-01

    Streptococcus pneumoniae is a diverse species causing invasive as well as localized infections that result in massive global morbidity and mortality. Strains vary markedly in pathogenic potential, but the molecular basis is obscured by the diversity and plasticity of the pneumococcal genome. We have previously reported that S. pneumoniae serotype 3 isolates belonging to the same multilocus sequence type (MLST) differed markedly in in vitro and in vivo phenotypes, in accordance with the clinical site of isolation, suggesting stable niche adaptation within a clonal lineage. In the present study, we have extended our analysis to serotype 14 clinical isolates from cases of sepsis or otitis media that belong to the same MLST (ST15). In a murine intranasal challenge model, five ST15 isolates (three from blood and two from ears) colonized the nasopharynx to similar extents. However, blood and ear isolates exhibited significant differences in bacterial loads in other host niches (lungs, ear, and brain) at both 24 and 72 h postchallenge. In spite of these differences, blood and ear isolates were present in the lungs at similar levels at 6 h postchallenge, suggesting that early immune responses may underpin the distinct virulence phenotypes. Transcriptional analysis of lung tissue from mice infected for 6 h with blood isolates versus ear isolates revealed 8 differentially expressed genes. Two of these were exclusively expressed in response to infection with the ear isolate. These results suggest a link between the differential capacities to elicit early innate immune responses and the distinct virulence phenotypes of clonally related S. pneumoniae strains.

  6. Dimers in α-pinene secondary organic aerosol: effect of hydroxyl radical, ozone, relative humidity and aerosol acidity

    NASA Astrophysics Data System (ADS)

    Kristensen, K.; Cui, T.; Zhang, H.; Gold, A.; Glasius, M.; Surratt, J. D.

    2014-04-01

    The formation of secondary organic aerosol (SOA) from both ozonolysis and hydroxyl radical (OH)-initiated oxidation of α-pinene under conditions of high nitric oxide (NO) concentrations with varying relative humidity (RH) and aerosol acidity was investigated in the University of North Carolina dual outdoor smog chamber facility. SOA formation from ozonolysis of α-pinene was enhanced relative to that from OH-initiated oxidation in the presence of initially high-NO conditions. However, no effect of RH on SOA mass was evident. Ozone (O3)-initiated oxidation of α-pinene in the presence of ammonium sulfate (AS) seed coated with organic aerosol from OH-initiated oxidation of α-pinene showed reduced nucleation compared to ozonolysis in the presence of pure AS seed aerosol. The chemical composition of α-pinene SOA was investigated by ultra-performance liquid chromatography/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry (UPLC/ESI-HR-Q-TOFMS), with a focus on the formation of carboxylic acids and high-molecular weight dimers. A total of eight carboxylic acids and four dimers were identified, constituting between 8 and 12% of the total α-pinene SOA mass. OH-initiated oxidation of α-pinene in the presence of nitrogen oxides (NOx) resulted in the formation of highly oxidized carboxylic acids, such as 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA) and diaterpenylic acid acetate (DTAA). The formation of dimers was observed only in SOA produced from the ozonolysis of α-pinene in the absence of NOx, with increased concentrations by a factor of two at higher RH (50-90%) relative to lower RH (30-50%). The increased formation of dimers correlates with an observed increase in new particle formation at higher RH due to nucleation. Increased aerosol acidity was found to have a negligible effect on the formation of the dimers. SOA mass yield did not influence the chemical composition of SOA formed from α-pinene ozonolysis with respect to

  7. The influence of delta formation mechanism on geotechnical property sequence of the late Pleistocene-Holocene sediments in the Mekong River Delta.

    PubMed

    Hoang, Truong Minh; van Lap, Nguyen; Oanh, Ta Thi Kim; Jiro, Takemura

    2016-11-01

    The aim of the study was to characterize a variety of microstructure development-levels and geotechnical property sequences of the late Pleistocene-Holocene deposits in the Mekong River delta (MRD), and the paper furthermore discusses the influences of delta formation mechanisms on them. The survey associated the geotechnical engineering and the sedimentary geology of the late Pleistocene-Holocene deposits at five sites and also undifferentiated Pleistocene sediments. A cross-section which was rebuilt in the delta progradation-direction and between the Mekong and Bassac rivers represents the stratigraphy. Each sedimentary unit was formed under a different delta formation mechanism and revealed a typical geotechnical property sequence. The mechanical behaviors of the sediment succession in the tide-dominated delta with significant fluvial-activity and material source tend to be more cohesionless soils and strengths than those in the tide- and wave-dominated delta and even the coast. The particular tendency of the mechanical behavior of the deposit succession can be reasonably estimated from the delta formation mechanism. The characteristics of the clay minerals from the Mekong River produced the argillaceous soil which does not have extremely high plasticity. The microstructure development-levels are low to very high indicating how to choose hydraulic conductivity value, k, for estimating overconsolidation ratio, OCR, by the piezocone penetration tests (CPTU). The OCR of sediments in the delta types strangely change with depth but none less than 1. The post-depositional processes significantly influenced the microstructure development, particularly the dehydrating and oxidizing processes.

  8. Role of a Putative gp41 Dimerization Domain in Human Immunodeficiency Virus Type 1 Membrane Fusion

    SciTech Connect

    Liu, J.; Deng, Y; Li, Q; Dey, A; Moore, J; Lu, M

    2010-01-01

    The entry of human immunodeficiency virus type 1 (HIV-1) into a target cell entails a series of conformational changes in the gp41 transmembrane glycoprotein that mediates the fusion of the viral and target cell membranes. A trimer-of-hairpins structure formed by the association of two heptad repeat (HR) regions of the gp41 ectodomain has been implicated in a late step of the fusion pathway. Earlier native and intermediate states of the protein are postulated to mediate the antiviral activity of the fusion inhibitor enfuvirtide and of broadly neutralizing monoclonal antibodies (NAbs), but the details of these structures remain unknown. Here, we report the identification and crystal structure of a dimerization domain in the C-terminal ectodomain of gp41 (residues 630 to 683, or C54). Two C54 monomers associate to form an asymmetric, antiparallel coiled coil with two distinct C-terminal {alpha}-helical overhangs. This dimer structure is conferred largely by interactions within a central core that corresponds to the sequence of enfuvirtide. The mutagenic alteration of the dimer interface severely impairs the infectivity of Env-pseudotyped viruses. Moreover, the C54 structure binds tightly to both the 2F5 and 4E10 NAbs and likely represents a potential intermediate conformation of gp41. These results should enhance our understanding of the molecular basis of the gp41 fusogenic structural transitions and thereby guide rational, structure-based efforts to design new fusion inhibitors and vaccine candidates intended to induce broadly neutralizing antibodies.

  9. Formation of cyclobutane thymine dimers photosensitized by pyridopsoralens: Quantitative and qualitative distribution within DNA

    SciTech Connect

    Moysan, A.; Viari, A.; Vigny, P. ); Voituriez, L.; Cadet J. ); Moustacchi, E.; Sage, E. )

    1991-07-23

    As after irradiation with 254-nm UV light, exposure of thymidine and three isomeric pyridopsoralen derivatives to UVA radiation, in the dry state, leads to the formation of the six diastereomers of cyclobutadithymidine as the predominant reaction. This unexpected photosensitized reaction, which also gives rise to both 5R* and 5S* diastereomers of 5,6-dihydro-5-({alpha}-thymidylyl)thymidine (or spore photoproduct), is selective since (2+2) dimerization of 2{prime}-deoxycytidine was not detected under the same experimental conditions. The cis-syn isomer of cyclobutadithymine was also found to be produced within isolated DNA following UVA irradiation in aqueous solutions containing 7-methylpyrido (3,4-c)psoralen. Quantitatively, this photoproduct represents about one-fifth of the overall yield of the furan-side pyridopsoralen (2+2) photocycloadducts the thymine. DNA sequencing methodology was used to demonstrate that pyridopsoralen-photosensitized DNA is a substrate for T4 endonuclease V and Escherichia coli photoreactivating enzyme, two enzymes acting specifically on cyclobutane pyrimidine dimers. The formation of cyclobutane thymine dimers concomitant to that of thymine-furocoumarin photoadducts and their eventual implication in the photobiological effects of the pyridopsoralens are discussed.

  10. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.

    PubMed

    Tsai, Shengdar Q; Wyvekens, Nicolas; Khayter, Cyd; Foden, Jennifer A; Thapar, Vishal; Reyon, Deepak; Goodwin, Mathew J; Aryee, Martin J; Joung, J Keith

    2014-06-01

    Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we describe dimeric RNA-guided FokI nucleases (RFNs) that can recognize extended sequences and edit endogenous genes with high efficiencies in human cells. RFN cleavage activity depends strictly on the binding of two guide RNAs (gRNAs) to DNA with a defined spacing and orientation substantially reducing the likelihood that a suitable target site will occur more than once in the genome and therefore improving specificities relative to wild-type Cas9 monomers. RFNs guided by a single gRNA generally induce lower levels of unwanted mutations than matched monomeric Cas9 nickases. In addition, we describe a simple method for expressing multiple gRNAs bearing any 5' end nucleotide, which gives dimeric RFNs a broad targeting range. RFNs combine the ease of RNA-based targeting with the specificity enhancement inherent to dimerization and are likely to be useful in applications that require highly precise genome editing.

  11. CENPT bridges adjacent CENPA nucleosomes on young human α-satellite dimers

    PubMed Central

    Thakur, Jitendra; Henikoff, Steven

    2016-01-01

    Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. Two components of the CCAN, CENPC and the histone-fold protein CENPT, provide independent connections from the ∼171-bp centromeric α-satellite repeat units to the outer kinetochore. However, the spatial relationship between CENPA nucleosomes and these two branches remains unclear. To address this issue, we use a base-pair resolution genomic readout of protein–protein interactions, comparative chromatin immunoprecipitation (ChIP) with sequencing, together with sequential ChIP, to infer the in vivo molecular architecture of the human CCAN. In contrast to the currently accepted model in which CENPT associates with H3 nucleosomes, we find that CENPT is centered over the CENPB box between two well-positioned CENPA nucleosomes on the most abundant centromeric young α-satellite dimers and interacts with the CENPB/CENPC complex. Upon cross-linking, the entire CENPA/CENPB/CENPC/CENPT complex is nuclease-protected over an α-satellite dimer that comprises the fundamental unit of centromeric chromatin. We conclude that CENPA/CENPC and CENPT pathways for kinetochore assembly are physically integrated over young α-satellite dimers. PMID:27384170

  12. Pentapeptide-repeat proteins that act as topoisomerase poison resistance factors have a common dimer interface

    PubMed Central

    Vetting, Matthew W.; Hegde, Subray S.; Zhang, Yong; Blanchard, John S.

    2011-01-01

    The protein AlbG is a self-resistance factor against albicidin, a nonribosomally encoded hybrid polyketide-peptide with antibiotic and phytotoxic properties produced by Xanthomonas albilineans. Primary-sequence analysis indicates that AlbG is a member of the pentapeptide-repeat family of proteins (PRP). The structure of AlbG from X. albilineans was determined at 2.0 Å resolution by SAD phasing using data collected from a single trimethyllead acetate derivative on a home source. AlbG folds into a right-handed quadrilateral β-helix composed of approximately eight semi-regular coils. The regularity of the β-­helix is blemished by a large loop/deviation in the β-helix between coils 4 and 5. The C-terminus of the β-helix is capped by a dimerization module, yielding a dimer with a 110 Å semi-collinear β-helical axis. This method of dimer formation appears to be common to all PRP proteins that confer resistance to topoisomerase poisons and contrasts with most PRP proteins, which are typically monomeric. PMID:21393830

  13. System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids

    PubMed Central

    Gao, Rong; Tao, Yuan; Stock, Ann M

    2008-01-01

    Two-component signal transduction, featuring highly conserved histidine kinases (HKs) and response regulators (RRs), is one of the most prevalent signalling schemes in prokaryotes. RRs function as phosphorylation-activated switches to mediate diverse output responses, mostly via transcription regulation. As bacterial genomes typically encode multiple two-component proteins for distinct signalling pathways, the sequence and structural similarities of RR receiver domains create significant challenges to maintain interaction specificity. It is especially demanding for members of the OmpR/PhoB subfamily, the largest RR subfamily, which share a conserved dimerization interface for phosphorylation-mediated transcription regulation. We developed a strategy to investigate RR interaction by analysing Förster resonance energy transfer (FRET) between cyan fluorescent protein (CFP)- and yellow fluorescent protein (YFP)-fused RRs in vitro. Using the Escherichia coli RR PhoB as a model system, we were able to observe phosphorylation-dependent FRET between fluorescent protein (FP)–PhoB proteins and validated the FRET method by determining dimerization affinity and dimerization-coupled phosphorylation kinetics that recapitulated values determined by alternative methods. Further application of the FRET method to all E. coli OmpR/PhoB subfamily RRs revealed that phosphorylation–activated RR interaction is indeed a common theme for OmpR/PhoB subfamily RRs and these RRs display significant interaction specificity. Weak hetero-pair interactions were also identified between several different RRs, suggesting potential cross-regulation between distinct pathways. PMID:18631241

  14. Homing endonuclease I-TevIII: dimerization as a means to a double-strand break

    PubMed Central

    Robbins, Justin B.; Stapleton, Michelle; Stanger, Matthew J.; Smith, Dorie; Dansereau, John T.; Derbyshire, Victoria; Belfort, Marlene

    2007-01-01

    Homing endonucleases are unusual enzymes, capable of recognizing lengthy DNA sequences and cleaving site-specifically within genomes. Many homing endonucleases are encoded within group I introns, and such enzymes promote the mobility reactions of these introns. Phage T4 has three group I introns, within the td, nrdB and nrdD genes. The td and nrdD introns are mobile, whereas the nrdB intron is not. Phage RB3 is a close relative of T4 and has a lengthier nrdB intron. Here, we describe I-TevIII, the H–N–H endonuclease encoded by the RB3 nrdB intron. In contrast to previous reports, we demonstrate that this intron is mobile, and that this mobility is dependent on I-TevIII, which generates 2-nt 3′ extensions. The enzyme has a distinct catalytic domain, which contains the H–N–H motif, and DNA-binding domain, which contains two zinc fingers required for interaction with the DNA substrate. Most importantly, I-TevIII, unlike the H–N–H endonucleases described so far, makes a double-strand break on the DNA homing site by acting as a dimer. Through deletion analysis, the dimerization interface was mapped to the DNA-binding domain. The unusual propensity of I-TevIII to dimerize to achieve cleavage of both DNA strands underscores the versatility of the H–N–H enzyme family. PMID:17289754

  15. Distribution of ions around thymine dimer containing DNA: A possible recognition element for endonuclease V

    SciTech Connect

    Osman, R.; Luo, N.; Miaskiewicz, K.; Miller, J.

    1995-10-01

    The molecular link between sunlight exposure and skin cancer can be traced to the formation of cyclobutane pyrimidine dimers together with (6-4) photoadducts of pyrimidines in DNA upon exposure to UV radiation. The mutagenicity of these lesions is frequently explained by miscoding during DNA replication due to perturbations of base-pairing interactions. However the mutagenicity of UV photoproducts depends of their sequence context, suggesting that more global structural changes in DNA contribute to mutation induction. One of the most effective protections against the deleterious effects of cyclobutane pyrimidine dimers is the wide range of repair of this lesion by different enzymatic pathways. This paper presents the results of a 200 ps molecular dynamics simulation on the dodecarner d(CGCGAATTCGCG){sub 2} containing a cis, syn-cyclobutane thymine dimer, explicit water and counterions. The averaged structure calculated from the simulation shows good agreement with the available NMR data. The distribution of counterions around the damaged DNA is different from that around a non damaged DNA and suggests a possible mechanism of damage recognition by the enzyme.

  16. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  17. Targeted Next-Generation Sequencing of Plasma DNA from Cancer Patients: Factors Influencing Consistency with Tumour DNA and Prospective Investigation of Its Utility for Diagnosis

    PubMed Central

    Kaisaki, Pamela J.; Cutts, Anthony; Popitsch, Niko; Camps, Carme; Pentony, Melissa M.; Wilson, Gareth; Page, Suzanne; Kaur, Kulvinder; Vavoulis, Dimitris; Henderson, Shirley; Gupta, Avinash; Middleton, Mark R.; Karydis, Ioannis; Talbot, Denis C.; Schuh, Anna; Taylor, Jenny C.

    2016-01-01

    Use of circulating tumour DNA (ctDNA) as a liquid biopsy has been proposed for potential identification and monitoring of solid tumours. We investigate a next-generation sequencing approach for mutation detection in ctDNA in two related studies using a targeted panel. The first study was retrospective, using blood samples taken from melanoma patients at diverse timepoints before or after treatment, aiming to evaluate correlation between mutations identified in biopsy and ctDNA, and to acquire a first impression of influencing factors. We found good concordance between ctDNA and tumour mutations of melanoma patients when blood samples were collected within one year of biopsy or before treatment. In contrast, when ctDNA was sequenced after targeted treatment in melanoma, mutations were no longer found in 9 out of 10 patients, suggesting the method might be useful for detecting treatment response. Building on these findings, we focused the second study on ctDNA obtained before biopsy in lung patients, i.e. when a tentative diagnosis of lung cancer had been made, but no treatment had started. The main objective of this prospective study was to evaluate use of ctDNA in diagnosis, investigating the concordance of biopsy and ctDNA-derived mutation detection. Here we also found positive correlation between diagnostic lung biopsy results and pre-biopsy ctDNA sequencing, providing support for using ctDNA as a cost-effective, non-invasive solution when the tumour is inaccessible or when biopsy poses significant risk to the patient. PMID:27626278

  18. Influence of pH, soil humic/fulvic acid, ionic strength, foreign ions and addition sequences on adsorption of Pb(II) onto GMZ bentonite.

    PubMed

    Wang, Suowei; Hu, Jun; Li, Jiaxing; Dong, Yunhui

    2009-08-15

    This work contributed to the adsorption of Pb(II) onto GMZ bentonite in the absence and presence of soil humic acid (HA)/fulvic acid (FA) using a batch technique. The influences of pH from 2 to 12, ionic strengths from 0.004M to 0.05M NaNO(3), soil HA/FA concentrations from 1.6 mg/L to 20mg/L, foreign cations (Li+, Na+, K+), anions (Cl(-), NO(3)(-)), and addition sequences on the adsorption of Pb(II) onto GMZ bentonite were tested. The adsorption isotherms of Pb(II) were determined at pH 3.6+/-0.1 and simulated with the Langmuir, Freundlich, and D-R adsorption models, respectively. The results demonstrated that the adsorption of Pb(II) onto GMZ bentonite increased with increasing pH from 2 to 6. HA was shown to enhance Pb(II) adsorption at low pH, but to reduce Pb(II) adsorption at high pH, whereas FA was shown to decrease Pb(II) adsorption at pH from 2 to 11. The results also demonstrated that the adsorption was strongly dependent on ionic strength and slightly dependent on the concentration of HA/FA. The adsorption of Pb(II) onto GMZ bentonite was dependent on foreign ions in solution. The addition sequences of bentonite/Pb(II)/HA had no effect on the adsorption of Pb(II).

  19. Data completeness of the Kumamoto earthquake sequence in the JMA catalog and its influence on the estimation of the ETAS parameters

    NASA Astrophysics Data System (ADS)

    Zhuang, Jiancang; Ogata, Yosihiko; Wang, Ting

    2017-02-01

    This study investigates the missing data problem in the Japan Meteorological Agency catalog of the Kumamoto aftershock sequence, which occurred since April 15, 2016, in Japan. Based on the assumption that earthquake magnitudes are independent of their occurrence times, we replenish the short-term missing data of small earthquakes by using a bi-scale transformation and study their influence on the maximum likelihood estimate (MLE) of the epidemic-type aftershock sequences (ETAS) parameters by comparing the analysis results from the original and the replenished datasets. The results show that the MLEs of the ETAS parameters vary when this model is fitted to the recorded catalog with different cutoff magnitudes, while those MLEs remain stable for the replenished dataset. Further analysis shows that the seismicity becomes quiescent after the occurrence of the second major shock, which can be regarded as a precursory phenomenon of the occurrence of the subsequent M_J7.3 mainshock. This relative quiescence is demonstrated more clearly by the analysis of the replenished dataset.

  20. The dimerization motif of the glycophorin A transmembrane segment in membranes: importance of glycine residues.

    PubMed

    Brosig, B; Langosch, D

    1998-04-01

    The glycophorin A transmembrane segment homo-dimerizes to a right-handed pair of alpha-helices. Here, we identified the amino acid motif mediating this interaction within a natural membrane environment. Critical residues were grafted onto two different hydrophobic host sequences in a stepwise manner and self-assembly of the hybrid sequences was determined with the ToxR transcription activator system. Our results show that the motif LIxxGxxxGxxxT elicits a level of self-association equivalent to that of the original glycophorin A transmembrane segment. This motif is very similar to the one previously established in detergent solution. Interestingly, the central GxxxG motif by itself already induced strong self-assembly of host sequences and the three-residue spacing between both glycines proved to be optimal for the interaction. The GxxxG element thus appears to be the most crucial part of the interaction motif.

  1. The dimerization motif of the glycophorin A transmembrane segment in membranes: importance of glycine residues.

    PubMed Central

    Brosig, B.; Langosch, D.

    1998-01-01

    The glycophorin A transmembrane segment homo-dimerizes to a right-handed pair of alpha-helices. Here, we identified the amino acid motif mediating this interaction within a natural membrane environment. Critical residues were grafted onto two different hydrophobic host sequences in a stepwise manner and self-assembly of the hybrid sequences was determined with the ToxR transcription activator system. Our results show that the motif LIxxGxxxGxxxT elicits a level of self-association equivalent to that of the original glycophorin A transmembrane segment. This motif is very similar to the one previously established in detergent solution. Interestingly, the central GxxxG motif by itself already induced strong self-assembly of host sequences and the three-residue spacing between both glycines proved to be optimal for the interaction. The GxxxG element thus appears to be the most crucial part of the interaction motif. PMID:9568912

  2. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.

    PubMed

    Johnson, Rachel M; Rath, Arianna; Deber, Charles M

    2006-12-01

    Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (TM) helices. While the stability of helix-helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix-helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of alpha-helical TM segments.

  3. Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin.

