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Sample records for dimerization sequence influence

  1. Sequence-Specific DNA Binding by a Short Peptide Dimer

    NASA Astrophysics Data System (ADS)

    Talanian, Robert V.; McKnight, C. James; Kim, Peter S.

    1990-08-01

    A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4^circC. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

  2. The regulator of nitrate assimilation in ascomycetes is a dimer which binds a nonrepeated, asymmetrical sequence.

    PubMed

    Strauss, J; Muro-Pastor, M I; Scazzocchio, C

    1998-03-01

    The regulation of nitrate assimilation seems to follow the same pattern in all ascomycetes where this process has been studied. We show here by in vitro binding studies and a number of protection and interference techniques that the transcription factor mediating nitrate induction in Aspergillus nidulans, a protein containing a binuclear zinc cluster DNA binding domain, recognizes an asymmetrical sequence of the form CTCC GHGG. We further show that the protein binds to its consensus site as a dimer. We establish the role of the putative dimerization element by its ability to replace the analogous element of the cI protein of phage lambda. Mutagenesis of crucial leucines of the dimerization element affect both the binding ability of the dimer and the conformation of the resulting protein-DNA complex. This is the first case to be described where a dimer recognizes such an asymmetrical nonrepeated sequence, presumably by each monomeric subunit making different contacts with different DNA half-sites. PMID:9488449

  3. Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases.

    PubMed Central

    Arimitsu, E; Aoki, S; Ishikura, S; Nakanishi, K; Matsuura, K; Hara, A

    1999-01-01

    Cynomolgus and Japanese monkey kidneys, dog and pig livers and rabbit lens contain dimeric dihydrodiol dehydrogenase (EC 1.3.1.20) associated with high carbonyl reductase activity. Here we have isolated cDNA species for the dimeric enzymes by reverse transcriptase-PCR from human intestine in addition to the above five animal tissues. The amino acid sequences deduced from the monkey, pig and dog cDNA species perfectly matched the partial sequences of peptides digested from the respective enzymes of these animal tissues, and active recombinant proteins were expressed in a bacterial system from the monkey and human cDNA species. Northern blot analysis revealed the existence of a single 1.3 kb mRNA species for the enzyme in these animal tissues. The human enzyme shared 94%, 85%, 84% and 82% amino acid identity with the enzymes of the two monkey strains (their sequences were identical), the dog, the pig and the rabbit respectively. The sequences of the primate enzymes consisted of 335 amino acid residues and lacked one amino acid compared with the other animal enzymes. In contrast with previous reports that other types of dihydrodiol dehydrogenase, carbonyl reductases and enzymes with either activity belong to the aldo-keto reductase family or the short-chain dehydrogenase/reductase family, dimeric dihydrodiol dehydrogenase showed no sequence similarity with the members of the two protein families. The dimeric enzyme aligned with low degrees of identity (14-25%) with several prokaryotic proteins, in which 47 residues are strictly or highly conserved. Thus dimeric dihydrodiol dehydrogenase has a primary structure distinct from the previously known mammalian enzymes and is suggested to constitute a novel protein family with the prokaryotic proteins. PMID:10477285

  4. Blue Light-induced Dimerization of Monomeric Aureochrome-1 Enhances Its Affinity for the Target Sequence*

    PubMed Central

    Hisatomi, Osamu; Nakatani, Yoichi; Takeuchi, Ken; Takahashi, Fumio; Kataoka, Hironao

    2014-01-01

    Aureochrome-1 (AUREO1) is a blue light (BL) receptor that mediates the branching response in stramenopile alga, Vaucheria frigida. AUREO1 contains a basic leucine zipper (bZIP) domain in the central region and a light-oxygen-voltage sensing (LOV) domain at the C terminus, and has been suggested to function as a light-regulated transcription factor. We have previously reported that preparations of recombinant AUREO1 contained the complete coding sequence (full-length, FL) and N-terminal truncated protein (ZL) containing bZIP and LOV domains, and suggested that wild-type ZL (ZLwt2) was in a dimer form with intermolecular disulfide linkages at Cys162 and Cys182 (Hisatomi, O., Takeuchi, K., Zikihara, K., Ookubo, Y., Nakatani, Y., Takahashi, F., Tokutomi, S., and Kataoka, H. (2013) Plant Cell Physiol. 54, 93–106). In the present study, we report the photoreactions, oligomeric structures, and DNA binding of monomeric cysteine to serine-mutated ZL (ZLC2S), DTT-treated ZL (DTT-ZL), and FL (DTT-FL). Recombinant AUREO1 showed similar spectral properties and dark regeneration kinetics to those of dimeric ZLwt2. Dynamic light scattering and size exclusion chromatography revealed that ZLC2S and DTT-ZL were monomeric in the dark state. Dissociation of intermolecular disulfide bonds of ZLwt2 was in equilibrium with a midpoint oxidation-redox potential of approximately −245 ± 15 mV. BL induced the dimerization of monomeric ZL, which subsequently increased its affinity for the target sequence. Also, DTT-FL was monomeric in the dark state and underwent BL-induced dimerization, which led to formation of the FL2·DNA complex. Taken together, our results suggest that monomeric AUREO1 is present in vivo, with dimerization playing a key role in its role as a BL-regulated transcription factor. PMID:24790107