    PubMed

    Phang, Juanita M; Harrop, Stephen J; Duff, Anthony P; Sokolova, Anna V; Crossett, Ben; Walsh, James C; Beckham, Simone A; Nguyen, Cuong D; Davies, Roberta B; Glöckner, Carina; Bromley, Elizabeth H C; Wilk, Krystyna E; Curmi, Paul M G

    2016-09-15

    Ezrin is a member of the ERM (ezrin-radixin-moesin) family of proteins that have been conserved through metazoan evolution. These proteins have dormant and active forms, where the latter links the actin cytoskeleton to membranes. ERM proteins have three domains: an N-terminal FERM [band Four-point-one (4.1) ERM] domain comprising three subdomains (F1, F2, and F3); a helical domain; and a C-terminal actin-binding domain. In the dormant form, FERM and C-terminal domains form a stable complex. We have determined crystal structures of the active FERM domain and the dormant FERM:C-terminal domain complex of human ezrin. We observe a bistable array of phenylalanine residues in the core of subdomain F3 that is mobile in the active form and locked in the dormant form. As subdomain F3 is pivotal in binding membrane proteins and phospholipids, these transitions may facilitate activation and signaling. Full-length ezrin forms stable monomers and dimers. We used small-angle X-ray scattering to determine the solution structures of these species. As expected, the monomer shows a globular domain with a protruding helical coiled coil. The dimer shows an elongated dumbbell structure that is twice as long as the monomer. By aligning ERM sequences spanning metazoan evolution, we show that the central helical region is conserved, preserving the heptad repeat. Using this, we have built a dimer model where each monomer forms half of an elongated antiparallel coiled coil with domain-swapped FERM:C-terminal domain complexes at each end. The model suggests that ERM dimers may bind to actin in a parallel fashion.

  4. Threshold electron attachment and electron impact ionization involving oxygen dimers

    NASA Astrophysics Data System (ADS)

    Kreil, J.; Ruf, M.-W.; Hotop, H.; Ettischer, I.; Buck, U.

    1998-12-01

    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O 2) 2. In the electron attachment experiment we study electron transfer from state-selected Ar **(20d) Rydberg atoms to O 2 molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures ( T0) and stagnation pressures ( p0). The relative dimer density is determined through measurements of Penning ionization by metastable Ne *(3s 3P2,0) atoms and used to estimate the absolute cross-section for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 dimers to be nearly 10 -17 m 2, almost four orders of magnitude larger than that for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O 2) 2 only 3.6(4)% of the dimers are detected as dimer ions (O 2) 2+. In additional experiments involving SF 6 clusters we show that SF 6 dimers fragment nearly completely upon 70 eV electron impact, yielding SF 5+ ions (probability for (SF 6)·SF 5+ production at most 0.3%).

  5. The N-terminal tails of the H2A-H2B histones affect dimer structure and stability.

    PubMed

    Placek, Brandon J; Gloss, Lisa M

    2002-12-17

    The histone proteins of the core nucleosome are highly basic and form heterodimers in a "handshake motif." The N-terminal tails of the histones extend beyond the canonical histone fold of the hand-shake motif and are the sites of posttranslational modifications, including lysine acetylations and serine phosphorylations, which influence chromatin structure and activity as well as alter the charge state of the tails. However, it is not well understood if these modifications are signals for recruitment of other cellular factors or if the removal of net positive charge from the N-terminal tail plays a role in the overall structure of chromatin. To elucidate the effects of the N-terminal tails on the structure and stability of histones, the highly charged N-terminal tails were truncated from the H2A and H2B histones. Three mutant dimers were studied: DeltaN-H2A/WT H2B; WT H2A/DeltaN-H2B, and DeltaN-H2A/DeltaN-H2B. The CD spectra, stabilities to urea-denaturation, and the salt-dependent stabilization of the three truncated dimers were compared with those of the wild-type dimer. The data support four conclusions regarding the effects of the N-terminal tails of H2A and H2B: (1) Removal of the N-terminal tails of H2A and H2B enhance the helical structure of the mutant heterodimers. (2) Relative to the full-length WT heterodimer, the DeltaN-H2A/WT H2B dimer is destabilized, while the WT H2A/DeltaN-H2B and DeltaN-H2A/DeltaN-H2B dimers are slightly stabilized. (3) The truncated dimers exhibit decreased m values, relative to the WT dimer, supporting the hypothesis that the N-terminal tails in the isolated dimer adopt a collapsed structure. (4) Electrostatic repulsion in the N-terminal tails decreases the stability of the H2A-H2B dimer.

  6. Discovery of porcine miRNA-196a/b may influence porcine adipogenesis in longissimus dorsi muscle by miRNA sequencing.

    PubMed

    Liu, Linqing; Qian, Kun; Wang, Chonglong

    2017-04-01

    Intramuscular fat (IMF) is one of the fat traits that has economic importance in the pork industry. Longissimus dorsi muscle contains IMF and is suitable for studying adipogenesis. To discover further potential regulatory miRNAs that may influence adipogenesis, we analyzed miRNA in the longissimus dorsi muscle of Yorkshire (YY, lean-type) and Chinese Wannanhua (WH, fatty) pigs using miRNA sequencing (miRNA-seq). From this dataset, we identified 598 unique miRNAs comprising 325 pre-miRNAs and 273 novel pre-miRNAs through comparison with known miRNAs in miRBase version 21. We found 42 miRNAs including nine up- and 33 down-regulated between the YY and WH pigs. Moreover, we found two miRNAs, miR-196a/b (miR-196a, miR-196b-5p), that had the highest level of expression in WH pigs, and miR-196a/b may influence porcine adipogenesis in longissimus dorsi muscle through an adipocytokine signaling pathway.

  7. Plaquette order in a dimerized frustrated spin ladder

    NASA Astrophysics Data System (ADS)

    Shlagman, Ofer; Shimshoni, Efrat

    2014-11-01

    We study the effect of dimerization (due to, e.g., spin-Peierls instability) on the phase diagram of a frustrated antiferromagnetic spin-1/2 ladder, with weak transverse and diagonal rung coupling. Our analysis focuses on a one-dimensional version of the model (i.e., a single two-leg ladder) where we consider two forms of dimerization on the legs: columnar dimers (CDs) and staggered dimers (SDs). We examine in particular the regime of parameters (corresponding to an intermediate X X Z anisotropy) in which the leg dimerization and the rung coupling terms are equally relevant. In both the CD and SD cases, we find that the effective field theory describing the system is a self-dual sine-Gordon model, which favors ordering and the opening of a gap to excitations. The order parameter, which reflects the interplay between the leg and rung dimerization interactions, represents a crystal of 4-spin plaquettes on which longitudinal and transverse dimers are in a coherent superposition. Depending on the leg dimerization mode, these plaquettes are closed or open, however both types spontaneously break reflection symmetry across the ladder. The closed plaquettes are stable, while the open plaquette order is relatively fragile and the corresponding gap may be tuned to zero under extreme conditions. We further find that a first-order transition occurs from the plaquette order to a valence bond crystal (VBC) of dimers on the legs. This suggests that in a higher-dimensional version of this system, this variety of distinct VBC states with comparable energies leads to the formation of domains. Effectively one-dimensional gapless spinon modes on domain boundaries may account for the experimental observation of spin-liquid behavior in a physical realization of the model.

  8. Monofunctionalization and dimerization of nanoparticles using coordination chemistry.

    PubMed

    Dewi, Melissa R; Gschneidtner, Tina A; Elmas, Sait; Ranford, Michael; Moth-Poulsen, Kasper; Nann, Thomas

    2015-02-24

    This paper describes a strategy for controlled nanoparticle dimerization by using a solid support approach. Two types of nanoparticles have been linked by using a 5-([2,2':6',2″-terpyridine]-4'-yloxy)pentan-1-amine (terpy-amine) iron complex. The strategy includes two major steps: first, the monofunctionalization of individual nanoparticles with terpy-amine ligand molecules on a solid support, followed by release of monofunctionalized particles and subsequent dimerization. The versatility of the approach was demonstrated by dimerizing two different types of nanoparticles: spherical gold and cube-shaped iron oxide nanoparticles.

  9. Ballistic transport in one-dimensional random dimer photonic crystals

    NASA Astrophysics Data System (ADS)

    Cherid, Samira; Bentata, Samir; Zitouni, Ali; Djelti, Radouan; Aziz, Zoubir

    2014-04-01

    Using the transfer-matrix technique and the Kronig Penney model, we numerically and analytically investigate the effect of short-range correlated disorder in Random Dimer Model (RDM) on transmission properties of the light in one dimensional photonic crystals made of three different materials. Such systems consist of two different structures randomly distributed along the growth direction, with the additional constraint that one kind of these layers always appear in pairs. It is shown that the one dimensional random dimer photonic crystals support two types of extended modes. By shifting of the dimer resonance toward the host fundamental stationary resonance state, we demonstrate the existence of the ballistic response in these systems.

  10. [Dichotomizing method applied to calculating equilibrium constant of dimerization system].

    PubMed

    Cheng, Guo-zhong; Ye, Zhi-xiang

    2002-06-01

    The arbitrary trivariate algebraic equations are formed based on the combination principle. The univariata algebraic equation of equilibrium constant kappa for dimerization system is obtained through a series of algebraic transformation, and it depends on the properties of monotonic functions whether the equation is solvable or not. If the equation is solvable, equilibrium constant of dimerization system is obtained by dichotomy and its final equilibrium constant of dimerization system is determined according to the principle of error of fitting. The equilibrium constants of trisulfophthalocyanine and biosulfophthalocyanine obtained with this method are 47,973.4 and 30,271.8 respectively. The results are much better than those reported previously.

  11. Scattering properties of weakly-bound dimers of Fermi atoms

    NASA Astrophysics Data System (ADS)

    Petrov, Dmitry

    2005-03-01

    We discuss the behavior of weakly bound bosonic dimers formed in a two-component Fermi gas with a large positive scattering length for the interspecies interaction. We present a theoretical approach for solving a few-body scattering problem and describe the physics of dimer-dimer elastic and inelastic scattering. We explain why these diatomic molecules, while in the highest ro-vibrational level, are characterized by remarkable collisional stability. Co-authors are Christophe Salomon, LKB, Ecole Normale Superieure, Paris, France; Georgy Shlyapnikov, LPTMS, University of South Paris, Orsay, France.

  12. Adsorption of silver dimer on graphene - A DFT study

    SciTech Connect

    Kaur, Gagandeep; Gupta, Shuchi; Rani, Pooja; Dharamvir, Keya

    2014-04-24

    We performed a systematic density functional theory (DFT) study of the adsorption of silver dimer (Ag{sub 2}) on graphene using SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Ag2-graphene system are calculated. The minimum energy configuration for a silver dimer is parallel to the graphene sheet with its two atoms directly above the centre of carbon-carbon bond. The negligible charge transfer between the dimer and the surface is also indicative of a weak bond. The methodology demonstrated in this paper may be applied to larger silver clusters on graphene sheet.

  13. Electric and magnetic hotspots in dielectric nanowire dimers

    NASA Astrophysics Data System (ADS)

    Mirzaei, Ali; Miroshnichenko, Andrey E.

    2015-03-01

    We study the formation of the electric and magnetic near-field hotspots in dielectric cylindrical dimers. We compare dielectric and metallic dimers by using experimental data for all materials and consider both TM and TE polarizations of light. We demonstrate that dielectric dimers allow us to simultaneously achieve pure magnetic and electric near-field hotspots for both polarizations in contrast to plasmonic structures. This offers new approaches for near-field engineering such as sensing, control of spontaneous emission, and enhanced Raman scattering.

  14. Vibrations of the carbon dioxide dimer

    NASA Astrophysics Data System (ADS)

    Chen, Hua; Light, J. C.

    2000-03-01

    Fully coupled four-dimensional quantum-mechanical calculations are presented for intermolecular vibrational states of rigid carbon dioxide dimer for J=0. The Hamiltonian operator is given in collision coordinates. The Hamiltonian matrix elements are evaluated using symmetrized products of spherical harmonics for angles and a potential optimized discrete variable representation (PO-DVR) for the intermolecular distance. The lowest ten or so states of each symmetry are reported for the potential energy surface (PES) given by Bukowski et al. [J. Chem. Phys. 110, 3785 (1999)]. Due to symmetries, there is no interconversion tunneling splitting for the ground state. Our calculations show that there is no tunneling shift of the ground state within our computation precision (0.01 cm-1). Analysis of the wave functions shows that only the ground states of each symmetry are nearly harmonic. The van der Waals frequencies and symmetry adapted force constants are found and compared to available experimental values. Strong coupling between the stretching coordinates and the bending coordinates are found for vibrationally excited states. The interconversion tunneling shifts are discussed for the vibrationally excited states.

  15. Smectic Phase Formed by DNA Dimers

    NASA Astrophysics Data System (ADS)

    Salamonczyk, Miroslaw; Gleeson, James; Jakli, Antal; Sprunt, Samuel; Dhont, Jan; Stiakakis, Emmanuel

    The rapidly expanding bio market is driving the development and characterization of new multifunctional materials. In particular, nucleic acids are under intense study for gene therapy, drug delivery and other bio-safe applications [1,2,3]. DNA is well-known to form a cholesteric nematic liquid crystal in its native form; however, much recent research has focused on self-assembly and mesomorphic behavior in concentrated solutions of short DNA helices [4]. Our work focuses on DNA dimers, consisting of 48 base-pair double-stranded helices connected by a 5 to 20 base flexible single strand, and suspended in a natural buffer. Depending on temperature, concentration and length of the flexible spacer, polarizing optical microscopy and small angle x-ray scattering reveal cholesteric nematic and, remarkably, smectic liquid crystalline phases. A model for smectic phase formation in this system will be presented. 1] J.-L. Lim et al., Int. J. of. Pharm. 490 (2015) 2652] D.-H. Kim et al., Nature Biotech. 23 (2005) 2223] K. Liu et al., Chem. Eur. J. 21 (2015) 48984] M. Nakata et al., Science 318 (2007) 1276 NSF DMR 1307674.

  16. Repressor Dimerization in the Zebrafish Somitogenesis Clock

    PubMed Central

    Cinquin, Olivier

    2007-01-01

    The oscillations of the somitogenesis clock are linked to the fundamental process of vertebrate embryo segmentation, yet little is known about their generation. In zebrafish, it has been proposed that Her proteins repress the transcription of their own mRNA. However, in its simplest form, this model is incompatible with the fact that morpholino knockdown of Her proteins can impair expression of their mRNA. Simple self-repression models also do not account for the spatiotemporal pattern of gene expression, with waves of gene expression shrinking as they propagate. Here we study computationally the networks generated by the wealth of dimerization possibilities amongst transcriptional repressors in the zebrafish somitogenesis clock. These networks can reproduce knockdown phenotypes, and strongly suggest the existence of a Her1–Her7 heterodimer, so far untested experimentally. The networks are the first reported to reproduce the spatiotemporal pattern of the zebrafish somitogenesis clock; they shed new light on the role of Her13.2, the only known link between the somitogenesis clock and positional information in the paraxial mesoderm. The networks can also account for perturbations of the clock by manipulation of FGF signaling. Achieving an understanding of the interplay between clock oscillations and positional information is a crucial first step in the investigation of the segmentation mechanism. PMID:17305423

  17. Ab initio calculations of nitramine dimers

    NASA Astrophysics Data System (ADS)

    Koh-Fallet, Sharon; Schweigert, Igor

    2015-06-01

    Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.

  18. Dimer packings with gaps and electrostatics

    PubMed Central

    Ciucu, Mihai

    2008-01-01

    Fisher and Stephenson conjectured in 1963 that the correlation function (defined by dimer packings) of two unit holes on the square lattice is rotationally invariant in the limit of large separation between the holes. We consider the same problem on the hexagonal lattice, extend it to an arbitrary finite collection of holes, and present an explicit conjectural answer. In recent work we managed to prove this conjecture in two fairly general cases. The quantity giving the answer can be regarded as the exponential of the negative of the two-dimensional electrostatic energy of a system of charges naturally associated with the holes. We further develop this analogy to electrostatics by presenting two different natural ways to define a field in our setup, and showing that both lead to the electric field, in the limit of large separations between the holes. For one of the fields, this is also stated as a limit shape theorem for random surfaces, with the continuum limit being a sum of helicoids. We conclude by explaining the relationship of our results to previous results in the physics literature on spin correlations in the Ising model.

  19. Self-aggregation of cationic dimeric surfactants in water-ionic liquid binary mixtures.

    PubMed

    Martín, Victoria Isabel; Rodríguez, Amalia; Laschewsky, André; Moyá, María Luisa

    2014-09-15

    The micellization of four dimeric cationic surfactants ("gemini surfactants") derived from N-dodecyl-N,N,N-trimethylammonium chloride was studied in pure water and in water-ionic liquid (IL) solutions by a wide range of techniques. The dimeric surfactants are distinguished by their rigid spacer groups separating the two surfactant motifs, which range from C3 to C5 in length. In order to minimize organic ion pairing effects as well as the role of the ionic liquids as potential co-surfactants, ILs with inorganic hydrophilic anions and organic cations of limited hydrophobicity were chosen, namely ethyl, butyl, and hexyl-3-imidazolium chlorides. (1)H NMR two-dimensional, 2D, rotating frame nuclear Overhauser effect spectroscopy measurements, ROESY, supported this premise. The spacer nature hardly affects the micellization process, neither in water nor in water-IL solutions. However, it does influence the tendency of the dimeric surfactants to form elongated micelles when surfactant concentration increases. In order to have a better understanding of the ternary water-IL surfactant systems, the micellization of the surfactants was also studied in aqueous NaCl solutions, in water-ethylene glycol and in water-formamide binary mixtures. The combined results show that the ionic liquids play a double role in the mixed systems, operating simultaneously as background electrolytes and as polar organic solvents. The IL role as organic co-solvent becomes more dominant when its concentration increases, and when the IL alkyl chain length augments.

  20. CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling.

    PubMed

    Rajakulendran, Thanashan; Sahmi, Malha; Kurinov, Igor; Tyers, Mike; Therrien, Marc; Sicheri, Frank

    2008-02-26

    RAF kinase functions in the mitogen-activated protein kinase (MAPK) pathway to transmit growth signals to the downstream kinases MEK and ERK. Activation of RAF catalytic activity is facilitated by a regulatory complex comprising the proteins CNK (Connector enhancer of KSR), HYP (Hyphen), and KSR (Kinase Suppressor of Ras). The sterile alpha-motif (SAM) domain found in both CNK and HYP plays an essential role in complex formation. Here, we have determined the x-ray crystal structure of the SAM domain of CNK in complex with the SAM domain of HYP. The structure reveals a single-junction SAM domain dimer of 1:1 stoichiometry in which the binding mode is a variation of polymeric SAM domain interactions. Through in vitro and in vivo mutational analyses, we show that the specific mode of dimerization revealed by the crystal structure is essential for RAF signaling and facilitates the recruitment of KSR to form the CNK/HYP/KSR regulatory complex. We present two docking-site models to account for how SAM domain dimerization might influence the formation of a higher-order CNK/HYP/KSR complex.

  1. Emergence of long-range order in sheets of magnetic dimers

    PubMed Central

    Haravifard, S.; Banerjee, A.; van Wezel, J.; Silevitch, D. M.; dos Santos, A. M.; Lang, J. C.; Kermarrec, E.; Srajer, G.; Gaulin, B. D.; Molaison, J. J.; Dabkowska, H. A.; Rosenbaum, T. F.

    2014-01-01

    Quantum spins placed on the corners of a square lattice can dimerize and form singlets, which then can be transformed into a magnetic state as the interactions between dimers increase beyond threshold. This is a strictly 2D transition in theory, but real-world materials often need the third dimension to stabilize long-range order. We use high pressures to convert sheets of Cu2+ spin 1/2 dimers from local singlets to global antiferromagnet in the model system SrCu2(BO3)2. Single-crystal neutron diffraction measurements at pressures above 5 GPa provide a direct signature of the antiferromagnetic ordered state, whereas high-resolution neutron powder and X-ray diffraction at commensurate pressures reveal a tilting of the Cu spins out of the plane with a critical exponent characteristic of 3D transitions. The addition of anisotropic, interplane, spin–orbit terms in the venerable Shastry–Sutherland Hamiltonian accounts for the influence of the third dimension. PMID:25246541

  2. Structural Role of the Conserved Cysteines in the Dimerization of the Viral Transmembrane Oncoprotein E5

    PubMed Central

    Windisch, Dirk; Hoffmann, Silke; Afonin, Sergii; Vollmer, Stefanie; Benamira, Soraya; Langer, Birgid; Bürck, Jochen; Muhle-Goll, Claudia; Ulrich, Anne S.

    2010-01-01

    The E5 oncoprotein is the major transforming protein of bovine papillomavirus type 1. This 44-residue transmembrane protein can interact with the platelet-derived growth factor receptor β, leading to ligand-independent activation and cell transformation. For productive interaction, E5 needs to dimerize via a C-terminal pair of cysteines, though a recent study suggested that its truncated transmembrane segment can dimerize on its own. To analyze the structure of the full protein in a membrane environment and elucidate the role of the Cys-Ser-Cys motif, we produced recombinantly the wild-type protein and four cysteine mutants. Comparison by circular dichroism in detergent micelles and lipid vesicular dispersion and by NMR in trifluoroethanol demonstrates that the absence of one or both cysteines does not influence the highly α-helical secondary structure, nor does it impair the ability of E5 to dimerize, observations that are further supported by sodium dodecylsulfate polyacrylamide gel electrophoresis. We also observed assemblies of higher order. Oriented circular dichroism in lipid bilayers shows that E5 is aligned as a transmembrane helix with a slight tilt angle, and that this membrane alignment is also independent of any cysteines. We conclude that the Cys-containing motif represents a disordered region of the protein that serves as an extra covalent connection for stabilization. PMID:20858420

  3. Global properties and propensity to dimerization of the amyloid-beta (12-28) peptide fragment through the modeling of its monomer and dimer diffusion coefficients and electrophoretic mobilities.

    PubMed

    Deiber, Julio A; Peirotti, Marta B; Piaggio, Maria V

    2015-03-01

    Neuronal activity loss may be due to toxicity caused mainly by amyloid-beta (1-40) and (1-42) peptides forming soluble oligomers. Here the amyloid-beta (12-28) peptide fragment (monomer) and its dimer are characterized at low pH through the modeling of their diffusion coefficients and effective electrophoretic mobilities. Translational diffusion coefficient experimental values of monomer and dimer analogs of this peptide fragment and monomer and dimer mixtures at thermodynamic equilibrium are used as reported in the literature for different monomer initial concentrations. The resulting electrokinetic and hydrodynamic global properties are employed to evaluate the amyloid-beta (12-28) peptide fragment propensity to dimerization through a thermodynamic theoretical framework. Therefore equilibrium constants are considered at pH 2.9 to elucidate one of the amyloidogenic mechanisms involving the central hydrophobic region LVFFA of the peptide spanning residues 17-21 associated with phenylalanine at positions 19 and 20 in the amino acid sequence of amyloid-beta peptides. An analysis demonstrating that peptide aggregation is a concentration-dependent process is provided, where both pair and intraparticle charge regulation phenomena become relevant. It is shown that the modeling of the effective electrophoretic mobility of the amyloid-beta (12-28) peptide fragment is crucial to understand the effect of hydrophobic region LVFFA in the amyloidogenic process.

  4. Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization.

    PubMed Central

    Mougel, M; Tounekti, N; Darlix, J L; Paoletti, J; Ehresmann, B; Ehresmann, C

    1993-01-01

    Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region. Images PMID:8233816

  5. The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization

    SciTech Connect

    Lalime, Erin N.; Pekosz, Andrew

    2014-06-15

    The influenza A virus NS1 protein has a nuclear localization sequence (NLS) in the amino terminal region. This NLS overlaps sequences that are important for RNA binding as well as protein dimerization. To assess the significance of the NS1 NLS on influenza virus replication, the NLS amino acids were individually mutated to alanines and recombinant viruses encoding these mutations were rescued. Viruses containing NS1 proteins with mutations at R37, R38 and K41 displayed minimal changes in replication or NS1 protein nuclear localization. Recombinant viruses encoding NS1 R35A were not recovered but viruses containing second site mutations at position D39 in addition to the R35A mutation were isolated. The mutations at position 39 were shown to partially restore NS1 protein dimerization but had minimal effects on nuclear localization. These data indicate that the amino acids in the NS1 NLS region play a more important role in protein dimerization compared to nuclear localization. - Highlights: • Mutations were introduced into influenza NS1 NLS1. • NS1 R37A, R38A, K41A viruses had minimal changes in replication and NS1 localization. • Viruses from NS1 R35A rescue all contained additional mutations at D39. • NS1 R35A D39X mutations recover dimerization lost in NS1 R35A mutations. • These results reaffirm the importance of dimerization for NS1 protein function.

  6. One Sequence, Two Folds: A Metastable Structure of CD2

    NASA Astrophysics Data System (ADS)

    Murray, Alison J.; Lewis, Sally J.; Barclay, A. Neil; Brady, R. Leo

    1995-08-01

    When expressed as part of a glutathione S-transferase fusion protein the NH_2-terminal domain of the lymphocyte cell adhesion molecule CD2 is shown to adopt two different folds. The immunoglobulin superfamily structure of the major (85%) monomeric component has previously been determined by both x-ray crystallography and NMR spectroscopy. We now describe the structure of a second, dimeric, form present in about 15% of recombinant CD2 molecules. After denaturation and refolding in the absence of the fusion partner, dimeric CD2 is converted to monomer, illustrating that the dimeric form represents a metastable folded state. The crystal structure of this dimeric form, refined to 2.0-Å resolution, reveals two domains with overall similarity to the IgSF fold found in the monomer. However, in the dimer each domain is formed by the intercalation of two polypeptide chains. Hence each domain represents a distinct folding unit that can assemble in two different ways. In the dimer the two domains fold around a hydrophilic interface believed to mimic the cell adhesion interaction at the cell surface, and the formation of dimer can be regulated by mutating single residues at this interface. This unusual misfolded form of the protein, which appears to result from inter- rather than intramolecular interactions being favored by an intermediate structure formed during the folding process, illustrates that evolution of protein oligomers is possible from the sequence for a single protein domain.

  7. Dimer model for Tau proteins bound in microtubule bundles

    NASA Astrophysics Data System (ADS)

    Hall, Natalie; Kluber, Alexander; Hayre, N. Robert; Singh, Rajiv; Cox, Daniel

    2013-03-01

    The microtubule associated protein tau is important in nucleating and maintaining microtubule spacing and structure in neuronal axons. Modification of tau is implicated as a later stage process in Alzheimer's disease, but little is known about the structure of tau in microtubule bundles. We present preliminary work on a proposed model for tau dimers in microtubule bundles (dimers are the minimal units since there is one microtubule binding domain per tau). First, a model of tau monomer was created and its characteristics explored using implicit solvent molecular dynamics simulation. Multiple simulations yield a partially collapsed form with separate positively/negatively charged clumps, but which are a factor of two smaller than required by observed microtubule spacing. We argue that this will elongate in dimer form to lower electrostatic energy at a cost of entropic ``spring'' energy. We will present preliminary results on steered molecular dynamics runs on tau dimers to estimate the actual force constant. Supported by US NSF Grant DMR 1207624.

  8. DLTS study of the oxygen dimer formation kinetics in silicon

    NASA Astrophysics Data System (ADS)

    Yarykin, Nikolai; Weber, Jörg

    2009-12-01

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480∘ C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  9. Non-stripe charge order in dimerized organic conductors

    NASA Astrophysics Data System (ADS)

    Mori, Takehiko

    2016-06-01

    This paper demonstrates charge order is important in dimerized β - and κ -phase organic conductors similar to the uniform θ - and α -phase conductors. Here the magnitude of the dimerization represents the deviation from the ideal triangular lattice in analogy with the anisotropy in the θ phase. Since the ratio of the intradimer transfer integral to the interdimer transfer integral is as large as ˜2.6 , these dimerized phases lead to a dimer Mott insulator, whereas the Coulomb repulsion is closer to the triangular lattice because the ratio of the intradimer Coulomb repulsion to the interdimer Coulomb repulsion is comparatively small (˜1.7 ). Accordingly, in the static-limit calculation, non-stripe charge order with threefold periodicity appears between the uniform and the stripe phases, and the analogy with the θ phase suggests the first-order nature of the metal-insulator transition.

  10. [Antioxidant and antibacterial activities of dimeric phenol compounds].

    PubMed

    Ogata, Masahiro

    2008-08-01

    We studied the antioxidant and antibacterial activities of monomeric and dimeric phenol compounds. Dimeric compounds had higher antioxidant activities than monomeric compounds. Electron spin resonance spin-trapping experiments showed that phenol compounds with an allyl substituent on their aromatic rings directly scavenged superoxide, and that only eugenol trapped hydroxyl radicals. We developed a generation system of the hydroxyl radical without using any metals by adding L-DOPA and DMPO to PBS or MiliQ water in vitro. We found that eugenol trapped hydroxyl radicals directly and is metabolized to a dimer. On the other hand, dipropofol, a dimer of propofol, has strong antibacterial activity against Gram-positive bacteria. However, it lacks solubility in water and this property is assumed to limit its efficacy. We tried to improve the solubility and found a new solubilization method of dipropofol in water with the addition of a monosaccharide or ascorbic acid.

  11. Sodium dimers on the surface of liquid {sup 4}He

    SciTech Connect

    Ancilotto, F.; DeToffol, G.; Toigo, F.

    1995-12-01

    We have studied the structure of a sodium dimer interacting with liquid {sup 4}He. We calculated the equilibrium configuration and binding energy of a Na{sub 2} molecule solvated in a bulk liquid {sup 4}He ``bubble`` and near the liquid-vapor interface ``dimple`` by using a density-functional approach. We find that the solvated molecule is a metastable state, while the the lowest energy bound state occurs when the molecule lies flat on the surface of the liquid. The binding energy for the ``erect`` dimer is only {similar_to}1 K higher than the flat dimer, with no potential energy barrier between the two orientations, implying relatively free rotations of the molecule on the surface. The small effects of the liquid environment on the vibrational properties of the dimer are investigated.

  12. Metallothionein dimers studied by nano-spray mass spectrometry.

    PubMed

    Hathout, Yetrib; Reynolds, Kristy J; Szilagyi, Zoltan; Fenselau, Catherine

    2002-01-15

    Both transient and stable dimers of metallothionein have been characterized, based on earlier studies using NMR, circular dichroism and size-exclusion chromatography. Here additional characterization is provided by nanospray mass spectrometry. Rapid redistribution of metal ions between monomeric Cd7- and Zn7-metallothionein 2a is monitored by nanospray. An experiment in which theses two forms of the monomeric protein are separated by a dialysis membrane, which will pass metal ions but not proteins, confirms that a transient dimer must form for metal ions to be redistributed. On the other hand, size-exclusion chromatography of reconstituted Zn7- or Cd7-metallothionein revealed the presence of monomeric and dimeric species. These dimers do not equilibrate readily to form monomers and they are shown to be covalent.

  13. New Insights into Poly(Lactic-co-glycolic acid) Microstructure: Using Repeating Sequence Copolymers to Decipher Complex NMR and Thermal Behavior

    PubMed Central

    Stayshich, Ryan M.; Meyer, Tara Y.

    2012-01-01

    Sequence, which Nature uses to spectacular advantage, has not been fully exploited in synthetic copolymers. To investigate the effect of sequence and stereosequence on the physical properties of copolymers a family of complex isotactic, syndiotactic and atactic repeating sequence poly(lactic-co-glycolic acid) copolymers (RSC PLGAs) were prepared and their NMR and thermal behavior was studied. The unique suitability of polymers prepared from the bioassimilable lactic and glycolic acid monomers for biomedical applications makes them ideal candidates for this type of sequence engineering. Polymers with repeating units of LG, GLG and LLG (L = lactic, G = glycolic) with controlled and varied tacticities were synthesized by assembly of sequence specific, stereopure dimeric, trimeric and hexameric segmer units. Specifically labeled deuterated lactic and glycolic acid segmers were likewise prepared and polymerized. Molecular weights for the copolymers ranged from Mn = 12-40 kDa by size exclusion chromatography in THF. Although the effects of sequence-influenced solution conformation were visible in all resonances of the 1H and 13C NMR spectra, the diastereotopic methylene resonances in the 1H NMR (CDCl3) for the glycolic units of the copolymers proved most sensitive. An octad level of resolution, which corresponds to an astounding 31-atom distance between the most separated stereocenters, was observed in some mixed sequence polymers. Importantly, the level of sensitivity of a particular NMR resonance to small differences in sequence was found to depend on the sequence itself. Thermal properties were also correlated with sequence. PMID:20681726

  14. Changes in apparent free energy of helix-helix dimerization in a biological membrane due to point mutations

    PubMed Central

    Duong, Mylinh T.; Jaszewski, Todd M.; Fleming, Karen G.; MacKenzie, Kevin R.

    2009-01-01

    Summary We present an implementation of the TOXCAT membrane protein self-association assay that measures the change in apparent free energy of transmembrane helix dimerization caused by point mutations. Quantifying the reporter gene expression from cells carrying wild type and mutant constructs shows that single point mutations that disrupt dimerization of the transmembrane domain of glycophorin A reproducibly lower the TOXCAT signal more than one hundred-fold. Replicate cultures can show up to three-fold changes in the level of expression of the membrane bound fusion construct, and correcting for these variations improves the precision of the calculated apparent free energy change. The remarkably good agreement between our TOXCAT apparent free energy scale and free energy differences from sedimentation equilibrium studies for point mutants of the glycophorin A transmembrane domain dimer indicate that sequence changes usually affect membrane helix-helix interactions quite similarly in these two very different environments. However, the effects of point mutations at threonine 87 suggest that intermonomer polar contacts by this side chain contribute significantly to dimer stability in membranes but not in detergents. Our findings demonstrate that a comparison of quantitative measurements of helix-helix interactions in biological membranes and genuine thermodynamic data from biophysical measurements on purified proteins can elucidate how changes in the lipidic environment modulate membrane protein stability. PMID:17570394

  15. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites

    PubMed Central

    Wu, Qian; Paul, Atanu; Su, Dan; Mehmood, Shahid; Foo, Tzeh Keong; Ochi, Takashi; Bunting, Emma L.; Xia, Bing; Robinson, Carol V.; Wang, Bin; Blundell, Tom L.

    2016-01-01

    Summary BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR. PMID:26778126

  16. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites.

    PubMed

    Wu, Qian; Paul, Atanu; Su, Dan; Mehmood, Shahid; Foo, Tzeh Keong; Ochi, Takashi; Bunting, Emma L; Xia, Bing; Robinson, Carol V; Wang, Bin; Blundell, Tom L

    2016-02-04

    BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR.

  17. Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS.

    PubMed

    Teplova, Marianna; Farazi, Thalia A; Tuschl, Thomas; Patel, Dinshaw J

    2016-01-01

    RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.

  18. Design and Preparation of Nanoparticle Dimers for SERS Detection

    DTIC Science & Technology

    2012-09-10

    aptamers (aptatags) or antibodies (antitags) as the recognition elements. Preparation of 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 09-10...resulting dimeric structures incorporate aptamers (aptatags) or antibodies (antitags) as the recognition elements. Preparation of suitable sensing...signal   enhancement   is   at   its   maximum.     The   resulting   dimeric   structures   incorporate   aptamers

  19. Anomalous atmospheric absorption spectra due to water dimer

    NASA Astrophysics Data System (ADS)

    Cai, Peipei; Zhang, Hansheng; Shen, Shanxiong; Cheng, I.-Shan

    1986-11-01

    The anomalous atmospheric absorption spectra in the window wavelength region of 8-14 microns have been suggested due to the water dimer. Based on laboratory measurements, water continuum CO2 laser absorption spectra and a resonance absorption line due to the weak local wave vapor pure rotational transition have been reported. The equilibrium concentration of water dimers in the atmosphere, the electronic binding energy and the theoretical calculations for absorption attenuation have been obtained in agreement with published data.

  20. Superconductivity in the liquid-dimer valence-bond state

    SciTech Connect

    Ioffe, L.B.; Larkin, A.I. )

    1989-10-01

    Introducing an unambiguous prescription which converts singlet dimers into quasidipoles, we describe the low-energy excitations in the liquid-dimer state as fluctuations of the average dipole moment. The exchange of these fluctuations leads to a long-range interaction between holes in this state. This interaction favors the two-particle Bose condensate and destroys the order parameter of the one-particle Bose condensate even at zero temperature.

  1. Absorption cross sections of the ClO dimer

    NASA Technical Reports Server (NTRS)

    Huder, K. J.; DeMore, W. B.

    1995-01-01

    The absorption cross sections of the ClO dimer, ClOOCl, are important to the photochemistry of ozone depletion in the Antarctic. In this work, new measurements were made of the dimer cross sections at 195 K. the results yield somewhat lower values in the long wavelength region, compared to those currently recommended in the NASA data evaluation (JPL 94-26). The corresponding solar photodissociation rates in the Antarctic are reduced by about 40%.

  2. The amino acid sequence of Neisseria lactamica PorB surface-exposed loops influences Toll-like receptor 2-dependent cell activation.

    PubMed

    Toussi, Deana N; Carraway, Margaretha; Wetzler, Lee M; Lewis, Lisa A; Liu, Xiuping; Massari, Paola

    2012-10-01

    Toll-like receptors (TLRs) play a major role in host mucosal and systemic defense mechanisms by recognizing a diverse array of conserved pathogen-associated molecular patterns (PAMPs). TLR2, with TLR1 and TLR6, recognizes structurally diverse bacterial products such as lipidated factors (lipoproteins and peptidoglycans) and nonlipidated proteins, i.e., bacterial porins. PorB is a pan-neisserial porin expressed regardless of organisms' pathogenicity. However, commensal Neisseria lactamica organisms and purified N. lactamica PorB (published elsewhere as Nlac PorB) induce TLR2-dependent proinflammatory responses of lower magnitude than N. meningitidis organisms and N. meningitidis PorB (published elsewhere as Nme PorB). Both PorB types bind to TLR2 in vitro but with different apparent specificities. The structural and molecular details of PorB-TLR2 interaction are only beginning to be unraveled and may be due to electrostatic attraction. PorB molecules have significant strain-specific sequence variability within surface-exposed regions (loops) putatively involved in TLR2 interaction. By constructing chimeric recombinant PorB loop mutants in which surface-exposed loop residues have been switched between N. lactamica PorB and N. meningitidis PorB, we identified residues in loop 5 and loop 7 that influence TLR2-dependent cell activation using HEK cells and BEAS-2B cells. These loops are not uniquely responsible for PorB interaction with TLR2, but NF-κB and MAP kinases signaling downstream of TLR2 recognition are likely influenced by a hypothetical "TLR2-binding signature" within the sequence of PorB surface-exposed loops. Consistent with the effect of purified PorB in vitro, a chimeric N. meningitidis strain expressing N. lactamica PorB induces lower levels of interleukin 8 (IL-8) secretion than wild-type N. meningitidis, suggesting a role for PorB in induction of host cell activation by whole bacteria.

  3. Cholesterol-dependent Conformational Plasticity in GPCR Dimers

    PubMed Central

    Prasanna, Xavier; Sengupta, Durba; Chattopadhyay, Amitabha

    2016-01-01

    The organization and function of the serotonin1A receptor, an important member of the GPCR family, have been shown to be cholesterol-dependent, although the molecular mechanism is not clear. We performed a comprehensive structural and dynamic analysis of dimerization of the serotonin1A receptor by coarse-grain molecular dynamics simulations totaling 3.6 ms to explore the molecular details of its cholesterol-dependent association. A major finding is that the plasticity and flexibility of the receptor dimers increase with increased cholesterol concentration. In particular, a dimer interface formed by transmembrane helices I-I was found to be sensitive to cholesterol. The modulation of dimer interface appears to arise from a combination of direct cholesterol occupancy and indirect membrane effects. Interestingly, the presence of cholesterol at the dimer interface is correlated with increased dimer plasticity and flexibility. These results represent an important step in characterizing the molecular interactions in GPCR organization with potential relevance to therapeutic interventions. PMID:27535203

  4. Mechanism of dimerization of the human melanocortin 1 receptor

    SciTech Connect

    Zanna, Paola T.; Sanchez-Laorden, Berta L.; Perez-Oliva, Ana B.; Turpin, Maria C.; Herraiz, Cecilia; Jimenez-Cervantes, Celia; Garcia-Borron, Jose C.

    2008-04-04

    The melanocortin 1 receptor (MC1R) is a dimeric G protein-coupled receptor expressed in melanocytes, where it regulates the amount and type of melanins produced and determines the tanning response to ultraviolet radiation. We have studied the mechanisms of MC1R dimerization. Normal dimerization of a deleted mutant lacking the seventh transmembrane fragment and the C-terminal cytosolic extension excluded coiled-coil interactions as the basis of dimerization. Conversely, the electrophoretic pattern of wild type receptor and several Cys {yields} Ala mutants showed that four disulfide bonds are established between the monomers. Disruption of any of these bonds abolished MC1R function, but only the one involving Cys35 was essential for traffic to the plasma membrane. A quadruple Cys35-267-273-275Ala mutant migrating as a monomer in SDS-PAGE in the absence of reducing agents was able to dimerize with WT, suggesting that in addition to disulfide bond formation, dimerization involves non-covalent interactions, likely of domain swap type.

  5. Mobile Monomers and Dimers in Precipitation Kinetics: a Microscopic Approach.

    PubMed

    Berim, Gersh O; Brim, Lana I; Ruckenstein, Eli

    2017-02-02

    A microscopic theory of precipitation kinetics in solution developed previously by Ruckenstein and co-workers [ Dadyburjor , D. B. ; Ruckenstein , E. J. Cryst. Growth 1977 , 40 , 279 - 290 ; Bhakta , A. ; Ruckenstein , E. J. Chem. Phys. 1995 , 103 , 7120 - 7135 ] is generalized. The processes (not considered in the original approach) of monomer-monomer agglomeration, leading to the creation of dimers, as well as absorption (emission) of dimers by solute particles due to dimer mobility are included in the theory. The theory is applied to a model system in which particles grow up to a certain largest size and then precipitate from solution. The most important change in the system kinetics due to those two processes (monomer agglomeration to form dimers and dimer absorption and emission) is tremendous slowing of the asymptotic time behavior of the concentration of particles of largest size. This can be used to obtain experimental evidence for agglomeration of monomers and dimer mobility in the kinetics of real systems. The effect of trimer absorption (emission) is estimated, and it is shown that it is negligible in many situations.

  6. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    PubMed

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  7. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    SciTech Connect

    Aravind, G.; Klaerke, B.; Rajput, J.; Toker, Y.; Andersen, L. H.; Bochenkova, A. V.; Antoine, R.; Racaud, A.; Dugourd, P.; Lemoine, J.

    2012-01-07

    Photodissociation lifetimes and fragment channels of gas-phase, protonated YA{sub n} (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of {approx}200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of {approx}2 {mu}s. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.

  8. Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation.

    PubMed Central

    Neet, K. E.; Timm, D. E.

    1994-01-01

    The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed. PMID:7756976

  9. Magneto-association near an atom-dimer resonance

    NASA Astrophysics Data System (ADS)

    Luo, D.; Nguyen, J. H. V.; Hulet, R. G.

    2015-05-01

    Over the past decade the universal scaling of Efimov trimers has been explored in various atomic species by measuring the three-body loss coefficient. An enhancement of the three-body loss at the atom-dimer resonance has been observed, but remains unexplained. It has been attributed to an ``avanlanche mechanism'' based on resonant atom-dimer scattering, yet the effectiveness of the hypothesis is under scrutiny. We present a new piece to the puzzle. In our work, Feshbach dimers and Efimov trimers are formed near the atom-dimer resonance by RF-association, from a Bose-Einstein condensate of 7Li atoms. The molecular binding energies are tunable by the broad Feshbach resonance of the atoms in the | 1 , 1 > state. We observe that the dimer formation rate is significantly enhanced at the atom-dimer resonance. The origin of this enhanement is unclear, but it may be closely related to the enhancement of the three-body loss rate. Work supported by the NSF, ARO, and the Welch Foundation.

  10. Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.