  5. Clinical conditions and patient factors significantly influence diagnostic utility of D-dimer in venous thromboembolism.

    PubMed

    Qasim, Asghar; Duggan, Mary; O'Connell, Niamh; O'Driscoll, Anne

    2009-06-01

    Determining D-dimer levels remains important in the diagnostic algorithms for venous thromboembolism (VTE). The present study aimed to identify factors influencing D-dimer utility in diagnosing VTE. Consecutive symptomatic medical patients, who attended our emergency department from 1 November 2006 to 31 December 2006, had D-dimer levels measured as fibrinogen equivalent units (FEU), following clinical risk assessment. Diagnosis of VTE was established by venous compression ultrasonography and computed tomographic pulmonary angiography. VTE-negative patients were followed for 2 months to detect future occurrence of thromboembolism. Impact of various factors on D-dimer levels was analyzed. Four thousand and twenty-six patients attended our emergency department, and 525 patients (median age 52 years) had D-dimer assessed. Final diagnosis of VTE was established in 25 (4.7%) patients on radiological investigations. Median D-dimer levels for VTE-negative patients less than 60 years old, with normal renal function and chest radiology were 0.38 microgFEU/ml (range 0.19-2.3), 0.39 microgFEU/ml (range 0.17-3.5) and 0.39 microgFEU/ml (range 0.1-4.3), respectively. Similar figures for those at least 60 years, with renal impairment and abnormal chest radiology, were 0.75 microgFEU/ml (range 0.22-4.3), 0.52 microgFEU/ml (range 0.17-4.4) and 0.92 microgFEU/ml (range 0.26-5.6), respectively. Factors including patient age, renal function and chest radiology had significant influence on D-dimer levels (P < 0.01). A triad of patient age at least 60 years, renal impairment (modification of diet in renal disease stage 2-5) and abnormal chest radiology had a false positive D-dimer in 96% of patients (n = 72). Use of D-dimer in patients with a triad of advanced age, renal impairment and abnormal chest radiology has no practical diagnostic value in VTE. PMID:19276796

  6. Sequence analysis of the dimerization initiation site of concordant and discordant viral variants superinfecting HIV type 1 patients.

    PubMed

    Mayr, Luzia; Powell, Rebecca; Kinge, Thompson; Nyambi, Phillipe N

    2011-11-01

    For HIV recombination to occur, the RNAs from two infecting strains within a cell must dimerize at the dimerization initiation site (DIS). We examined the sequence identity at the DIS (697-731 bp, Hxb2 numbering engine) in patients superinfected with concordant HIV-1 strains and compared them to those with discordant strains. Viral RNA in sequential plasma from four subjects superinfected with subtype-discordant and two subjects superinfected with subtype-concordant HIV-1 strains was extracted, amplified (5' LTR-early gag: 526-1200 bp, Hxb2 numbering engine), sequenced, and analyzed to determine their compatibility for dimerization in vivo. The concordant viruses infecting the two subjects exhibited identical sequences in the 35-bp-long DIS region while sequences from the discordant viruses revealed single nucleotide changes that were located in the DIS loop (715 bp), its flanking nucleotides (710 bp and 717 bp), and the DIS stem (719 bp). Evidence from in vitro experiments demonstrates that these in vivo changes identified can abolish dimerization and reduce recombination frequency. Therefore, these results revealing differences in the DIS of discordant strains versus the similarity noted for the concordant strains may contribute to the differences in the frequency of recombination in patients superinfected with such HIV-1 variants. PMID:21453132

  7. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

    PubMed Central

    Malinverni, Duccio; Marsili, Simone; Barducci, Alessandro; De Los Rios, Paolo

    2015-01-01

    Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex biochemical cycle involving large-scale structural rearrangements. Here we show that an analysis of coevolution at the residue level fully captures the characteristic large-scale conformational transitions of this protein family, and predicts an evolutionary conserved–and thus functional–homo-dimeric arrangement. Furthermore, we highlight that the features encoding the Hsp70 dimer are more conserved in bacterial than in eukaryotic sequences, suggesting that the known Hsp70/Hsp110 hetero-dimer is a eukaryotic specialization built on a pre-existing template. PMID:26046683

  8. Sequence-selective carbohydrate-DNA interaction: dimeric and monomeric forms of the calicheamicin oligosaccharide interfere with transcription factor function.