    PubMed

    Nagai, Satoshi; Hida, Kohsuke; Urushizaki, Shingo; Onitsuka, Goh; Yasuike, Motoshige; Nakamura, Yoji; Fujiwara, Atushi; Tajimi, Seisuke; Kimoto, Katsunori; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

    2016-02-01

    In this study, we investigated the influence of diurnal sampling bias on the community structure of plankton by comparing the biodiversity among seawater samples (n=9) obtained every 3h for 24h by using massively parallel sequencing (MPS)-based plankton monitoring at a fixed point conducted at Himedo seaport in Yatsushiro Sea, Japan. The number of raw operational taxonomy units (OTUs) and OTUs after re-sampling was 507-658 (558 ± 104, mean ± standard deviation) and 448-544 (467 ± 81), respectively, indicating high plankton biodiversity at the sampling location. The relative abundance of the top 20 OTUs in the samples from Himedo seaport was 48.8-67.7% (58.0 ± 5.8%), and the highest-ranked OTU was Pseudo-nitzschia species (Bacillariophyta) with a relative abundance of 17.3-39.2%, followed by Oithona sp. 1 and Oithona sp. 2 (Arthropoda). During seawater sampling, the semidiurnal tidal current having an amplitude of 0.3ms(-1) was dominant, and the westward residual current driven by the northeasterly wind was continuously observed during the 24-h monitoring. Therefore, the relative abundance of plankton species apparently fluctuated among the samples, but no significant difference was noted according to G-test (p>0.05). Significant differences were observed between the samples obtained from a different locality (Kusuura in Yatsushiro Sea) and at different dates, suggesting that the influence of diurnal sampling bias on plankton diversity, determined using the MPS-based survey, was not significant and acceptable.

  11. Mass Analyzed Threshold Ionization of Lutetium Dimer

    NASA Astrophysics Data System (ADS)

    Wu, Lu; Roudjane, Mourad; Liu, Yang; Yang, Dong-Sheng

    2013-06-01

    Lu_2 is produced in a pulsed laser-vaporization metal-cluster source and studied by mass-analyzed threshold ionization (MATI) spectroscopy. The MATI spectrum displays several long progressions from the transitions between various vibrational levels of the neutral and ion electronic states. From the spectrum, the upper limit of the ionization energy of the dimer is determined to be 43996 cm^{-1}, and the vibrational frequencies are measured to be 121 cm^{-1} in the neutral state and 90 cm^{-1} in the ion state. By combining with ab initio calculations at CASPT2 level, the ground state of Lu_2 is identified as ^3Σ_g^-. The ^3Σ_g^- state has an electron configuration of 6sσ_g^25dπ_u^15dπ_u^16sσ_u^2, which is formed by the interactions of two Lu atoms in the ^2D(5d6s^2) ground state. Ionization of the neutral state removes a 5dπ_u bonding electron and yields a ion state with a considerably longer bond distance. Lu_2 has a very different bonding feature from La_2, for which a ^1Σ_g^+ ground state was previously identified with an electron configuration of 5dπ_u^46sσ_g^2 formed by the interactions of two La atoms in the ^4F(5d^26s) excited state. Yang Liu, Lu Wu, Chang-Hua Zhang, Serge A. Krasnokutski, and Dong-Sheng Yang, J. Chem. Phys. 135, 034309 (2011).

  12. UVA Generates Pyrimidine Dimers in DNA Directly

    PubMed Central

    Jiang, Yong; Rabbi, Mahir; Kim, Minkyu; Ke, Changhong; Lee, Whasil; Clark, Robert L.; Mieczkowski, Piotr A.; Marszalek, Piotr E.

    2009-01-01

    There is increasing evidence that UVA radiation, which makes up ∼95% of the solar UV light reaching the Earth's surface and is also commonly used for cosmetic purposes, is genotoxic. However, in contrast to UVC and UVB, the mechanisms by which UVA produces various DNA lesions are still unclear. In addition, the relative amounts of various types of UVA lesions and their mutagenic significance are also a subject of debate. Here, we exploit atomic force microscopy (AFM) imaging of individual DNA molecules, alone and in complexes with a suite of DNA repair enzymes and antibodies, to directly quantify UVA damage and reexamine its basic mechanisms at a single-molecule level. By combining the activity of endonuclease IV and T4 endonuclease V on highly purified and UVA-irradiated pUC18 plasmids, we show by direct AFM imaging that UVA produces a significant amount of abasic sites and cyclobutane pyrimidine dimers (CPDs). However, we find that only ∼60% of the T4 endonuclease V-sensitive sites, which are commonly counted as CPDs, are true CPDs; the other 40% are abasic sites. Most importantly, our results obtained by AFM imaging of highly purified native and synthetic DNA using T4 endonuclease V, photolyase, and anti-CPD antibodies strongly suggest that CPDs are produced by UVA directly. Thus, our observations contradict the predominant view that as-yet-unidentified photosensitizers are required to transfer the energy of UVA to DNA to produce CPDs. Our results may help to resolve the long-standing controversy about the origin of UVA-produced CPDs in DNA. PMID:19186150

  13. Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization

    NASA Astrophysics Data System (ADS)

    Elkin, Carl D.; Zuccola, Harmon J.; Hogle, James M.; Joseph-McCarthy, Diane

    2000-11-01

    Hepatitis delta virus (HDV) encodes a single polypeptide called hepatitis delta antigen (DAg). Dimerization of DAg is required for viral replication. The structure of the dimerization region, residues 12 to 60, consists of an anti-parallel coiled coil [Zuccola et al., Structure, 6 (1998) 821]. Multiple Copy Simultaneous Searches (MCSS) of the hydrophobic core region formed by the bend in the helix of one monomer of this structure were carried out for many diverse functional groups. Six critical interaction sites were identified. The Protein Data Bank was searched for backbone templates to use in the subsequent design process by matching to these sites. A 14 residue helix expected to bind to the d-isomer of the target structure was selected as the template. Over 200 000 mutant sequences of this peptide were generated based on the MCSS results. A secondary structure prediction algorithm was used to screen all sequences, and in general only those that were predicted to be highly helical were retained. Approximately 100 of these 14-mers were model built as d-peptides and docked with the l-isomer of the target monomer. Based on calculated interaction energies, predicted helicity, and intrahelical salt bridge patterns, a small number of peptides were selected as the most promising candidates. The ligand design approach presented here is the computational analogue of mirror image phage display. The results have been used to characterize the interactions responsible for formation of this model anti-parallel coiled coil and to suggest potential ligands to disrupt it.

  14. Effect of phosphorylation on EGFR dimer stability probed by single-molecule dynamics and FRET/FLIM.

    PubMed

    Coban, Oana; Zanetti-Dominguez, Laura C; Matthews, Daniel R; Rolfe, Daniel J; Weitsman, Gregory; Barber, Paul R; Barbeau, Jody; Devauges, Viviane; Kampmeier, Florian; Winn, Martyn; Vojnovic, Borivoj; Parker, Peter J; Lidke, Keith A; Lidke, Diane S; Ameer-Beg, Simon M; Martin-Fernandez, Marisa L; Ng, Tony

    2015-03-10

    Deregulation of epidermal growth factor receptor (EGFR) signaling has been correlated with the development of a variety of human carcinomas. EGF-induced receptor dimerization and consequent trans- auto-phosphorylation are among the earliest events in signal transduction. Binding of EGF is thought to induce a conformational change that consequently unfolds an ectodomain loop required for dimerization indirectly. It may also induce important allosteric changes in the cytoplasmic domain. Despite extensive knowledge on the physiological activation of EGFR, the effect of targeted therapies on receptor conformation is not known and this particular aspect of receptor function, which can potentially be influenced by drug treatment, may in part explain the heterogeneous clinical response among cancer patients. Here, we used Förster resonance energy transfer/fluorescence lifetime imaging microscopy (FRET/FLIM) combined with two-color single-molecule tracking to study the effect of ATP-competitive small molecule tyrosine kinase inhibitors (TKIs) and phosphatase-based manipulation of EGFR phosphorylation on live cells. The distribution of dimer on-times was fitted to a monoexponential to extract dimer off-rates (koff). Our data show that pretreatment with gefitinib (active conformation binder) stabilizes the EGFR ligand-bound homodimer. Overexpression of EGFR-specific DEP-1 phosphatase was also found to have a stabilizing effect on the homodimer. No significant difference in the koff of the dimer could be detected when an anti-EGFR antibody (425 Snap single-chain variable fragment) that allows for dimerization of ligand-bound receptors, but not phosphorylation, was used. These results suggest that both the conformation of the extracellular domain and phosphorylation status of the receptor are involved in modulating the stability of the dimer. The relative fractions of these two EGFR subpopulations (interacting versus free) were obtained by a fractional-intensity analysis of

  15. Reptation Quantum Monte Carlo Calculation of Charge Transfer in The Na-Cl Dimer

    NASA Astrophysics Data System (ADS)

    Yao, Yi; Kanai, Yosuke

    2015-03-01

    Reptation Quantum Monte Carlo (QMC) calculations are performed to describe the charge transfer behavior in a NaCl dimer. Influence of fixed node approximation on the charge transfer was examined by obtaining electron density via reputation QMC. We employ Slater-Jastrow wavefunction as the trial wavefunction, and the fermion nodes are obtained from single particle orbitals of Hartree-Fock and Density Functional Theory (DFT) with several exchange-correlation approximations. We will discuss our QMC results together with DFT calculations to give insights into observed dependence of the charge transfer behavior on the fixed-node approximation.

  16. Influence of the cycle length on the production of PHA and polyglucose from glycerol by bacterial enrichments in sequencing batch reactors.

    PubMed

    Moralejo-Gárate, Helena; Palmeiro-Sánchez, Tania; Kleerebezem, Robbert; Mosquera-Corral, Anuska; Campos, José Luis; van Loosdrecht, Mark C M

    2013-12-01

    PHA, a naturally occurring biopolymer produced by a wide range of microorganisms, is known for its applications as bioplastic. In recent years the use of agro-industrial wastewater as substrate for PHA production by bacterial enrichments has attracted considerable research attention. Crude glycerol as generated during biodiesel production is a waste stream that due to its high organic matter content and low price could be an interesting substrate for PHA production. Previously we have demonstrated that when glycerol is used as substrate in a feast-famine regime, PHA and polyglucose are simultaneously produced as storage polymers. The work described in this paper aimed at understanding the effect of the cycle length on the bacterial enrichment process with emphasis on the distribution of glycerol towards PHA and polyglucose. Two sequencing batch reactors where operated with the same hydraulic and biomass retention time. A short cycle length (6 h) favored polyglucose production over PHA, whereas at long cycle length (24 h) PHA was more favored. In both communities the same microorganism appeared dominating, suggesting a metabolic rather than a microbial competition response. Moreover, the presence of ammonium during polymer accumulation did not influence the maximum amount of PHA that was attained.

  17. Influence of CeO2 NPs on biological phosphorus removal and bacterial community shifts in a sequencing batch biofilm reactor with the differential effects of molecular oxygen.

    PubMed

    Xu, Yi; Wang, Chao; Hou, Jun; Wang, Peifang; You, Guoxiang; Miao, Lingzhan; Lv, Bowen; Yang, Yangyang

    2016-11-01

    The effects of CeO2 nanoparticles (CeO2 NPs) on a sequencing batch biofilm reactor (SBBR) with established biological phosphorus (P) removal were investigated from the processes of anaerobic P release and aerobic P uptake. At low concentration (0.1mg/L), no significant impact was observed on total phosphorus (TP) removal after operating for 8h. However, at a concentration of 20mg/L, TP removal efficiency decreased from 83.68% to 55.88% and 16.76% when the CeO2 NPs were added at the beginning of the anaerobic and aerobic periods, respectively. Further studies illustrated that the inhibition of the specific P release rate was caused by the reversible states of Ce(3+) and Ce(4+), which inhibited the activity of exopolyphosphatase (PPX) and transformation of poly-β-hydoxyalkanoates (PHA) and glycogen, as well as the uptake of volatile fatty acids (VFAs). The decrease in the specific P uptake rate was mainly attributed to the significantly suppressed energy generation and decreased abundance of Burkholderia caused by excess reactive oxygen species. The removal of chemical oxygen demand (COD) was not influenced by CeO2 NPs under aerobic conditions, due to the increased abundance of Acetobacter and Acidocella after exposure. The inhibitory effects of CeO2 NPs with molecular oxygen were reduced after anaerobic exposure due to the enhanced particle size and the presence of Ce(3+).

  18. Products and mechanism of acene dimerization. A computational study.

    PubMed

    Zade, Sanjio S; Zamoshchik, Natalia; Reddy, A Ravikumar; Fridman-Marueli, Galit; Sheberla, Dennis; Bendikov, Michael

    2011-07-20

    The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso

  19. Physico-chemical properties of molten dimer ascorbate oxidase.

    PubMed

    Nicolai, Eleonora; Di Venere, Almerinda; Rosato, Nicola; Rossi, Antonello; Finazzi Agro', Alessandro; Mei, Giampiero

    2006-11-01

    The possible presence of dimeric unfolding intermediates might offer a clue to understanding the relationship between tertiary and quaternary structure formation in dimers. Ascorbate oxidase is a large dimeric enzyme that displays such an intermediate along its unfolding pathway. In this study the combined effect of high pressure and denaturing agents gave new insight on this intermediate and on the mechanism of its formation. The transition from native dimer to the dimeric intermediate is characterized by the release of copper ions forming the tri-nuclear copper center located at the interface between domain 2 and 3 of each subunit. This transition, which is pH-dependent, is accompanied by a decrease in volume, probably associated to electrostriction due to the loosening of intra-subunit electrostatic interactions. The dimeric species is present even at 3 x 10(8) Pa, providing evidence that mechanically or chemically induced unfolding lead to a similar intermediate state. Instead, dissociation occurs with an extremely large and negative volume change (DeltaV approximately -200 mL.mol(-1)) by pressurization in the presence of moderate amounts of denaturant. This volume change can be ascribed to the elimination of voids at the subunit interface. Furthermore, the combination of guanidine and high pressure uncovers the presence of a marginally stable (DeltaG approximately 2 kcal.mol(-1)) monomeric species (which was not observed in previous equilibrium unfolding measurements) that might be populated in the early folding steps of ascorbate oxidase. These findings provide new aspects of the protein folding pathway, further supporting the important role of quaternary interactions in the folding strategy of large dimeric enzymes.

  20. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Monomucleotides

    NASA Astrophysics Data System (ADS)

    Kanavarioti, Anastassia

    1997-08-01

    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2-methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2+ in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MeImpU and 2-MeImpC produce about 65% of oligomers including 4% of the 3',5'-linked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of internucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MeImpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  1. Integrability and conformal data of the dimer model

    NASA Astrophysics Data System (ADS)

    Morin-Duchesne, Alexi; Rasmussen, Jørgen; Ruelle, Philippe

    2016-04-01

    The central charge of the dimer model on the square lattice is still being debated in the literature. In this paper, we provide evidence supporting the consistency of a c=-2 description. Using Lieb’s transfer matrix and its description in terms of the Temperley-Lieb algebra {{TL}}n at β =0, we provide a new solution of the dimer model in terms of the model of critical dense polymers on a tilted lattice and offer an understanding of the lattice integrability of the dimer model. The dimer transfer matrix is analyzed in the scaling limit, and the result for {L}0-\\frac{c}{24} is expressed in terms of fermions. Higher Virasoro modes are likewise constructed as limits of elements of {{TL}}n and are found to yield a c=-2 realization of the Virasoro algebra, familiar from fermionic bc ghost systems. In this realization, the dimer Fock spaces are shown to decompose, as Virasoro modules, into direct sums of Feigin-Fuchs modules, themselves exhibiting reducible yet indecomposable structures. In the scaling limit, the eigenvalues of the lattice integrals of motion are found to agree exactly with those of the c=-2 conformal integrals of motion. Consistent with the expression for {L}0-\\frac{c}{24} obtained from the transfer matrix, we also construct higher Virasoro modes with c = 1 and find that the dimer Fock space is completely reducible under their action. However, the transfer matrix is found not to be a generating function for the c = 1 integrals of motion. Although this indicates that Lieb’s transfer matrix description is incompatible with the c = 1 interpretation, it does not rule out the existence of an alternative, c = 1 compatible, transfer matrix description of the dimer model.

  2. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

    NASA Technical Reports Server (NTRS)

    Kanavarioti, Anastassia

    1997-01-01

    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  3. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68

    PubMed Central

    Feracci, Mikael; Foot, Jaelle N.; Grellscheid, Sushma N.; Danilenko, Marina; Stehle, Ralf; Gonchar, Oksana; Kang, Hyun-Seo; Dalgliesh, Caroline; Meyer, N. Helge; Liu, Yilei; Lahat, Albert; Sattler, Michael; Eperon, Ian C.; Elliott, David J.; Dominguez, Cyril

    2016-01-01

    Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome. PMID:26758068

  4. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.

    PubMed

    Feracci, Mikael; Foot, Jaelle N; Grellscheid, Sushma N; Danilenko, Marina; Stehle, Ralf; Gonchar, Oksana; Kang, Hyun-Seo; Dalgliesh, Caroline; Meyer, N Helge; Liu, Yilei; Lahat, Albert; Sattler, Michael; Eperon, Ian C; Elliott, David J; Dominguez, Cyril

    2016-01-13

    Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome.

  5. [Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

    PubMed

    Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

    2011-01-01

    The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

  6. Factors contributing to deletion within Mungbean yellow mosaic virus partial dimers in binary vectors used for agroinoculation.

    PubMed

    Shivaprasad, P V; Thomas, M; Balamani, V; Biswas, D; Vanitharani, R; Karthikeyan, A S; Veluthambi, K

    2006-10-01

    Mungbean yellow mosaic virus-Vigna (MYMV) sequences cloned as partial dimers within the T-DNA of a binary vector were deleted at a high frequency upon conjugal mobilization from Escherichia coli into Agrobacterium tumefaciens. This deletion involving the genome-length viral DNA did not occur when the binary plasmid was inside E. coli and when the binary plasmid was introduced into Agrobacterium by electroporation. Deletions occurred in both DNA A and DNA B partial dimers. A minimum of 500-nt continuity on either side of the nonanucleotide in the duplicated common region is required for deletion. A. tumefaciens cells in which deletion was complete, grew as larger colonies reflecting a growth advantage. The small, slow-growing colonies eventually lost the genome-length viral sequences after a few more cycles of growth. Partial dimers in binary plasmids pGA472 and pBin19 with RK2 replicon underwent deletion while those in pPZP with pVS1 replicon did not undergo deletion. Deletion was observed in A. tumefaciens strains C58, A136, A348 and A281 with C58 chromosome background, but not in Ach5 and T37. Interestingly, deletion did not occur in A. tumefaciens strain AGL1 with a recA mutation in C58 chromosome, implying a clear role for recombination in deletion. These observations suggest the choice of Agrobacterium strains and binary vectors for agroinoculation of geminiviruses.

  7. Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach

    PubMed Central

    Aljabr, Waleed; Touzelet, Olivier; Pollakis, Georgios; Wu, Weining; Munday, Diane C.; Hughes, Margaret; Hertz-Fowler, Christiane; Kenny, John; Fearns, Rachel; Barr, John N.

    2015-01-01

    ABSTRACT Human respiratory syncytial virus (HRSV) is a major cause of serious respiratory tract infection. Treatment options include administration of ribavirin, a purine analog, although the mechanism of its anti-HRSV activity is unknown. We used transcriptome sequencing (RNA-seq) to investigate the genome mutation frequency and viral mRNA accumulation in HRSV-infected cells that were left untreated or treated with ribavirin. In the absence of ribavirin, HRSV-specific transcripts accounted for up to one-third of total RNA reads from the infected-cell RNA population. Ribavirin treatment resulted in a >90% reduction in abundance of viral mRNA reads, while at the same time no such reduction was detected for the abundance of cellular transcripts. The presented data reveal that ribavirin significantly increases the frequency of HRSV-specific RNA mutations, suggesting a direct influence on the fidelity of the HRSV polymerase. The presented data show that transitions and transversions occur during HRSV replication and that these changes occur in hot spots along the HRSV genome. Examination of nucleotide substitution rates in the viral genome indicated an increase in the frequency of transition but not transversion mutations in the presence of ribavirin. In addition, our data indicate that in the continuous cell types used and at the time points analyzed, the abundances of some HRSV mRNAs do not reflect the order in which the mRNAs are transcribed. IMPORTANCE Human respiratory syncytial virus (HRSV) is a major pediatric pathogen. Ribavirin can be used in children who are extremely ill to reduce the amount of virus and to lower the burden of disease. Ribavirin is used as an experimental therapy with other viruses. The mechanism of action of ribavirin against HRSV is not well understood, although it is thought to increase the mutation rate of the viral polymerase during replication. To investigate this hypothesis, we used a high-resolution approach that allowed us to

  8. Visualization of Myc/Max/Mad family dimers and the competition for dimerization in living cells.

    PubMed

    Grinberg, Asya V; Hu, Chang-Deng; Kerppola, Tom K

    2004-05-01

    Myc and Mad family proteins play opposing roles in the control of cell growth and proliferation. We have visualized the subcellular locations of complexes formed by Myc/Max/Mad family proteins using bimolecular fluorescence complementation (BiFC) analysis. Max was recruited to different subnuclear locations by interactions with Myc versus Mad family members. Complexes formed by Max with Mxi1, Mad3, or Mad4 were enriched in nuclear foci, whereas complexes formed with Myc were more uniformly distributed in the nucleoplasm. Mad4 was localized to the cytoplasm when it was expressed separately, and Mad4 was recruited to the nucleus through dimerization with Max. The cytoplasmic localization of Mad4 was determined by a CRM1-dependent nuclear export signal located near the amino terminus. We compared the relative efficiencies of complex formation among Myc, Max, and Mad family proteins in living cells using multicolor BiFC analysis. Max formed heterodimers with the basic helix-loop-helix leucine zipper (bHLHZIP) domain of Myc (bMyc) more efficiently than it formed homodimers. Replacement of two amino acid residues in the leucine zipper of Max reversed the relative efficiencies of homo- and heterodimerization in cells. Surprisingly, Mad3 formed complexes with Max less efficiently than bMyc, whereas Mad4 formed complexes with Max more efficiently than bMyc. The distinct subcellular locations and the differences between the efficiencies of dimerization with Max indicate that Mad3 and Mad4 are likely to modulate transcription activation by Myc at least in part through distinct mechanisms.

  9. Visualization of Myc/Max/Mad Family Dimers and the Competition for Dimerization in Living Cells†

    PubMed Central

    Grinberg, Asya V.; Hu, Chang-Deng; Kerppola, Tom K.