    PubMed Central

    Liu, C; Smith, B M; Ajito, K; Komatsu, H; Gomez-Paloma, L; Li, T; Theodorakis, E A; Nicolaou, K C; Vogt, P K

    1996-01-01

    The synthetic oligosaccharide moiety of the antibiotic calicheamicin and the head-to-head dimer of this oligosaccharide are known to bind to the minor groove of DNA in a sequence-selective manner preferring distinct target sequences. We tested these carbohydrates for their ability to interfere with transcription factor function. The oligosaccharides inhibit binding of transcription factors to DNA in a sequence-selective manner, probably by inducing a conformational change in DNA structure. They also interfere with transcription by polymerase II in vitro. The effective concentrations of the oligosaccharides for inhibition of transcription factor binding and for transcriptional inhibition are in the micromolar range. The dimer is a significantly more active inhibitor than is the monomer. Images Fig. 2 Fig. 3 PMID:8570664

  9. Chromomycin dimer-DNA oligomer complexes. Sequence selectivity and divalent cation specificity.

    PubMed

    Gao, X L; Patel, D J

    1990-12-11

    This paper reports on a solution NMR characterization of the sequence selectivity and metal ion specificity in chromomycin-DNA oligomer complexes in the presence of divalent cations. The sequence selectivity studies have focused on chromomycin complexes with the self-complementary d(A1-A2-G3-G4-C5-C6-T7-T8) duplex containing a pair of adjacent (G3-G4).(C5-C6) steps and the self-complementary d(A1-G2-G3-A4-T5-C6-C7-T8) duplex containing a pair of separated (G2-G3).(C6-C7) steps in aqueous solution. The antitumor agent (chromomycin) and nucleic acid protons have been assigned following analysis of distance connectivities in NOESY spectra and coupling connectivities in DQF-COSY spectra for both complexes in H2O and D2O solution. The observed intermolecular NOEs establish that chromomycin binds as a Mg(II)-coordinated dimer [1 Mg(II) per complex] and contacts the minor-groove edge with retention of 2-fold symmetry centered about the (G3-G4-C5-C6).(G3-G4-C5-C6) segment of the d(A2G2C2T2) duplex. By contrast, complex formation is centered about the (G2-G3-A4-T5).(A4-T5-C6-C7) segment and results in removal of the two fold symmetry of the d(AG2ATC2T) duplex. Thus, the binding of one subunit of the chromomycin dimer at its preferred (G-G).(C-C) site assists in the binding of the second subunit to the less preferred adjacent (A-T).(A-T) site. These observations suggest a hierarchy of chromomycin binding sites, with a strong site detected at the (G-G) step due to the hydrogen-bonding potential of acceptor N3 and donor NH2 groups of guanosine that line the minor groove. The divalent cation specificity has been investigated by studies on the symmetric chromomycin-d(A2G2C2T2) complex in the presence of diamagnetic Mg(II), Zn(II), and Cd(II) cations and paramagnetic Ni(II) and Co(II) cations. A comparative NOESY study of the Mg(II) and Ni(II) symmetric complexes suggests that a single tightly bound divalent cation aligns the two chromomycins in the dimer through coordination to

  10. Temperature influences epimerization and composition of flavanol monomers, dimers and trimers during cocoa bean roasting.

    PubMed

    Kothe, Lisa; Zimmermann, Benno F; Galensa, Rudolf

    2013-12-15

    Cocoa consumption is suggested to promote many health benefits, since cocoa is a rich source of flavanols; but amounts and profiles of flavanols depend strongly on the bean type, origin and manufacturing process. Roasting is known as a crucial step in technical treatment of cocoa, which leads to flavanol losses and modifications, especially the epimerization of (-)-epicatechin to (-)-catechin. This study monitors the influence of cocoa bean roasting on the composition of flavanol monomers to trimers, with special focus on epimerization, which was quantified for procyanidin dimers, and also observed for trimers for the first time. Five dimeric and two trimeric potential epimerization products were detected and the extent of epimerization during cocoa roasting was shown to be a function of temperature. The data also showed remarkable variations in the change of flavanol content. The quantified flavanols decreased about 50% in Java beans and increased about 30% in Ivory Coast beans, despite being roasted under equal conditions. PMID:23993533

  11. The influence of zeolitic water on the rate of butadiene dimerization

    SciTech Connect

    1995-02-01

    Zeolites find widespread usage as catalysts for a variety of chemical transformations. Frequently, the catalytically active agent is a transition metal ion located at an exchange site in contact with the zeolitic surface. Although the extraframework cation positions and relative populations can often be determined by spectroscopic methods, the influence of cation sitting and adsorbed reactant induced migration under reaction conditions is less well understood. This note describes the role which water exerts on the activity of copper-exchanged zeolite Y for the dimerization of butadiene to 4-vinylcyclohexene (4-VCH). 12 refs., 1 fig., 1 tab.

  12. Detergent Properties Influence the Stability of the Glycophorin A Transmembrane Helix Dimer in Lysophosphatidylcholine Micelles

    PubMed Central

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

    2012-01-01

    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. PMID:23260047

  13. Cooperative binding of the yeast Spt10p activator to the histone upstream activating sequences is mediated through an N-terminal dimerization domain

    PubMed Central

    Mendiratta, Geetu; Eriksson, Peter R.; Clark, David J.

    2007-01-01

    The yeast Spt10p activator is a putative histone acetyltransferase (HAT) possessing a sequence-specific DNA-binding domain (DBD) which binds to the upstream activation sequences (UAS elements) in the histone gene promoters. Spt10p binds to a pair of histone UAS elements with extreme positive cooperativity. The molecular basis of this cooperativity was addressed. Spt10p (640 residues) is an elongated dimer, but the isolated DBD (residues 283–396) is a monomer and binds non-cooperatively to DNA. A Spt10p fragment comprising the N-terminal domain (NTD), HAT domain and DBD (residues 1–396) binds cooperatively and is a dimer, whereas an overlapping Spt10p fragment comprising the DBD and C-terminal domains (residues 283–640) binds non-cooperatively and is a monomer. These observations imply that cooperative binding requires dimerization. The isolated NTD (residues 1–98) is a dimer and is responsible for dimerization. We propose that cooperativity involves a conformational change in the Spt10p dimer which facilitates the simultaneous recognition of two UAS elements. In vivo, deletion of the NTD results in poor growth, but does not prevent the binding at the HTA1 promoter, suggesting that dimerization is biologically important. Residues 1–396 are sufficient for normal growth, indicating that the critical functions of Spt10p reside in the N-terminal domains. PMID:17202156

  14. A Short Sequence Motif in the 5′ Leader of the HIV-1 Genome Modulates Extended RNA Dimer Formation and Virus Replication*

    PubMed Central

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

    2014-01-01

    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. PMID:25368321

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

    PubMed Central

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

    2016-01-01

    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. PMID:27364008

  16. 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. PMID:27364008

  17. Single-Molecule Analysis of Thymine Dimer-Containing G-Quadruplexes Formed from the Human Telomere Sequence

    PubMed Central

    2015-01-01

    The human telomere plays crucial roles in maintaining genome stability. In the presence of suitable cations, the repetitive 5′-TTAGGG-3′ human telomere sequence can fold into G-quadruplexes that adopt the hybrid, basket, or propeller fold. The telomere sequence is hypersensitive to UV-induced thymine dimer (T=T) formation, yet it does not cause telomere shortening. In this work, the potential structural disruption and thermodynamic stability of the T=T-containing natural telomere sequences were studied to understand why this damage is tolerated in telomeres. First, established methods, such as thermal melting measurements, electrophoretic mobility shift assays, and circular dichroism spectroscopy, were utilized to determine the effects of the damage on these structures. Second, a single-molecule ion channel recording technique using α-hemolysin (α-HL) was employed to examine further the structural differences between the damaged sequences. It was observed that the damage caused slightly lower thermal stabilities and subtle changes in the circular dichroism spectra for hybrid and basket folds. The α-HL experiments determined that T=Ts disrupt double-chain reversal loop formation but are tolerated in edgewise and diagonal loops. The largest change was observed for the T=T-containing natural telomere sequence when the propeller fold (all double-chain reversal loops) was studied. On the basis of the α-HL experiments, it was determined that a triplexlike structure exists under conditions that favor a propeller structure. The biological significance of these observations is discussed. PMID:25407781

  18. Application of systematic sequences of wave functions to the water dimer

    SciTech Connect

    Feller, D. )