    2004-01-01

    Myc and Mad family proteins play opposing roles in the control of cell growth and proliferation. We have visualized the subcellular locations of complexes formed by Myc/Max/Mad family proteins using bimolecular fluorescence complementation (BiFC) analysis. Max was recruited to different subnuclear locations by interactions with Myc versus Mad family members. Complexes formed by Max with Mxi1, Mad3, or Mad4 were enriched in nuclear foci, whereas complexes formed with Myc were more uniformly distributed in the nucleoplasm. Mad4 was localized to the cytoplasm when it was expressed separately, and Mad4 was recruited to the nucleus through dimerization with Max. The cytoplasmic localization of Mad4 was determined by a CRM1-dependent nuclear export signal located near the amino terminus. We compared the relative efficiencies of complex formation among Myc, Max, and Mad family proteins in living cells using multicolor BiFC analysis. Max formed heterodimers with the basic helix-loop-helix leucine zipper (bHLHZIP) domain of Myc (bMyc) more efficiently than it formed homodimers. Replacement of two amino acid residues in the leucine zipper of Max reversed the relative efficiencies of homo- and heterodimerization in cells. Surprisingly, Mad3 formed complexes with Max less efficiently than bMyc, whereas Mad4 formed complexes with Max more efficiently than bMyc. The distinct subcellular locations and the differences between the efficiencies of dimerization with Max indicate that Mad3 and Mad4 are likely to modulate transcription activation by Myc at least in part through distinct mechanisms. PMID:15121849

  10. Synthesis and Applications of Non-spherical Dimer Colloids

    NASA Astrophysics Data System (ADS)

    Yoon, Kisun

    Colloids are promising building blocks in material synthesis because of their controllability of size and surface properties. The synthesis of chemically and/or geometrically anisotropic colloidal particles has received attentions with the expectation of building blocks for complex structures. However, the synthesis of anisotropic colloidal particles is by far more difficult than the synthesis of spherical colloidal particles. Lack of monodispersity and productivity of many anisotropic particles often limits their applications as a building block for complex structures. Thus, it is highly desirable to develop methods which can produce a large amount of monodisperse non-spherical particles with controllable asymmetric surface properties. This dissertation details the work for developing such a method. The major result of this dissertation is a synthetic method to produce monodisperse non-spherical colloids with anisotropic surface property in a large quantity. The anisotropic colloid, which we call it as Dimer particle, has two fused lobes like a dumbbell and each lobe's size can be independently controlled. We present a novel method to synthesize sub-micron size Dimer particles. This method can produce a large amount of submicron-sized Dimer particles with good monodispersity and well-controlled shape. Submicron-sized Dimer particles have been highly desired since they can be used as a building block for self assembly using Brownian motion, colloidal surfactant for Pickering emulsion, and photonic materials. To fully take advantage of the anisotropy of the particles, we develop a facile method to tailor the surface property of each lobe independently by asymmetrically coating the particles with gold nanoparticles. This method doesn't need the arrangement of particles onto any type of interfaces. Asymmetric coating of gold nanoparticles can be carried out simply by mixing Dimer particles with gold nanoparticles. The formation mechanism of the submicron-sized Dimer

  11. Hydrogenated fullerenes dimer, peanut and capsule: An atomic comparison

    NASA Astrophysics Data System (ADS)

    EL-Barbary, A. A.

    2016-04-01

    Hydrogenated fullerenes are detected in the Universe in space but their identification is still unsolved task. Therefore, this paper provides useful information about hydrogenated fullerenes (dimer, peanut and capsule) using DFT method at the B3LYP/6-31G(d) level of theory. The stability, geometric structures, hydrogen adsorption energies and NMR chemical shifts are calculated. The results show that the energy of most stable isomer of C118 dimer is lower than the energies sum of C60 and C58 cages by 1.77 eV and the energy per carbon atom of C144 capsule is more stable than C60 cage by 126.98 meV. Also, endohedral Ti-doped C118 dimer and C128 peanut are found to be most stable structures than exohedral Ti-doped C118 dimer and C128 peanut by 2.19 eV/Ti and 3.52 eV/Ti, respectively. The hydrogenation process is found to be enhanced (especially at the caps) for endohedral Ti-doped C118 dimer and C128 peanut through electronic surface modifications. The most active hydrogenation sites are selected and it is found that the most stable hydrogenation sites are Houts1 and Houts3 for fullerenes and endohedral Ti-doped fullerenes, respectively.

  12. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

    SciTech Connect

    Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

    2007-02-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

  13. Highly stable tetrathiafulvalene radical dimers in [3]catenanes

    SciTech Connect

    Spruell, Jason M.; Coskun, Ali; Friedman, Douglas C.; Forgan, Ross S.; Sarjeant, Amy A.; Trabolsi, Ali; Fahrenbach, Albert C.; Barin, Gokhan; Paxton, Walter F.; Dey, Sanjeev K.; Olson, Mark A.; Benítez, Diego; Tkatchouk, Ekaterina; Colvin, Michael T.; Carmielli, Raanan; Caldwell, Stuart T.; Rosair, Georgina M.; Hewage, Shanika Gunatilaka; Duclairoir, Florence; Seymour, Jennifer L.; Slawin, Alexandra M.Z.; Goddard, III, William A.; Wasielewski, Michael R.; Cooke, Graeme; Stoddart, J. Fraser

    2010-12-03

    Two [3]catenane 'molecular flasks' have been designed to create stabilized, redox-controlled tetrathiafulvalene (TTF) dimers, enabling their spectrophotometric and structural properties to be probed in detail. The mechanically interlocked framework of the [3]catenanes creates the ideal arrangement and ultrahigh local concentration for the encircled TTF units to form stable dimers associated with their discrete oxidation states. These dimerization events represent an affinity umpolung, wherein the inversion in electronic affinity replaces the traditional TTF-bipyridinium interaction, which is over-ridden by stabilizing mixed-valence (TTF){sub 2}{sup {sm_bullet}+} and radical-cation (TTF{sup {sm_bullet}+}){sub 2} states inside the 'molecular flasks.' The experimental data, collected in the solid state as well as in solution under ambient conditions, together with supporting quantum mechanical calculations, are consistent with the formation of stabilized paramagnetic mixed-valence dimers, and then diamagnetic radical-cation dimers following subsequent one-electron oxidations of the [3]catenanes.

  14. Altered Dimer Interface Decreases Stability in an Amyloidogenic Protein

    SciTech Connect

    Baden, Elizabeth M.; Owen, Barbara A.L.; Peterson, Francis C.; Volkman, Brian F.; Ramirez-Alvarado, Marina; Thompson, James R.

    2008-07-21

    Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kl O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kl O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kl O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.

  15. Structure determination and conformation analysis of symmetrical dimers.

    PubMed

    Buevich, Alexei V; Chan, Tze-Ming; Wang, C H; McPhail, Andrew T; Ganguly, A K

    2005-03-01

    Conformational and stereochemical analysis of six new symmetrical dimers was performed using proton-proton vicinal coupling measured from (1)H NMR and (13)C satellites of (1)H NMR signals, natural abundance (13)C-edited nuclear overhauser effect (NOE) experiments, comprehensive NOE analysis and molecular modeling. The (13)C satellite analysis and (13)C-edited NOE experiments were carried out to extract spectral information between equivalent protons. Molecular modeling was applied for estimations of three-dimensional parameters of the studied dimers, which were subsequently used to generate a set of theoretical NOE for each possible conformation. The J-coupling, (13)C-edited NOE and quantitative NOE analyses showed the predominance of gauche conformation for three dimers, whereas a mixture of gauche and anti conformations (45:55) for three other dimers was established by quantitative NOE analysis. X-ray crystallographic study confirmed the stereochemistry of one of the dimers and revealed a discrepancy in conformation stability between liquid and solid states.

  16. Secreted CXCL12 (SDF-1) Forms Dimers under Physiologic Conditions

    PubMed Central

    Ray, Paramita; Lewin, Sarah A.; Mihalko, Laura Anne; Lesher-Perez, Sasha Cai; Takayama, Shuichi; Luker, Kathryn E.; Luker, Gary D.

    2015-01-01

    Chemokine CXCL12 signaling through receptors CXCR4 and CXCR7 has essential functions in development and underlies diseases including cancer, atherosclerosis, and autoimmunity. Chemokines may form homodimers that regulate receptor binding and signaling, but previous studies with synthetic CXCL12 have produced conflicting evidence for homodimerization. We used bioluminescence imaging with Gaussia luciferase fusions to investigate dimerization of CXCL12 secreted from mammalian cells. By column chromatography and Gaussia luciferase complementation, we established that CXCL12 was secreted from mammalian cells as both monomers and dimers. Secreted CXCL12 also formed homodimers in the extracellular space. Monomeric CXCL12 preferentially activated CXCR4 signaling through Gαi and AKT, while dimeric CXCL12 more effectively promoted recruitment of β-arrestin 2 to CXCR4 and chemotaxis of CXCR4-expressing breast cancer cells. We also showed that CXCR7 preferentially sequestered monomeric CXCL12 from the extracellular space and had minimal effects on dimeric CXCL12 in cell-based assays and an orthotopic tumor xenograft model of human breast cancer. These studies establish that CXCL12 secreted from mammalian cells forms homodimers under physiologic conditions. Since monomeric and dimeric CXCL12 have distinct effects on cell signaling and function, our results have important implications for ongoing efforts to target CXCL12 pathways for therapy. PMID:22142194

  17. Palladium dimers adsorbed on graphene: A DFT study

    SciTech Connect

    Kaur, Gagandeep; Gupta, Shuchi; Dharamvir, Keya

    2015-05-15

    The 2D structure of graphene shows a great promise for enhanced catalytic activity when adsorbed with palladium. We performed a systematic density functional theory (DFT) study of the adsorption of palladium dimer (Pd{sub 2}) on graphene using SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Pd{sub 2}-graphene system are calculated. Both horizontal and vertical orientations of Pd{sub 2} on graphene are studied. Our calculations revealed that the minimum energy configuration for Pd dimer is parallel to the graphene sheet with its two atoms occupying centre of adjacent hexagonal rings of graphene sheet. Magnetic moment is induced for Pd dimer adsorbed on graphene in vertical orientation while horizontal orientation of Pd dimer on graphene do not exhibit magnetism. Insignificant energy differences among adsorption sites means that dimer mobility on the graphene sheet is high. There is imperceptible distortion of graphene sheet perpendicular to its plane. However, some lateral displacements are seen.

  18. Antineoplastic agents. 595. Structural modifications of betulin and the X-ray crystal structure of an unusual betulin amine dimer.

    PubMed

    Pettit, George R; Melody, Noeleen; Hempenstall, Frank; Chapuis, Jean-Charles; Groy, Thomas L; Williams, Lee

    2014-04-25

    The lupane-type triterpene betulin (1) has been subjected to a series of structural modifications for the purpose of evaluating resultant cancer cell growth inhibitory activity. The reaction sequence 7→11→12 was especially noteworthy in providing a betulin-derived amine dimer. Other unexpected synthetic results included the 11 and 13/14→17 conversions, which yielded an imidazo derivative. X-ray crystal structures of dimer 12 and intermediate 25 are reported. All of the betulin modifications were examined for anticancer activity against the P388 murine and human cell lines. Significant cancer cell growth inhibition was found for 4, 8, 9, 15/16, 19, 20, 24, and 26, which further defines the utility of the betulin scaffold.

  19. Mio-Pliocene to Pleistocene paleotopographic evolution of Brittany (France) from a sequence stratigraphic analysis: relative influence of tectonics and climate

    NASA Astrophysics Data System (ADS)

    Brault, N.; Bourquin, S.; Guillocheau, F.; Dabard, M.-P.; Bonnet, S.; Courville, P.; Estéoule-Choux, J.; Stepanoff, F.

    2004-01-01

    The Mio-Pliocene in Western Europe is a period of major climatic and tectonic change with important topographic consequences. The aim of this paper is to reconstruct these topographic changes (based on sedimentological analysis and sequence stratigraphy) for the Armorican Massif (western France) and to discuss their significance. The Mio-Pliocene sands of the Armorican Massif (Red Sands) are mainly preserved in paleovalleys and are characterized by extensive fluvial sheetflood deposits with low-preservation and by-pass facies. This sedimentological study shows that the Red Sands correspond to three main sedimentary environments: fluvial (alluvial fan, low-sinuosity rivers and braided rivers), estuarine and some rare open marine deposits (marine bioclastic sands: "faluns" of French authors). Two orders of sequences have been correlated across Brittany with one or two minor A/ S cycles comprised within the retrogradational trend of a major cycle. The unconformity at the base of the lower cycle is more marked than the unconformity observed at the top, which corresponds to a re-incision of the paleovalley network. A comparison of the results of the sequence stratigraphy analysis with eustatic variations and tectonic events during the Mio-Pliocene allows (1) to discuss their influence on the evolution of the Armorican Massif and (2) to compare the stratigraphic record with other west-European basins. The unconformity observed at the base of the first minor cycle may be attributed to Serravallian-Tortonian tectonic activity and/or eustatic fall, and the unconformity of the second minor cycle may be attributed to Late Tortonian-Early Messinian tectonic activity. The earlier unconformity is coeval with the development of a "smooth" paleovalley network compared to the jagged present-day relief. A single episode of Mio-Pliocene deformation recorded in Brittany may be dated as Zanclean, thus explaining the lack of the maximum flooding surface except in isolated areas. From

  20. Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

    PubMed Central

    Bledsoe, Jacob W.; Peterson, Brian C.; Swanson, Kelly S.; Small, Brian C.

    2016-01-01

    Aquaculture recently overtook capture fisheries as the largest producer of food fish, but to continue increasing fish production the industry is in search of better methods of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high-throughput DNA sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (dph), while also characterizing the environmental microbes derived from the water supply and the administered diets. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 dph when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 dph. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the species Cetobacterium somerae and Plesiomonas shigelloides showing the highest abundance in the catfish microbiota after 3 dph. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water-supply. Although, there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Our results have implications for future research related to channel catfish biology and culture, and increase our

  1. A DNA Sequence Recognition Loop on APOBEC3A Controls Substrate Specificity

    PubMed Central

    Dhuey, Erica; Zhang, Ruonan; Cao, Ping; Herate, Cecile; Chauveau, Lise; Hubbard, Stevan R.; Landau, Nathaniel R.

    2014-01-01

    APOBEC3A (A3A), one of the seven-member APOBEC3 family of cytidine deaminases, lacks strong antiviral activity against lentiviruses but is a potent inhibitor of adeno-associated virus and endogenous retroelements. In this report, we characterize the biochemical properties of mammalian cell-produced and catalytically active E. coli-produced A3A. The enzyme binds to single-stranded DNA with a Kd of 150 nM and forms dimeric and monomeric fractions. A3A, unlike APOBEC3G (A3G), deaminates DNA substrates nonprocessively. Using a panel of oligonucleotides that contained all possible trinucleotide contexts, we identified the preferred target sequence as TC (A/G). Based on a three-dimensional model of A3A, we identified a putative binding groove that contains residues with the potential to bind substrate DNA and to influence target sequence specificity. Taking advantage of the sequence similarity to the catalytic domain of A3G, we generated A3A/A3G chimeric proteins and analyzed their target site preference. We identified a recognition loop that altered A3A sequence specificity, broadening its target sequence preference. Mutation of amino acids in the predicted DNA binding groove prevented substrate binding, confirming the role of this groove in substrate binding. These findings shed light on how APOBEC3 proteins bind their substrate and determine which sites to deaminate. PMID:24827831

  2. pH dependent unfolding characteristics of DLC8 dimer: Residue level details from NMR.

    PubMed

    Mohan, P M Krishna; Hosur, Ramakrishna V

    2008-11-01

    Environment dependence of folding and unfolding of a protein is central to its function. In the same vein, knowledge of pH dependence of stability and folding/unfolding is crucial for many biophysical equilibrium and kinetic studies designed to understand protein folding mechanisms. In the present study we investigated the guanidine induced unfolding transition of dynein light chain protein (DLC8), a cargo adaptor of the dynein complex in the pH range 7-10. It is observed that while the protein remains a dimer in the entire pH range, its stability is somewhat reduced at alkaline pH. Global unfolding features monitored using fluorescence spectroscopy revealed that the unfolding transition of DLC8 at pH 7 is best described by a three-state model, whereas, that at pH 10 is best described by a two-state model. Chemical shift perturbations due to pH change provided insights into the corresponding residue level structural perturbations in the DLC8 dimer. Likewise, backbone (15)N relaxation measurements threw light on the corresponding motional changes in the dimeric protein. These observations have been rationalized on the basis of expected changes with increasing pH in the protonation states of the titratable residues on the structure of the protein. These, in turn provide an explanation for the change from three-state to two-state guanidine induced unfolding transition as the pH is increased from 7 to 10. All these results exemplify and highlight the role of environment vis-à-vis the sequence and structure of a given protein in dictating its folding/unfolding characteristics.

  3. Engineering of Helicobacter pylori Dimeric Oxidoreductase DsbK (HP0231)

    PubMed Central

    Bocian-Ostrzycka, Katarzyna M.; Grzeszczuk, Magdalena J.; Banaś, Anna M.; Jastrząb, Katarzyna; Pisarczyk, Karolina; Kolarzyk, Anna; Łasica, Anna M.; Collet, Jean-François; Jagusztyn-Krynicka, Elżbieta K.

    2016-01-01

    The formation of disulfide bonds that are catalyzed by proteins of the Dsb (disulfide bond) family is crucial for the correct folding of many extracytoplasmic proteins. Thus, this formation plays an essential, pivotal role in the assembly of many virulence factors. The Helicobacter pylori disulfide bond-forming system is uncomplicated compared to the best-characterized Escherichia coli Dsb pathways. It possesses only two extracytoplasmic Dsb proteins named HP0377 and HP0231. As previously shown, HP0377 is a reductase involved in the process of cytochrome c maturation. Additionally, it also possesses disulfide isomerase activity. HP0231 was the first periplasmic dimeric oxidoreductase involved in disulfide generation to be described. Although HP0231 function is critical for oxidative protein folding, its structure resembles that of dimeric EcDsbG, which does not confer this activity. However, the HP0231 catalytic motifs (CXXC and the so-called cis-Pro loop) are identical to that of monomeric EcDsbA. To understand the functioning of HP0231, we decided to study the relations between its sequence, structure and activity through an extensive analysis of various HP0231 point mutants, using in vivo and in vitro strategies. Our work shows the crucial role of the cis-Pro loop, as changing valine to threonine in this motif completely abolishes the protein function in vivo. Functioning of HP0231 is conditioned by the combination of CXXC and the cis-Pro loop, as replacing the HP0231 CXXC motif by the motif from EcDsbG or EcDsbC results in bifunctional protein, at least in E. coli. We also showed that the dimerization domain of HP0231 ensures contact with its substrates. Moreover, the activity of this oxidase is independent on the structure of the catalytic domain. Finally, we showed that HP0231 chaperone activity is independent of its redox function. PMID:27507968

  4. Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study.

    PubMed

    Do, Ngoc Quang; Phan, Anh Tuân

    2012-11-12

    Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.

  5. Electron attachment to hydrated oligonucleotide dimers: guanylyl-3',5'-cytidine and cytidylyl-3',5'-guanosine.

    PubMed

    Gu, Jiande; Xie, Yaoming; Schaefer, Henry F

    2010-05-03

    The dinucleoside phosphate deoxycytidylyl-3',5'-deoxyguanosine (dCpdG) and deoxyguanylyl-3',5'-deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5' end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3' end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine-containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The pi-stacking interaction between nucleobases G and C seems unlikely to improve the electron-capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron-capturing ability of cytosine should be attributed to the intensified proton accepting-donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O-C sigma bond and N-glycosidic bond breakage, might be expected for the radical anions of the guanosine-cytosine mixed oligonucleotides.

  6. Revisiting the putative TCR Cα dimerization model through structural analysis.

    PubMed

    Wang, Jia-Huai; Reinherz, Ellis L

    2013-01-01

    Despite major advances in T cell receptor (TCR) biology and structure, how peptide-MHC complex (pMHC) ligands trigger αβ TCR activation remains unresolved. Two views exist. One model postulates that monomeric TCR-pMHC ligation events are sufficient while a second proposes that TCR-TCR dimerization in cis via Cα domain interaction plus pMHC binding is critical. We scrutinized 22 known TCR/pMHC complex crystal structures, and did not find any predicted molecular Cα-Cα contacts in these crystals that would allow for physiological TCR dimerization. Moreover, the presence of conserved glycan adducts on the outer face of the Cα domain preclude the hypothesized TCR dimerization through the Cα domain. Observed functional consequences of Cα mutations are likely indirect, with TCR microclusters at the immunological synapse driven by TCR transmembrane/cytoplasmic interactions via signaling molecules, scaffold proteins, and/or cytoskeletal elements.

  7. Polarization to the field enhancement by a gold dimer

    NASA Astrophysics Data System (ADS)

    Hong, Xin; Jin, Zheng

    2016-11-01

    Due to the effect of plasmonic coupling, gold nanoparticle dimers have been paid more attentions in bio-imaging. The coupling effect existing at the gap between a closely linked particle pair can make the local field strongly enhanced and in which the angle between the excitation polarization and the dimer axis plays a dominant role. We calculated the amplitude distribution under a highly focused illumination objective. The simulation results show that for such a model, 45 degrees between the excitation polarization and the dimer axis can produce an optimum signal. The enhancement thus obtained is 10.78 fold while the variation between peak-peak can reach 6.59 fold compared to a single plasmoic particle during the rotation of the polarization.

  8. Optofluidic taming of a colloidal dimer with a silicon nanocavity

    SciTech Connect

    Pin, C.; Renaut, C.; Cluzel, B. Fornel, F. de; Peyrade, D.; Picard, E.; Hadji, E.

    2014-10-27

    We report here the optical trapping of a heterogeneous colloidal dimer above a photonic crystal nanocavity used as an on-chip optical tweezer. The trapped dimer consists of a cluster of two dielectric microbeads of different sizes linked by van der Waals forces. The smallest bead, 1 μm in diameter, is observed to be preferentially trapped by the nanotweezer, leaving the second bead untrapped. The rotational nature of the trapped dimer Brownian motion is first evidenced. Then, in the presence of a fluid flow, control of its orientation and rotation is achieved. The whole system is found to show high rotational degrees of freedom, thereby acting as an effective flow-sensitive microscopic optical ball joint.