    1992-04-15

    A systematic series of calculations encompassing a wide range of basis sets and correlated methods has been used to estimate the complete basis set, full CI hydrogen bond strength in the water dimer system. The largest basis set included up through {ital h} polarization functions on oxygen and {ital g} functions on hydrogen. The complete basis set limit for the self-consistent-field (SCF) interaction energy is estimated to be {minus}3.55 kcal/mol with an accompanying correlation contribution of {similar to}{minus}1.5 kcal/mol. This leads to an interaction energy of {minus}5.1 kcal/mol, exclusive of vibrational zero-point considerations, and is in good agreement with experimental measurements of {minus}5.4{plus minus}0.7 kcal/mol. Inclusion of an approximate adjustment for the basis set superposition error via the Boys/Bernardi counterpoise correction was found to substantially improve agreement with {Delta}{ital E}{sub {infinity}}, our estimate of the complete basis set interaction energy, at the both the SCF and correlated levels for basis sets that were lacking in sufficient near-valence diffuse functions. For diffuse-function-augmented basis sets, application of the CP correction was found to sometimes worsen agreement with {Delta}{ital E}{sub {infinity}}.

  19. 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. PMID:25524231

  20. Single Point Mutation in Bin/Amphiphysin/Rvs (BAR) Sequence of Endophilin Impairs Dimerization, Membrane Shaping, and Src Homology 3 Domain-mediated Partnership*

    PubMed Central

    Gortat, Anna; San-Roman, Mabel Jouve; Vannier, Christian; Schmidt, Anne A.

    2012-01-01

    Bin/Amphiphysin/Rvs (BAR) domain-containing proteins are essential players in the dynamics of intracellular compartments. The BAR domain is an evolutionarily conserved dimeric module characterized by a crescent-shaped structure whose intrinsic curvature, flexibility, and ability to assemble into highly ordered oligomers contribute to inducing the curvature of target membranes. Endophilins, diverging into A and B subgroups, are BAR and SH3 domain-containing proteins. They exert activities in membrane dynamic processes such as endocytosis, autophagy, mitochondrial dynamics, and permeabilization during apoptosis. Here, we report on the involvement of the third α-helix of the endophilin A BAR sequence in dimerization and identify leucine 215 as a key residue within a network of hydrophobic interactions stabilizing the entire BAR dimer interface. With the combination of N-terminal truncation retaining the high dimerization capacity of the third α-helices of endophilin A and leucine 215 substitution by aspartate (L215D), we demonstrate the essential role of BAR sequence-mediated dimerization on SH3 domain partnership. In comparison with wild type, full-length endophilin A2 heterodimers with one protomer bearing the L215D substitution exhibit very significant changes in membrane binding and shaping activities as well as a dramatic decrease of SH3 domain partnership. This suggests that subtle changes in the conformation and/or rigidity of the BAR domain impact both the control of membrane curvature and downstream binding to effectors. Finally, we show that expression, in mammalian cells, of endophilin A2 bearing the L215D substitution impairs the endocytic recycling of transferrin receptors. PMID:22167186

  1. 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.

  2. Influence of C5-methylation of cytosine on the formation of cyclobutane pyrimidine dimers

    NASA Astrophysics Data System (ADS)

    Li, Xiaoyi; Eriksson, Leif A.

    2005-01-01

    The reaction pathways for thermal and photochemical formation of 5-methylcytosine (m 5C) pyrimidine dimers (CPD) are explored using density functional theory techniques. It is shown that the methylation of cytosine does not contribute to an increased yield of CPDs after UV irradiation due to an even lower excitation energy at the reactant complex of m 5C as compared to cytosine, a larger barrier to reach the decay channel corresponding to the transition state structure along the ground state reaction path, and a higher-lying decay channel.

  3. 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.

  4. Resolution of mixed site DNA complexes with dimer-forming minor groove binders by using electrospray ionization mass spectrometry: Compound structure and DNA sequence effects

    PubMed Central

    Laughlin, Sarah; Wang, Siming; Kumar, Arvind; Farahat, Abdelbasset A.; Boykin, David W.; Wilson, W. David

    2015-01-01

    Small molecule targeting of the DNA minor groove is a promising approach to modulate genomic processes necessary for normal cellular function. For instance, dicationic diamindines, a well-known class of minor groove binding compounds, have been shown to inhibit interactions of transcription factors binding to genomic DNA. The applications of these compounds could be significantly expanded if we understand sequence-specific recognition of DNA better and could use the information to design more sequence-specific compounds. Aside from polyamides, minor groove binders typically recognize DNA at A-tract or alternating AT base pair sites. Targeting sites with GC base pairs, referred to here as mixed base pair sequences, is much more difficult than those rich in AT base pairs. Compound 1 is the first dicationic diamidine reported to recognize a mixed base pair site. It binds in the minor groove of ATGA sequences as a dimer with positive cooperativity. Due to the well-characterized behavior of 1 with ATGA and AT rich sequences, it provides a paradigm for understanding the elements that are key for recognition of mixed sequence sites. Electrospray ionization mass spectrometry (ESI-MS) is a powerful method to screen DNA complexes formed by analogs of 1 for specific recognition. We also report a novel approach to determine patterns of recognition by 1 for cognate ATGA and ATGA-mutant sequences. We found that functional group modifications and mutating the DNA target site significantly affect binding and stacking, respectively. Both compound conformation and DNA sequence directionality are crucial for recognition. PMID:25703690

  5. 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

  6. Dimeric Sesquiterpenoids.

    PubMed

    Liao, Shang-Gao; Yue, Jian-Min

    2016-01-01

    It is widely accepted that a large number of proteins that are responsible for cellular function exist as dimers or need to be activated by dimerization before mediating certain signaling pathways. Simultaneously targeting both monomeric moieties of the dimeric proteins has shown potential in the development of various therapeutic agents. As dimeric molecules might be able to act on both moieties of a dimeric protein, dimeric sesquiterpenoids (DSs), which are generated biogenetically from coupling of two sesquiterpenoid molecules, are in essence potential biologically active molecules, and have attracted in recent years great attention for their peculiar structures and biological activities. In fact, a number of DSs are more potent than their monomeric precursors for some activities such as anti-inflammatory, anti-tumor, immunosuppressive, potassium channel blocking, antimalarial, anti-virus, and neurotrophic activities.The complex and diversified structures of DSs also attracted attention of chemists in their isolation, structural elucidation, and synthetic construction.In the contribution, a general view of the classification and distribution of DSs will be provided. Strategies for the structural elucidation of DSs and their analogues is presented. Chemical strategies for the convergence of the two sesquiterpenoid units is reviewed. Biological activities are discussed under each type of activity. PMID:26659108

  7. Evaluation of performance including influence by interfering substances of the Innovance D-dimer assay on the Sysmex coagulation analyzer.

    PubMed

    Park, Seo-Jin; Chi, Hyun-Sook; Chun, Soh Hyun; Jang, Seongsoo; Park, Chan-Jeoung

    2011-01-01

    D-dimer is formed during activation of the coagulation system and is commonly assayed in order to diagnose disseminated intravascular coagulation, deep vein thrombosis, and pulmonary embolism. Enzyme-linked immunosorbent assay has been validated as the reference method, but it is a time-consuming procedure. The objective of this study was to evaluate a new immunoturbidimetric, particle-enhanced, Innovance(®) D-dimer immunoassay. A total of 129 plasma samples from apparently healthy individuals and 298 samples from patients were collected for linearity, precision, and correlation studies. Testing the precision of low- and high-controls yielded CV values of 2.08% and 1.76%, respectively. The central 95% non-parametric reference interval estimated from healthy controls was 0.093-0.68 mg/L Fibrinogen Equivalent Units (FEU; median, 0.26 mg/L FEU). Comparison analysis yielded acceptable correlation with the STA Liatest(®) D-dimer assay (R(2) = 0.9471). At a cut-off level of <0.5 mg/L FEU, the sensitivity and specificity indices of the Innovance D-dimer assay were 99.7% and 89.1%, respectively. Thus the Innovance D-dimer method showed acceptable precision and linearity, and the assay results showed acceptable correlation with the STA Liatest D-dimer method. The Innovance method was relatively unaffected by potential interfering substances such as bilirubin and hemoglobin. In conclusion, the Innovance D-dimer assay is suitable for monitoring D-dimer concentrations in various clinical conditions and should be useful in clinical laboratories. PMID:21325250

  8. Transport of rice cyclobutane pyrimidine dimer photolyase into mitochondria relies on a targeting sequence located in its C-terminal internal region.

    PubMed

    Takahashi, Sayaka; Teranishi, Mika; Izumi, Masanori; Takahashi, Masaaki; Takahashi, Fumio; Hidema, Jun

    2014-09-01

    The cyclobutane pyrimidine dimer (CPD), which represents a major type of DNA damage induced by ultraviolet-B (UVB) radiation, is a principal cause of UVB-induced growth inhibition in plants. CPD photolyase is the primary enzyme for repairing CPDs and is crucial for determining the sensitivity of Oryza sativa (rice) to UVB radiation. CPD photolyase is widely distributed among species ranging from eubacteria to eukaryotes, and is classified into class I or II based on its primary structure. We previously demonstrated that rice CPD photolyase (OsPHR), which belongs to class II and is encoded by a single-copy gene, is a unique nuclear/mitochondrial/chloroplast triple-targeting protein; however, the location and nature of the organellar targeting information contained within OsPHR are unknown. Here, the nuclear and mitochondrial targeting signal sequences of OsPHR were identified by systematic deletion analysis. The nuclear and mitochondrial targeting sequences are harbored within residues 487-489 and 391-401 in the C-terminal region of OsPHR (506 amino acid residues), respectively. The mitochondrial targeting signal represents a distinct topogenic sequence that differs structurally and functionally from classical N-terminal pre-sequences, and this region, in addition to its role in localization to the mitochondria, is essential for the proper functioning of the CPD photolyase. Furthermore, the mitochondrial targeting sequence, which is characteristic of class-II CPD photolyases, was acquired before the divergence of class-II CPD photolyases in eukaryotes. These results indicate that rice plants have evolved a CPD photolyase that functions in mitochondria to protect cells from the harmful effects of UVB radiation. PMID:24947012