  9. D-dimer is elevated in acute aortic dissection.

    PubMed

    Martin, Thomas; Shariq, Sohail

    2010-08-31

    This case illustrates that d-dimer is elevated in patients with acute aortic dissection. A 49-year-old woman presented with central, crushing chest pain exacerbated on inspiration. The chest pain was associated with right-leg numbness and pain, although peripheral pulses and blood pressures were normal. Routine bloods demonstrated an elevated d-dimer with a normal ECG and chest x-ray radiograph. A differential diagnosis of pulmonary embolism and acute aortic dissection was made. CT-angiogram showed type B aortic dissection. This case report highlights the mounting evidence that d-dimer is elevated in practically all incidents of aortic dissection and could be useful as a negative predictive marker.

  10. An exploration of the ozone dimer potential energy surface

    SciTech Connect

    Azofra, Luis Miguel; Alkorta, Ibon; Scheiner, Steve

    2014-06-28

    The (O{sub 3}){sub 2} dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O{sub 3} monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal vibrational frequencies are shifted to the red by dimerization, particularly the antisymmetric stretching mode whose shift is as high as 111 cm{sup −1}. In addition to the five minima, 11 higher-order stationary points are identified.

  11. Epoxidation of propylene dimers and isomerization of mixtures obtained

    SciTech Connect

    Dobrev, D.M.; Kurtev, K.S.

    1988-05-10

    Mixtures of hexenes are obtained in the dimerization of propylene on a Ziegler catalyst. By the epoxidation of this mixture by organic peroxides, followed by isomerization of the oxides, C/sub 6/ ketones, which are used as solvents, can be obtained. The hexenes were obtained by dimerization of propylene in the presence of a Ni(C/sub 5/H/sub 7/O/sub 2/)/sub 2/-P(C/sub 6/H/sub 5/)/sub 3/-(C/sub 3/H/sub 5/)/sub 2/AlCl catalytic system. The epoxidation was carried with technical grade isopropylbenzyl hydroperoxide (IPBHP). MoO/sub 2/(C/sub 5/H/sub 7/O/sub 2/)/sub 2/ was used as the catalyst. The relative rates of epoxidation of different isomers contained in the dimeric fraction, with respect to 2-methyl-1-pentene, was determined by means of competing reactions.

  12. Micellisation and immunoreactivities of dimeric beta-caseins.

    PubMed

    Yousefi, Reza; Gaudin, Jean-Charles; Chobert, Jean-Marc; Pourpak, Zahra; Moin, Mostafa; Moosavi-Movahedi, Ali Akbar; Haertle, Thomas

    2009-12-01

    Bovine beta-casein (beta-CN) is a highly amphiphilic micellising phospho-protein showing chaperone-like activity in vitro. Recently, existence of multiple sequential epitopes on beta-CN polypeptide chain in both hydrophilic-polar (psi) and hydrophobic-apolar domains (phi) has been evidenced. In order to clarify specific contribution of polar and apolar domains in micellisation process and in shaping immunoreactivity of beta-CN, its dimeric/bi-amphiphilic "quasi palindromic" forms covalently connected by a disulfide bond linking either N-terminal (C4 beta-CND) or C-terminal domain (C208 beta-CND) were produced and studied. Depending on the C- or N-terminal position of inserted cysteine, each dimeric beta-CN contains one polar/apolar region at the centre and two external hydrophobic/hydrophilic ends. Consequently, such casein dimers have radically different polarities/hydrophobicities on their outside surfaces. Dynamic light scattering (DLS) measurements indicate that these dimeric casein molecules form micelles of different sizes depending on arrangement of polar fragments of the beta-CN mutants in their constrained dimers. Non-aggregated dimers have different hydrodynamic diameters that could be explained by their different geometries. Measurements of fluorescence showed more hydrophobic environment of Trp residues of C208 beta-CND, while in similar experimental conditions Trp residues of C4 beta-CND and native beta-CN were more exposed to the polar medium. Both fluorescence and DLS studies showed greater propensity for micellisation of the dimeric beta-CNs, suggesting that the factors inducing the formation of micelles are stronger in the bi-amphiphilic dimers. 1-anilino-naphthalene-8-sulfonate (ANS) binding studies showed different binding of ANS by these dimers as well as different exposition of ANS binding (hydrophobic) regions in the micellar states. The differences in fluorescence resonance energy transfer (FRET) profiles of C4 beta-CND and C208 beta-CND can

  13. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  14. Using Surface Curvature to Control the Dimerization of a Surface-Active Protein

    NASA Astrophysics Data System (ADS)

    Kurylowicz, Martin; Giuliani, Maximiliano; Dutcher, John

    2012-02-01

    Understanding the influence of surface geometry on adsorbed proteins promises new possibilities in biophysics, such as topographical catalysis, molecular recognition of geometric cues, and modulations of oligomerization or ligand binding. We have created nano-textured hydrophobic surfaces that are stable in buffer by spin coating polystyrene (PS) nanoparticles (NPs) to form patchy NP monolayers on a PS substrate, yielding flat and highly curved areas on the same sample. Moreover, we have separated surface chemistry from texture by floating a 10 nm thick film of monodisperse PS onto the NP-functionalized surface. Using Single Molecule Force Spectroscopy we have compared in situ the distribution of detachment lengths for proteins on curved surfaces to that measured on flat surfaces. We have shown that β-Lactoglobulin (β-LG), a surface-active protein which helps to stabilize oil droplets in milk, forms dimers on both flat PS surfaces and surfaces with a radius of curvature of 100 nm, whereas β-LG monomers exist for more highly curved surfaces with radii of curvature of 25 and 40 nm. It is surprising that rather large radii of curvature have such a strong influence on proteins whose radius is only ˜2 nm. Furthermore, the transition from dimer to monomer with changes in surface curvature offers promising applications for proteins whose function can be modified by their oligomerization state.

  15. Fluxional σ-Bonds of the 2,5,8-Trimethylphenalenyl Dimer: Direct Observation of the Sixfold σ-Bond Shift via a π-Dimer.

    PubMed

    Uchida, Kazuyuki; Mou, Zhongyu; Kertesz, Miklos; Kubo, Takashi

    2016-04-06

    Direct evidence for σ-bond fluxionality in a phenalenyl σ-dimer was successfully obtained by a detailed investigation of the solution-state dynamics of 2,5,8-trimethylphenalenyl (TMPLY) using both experimental and theoretical approaches. TMPLY formed three diamagnetic dimers, namely, the σ-dimer (RR/SS), σ-dimer (RS), and π-dimer, which were fully characterized by (1)H NMR spectroscopy and electronic absorption measurements. The experimental findings gave the first quantitative insights into the essential preference of these competitive and unusual dimerization modes. The spectroscopic analyses suggested that the σ-dimer (RR/SS) is the most stable in terms of energy, whereas the others are metastable; the energy differences between these three isomers are less than 1 kcal mol(-1). Furthermore, the intriguing dynamics of the TMPLY dimers in the solution state were fully revealed by means of (1)H-(1)H exchange spectroscopy (EXSY) measurements and variable-temperature (1)H NMR studies. Surprisingly, the σ-dimer (RR/SS) demonstrated a sixfold σ-bond shift between the six sets of α-carbon pairs. This unusual σ-bond fluxionality is ascribed to the presence of a direct interconversion pathway between the σ-dimer (RR/SS) and the π-dimer, which was unambiguously corroborated by the EXSY measurements. The proposed mechanism of the sixfold σ-bond shift based on the experimental findings was well-supported by theoretical calculations.

  16. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  17. Dimeric α-Cobratoxin X-ray Structure

    PubMed Central

    Osipov, Alexey V.; Rucktooa, Prakash; Kasheverov, Igor E.; Filkin, Sergey Yu.; Starkov, Vladislav G.; Andreeva, Tatyana V.; Sixma, Titia K.; Bertrand, Daniel; Utkin, Yuri N.; Tsetlin, Victor I.

    2012-01-01

    In Naja kaouthia cobra venom, we have earlier discovered a covalent dimeric form of α-cobratoxin (αCT-αCT) with two intermolecular disulfides, but we could not determine their positions. Here, we report the αCT-αCT crystal structure at 1.94 Å where intermolecular disulfides are identified between Cys3 in one protomer and Cys20 of the second, and vice versa. All remaining intramolecular disulfides, including the additional bridge between Cys26 and Cys30 in the central loops II, have the same positions as in monomeric α-cobratoxin. The three-finger fold is essentially preserved in each protomer, but the arrangement of the αCT-αCT dimer differs from those of noncovalent crystallographic dimers of three-finger toxins (TFT) or from the κ-bungarotoxin solution structure. Selective reduction of Cys26-Cys30 in one protomer does not affect the activity against the α7 nicotinic acetylcholine receptor (nAChR), whereas its reduction in both protomers almost prevents α7 nAChR recognition. On the contrary, reduction of one or both Cys26-Cys30 disulfides in αCT-αCT considerably potentiates inhibition of the α3β2 nAChR by the toxin. The heteromeric dimer of α-cobratoxin and cytotoxin has an activity similar to that of αCT-αCT against the α7 nAChR and is more active against α3β2 nAChRs. Our results demonstrate that at least one Cys26-Cys30 disulfide in covalent TFT dimers, similar to the monomeric TFTs, is essential for their recognition by α7 nAChR, although it is less important for interaction of covalent TFT dimers with the α3β2 nAChR. PMID:22223648

  18. Dimeric RNA recognition regulates HIV-1 genome packaging.

    PubMed

    Nikolaitchik, Olga A; Dilley, Kari A; Fu, William; Gorelick, Robert J; Tai, S-H Sheldon; Soheilian, Ferri; Ptak, Roger G; Nagashima, Kunio; Pathak, Vinay K; Hu, Wei-Shau

    2013-03-01

    How retroviruses regulate the amount of RNA genome packaged into each virion has remained a long-standing question. Our previous study showed that most HIV-1 particles contain two copies of viral RNA, indicating that the number of genomes packaged is tightly regulated. In this report, we examine the mechanism that controls the number of RNA genomes encapsidated into HIV-1 particles. We hypothesize that HIV-1 regulates genome packaging by either the mass or copy number of the viral RNA. These two distinct mechanisms predict different outcomes when the genome size deviates significantly from that of wild type. Regulation by RNA mass would result in multiple copies of a small genome or one copy of a large genome being packaged, whereas regulation by copy number would result in two copies of a genome being packaged independent of size. To distinguish between these two hypotheses, we examined the packaging of viral RNA that was larger (≈17 kb) or smaller (≈3 kb) than that of wild-type HIV-1 (≈9 kb) and found that most particles packaged two copies of the viral genome regardless of whether they were 17 kb or 3 kb. Therefore, HIV-1 regulates RNA genome encapsidation not by the mass of RNA but by packaging two copies of RNA. To further explore the mechanism that governs this regulation, we examined the packaging of viral RNAs containing two packaging signals that can form intermolecular dimers or intramolecular dimers (self-dimers) and found that one self-dimer is packaged. Therefore, HIV-1 recognizes one dimeric RNA instead of two copies of RNA. Our findings reveal that dimeric RNA recognition is the key mechanism that regulates HIV-1 genome encapsidation and provide insights into a critical step in the generation of infectious viruses.

  19. Fractal analysis of DNA sequence data

    SciTech Connect

    Berthelsen, C.L.

    1993-01-01

    DNA sequence databases are growing at an almost exponential rate. New analysis methods are needed to extract knowledge about the organization of nucleotides from this vast amount of data. Fractal analysis is a new scientific paradigm that has been used successfully in many domains including the biological and physical sciences. Biological growth is a nonlinear dynamic process and some have suggested that to consider fractal geometry as a biological design principle may be most productive. This research is an exploratory study of the application of fractal analysis to DNA sequence data. A simple random fractal, the random walk, is used to represent DNA sequences. The fractal dimension of these walks is then estimated using the [open quote]sandbox method[close quote]. Analysis of 164 human DNA sequences compared to three types of control sequences (random, base-content matched, and dimer-content matched) reveals that long-range correlations are present in DNA that are not explained by base or dimer frequencies. The study also revealed that the fractal dimension of coding sequences was significantly lower than sequences that were primarily noncoding, indicating the presence of longer-range correlations in functional sequences. The multifractal spectrum is used to analyze fractals that are heterogeneous and have a different fractal dimension for subsets with different scalings. The multifractal spectrum of the random walks of twelve mitochondrial genome sequences was estimated. Eight vertebrate mtDNA sequences had uniformly lower spectra values than did four invertebrate mtDNA sequences. Thus, vertebrate mitochondria show significantly longer-range correlations than to invertebrate mitochondria. The higher multifractal spectra values for invertebrate mitochondria suggest a more random organization of the sequences. This research also includes considerable theoretical work on the effects of finite size, embedding dimension, and scaling ranges.

  20. A theoretical kinetic model of the temperature and pH dependent dimerization of orthosilicic acid in aqueous solution.

    PubMed

    McIntosh, Grant J

    2012-01-14

    The first steps in a pH- and temperature-dependent theoretical kinetic model of silicate polymerization and dissolution are examined in this work with a combined ab initio and transition state theory based study of the dimerization of H(4)SiO(4). The role of solvation has been of primary concern in this work, and its influence on theoretical activation energies and pre-exponential factors has been thoroughly benchmarked. Relatively inexpensive MP2/6-31+G(d)//HF/6-31+G(d) calculations of octahydrate clusters, with conductor-like polarizable continuum model corrections obtained in the MP2-level single-point calculations, have been shown to lead to a good description of the limited experimentally determined energetics of dimerization for most elementary reactions. Pre-exponential factors computed from this level of theory are found to be relatively insensitive to the level of theory utilized for geometry optimizations, the number of explicit waters, hindered rotor corrections, and variational effects arising from the minimization of rate constants. Within this framework, a kinetic model of the chemistry of H(4)SiO(4) and H(3)SiO(4)(-), forming H(6)Si(2)O(7) and H(5)Si(2)O(7)(-), has been compiled. Numerical simulations over pH = 3-12 show that a number of pH- and temperature dependent trends in reaction rates and positions of equilibrium are well described with this simple dimerization model. More specifically to the dimerization process, we obtain dimerization constants, log K(dim), of 1.85 and -7.15 for the formation of H(6)Si(2)O(7) and H(5)Si(2)O(7)(-) respectively, which compare well with experimentally determined values of 1.2 and -8.5, respectively.

  1. Dimerization of argon and the properties of its small clusters

    NASA Astrophysics Data System (ADS)

    Titov, S. V.; Serov, S. A.; Ostrovskii, G. M.

    2016-12-01

    Statistical thermodynamic means are used to study the bound state of a small cluster AN (2 ≤ N ≤ 5) of Lennard-Jones particles in a spherical cavity. The statistical sum is calculated by the Monte Carlo method. For the dimer, integration is reduced to quadratures. The integration region contains only phase space points corresponding to the bound cluster state. Dimerization constant 2A = A2 is calculated via the probability of finding a molecule in the bound state using the example of argon.

  2. Antagonizing STAT5B dimerization with an osmium complex

    PubMed Central

    Liu, Li-Juan; Wang, Wanhe; Kang, Tian-Shu; Liang, Jia-Xin; Liu, Chenfu; Kwong, Daniel W. J.; Wong, Vincent Kam Wai; Ma, Dik-Lung; Leung, Chung-Hang

    2016-01-01

    Targeting STAT5 is an appealing therapeutic strategy for the treatment of hematologic malignancies and inflammation. Here, we present the novel osmium(II) complex 1 as the first metal-based inhibitor of STAT5B dimerization. Complex 1 exhibited superior inhibitory activity against STAT5B DNA binding compared to STAT5A DNA binding. Moreover, 1 repressed STAT5B transcription and blocked STAT5B dimerization via binding to the STAT5B protein, thereby inhibiting STAT5B translocation to the nucleus. Furthermore, 1 was able to selectively inhibit STAT5B phosphorylation without affecting the expression level of STAT5B. PMID:27853239

  3. A Pfaffian Formula for Monomer-Dimer Partition Functions

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Jauslin, Ian; Lieb, Elliott H.

    2016-04-01

    We consider the monomer-dimer partition function on arbitrary finite planar graphs and arbitrary monomer and dimer weights, with the restriction that the only non-zero monomer weights are those on the boundary. We prove a Pfaffian formula for the corresponding partition function. As a consequence of this result, multipoint boundary monomer correlation functions at close packing are shown to satisfy fermionic statistics. Our proof is based on the celebrated Kasteleyn theorem, combined with a theorem on Pfaffians proved by one of the authors, and a careful labeling and directing procedure of the vertices and edges of the graph.

  4. Styrene dimers and trimers affect reproduction of daphnid (Ceriodaphnia dubia).

    PubMed

    Tatarazako, Norihisa; Takao, Yuji; Kishi, Katsuyuki; Onikura, Norio a; Arizono, Koji; Iguchi, Taisen

    2002-08-01

    The endocrine disruptor activity of styrene in humans and other vertebrates appears to be negligible. However, offspring numbers were reduced in Ceriodaphnia dubia bred in polystyrene cups. Styrene dimers and trimers were found to be eluted from the polystyrene cups by hexane and methanol with gas chromatography-mass spectrometry. Styrene dimers and trimers at concentrations of 0.04-1.7 microg/l affected C. dubia fertility (25% reduction after seven days), suggesting that styrenes have the potential to impair crustacean populations in the aquatic environment.

  5. Dimerization of polycyclic aromatic hydrocarbons in soot nucleation.

    PubMed

    Zhang, Hong-Bo; You, Xiaoqing; Wang, Hongmiao; Law, Chung K

    2014-02-27

    A possible pathway of soot nucleation, in which localized π electrons play an important role in binding the polycyclic aromatic hydrocarbon (PAH) molecules having multiradical characteristics to form stable polymer molecules through covalent bonds, is studied using density functional and semiempirical methods. Results show that the number of covalent bonds formed in the dimerization of two identical PAHs is determined by the radical character, and the sites to form bonds are related to the aromaticity of individual six-membered ring structure. It is further shown that the binding energy of dimerization increases linearly with the diradical character in the range relevant to soot nucleation.

  6. Dimeric acylphloroglucinols from Hypericum austrobrasiliense exhibiting antinociceptive activity in mice.

    PubMed

    Bridi, Henrique; Ccana-Ccapatinta, Gari V; Stolz, Eveline D; Meirelles, Gabriela C; Bordignon, Sérgio A L; Rates, Stela M K; von Poser, Gilsane L

    2016-02-01

    Three dimeric acylphloroglucinols, austrobrasilol A, austrobrasilol B and isoaustrobrasilol B were isolated from the flowers of Hypericum austrobrasiliense (Hypericaceae, section Trigynobrathys). Their structures were elucidated using mass spectrometry and NMR experiments (1D and 2D), and by comparison with previously reported data for other dimeric acylphloroglucinols isolated from Hypericum and Elaphoglossum genera. The three compounds were orally administered in mice at equimolar doses to uliginosin B (15mg/kg, p.o.) displaying antinociceptive activity in the hot-plate test. The compounds did not induce motor impairment in the rotarod apparatus.

  7. The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.

    PubMed

    Booth, David S; Cheng, Yifan; Frankel, Alan D

    2014-12-08

    The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.

  8. Crystal structure of poxvirus thymidylate kinase: An unexpected dimerization has implications for antiviral therapy

    PubMed Central

    Caillat, Christophe; Topalis, Dimitri; Agrofoglio, Luigi A.; Pochet, Sylvie; Balzarini, Jan; Deville-Bonne, Dominique; Meyer, Philippe

    2008-01-01

    Unlike most DNA viruses, poxviruses replicate in the cytoplasm of host cells. They encode enzymes needed for genome replication and transcription, including their own thymidine and thymidylate kinases. Some herpes viruses encode only 1 enzyme catalyzing both reactions, a peculiarity used for prodrug activation to obtain maximum specificity. We have solved the crystal structures of vaccinia virus thymidylate kinase bound to TDP or brivudin monophosphate. Although the viral and human enzymes have similar sequences (42% identity), they differ in their homodimeric association and active-site geometry. The vaccinia TMP kinase dimer arrangement is orthogonal and not antiparallel as in human enzyme. This different monomer orientation is related to the presence of a canal connecting the edge of the dimer interface to the TMP base binding pocket. Consequently, the pox enzyme accommodates nucleotides with bulkier bases, like brivudin monophosphate and dGMP; these are efficiently phosphorylated and stabilize the enzyme. The brivudin monophosphate-bound structure explains the structural basis for this specificity, opening the way to the rational development of specific antipox agents that may also be suitable for poxvirus TMP kinase gene-based chemotherapy of cancer. PMID:18971333

  9. Crystal structure of poxvirus thymidylate kinase: an unexpected dimerization has implications for antiviral therapy.

    PubMed

    Caillat, Christophe; Topalis, Dimitri; Agrofoglio, Luigi A; Pochet, Sylvie; Balzarini, Jan; Deville-Bonne, Dominique; Meyer, Philippe

    2008-11-04

    Unlike most DNA viruses, poxviruses replicate in the cytoplasm of host cells. They encode enzymes needed for genome replication and transcription, including their own thymidine and thymidylate kinases. Some herpes viruses encode only 1 enzyme catalyzing both reactions, a peculiarity used for prodrug activation to obtain maximum specificity. We have solved the crystal structures of vaccinia virus thymidylate kinase bound to TDP or brivudin monophosphate. Although the viral and human enzymes have similar sequences (42% identity), they differ in their homodimeric association and active-site geometry. The vaccinia TMP kinase dimer arrangement is orthogonal and not antiparallel as in human enzyme. This different monomer orientation is related to the presence of a canal connecting the edge of the dimer interface to the TMP base binding pocket. Consequently, the pox enzyme accommodates nucleotides with bulkier bases, like brivudin monophosphate and dGMP; these are efficiently phosphorylated and stabilize the enzyme. The brivudin monophosphate-bound structure explains the structural basis for this specificity, opening the way to the rational development of specific antipox agents that may also be suitable for poxvirus TMP kinase gene-based chemotherapy of cancer.

  10. SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers.

    PubMed

    Hass, Matthew R; Liow, Hien-Haw; Chen, Xiaoting; Sharma, Ankur; Inoue, Yukiko U; Inoue, Takayoshi; Reeb, Ashley; Martens, Andrew; Fulbright, Mary; Raju, Saravanan; Stevens, Michael; Boyle, Scott; Park, Joo-Seop; Weirauch, Matthew T; Brent, Michael R; Kopan, Raphael

    2015-08-20

    We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level.

  11. Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes

    SciTech Connect

    Arnett, Kelly L.; Hass, Matthew; McArthur, Debbie G.; Ilagan, Ma Xenia G.; Aster, Jon C.; Kopan, Raphael; Blacklow, Stephen C.