  9. Crop sequence and tillage influences on dryland spring wheat production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cropping systems and management practices for spring wheat production have changed during the past half century. Greater emphasis on soil and water conservation has helped to stabilize crop yields. Our objectives were to determine the influences of six crop sequences and two tillage practices on spr...

  10. Perinatally Influenced Autonomic System Fluctuations Drive Infant Vocal Sequences.

    PubMed

    Zhang, Yisi S; Ghazanfar, Asif A

    2016-05-23

    The variable vocal behavior of human infants is the scaffolding upon which speech and social interactions develop. It is important to know what factors drive this developmentally critical behavioral output. Using marmoset monkeys as a model system, we first addressed whether the initial conditions for vocal output and its sequential structure are perinatally influenced. Using dizygotic twins and Markov analyses of their vocal sequences, we found that in the first postnatal week, twins had more similar vocal sequences to each other than to their non-twin siblings. Moreover, both twins and their siblings had more vocal sequence similarity with each other than with non-sibling infants. Using electromyography, we then investigated the physiological basis of vocal sequence structure by measuring respiration and arousal levels (via changes in heart rate). We tested the hypothesis that early-life influences on vocal output are via fluctuations of the autonomic nervous system (ANS) mediated by vocal biomechanics. We found that arousal levels fluctuate at ∼0.1 Hz (the Mayer wave) and that this slow oscillation modulates the amplitude of the faster, ∼1.0 Hz respiratory rhythm. The systematic changes in respiratory amplitude result in the different vocalizations that comprise infant vocal sequences. Among twins, the temporal structure of arousal level changes was similar and therefore indicates why their vocal sequences were similar. Our study shows that vocal sequences are tightly linked to respiratory patterns that are modulated by ANS fluctuations and that the temporal structure of ANS fluctuations is perinatally influenced. PMID:27068420

  11. 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. PMID:27108208

  12. Inhibiting EGFR Dimerization Using Triazolyl-Bridged Dimerization Arm Mimics

    PubMed Central

    Hanold, Laura E.; Oruganty, Krishnadev; Ton, Norman T.; Beedle, Aaron M.; Kannan, Natarajan; Kennedy, Eileen J.

    2015-01-01

    The epidermal growth factor receptor (EGFR) is overexpressed in multiple carcinomas and is the focus of a variety of targeted therapies. Here we report the design of peptide-based compounds that mimic the EGFR dimerization arm and inhibit allosteric activation of EGFR. These peptides are modified to contain a triazolyl bridge between the peptide strands to constrain the EGFR dimerization arm β-loop. In this study, we demonstrate that these peptides have significantly improved proteolytic stability over the non-modified peptide sequence, and their inhibitory effects are dependent on the number of the methylene units and orientation of the introduced triazolyl bridge. We identified a peptide, EDA2, which downregulates receptor phosphorylation and dimerization and reduces cell viability. This is the first example of a biologically active triazolyl-bridged peptide targeting the EGFR dimerization interface that effectively downregulates EGFR activation. PMID:25790232

  13. Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization

    PubMed Central

    Baumketner, A.; Shea, J.-E.

    2005-01-01

    The oligomerization of four peptide sequences, KFFE, KVVE, KLLE, and KAAE is studied using replica-exchange molecular dynamics simulations with an atomically detailed peptide model. Previous experimental studies reported that of these four peptides, only those containing phenylalanine and valine residues form fibrils. We show that the fibrillogenic propensities of these peptides can be rationalized in terms of the equilibrium thermodynamics of their early oligomers. Thermodynamic stability of dimers, as measured by the temperature of monomer association, is seen to be higher for those peptides that are able to form fibrils. Although the relative high and low stabilities of the KFFE and KAAE dimers arise from their respective high and low interpeptide interaction energies, the higher stability of the KVVE dimer over the KLLE system results from the smaller loss of configurational entropy accompanying the dimerization of KVVE. Free energy landscapes for dimerization are found to be strongly sequence-dependent, with a high free energy barrier separating the monomeric and dimeric states for KVVE, KLLE, and KAAE sequences. In contrast, the most fibrillogenic peptide, KFFE, displayed downhill assembly, indicating enhanced kinetic accessibility of its dimeric states. The dimeric phase for all peptide sequences is found to be heterogeneous, containing both antiparallel β-sheet structures that can grow into full fibrils as well as disordered dimers acting as on- or off-pathway intermediates for fibrillation. PMID:16127168