    2010-11-12

    Ligand-induced proteolysis of Notch produces an intracellular effector domain that transduces essential signals by regulating the transcription of target genes. This function relies on the formation of transcriptional activation complexes that include intracellular Notch, a Mastermind co-activator and the transcription factor CSL bound to cognate DNA. These complexes form higher-order assemblies on paired, head-to-head CSL recognition sites. Here we report the X-ray structure of a dimeric human Notch1 transcription complex loaded on the paired site from the human HES1 promoter. The small interface between the Notch ankyrin domains could accommodate DNA bending and untwisting to allow a range of spacer lengths between the two sites. Cooperative dimerization occurred on the human and mouse Hes5 promoters at a sequence that diverged from the CSL-binding consensus at one of the sites. These studies reveal how promoter organizational features control cooperativity and, thus, the responsiveness of different promoters to Notch signaling.

  12. Mechanism of amyloid β-protein dimerization determined using single-molecule AFM force spectroscopy

    NASA Astrophysics Data System (ADS)

    Lv, Zhengjian; Roychaudhuri, Robin; Condron, Margaret M.; Teplow, David B.; Lyubchenko, Yuri L.

    2013-10-01

    Aβ42 and Aβ40 are the two primary alloforms of human amyloid β-protein (Aβ). The two additional C-terminal residues of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single-molecule force microscopy to characterize interpeptide interactions for Aβ42 and Aβ40 and corresponding mutants. We discovered a dramatic difference in the interaction patterns of Aβ42 and Aβ40 monomers within dimers. Although the sequence difference between the two peptides is at the C-termini, the N-terminal segment plays a key role in the peptide interaction in the dimers. This is an unexpected finding as N-terminal was considered as disordered segment with no effect on the Aβ peptide aggregation. These novel properties of Aβ proteins suggests that the stabilization of N-terminal interactions is a switch in redirecting of amyloids form the neurotoxic aggregation pathway, opening a novel avenue for the disease preventions and treatments.

  13. Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae

    PubMed Central

    Ostrow, A. Zachary; Gan, Yan; Villwock, Sandra K.; Linke, Christian; Barberis, Matteo; Chen, Lin; Aparicio, Oscar M.

    2017-01-01

    Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance. PMID:28265091

  14. UV Radiation–Sensitive Norin 1 Rice Contains Defective Cyclobutane Pyrimidine Dimer Photolyase

    PubMed Central

    Hidema, Jun; Kumagai, Tadashi; Sutherland, Betsy M.

    2000-01-01

    Norin 1, a progenitor of many economically important Japanese rice strains, is highly sensitive to the damaging effects of UVB radiation (wavelengths 290 to 320 nm). Norin 1 seedlings are deficient in photorepair of cyclobutane pyrimidine dimers. However, the molecular origin of this deficiency was not known and, because rice photolyase genes have not been cloned and sequenced, could not be determined by examining photolyase structural genes or upstream regulatory elements for mutations. We therefore used a photoflash approach, which showed that the deficiency in photorepair in vivo resulted from a functionally altered photolyase. These results were confirmed by studies with extracts, which showed that the Norin 1 photolyase–dimer complex was highly thermolabile relative to the wild-type Sasanishiki photolyase. This deficiency results from a structure/function alteration of photolyase rather than of nonspecific repair, photolytic, or regulatory elements. Thus, the molecular origin of this plant DNA repair deficiency, resulting from a spontaneously occurring mutation to UV radiation sensitivity, is defective photolyase. PMID:11006332

  15. Activation of PKR by RNA misfolding: HDV ribozyme dimers activate PKR

    PubMed Central

    Heinicke, Laurie A.; Bevilacqua, Philip C.

    2012-01-01

    Protein Kinase R (PKR), the double-stranded RNA (dsRNA)-activated protein kinase, plays important roles in innate immunity. Previous studies have shown that PKR is activated by long stretches of dsRNA, RNA pseudoknots, and certain single-stranded RNAs; however, regulation of PKR by RNAs with globular tertiary structure has not been reported. In this study, the HDV ribozyme is used as a model of a mostly globular RNA. In addition to a catalytic core, the ribozyme contains a peripheral 13-bp pairing region (P4), which, upon shortening, affects neither the catalytic activity of the ribozyme nor its ability to crystallize. We report that the HDV ribozyme sequence alone can activate PKR. To elucidate the RNA structural basis for this, we prepared a number of HDV variants, including those with shortened or lengthened P4 pairing regions, with the anticipation that lengthening the P4 extension would yield a more potent activator since it would offer more base pairs of dsRNA. Surprisingly, the variant with a shortened P4 was the most potent activator. Through native gel mobility and enzymatic structure mapping experiments we implicate misfolded HDV ribozyme dimers as the PKR-activating species, and show that the shortened P4 leads to enhanced occupancy of the RNA dimer. These observations have implications for how RNA misfolding relates to innate immune response and human disease. PMID:23105000

  16. Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA

    SciTech Connect

    Dibrov, Sergey; McLean, Jaime; Hermann, Thomas

    2011-09-27

    A sequence around the start codon of the mRNA of human thymidylate synthase (TS) folds into a secondary-structure motif in which the initiation site is sequestered in a metastable hairpin. Binding of the protein to its own mRNA at the hairpin prevents the production of TS through a translation-repression feedback mechanism. Stabilization of the mRNA hairpin by other ligands has been proposed as a strategy to reduce TS levels in anticancer therapy. Rapidly proliferating cells require high TS activity to maintain the production of thymidine as a building block for DNA synthesis. The crystal structure of a model oligonucleotide (TS1) that represents the TS-binding site of the mRNA has been determined. While fluorescence studies showed that the TS1 RNA preferentially adopts a hairpin structure in solution, even at high RNA concentrations, an asymmetric dimer of two hybridized TS1 strands was obtained in the crystal. The TS1 dimer contains an unusual S-turn motif that also occurs in the 'off' state of the human ribosomal decoding site RNA.

  17. Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae.

    PubMed

    Ostrow, A Zachary; Kalhor, Reza; Gan, Yan; Villwock, Sandra K; Linke, Christian; Barberis, Matteo; Chen, Lin; Aparicio, Oscar M

    2017-03-21

    Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1 phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in a manner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.

  18. The effect of resonance interactions on the absorption spectra of (SF6)2 dimers in low-temperature matrices: Calculations and experiment

    NASA Astrophysics Data System (ADS)

    Tokhadze, I. K.; Kolomiĭtsova, T. D.; Tokhadze, K. G.; Shchepkin, D. N.

    2007-03-01

    The IR absorption spectra of (SF6)2 dimers in Ar and N2 matrices are investigated at 11 K. As a result of the resonance dipole-dipole interaction, the band of the triply degenerate vibration v 3 is split into two components v X, Y and v Z. In comparison with the gaseous state, the splitting Δv = v X, Y - v Z in the argon matrix decreases to 18.45 cm-1, whereas, in the nitrogen matrix, the band v X, Y is split into components v X and v Y, with the splitting being equal to δ ≈ 0.9 cm-1. A model that takes into account the influence of the matrix on the spectra of dimers is developed. The model makes it possible to successively (i) calculate the resonance spectrum of an isolated dimer in terms of the model of local modes taking into account resonance interactions, (ii) determine with the help of the Monte Carlo method the structure of a matrix consisting of 512 1440 Ar (or N2) atoms and a rigid (SF6)2 dimer, and (iii) take into account interactions of local dipole moments of a dimer with particles of the matrix in the approximation of dipole-induced dipole interactions. The model developed satisfactorily describes the experimental results. The calculated frequencies v Z, v X, and v Y of a dimer in the matrix are shifted toward smaller frequencies as compared to the gaseous state, while the resonance splitting decreases virtually by 2 cm-1. It is shown that, in an argon matrix with a symmetric arrangement of argon atoms nearest to a dimer, the splitting of v X, Y proves to be smaller than 0.05 cm-1. In a nitrogen matrix, this splitting increases virtually to 0.4 cm-1.

  19. Structure and Mechanism of the Influenza A M218-60 Dimer of Dimers.

    PubMed

    Andreas, Loren B; Reese, Marcel; Eddy, Matthew T; Gelev, Vladimir; Ni, Qing Zhe; Miller, Eric A; Emsley, Lyndon; Pintacuda, Guido; Chou, James J; Griffin, Robert G

    2015-12-02

    We report a magic angle spinning (MAS) NMR structure of the drug-resistant S31N mutation of M218-60 from Influenza A. The protein was dispersed in diphytanoyl-sn-glycero-3-phosphocholine lipid bilayers, and the spectra and an extensive set of constraints indicate that M218-60 consists of a dimer of dimers. In particular, ∼280 structural constraints were obtained using dipole recoupling experiments that yielded well-resolved (13)C-(15)N, (13)C-(13)C, and (1)H-(15)N 2D, 3D, and 4D MAS spectra, all of which show cross-peak doubling. Interhelical distances were measured using mixed (15)N/(13)C labeling and with deuterated protein, MAS at ωr/2π = 60 kHz, ω0H/2π = 1000 MHz, and (1)H detection of methyl-methyl contacts. The experiments reveal a compact structure consisting of a tetramer composed of four transmembrane helices, in which two opposing helices are displaced and rotated in the direction of the membrane normal relative to a four-fold symmetric arrangement, yielding a two-fold symmetric structure. Side chain conformations of the important gating and pH-sensing residues W41 and H37 are found to differ markedly from four-fold symmetry. The rmsd of the structure is 0.7 Å for backbone heavy atoms and 1.1 Å for all heavy atoms. This two-fold symmetric structure is different from all of the previous structures of M2, many of which were determined in detergent and/or with shorter constructs that are not fully active. The structure has implications for the mechanism of H(+) transport since the distance between His and Trp residues on different helices is found to be short. The structure also exhibits two-fold symmetry in the vicinity of the binding site of adamantyl inhibitors, and steric constraints may explain the mechanism of the drug-resistant S31N mutation.

  20. Biophysical Characterization of the Dimer and Tetramer Interface Interactions of the Human Cytosolic Malic Enzyme

    PubMed Central

    Murugan, Sujithkumar; Hung, Hui-Chih

    2012-01-01

    The cytosolic NADP+-dependent malic enzyme (c-NADP-ME) has a dimer-dimer quaternary structure in which the dimer interface associates more tightly than the tetramer interface. In this study, the urea-induced unfolding process of the c-NADP-ME interface mutants was monitored using fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation and enzyme activities. Here, we demonstrate the differential protein stability between dimer and tetramer interface interactions of human c-NADP-ME. Our data clearly demonstrate that the protein stability of c-NADP-ME is affected predominantly by disruptions at the dimer interface rather than at the tetramer interface. First, during thermal stability experiments, the melting temperatures of the wild-type and tetramer interface mutants are 8–10°C higher than those of the dimer interface mutants. Second, during urea denaturation experiments, the thermodynamic parameters of the wild-type and tetramer interface mutants are almost identical. However, for the dimer interface mutants, the first transition of the urea unfolding curves shift towards a lower urea concentration, and the unfolding intermediate exist at a lower urea concentration. Third, for tetrameric WT c-NADP-ME, the enzyme is first dissociated from a tetramer to dimers before the 2 M urea treatment, and the dimers then dissociated into monomers before the 2.5 M urea treatment. With a dimeric tetramer interface mutant (H142A/D568A), the dimer completely dissociated into monomers after a 2.5 M urea treatment, while for a dimeric dimer interface mutant (H51A/D90A), the dimer completely dissociated into monomers after a 1.5 M urea treatment, indicating that the interactions of c-NADP-ME at the dimer interface are truly stronger than at the tetramer interface. Thus, this study provides a reasonable explanation for why malic enzymes need to assemble as a dimer of dimers. PMID:23284632

  1. Packing interface energetics in different crystal forms of the λ Cro dimer.

    PubMed

    Ahlstrom, Logan S; Miyashita, Osamu

    2014-07-01

    Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures.

  2. Immunohistochemical evaluation of tissue factor, fibrin/fibrinogen and D-dimers in canine gliomas.

    PubMed

    de la Fuente, Cristian; Pumarola, Martí; Blasco, Ester; Fernández, Francisco; Viu, Judit; Añor, Sònia

    2014-06-01

    In human gliomas, tissue factor (TF) is overexpressed, associated with the grade of malignancy and influences tumour biology. Intra-tumoural fibrin/fibrinogen deposition and activation of the fibrinolytic system also play a role in tumour cell proliferation and angiogenesis. The first aim of the present study was to investigate TF expression and the presence of fibrin/fibrinogen and D-dimers in canine glioma biopsies, graded according to the World Health Organization (WHO) classification of tumours of the central nervous system. The second aim was to investigate the occurrence of intravascular thrombosis (IVT) in canine gliomas, as a potential histological marker of glioma type or grade of malignancy. An immunohistochemical study using antibodies against TF, fibrin/fibrinogen and D-dimers was performed with 24 glioma samples, including 15 oligodendrogliomas, 6 astrocytomas and 3 mixed gliomas. Immunohistochemical data were statistically analysed to determine whether there was any relationship between glioma type and grade of malignancy. All gliomas were moderate to strongly positive for TF and the staining score was significantly higher (P = 0.04) in high-grade (III or IV) than in low-grade (II) gliomas. Intra-tumoural fibrin/fibrinogen deposition was detected in all tumour biopsies assessed, and D-dimers were detected in 17/24 gliomas. IVT was a frequent finding, but was not linked to a specific glioma type or malignancy grade. TF expression, fibrin/fibrinogen deposition, extravascular fibrinolytic system activation and IVT occur in canine gliomas. Canine glioma might be a suitable model for studying coagulation and fibrinolysis as potential therapeutic targets for human gliomas.

  3. Comparative assay of antioxidant packages for dimer of estolide esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A series of 26 different antioxidants and commercial antioxidant packages, containing both natural and synthetic-based materials, were evaluated with dimeric coconut-oleic estolide 2-ethylhexyl ester. The different antioxidants were broken down into different classes of materials: phenolic, aminic, ...

  4. The Internal Structure of Nanoparticle Dimers Linked by DNA

    NASA Astrophysics Data System (ADS)

    Vargas Lara, Fernando; Cheng, Ching-Jung; Gang, Oleg; Starr, Francis W.

    2012-02-01

    The self-assembly of inorganic units controlled by the interactions of biological molecules, like DNA, has received attention for the possibility to specify higher-order structure, with potential biological, optical and electronic applications. In biology, self-assembly of complex materials (eg. bone, spider silk) frequently occurs in a stepwise, hierarchical fashion. Here, we consider a first step towards a hierarchical approach for synthetic nanostructures of nanoparticles (NPs) linked by DNA. The most basic unit in this multiscale approach is a dimer of NPs linked by DNA. We use a coarse-grained molecular model to explain experimental measurements of the separation of two DNA-coated NPs connected by linking single-stranded DNA (ssDNA). We show that the dimer separation is primarily controlled by the number of DNA links between NPs. If these links are not constrained to lie along the axis between NPs, the separation is limited by off-axis connections that force the NPs to be closer. We also determine how the number of connections alters the effective persistence length of the ssDNA that connects the dimer. We discuss how these dimers might be used for subsequent assembly at larger scales.

  5. Cantharimide dimers from the Chinese blister beetle, Mylabris phalerate PALLAS.

    PubMed

    Nakatani, Takafumi; Jinpo, Katsuaki; Noda, Naoki

    2007-01-01

    Five cantharidin-related compounds were isolated from the Chinese blister beetle, Mylabris phalerate PALLAS (Meloidae). Their structures were determined based on spectroscopic and chemical evidence. Three of them were identified as cantharimide dimers, which consist of two units of cantharimide combined with a tri-, tetra-, or penta-methylene group.

  6. Dimeric pyrrole-imidazole alkaloids: synthetic approaches and biosynthetic hypotheses.

    PubMed

    Wang, Xiao; Ma, Zhiqiang; Wang, Xiaolei; De, Saptarshi; Ma, Yuyong; Chen, Chuo

    2014-08-14

    The pyrrole-imidazole alkaloids are a group of structurally unique and biologically interesting marine sponge metabolites. Among them, the cyclic dimers have caught synthetic chemists' attention particularly. Numerous synthetic strategies have been developed and various biosynthetic hypotheses have been proposed for these fascinating natural products. We discuss herein the synthetic approaches and the biosynthetic insights obtained from these studies.

  7. Asymptotics of Height Change on Toroidal Temperleyan Dimer Models

    NASA Astrophysics Data System (ADS)

    Dubédat, Julien; Gheissari, Reza

    2015-04-01

    The dimer model is an exactly solvable model of planar statistical mechanics. In its critical phase, various aspects of its scaling limit are known to be described by the Gaussian free field. For periodic graphs, criticality is an algebraic condition on the spectral curve of the model, determined by the edge weights (Kenyon et al. in Ann Math (2) 163(3):1019-1056, 2006); isoradial graphs provide another class of critical dimer models, in which the edge weights are determined by the local geometry. In the present article, we consider another class of graphs: general Temperleyan graphs, i.e. graphs arising in the (generalized) Temperley bijection between spanning trees and dimer models. Building in particular on Forman's formula and representations of Laplacian determinants in terms of Poisson operators, and under a minimal assumption—viz. that the underlying random walk converges to Brownian motion—we show that the natural topological observable on macroscopic tori converges in law to its universal limit, i.e. the law of the periods of the dimer height function converges to that of the periods of a compactified free field.

  8. Potential Energy Surface Database of Group II Dimer

    National Institute of Standards and Technology Data Gateway

    SRD 143 NIST Potential Energy Surface Database of Group II Dimer (Web, free access)   This database provides critical atomic and molecular data needed in order to evaluate the feasibility of using laser cooled and trapped Group II atomic species (Mg, Ca, Sr, and Ba) for ultra-precise optical clocks or quantum information processing devices.

  9. Hydrazine-mediated strongly coupled Re(CO)3 dimers.

    PubMed

    Hasheminasab, A; Rhoda, H M; Crandall, L A; Ayers, J T; Nemykin, V N; Herrick, R S; Ziegler, C J

    2015-10-21

    Dimeric metal complexes can often exhibit coupling interactions via bridging ligands. In this report, we present two Re(CO)3 dimers, where the metals are linked via a bis(pyca) hydrazine (pyca = pyridine-2-carbaldehyde imine) Schiff base ligand. For the dimeric compounds 4 and 5, we observe strong coupling across the dimer as measured by cyclic voltammetry: ∼480 mV separations between the first and the second reduction waves that correspond to comproportionation constants close to 1.5 × 10(8). Evidence for a mixed valence state upon one electron reduction was also observed by spectroelectrochemistry in which a clear inter-valence charge-transfer (IVCT) band was observed in [4]- and [5]-complexes. The electronic structures of all target compounds were probed by DFT and TDDFT computational methods. DFT calculations indicate that reduction takes place at the diimine units, and that the observed coupling is a ligand-based phenomenon, rather than one that involves metal-based orbitals.

  10. Ising anyons in frustration-free Majorana-dimer models

    NASA Astrophysics Data System (ADS)

    Ware, Brayden; Son, Jun Ho; Cheng, Meng; Mishmash, Ryan V.; Alicea, Jason; Bauer, Bela

    2016-09-01

    Dimer models have long been a fruitful playground for understanding topological physics. Here, we introduce a class, termed Majorana-dimer models, wherein bosonic dimers are decorated with pairs of Majorana modes. We find that the simplest examples of such systems realize an intriguing, intrinsically fermionic phase of matter that can be viewed as the product of a chiral Ising theory, which hosts deconfined non-Abelian quasiparticles, and a topological px-i py superconductor. While the bulk anyons are described by a single copy of the Ising theory, the edge remains fully gapped. Consequently, this phase can arise in exactly solvable, frustration-free models. We describe two parent Hamiltonians: one generalizes the well-known dimer model on the triangular lattice, while the other is most naturally understood as a model of decorated fluctuating loops on a honeycomb lattice. Using modular transformations, we show that the ground-state manifold of the latter model unambiguously exhibits all properties of the Ising×(px-i py) theory. We also discuss generalizations with more than one Majorana mode per site, which realize phases related to Kitaev's 16-fold way in a similar fashion.

  11. Transporting testosterone and its dimers by serum proteins.

    PubMed

    Chanphai, P; Vesper, A R; Bekale, L; Bérubé, G; Tajmir-Riahi, H A

    2015-12-01

    A substantial part of steroids is bound to serum proteins in vivo. We report the association of testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) with human serum albumin (HSA) and bovine serum albumin (BSA) in aqueous solution at physiological pH. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-protein binding and protein aggregation process. Spectroscopic analysis showed that steroids bind protein via hydrophobic, hydrophilic and H-bonding interactions. HSA forms more stable complexes than BSA. The binding affinity of steroid-protein adducts is testosterone>dimer-aromatic>dimer-aliphatic. Transmission electron microscopy showed major changes in protein morphology as steroid-protein complexation occurred with increase in the diameter of the protein aggregate indicating encapsulation of steroids by serum proteins. Modeling showed the presence of H-bonding stabilized testosterone-protein complexes with the free binding energy of -12.95 for HSA and -11.55 kcal/mol for BSA, indicating that the interaction process is spontaneous at room temperature. Steroid complexation induced more perturbations of BSA conformation than HSA.

  12. Centrosymmetric dimer of quinuclidine betaine and squaric acid complex

    NASA Astrophysics Data System (ADS)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2012-12-01

    The complex of squaric acid (3,4-dihydroxy-3-cyclobuten-1,2-dion, H2SQ) with quinuclidine betaine (1-carboxymethyl-1-azabicyclo[2.2.2]octane inner salt, QNB), 1, has been characterized by single-crystal X-ray analysis, FTIR and NMR spectroscopies and by DFT calculations. In the crystal of 1, monoclinic space group P21/n, one proton from H2SQ is transferred to QNB. QNBH+ and HSQ- are linked together by a Osbnd H⋯O hydrogen bond of 2.553(2) Å. Two such QNBH+·HSQ- complexes form a centrosymmetric dimer bridged by two Osbnd H⋯O bonds of 2.536(2) Å. The FTIR spectrum is consistent with the X-ray results. The structures of monomer QNBH+·HSQ- (1a) and dimer [QNB·H2SQ]2 (2) have been optimized at the B3LYP/6-311++G(d,p) level of theory. Isolated dimer 2 optimized back to a molecular aggregate of H2SQ and QNB. The calculated frequencies for the optimized structure of dimer 2 have been used to explain the frequencies of the experimental FTIR spectrum. The interpretation of 1H and 13C NMR spectra has been based on the calculated GIAO/B3LYP/6-311++G(d,p) magnetic isotropic shielding constants for monomer 1a.

  13. Nanoparticle-nanoparticle vs. nanoparticle-substrate hot spot contributions to the SERS signal: studying Raman labelled monomers, dimers and trimers.

    PubMed

    Sergiienko, Sergii; Moor, Kamila; Gudun, Kristina; Yelemessova, Zarina; Bukasov, Rostislav

    2017-02-08

    We used a combination of Raman microscopy, AFM and TEM to quantify the influence of dimerization on the surface enhanced Raman spectroscopy (SERS) signal for gold and silver nanoparticles (NPs) modified with Raman reporters and situated on gold, silver, and aluminum films and a silicon wafer. The overall increases in the mean SERS enhancement factor (EF) upon dimerization (up by 43% on average) and trimerisation (up by 96% on average) of AuNPs and AgNPs on the studied metal films are within a factor of two, which is moderate when compared to most theoretical models. However, the maximum ratio of EFs for some dimers to the mean EF of monomers can be as high as 5.5 for AgNPs on a gold substrate. In contrast, for dimerization and trimerization of gold and silver NPs on silicon, the mean EF increases by 1-2 orders of magnitude relative to the mean EF of single NPs. Therefore, hot spots in the interparticle gap between gold nanoparticles rather than hot spots between Au nanoparticles and the substrate dominate SERS enhancement for dimers and trimers on a silicon substrate. However, Raman labeled noble metal nanoparticles on plasmonic metal films generate on average SERS enhancement of the same order of magnitude for both types of hot spot zones (e.g. NP/NP and NP/metal film).

  14. Nature and possible mechanisms of formation of potential mutations arising at emerging of thymine dimers after irradiation of double-stranded DNA by ultraviolet light

    NASA Astrophysics Data System (ADS)

    Grebneva, H. A.

    2003-01-01

    The mutagenesis under ultraviolet (UV)-irradiation is discussed. It is assumed, that the basic damages resulting in transitions, transversions, mutations of the frameshift and complex mutations are changes of the tautomeric state of the bases. The bases may be a part of dimers or may be not the dimer components. We consider such rare tautomeric states, which may influence the character of base pairing. A model of the formation of the above rare tautomeric forms of nucleotide bases under the UV-irradiation of the DNA is proposed. In the case of a radiation deexcitation of the DNA, which has absorbed the UV-quantum of the triplet energy level, there occur strong forced oscillations. They may result in changes of the lengths of hydrogen bonds between DNA bases. As a result, at H-bond shortening, the hydrogen atom may be almost in the center of H-bond. In the case of H-bond elongation, it may remain near the partner atom. Because of the H-bond breaking, during the formation of dimers, rare tautomeric forms of bases influencing the character of pairing can be realized. If a pair of the bases is not a part of dimer, then the only new stable configuration of the hydrogen atoms is the one that occurred at double-proton phototautomerism. It is shown that only those dimers are mutational, in which the change of a tautomeric state of the DNA bases have taken place. This is one of the differences between the proposed model and the standard one. The latter assumes, that from the point of view of ability of forming the mutations all the dimers are identical, and the DNA-polymerase is sometimes mistaken, incidentally building uncomplementary bases in. The consideration is only of qualitative character, it needs experimental verification, subsequent study by methods of quantum chemistry and theoretical physics. A list of problems to be studied in this respect is given.

  15. Synthesis, characterization, OFET and electrochemical properties of novel dimeric metallophthalocyanines.

    PubMed

    Ozer, Lale Meyancı; Ozer, Metin; Altındal, Ahmet; Ozkaya, Ali Rıza; Salih, Bekir; Bekaroğlu, Ozer

    2013-05-14

    The synthesis of 4,4'-[6,6'-methylenebis (2-(2-(3,4-dicyanophenoxy)-5-methylbenzyl)-4-methyl-6,1-phenylene)] bis (oxy) diphthalonitrile 1 was achieved starting from 4-nitrophthalonitrile and 6,6'-methylenebis(2-(2-hydroxy-5-methylbenzyl)-4-methylphenol in DMF at 50 °C by the catalysis of K2CO3 under argon. The corresponding dimeric metallophthalocyanines (Zn2Pc2 2 and Co2Pc2 3) were tetramerized in dimethylaminoethanol with the appropriate metal salt. Newly synthesized compounds were characterized by elemental analysis, UV-vis, FT-IR (ATR), MALDI-TOF mass and (1)H-NMR spectroscopy techniques. The electrochemical properties of the complexes were examined by cyclic voltammetry, differential pulse voltammetry, controlled potential coulometry and in situ spectroelectrochemistry in nonaqueous media. The results showed that while there is considerable weak interactions between the two metal phthalocyanine units in dimeric zinc phthalocyanine, these interactions in dimeric cobalt phthalocyanine is remarkable. The catalytic performances of dimeric cobalt phthalocyanine in the reduction of oxygen in a medium similar to the working conditions of the polymer electrolyte membrane fuel-cells were found to be much higher than that of dinuclear zinc phthalocyanine. Solution-processed films of the complexes were utilized as an active semiconducting layer in the fabrication of organic field-effect transistors (OFETs) in the bottom-gate configurations. The output characteristics of the resulting p-type OFET devices were investigated to evaluate the performances such as the field effect mobility (μF). A relatively high field effect mobility of 7.3 × 10(-3) cm(2) V(-1) s(-1) was observed for dimeric cobalt phthalocyanine.

  16. Radiation-enhanced optical antenna based on nonperiodic metallic nanoparticle dimer chain

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Yu, Wenhai; Yue, Wencheng; Yao, Peijun; Liu, Wen

    2015-07-01

    With the aid of multi-sphere dyadic Green's function, we present a design of optical nanoantenna which is composed of a nonperiodic nanoparticle dimer chain. By breaking the periodicity of the dimer chain, the radiative emission of the dimer chain is significantly enhanced because the strong coupling which limits radiation enhancement is inhibited when the separations between dimers are reduced. Our work clearly shows the crucial role of nonperiodicity in the design of the Yagi-Uda nanoantenna.

  17. The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization.

    PubMed

    Romero-López, Cristina; Barroso-delJesus, Alicia; Berzal-Herranz, Alfredo

    2017-02-24

    The RNA genome of the hepatitis C virus (HCV) establishes a network of long-distance RNA-RNA interactions that direct the progression of the infective cycle. This work shows that the dimerization of the viral genome, which is initiated at the dimer linkage sequence (DLS) within the 3'UTR, is promoted by the CRE region, while the IRES is a negative regulatory partner. Using differential 2'-acylation probing (SHAPE-dif) and molecular interference (HMX) technologies, the CRE activity was found to mainly lie in the critical 5BSL3.2 domain, while the IRES-mediated effect is dependent upon conserved residues within the essential structural elements JIIIabc, JIIIef and PK2. These findings support the idea that, along with the DLS motif, the IRES and CRE are needed to control HCV genome dimerization. They also provide evidences of a novel function for these elements as chaperone-like partners that fine-tune the architecture of distant RNA domains within the HCV genome.

  18. Nuclear Import and Dimerization of Tomato ASR1, a Water Stress-Inducible Protein Exclusive to Plants

    PubMed Central

    Ricardi, Martiniano M.; Guaimas, Francisco F.; González, Rodrigo M.; Burrieza, Hernán P.; López-Fernández, María P.; Estévez, José M.; Iusem, Norberto D.

    2012-01-01

    The ASR (for ABA/water stress/ripening) protein family, first described in tomato as nuclear and involved in adaptation to dry climates, is widespread in the plant kingdom, including crops of high agronomic relevance. We show both nuclear and cytosolic localization for ASR1 (the most studied member of the family) in histological plant samples by immunodetection, typically found in small proteins readily diffusing through nuclear pores. Indeed, a nuclear localization was expected based on sorting prediction software, which also highlight a monopartite nuclear localization signal (NLS) in the primary sequence. However, here we prove that such an “NLS” of ASR1 from tomato is dispensable and non-functional, being the transport of the protein to the nucleus due to simple diffusion across nuclear pores. We attribute such a targeting deficiency to the misplacing in that cryptic NLS of two conserved contiguous lysine residues. Based on previous in vitro experiments regarding quaternary structure, we also carried out live cell imaging assays through confocal microscopy to explore dimer formation in planta. We found homodimers in both the cytosol and the nucleus and demonstrated that assembly of both subunits together can occur in the cytosol, giving rise to translocation of preformed dimers. The presence of dimers was further corroborated by means of in vivo crosslinking of nuclei followed by SDS-PAGE. PMID:22899993

  19. The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization

    PubMed Central

    Romero-López, Cristina; Barroso-delJesus, Alicia; Berzal-Herranz, Alfredo

    2017-01-01

    The RNA genome of the hepatitis C virus (HCV) establishes a network of long-distance RNA-RNA interactions that direct the progression of the infective cycle. This work shows that the dimerization of the viral genome, which is initiated at the dimer linkage sequence (DLS) within the 3′UTR, is promoted by the CRE region, while the IRES is a negative regulatory partner. Using differential 2′-acylation probing (SHAPE-dif) and molecular interference (HMX) technologies, the CRE activity was found to mainly lie in the critical 5BSL3.2 domain, while the IRES-mediated effect is dependent upon conserved residues within the essential structural elements JIIIabc, JIIIef and PK2. These findings support the idea that, along with the DLS motif, the IRES and CRE are needed to control HCV genome dimerization. They also provide evidences of a novel function for these elements as chaperone-like partners that fine-tune the architecture of distant RNA domains within the HCV genome. PMID:28233845

  20. Nuclear import and dimerization of tomato ASR1, a water stress-inducible protein exclusive to plants.

    PubMed

    Ricardi, Martiniano M; Guaimas, Francisco F; González, Rodrigo M; Burrieza, Hernán P; López-Fernández, María P; Jares-Erijman, Elizabeth A; Estévez, José M; Iusem, Norberto D

    2012-01-01

    The ASR (for ABA/water stress/ripening) protein family, first described in tomato as nuclear and involved in adaptation to dry climates, is widespread in the plant kingdom, including crops of high agronomic relevance. We show both nuclear and cytosolic localization for ASR1 (the most studied member of the family) in histological plant samples by immunodetection, typically found in small proteins readily diffusing through nuclear pores. Indeed, a nuclear localization was expected based on sorting prediction software, which also highlight a monopartite nuclear localization signal (NLS) in the primary sequence. However, here we prove that such an "NLS" of ASR1 from tomato is dispensable and non-functional, being the transport of the protein to the nucleus due to simple diffusion across nuclear pores. We attribute such a targeting deficiency to the misplacing in that cryptic NLS of two conserved contiguous lysine residues. Based on previous in vitro experiments regarding quaternary structure, we also carried out live cell imaging assays through confocal microscopy to explore dimer formation in planta. We found homodimers in both the cytosol and the nucleus and demonstrated that assembly of both subunits together can occur in the cytosol, giving rise to translocation of preformed dimers. The presence of dimers was further corroborated by means of in vivo crosslinking of nuclei followed by SDS-PAGE.

  1. Dimeric States of Neural- and Epithelial-Cadherins are Distinguished by the Rate of Disassembly†

    PubMed Central

    Vunnam, Nagamani; Flint, Jon; Balbo, Andrea; Schuck, Peter; Pedigo, Susan

    2011-01-01

    Epithelial- and Neural-cadherins are specifically localized at synapses in neurons which can change shape and contact surface on a time scale of seconds to months. We have focused our studies on the role of the extracellular domains of cadherins in the dynamics of synapses. The kinetics of dimer disassembly of the first two extracellular domains of E- and N-cadherin, ECAD12 and NCAD12, were studied with analytical size exclusion chromatography and sedimentation velocity. NCAD12 forms three different dimers that are distinguished by assembly conditions and kinetics of dissociation. ECAD12 dimer disassembles rapidly regardless of the calcium concentration, whereas the disassembly of NCAD12 dimers was strongly dependent on calcium concentration. In addition to the apo- and saturated-dimeric forms of NCAD12, there is a third dimeric form that is a slow exchange dimer. This third dimeric form for NCAD12, formed by decalcification of the calcium-saturated dimer, was kinetically-trapped in apo-conditions and did not disassemble over a period of months. Sedimentation velocity experiments showed that this dimer, upon addition of calcium, had similar weighted averages as calcium-saturated dimer. These studies provide evidence that the kinetics of dimer disassembly of the extracellular domains may be a major contributor to the morphological dynamics of synapses in vivo. PMID:21375242

  2. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Dimer acid/rosin amidoamine reaction... Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... generically as Dimer acid/rosin amidoamine reaction product (PMN P-99-0143) is subject to reporting under...

  3. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Dimer acid/rosin amidoamine reaction... Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... generically as Dimer acid/rosin amidoamine reaction product (PMN P-99-0143) is subject to reporting under...

  4. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Dimer acid/rosin amidoamine reaction... Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... generically as Dimer acid/rosin amidoamine reaction product (PMN P-99-0143) is subject to reporting under...

  5. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Dimer acid/rosin amidoamine reaction... Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... generically as Dimer acid/rosin amidoamine reaction product (PMN P-99-0143) is subject to reporting under...

  6. 40 CFR 721.9484 - Dimer acid/rosin amidoamine reaction product (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Dimer acid/rosin amidoamine reaction... Specific Chemical Substances § 721.9484 Dimer acid/rosin amidoamine reaction product (generic). (a... generically as Dimer acid/rosin amidoamine reaction product (PMN P-99-0143) is subject to reporting under...

  7. A Designed “Nested” Dimer of Cyanovirin-N Increases Antiviral Activity

    PubMed Central

    Woodrum, Brian W.; Maxwell, Jason; Allen, Denysia M.; Wilson, Jennifer; Krumpe, Lauren R.H.; Bobkov, Andrey A.; Hill, R. Blake; Kibler, Karen V.; O’Keefe, Barry R.; Ghirlanda, Giovanna

    2016-01-01

    Cyanovirin-N (CV-N) is an antiviral lectin with potent activity against enveloped viruses, including HIV. The mechanism of action involves high affinity binding to mannose-rich glycans that decorate the surface of enveloped viruses. In the case of HIV, antiviral activity of CV-N is postulated to require multivalent interactions with envelope protein gp120, achieved through a pseudo-repeat of sequence that adopts two near-identical glycan-binding sites, and possibly involves a 3D-domain-swapped dimeric form of CV-N. Here, we present a covalent dimer of CV-N that increases the number of active glycan-binding sites, and we characterize its ability to recognize four glycans in solution. A CV-N variant was designed in which two native repeats were separated by the “nested” covalent insertion of two additional repeats of CV-N, resulting in four possible glycan-binding sites. The resulting Nested CV-N folds into a wild-type-like structure as assessed by circular dichroism and NMR spectroscopy, and displays high thermal stability with a Tm of 59 °C, identical to WT. All four glycan-binding domains encompassed by the sequence are functional as demonstrated by isothermal titration calorimetry, which revealed two sets of binding events to dimannose with dissociation constants Kd of 25 μM and 900 μM, assigned to domains B and B’ and domains A and A’ respectively. Nested CV-N displays a slight increase in activity when compared to WT CV-N in both an anti-HIV cellular assay and a fusion assay. This construct conserves the original binding specifityies of domain A and B, thus indicating correct fold of the two CV-N repeats. Thus, rational design can be used to increase multivalency in antiviral lectins in a controlled manner. PMID:27275831

  8. A Designed "Nested" Dimer of Cyanovirin-N Increases Antiviral Activity.

    PubMed

    Woodrum, Brian W; Maxwell, Jason; Allen, Denysia M; Wilson, Jennifer; Krumpe, Lauren R H; Bobkov, Andrey A; Hill, R Blake; Kibler, Karen V; O'Keefe, Barry R; Ghirlanda, Giovanna

    2016-06-06

    Cyanovirin-N (CV-N) is an antiviral lectin with potent activity against enveloped viruses, including HIV. The mechanism of action involves high affinity binding to mannose-rich glycans that decorate the surface of enveloped viruses. In the case of HIV, antiviral activity of CV-N is postulated to require multivalent interactions with envelope protein gp120, achieved through a pseudo-repeat of sequence that adopts two near-identical glycan-binding sites, and possibly involves a 3D-domain-swapped dimeric form of CV-N. Here, we present a covalent dimer of CV-N that increases the number of active glycan-binding sites, and we characterize its ability to recognize four glycans in solution. A CV-N variant was designed in which two native repeats were separated by the "nested" covalent insertion of two additional repeats of CV-N, resulting in four possible glycan-binding sites. The resulting Nested CV-N folds into a wild-type-like structure as assessed by circular dichroism and NMR spectroscopy, and displays high thermal stability with a Tm of 59 °C, identical to WT. All four glycan-binding domains encompassed by the sequence are functional as demonstrated by isothermal titration calorimetry, which revealed two sets of binding events to dimannose with dissociation constants Kd of 25 μM and 900 μM, assigned to domains B and B' and domains A and A' respectively. Nested CV-N displays a slight increase in activity when compared to WT CV-N in both an anti-HIV cellular assay and a fusion assay. This construct conserves the original binding specifityies of domain A and B, thus indicating correct fold of the two CV-N repeats. Thus, rational design can be used to increase multivalency in antiviral lectins in a controlled manner.

  9. Commonly-occurring polymorphisms in the COMT, DRD1 and DRD2 genes influence different aspects of motor sequence learning in humans.

    PubMed

    Baetu, Irina; Burns, Nicholas R; Urry, Kristi; Barbante, Girolamo Giovanni; Pitcher, Julia B

    2015-11-01

    Performing sequences of movements is a ubiquitous skill that involves dopamine transmission. However, it is unclear which components of the dopamine system contribute to which aspects of motor sequence learning. Here we used a genetic approach to investigate the relationship between different components of the dopamine system and specific aspects of sequence learning in humans. In particular, we investigated variations in genes that code for the catechol-O-methyltransferase (COMT) enzyme, the dopamine transporter (DAT) and dopamine D1 and D2 receptors (DRD1 and DRD2). COMT and the DAT regulate dopamine availability in the prefrontal cortex and the striatum, respectively, two key regions recruited during learning, whereas dopamine D1 and D2 receptors are thought to be involved in long-term potentiation and depression, respectively. We show that polymorphisms in the COMT, DRD1 and DRD2 genes differentially affect behavioral performance on a sequence learning task in 161 Caucasian participants. The DRD1 polymorphism predicted the ability to learn new sequences, the DRD2 polymorphism predicted the ability to perform a previously learnt sequence after performing interfering random movements, whereas the COMT polymorphism predicted the ability to switch flexibly between two sequences. We used computer simulations to explore potential mechanisms underlying these effects, which revealed that the DRD1 and DRD2 effects are possibly related to neuroplasticity. Our prediction-error algorithm estimated faster rates of connection strengthening in genotype groups with presumably higher D1 receptor densities, and faster rates of connection weakening in genotype groups with presumably higher D2 receptor densities. Consistent with current dopamine theories, these simulations suggest that D1-mediated neuroplasticity contributes to learning to select appropriate actions, whereas D2-mediated neuroplasticity is involved in learning to inhibit incorrect action plans. However, the

  10. Cloning and characterization of human inducible nitric oxide synthase splice variants: A domain, encoded by exons 8 and 9, is critical for dimerization

    PubMed Central

    Eissa, N. Tony; Yuan, Jean W.; Haggerty, Cynthia M.; Choo, Esther K.; Palmer, Celeste D.; Moss, Joel

    1998-01-01

    The inducible nitric oxide synthase (iNOS) contains an amino-terminal oxygenase domain, a carboxy-terminal reductase domain, and an intervening calmodulin-binding region. For the synthesis of nitric oxide (NO), iNOS is active as a homodimer. The human iNOS mRNA is subject to alternative splicing, including deletion of exons 8 and 9 that encode amino acids 242–335 of the oxygenase domain. In this study, iNOS8−9− and full-length iNOS (iNOSFL) were cloned from bronchial epithelial cells. Expression of iNOS8−9− in 293 cell line resulted in generation of iNOS8−9− mRNA and protein but did not lead to NO production. In contrast to iNOSFL, iNOS8−9− did not form dimers. Similar to iNOSFL, iNOS8−9− exhibited NADPH-diaphorase activity and contained tightly bound calmodulin, indicating that the reductase and calmodulin-binding domains were functional. To identify sequences in exons 8 and 9 that are critical for dimerization, iNOSFL was used to construct 12 mutants, each with deletion of eight residues in the region encoded by exons 8 and 9. In addition, two “control” iNOS deletion mutants were synthesized, lacking either residues 45–52 of the oxygenase domain or residues 1131–1138 of the reductase domain. Whereas both control deletion mutants generated NO and formed dimers, none of the 12 other mutants formed dimers or generated NO. The region encoded by exons 8 and 9 is critical for iNOS dimer formation and NO production but not for reductase activity. This region could be a potential target for therapeutic interventions aimed at inhibiting iNOS dimerization and hence NO synthesis. PMID:9636200

  11. Evaluation of stability difference between asymmetric homochiral dimer in (S)-thalidomide crystal and symmetric heterochiral dimer in (RS)-thalidomide crystal

    NASA Astrophysics Data System (ADS)

    Suzuki, Toshiya; Tanaka, Masahito; Shiro, Motoo; Shibata, Norio; Osaka, Tetsuya; Asahi, Toru

    2010-03-01

    This article discusses differences in physicochemical properties such as solubility and melting point between (S)-thalidomide and (RS)-thalidomide based on crystal structures determined by X-ray diffraction experiments. Investigation of such differences is of great importance because thalidomide has attracted considerable attention again due to its wide-range bioactivity for intractable diseases. In this article, structures of hydrogen-bonded rings were compared between asymmetric homochiral dimers in (S)-thalidomide crystal and symmetric heterochiral dimers in (RS)-thalidomide crystal. The heterochiral dimer was evaluated to be more stable than the homochiral dimer by the energy calculations for hydrogen-bonded rings in those dimers. These results indicate that differences in physicochemical properties between enantiomeric and racemic thalidomides originate from the difference of structural stability between homochiral and heterochiral dimers.

  12. A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation.

    PubMed

    Shi, Jing; Chen, Wei-Fei; Zhang, Bo; Fan, San-Hong; Ai, Xia; Liu, Na-Nv; Rety, Stephane; Xi, Xu-Guang

    2017-04-07

    Helicases play a critical role in processes such as replication or r