  14. 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) PMID:8056006

  15. Colon cancer-derived oncogenic EGFR G724S mutant identified by whole genome sequence analysis is dependent on asymmetric dimerization and sensitive to cetuximab

    PubMed Central

    2014-01-01

    Background Inhibition of the activated epidermal growth factor receptor (EGFR) with either enzymatic kinase inhibitors or anti-EGFR antibodies such as cetuximab, is an effective modality of treatment for multiple human cancers. Enzymatic EGFR inhibitors are effective for lung adenocarcinomas with somatic kinase domain EGFR mutations while, paradoxically, anti-EGFR antibodies are more effective in colon and head and neck cancers where EGFR mutations occur less frequently. In colorectal cancer, anti-EGFR antibodies are routinely used as second-line therapy of KRAS wild-type tumors. However, detailed mechanisms and genomic predictors for pharmacological response to these antibodies in colon cancer remain unclear. Findings We describe a case of colorectal adenocarcinoma, which was found to harbor a kinase domain mutation, G724S, in EGFR through whole genome sequencing. We show that G724S mutant EGFR is oncogenic and that it differs from classic lung cancer derived EGFR mutants in that it is cetuximab responsive in vitro, yet relatively insensitive to small molecule kinase inhibitors. Through biochemical and cellular pharmacologic studies, we have determined that cells harboring the colon cancer-derived G719S and G724S mutants are responsive to cetuximab therapy in vitro and found that the requirement for asymmetric dimerization of these mutant EGFR to promote cellular transformation may explain their greater inhibition by cetuximab than small-molecule kinase inhibitors. Conclusion The colon-cancer derived G719S and G724S mutants are oncogenic and sensitive in vitro to cetuximab. These data suggest that patients with these mutations may benefit from the use of anti-EGFR antibodies as part of the first-line therapy. PMID:24894453

  16. Dimerization-induced folding of MST1 SARAH and the influence of the intrinsically unstructured inhibitory domain: low thermodynamic stability of monomer.

    PubMed

    Constantinescu Aruxandei, Diana; Makbul, Cihan; Koturenkiene, Agne; Lüdemann, Maik-Borris; Herrmann, Christian

    2011-12-27

    The serine/threonine mammalian sterile 20-like kinase (MST1) is involved in promotion of caspase-dependent and independent apoptosis. Phosphorylation and oligomerization are required for its activation. The oligomerization domain, denoted as SARAH domain, forms an antiparallel coiled coil dimer, and it is important for both MST1 autophosphorylation and interactions with other proteins like the Rassf proteins containing also a SARAH domain. Here we show that the monomeric state of SARAH is thermodynamically unstable and that homodimerization is coupled with folding. Moreover, the influence of the inhibitory domain on SARAH stability and affinity is addressed. By investigating the thermal denaturation using differential scanning calorimetry and circular dichroism, we have found that the SARAH domain dissociates and unfolds cooperatively, without a stable intermediate monomeric state. Combining the data with information from isothermal titration calorimetry, a low thermodynamic stability of the monomeric species is obtained. Thus, it is proposed that the transition from MST1 SARAH homodimer to some specific heterodimer implies a non-native monomer intermediate. The inhibitory domain is found to be highly flexible and intrinsically unfolded, not only in isolation but also in the dimeric state of the inhibitory-SARAH construct. The existence of two caspase recognition motifs within the inhibitory domain suggests that its structural flexibility might be important for activation of MST1 during apoptosis. Moreover, the inhibitory domain increases the thermodynamic stability of the SARAH dimer and the homodimer affinity, while having almost no effect on the SARAH domain in the monomeric state. These results emphasize the importance of flexibility and binding-induced folding for specificity, affinity, and the capacity to switch from one state to another. PMID:22112013

  17. Influence of flanking sequences on presentation efficiency of a CD8+ cytotoxic T-cell epitope delivered by parvovirus-like particles.

    PubMed

    Rueda, P; Morón, G; Sarraseca, J; Leclerc, C; Casal, J I

    2004-03-01

    We have previously developed an antigen-delivery system based on hybrid recombinant porcine parvovirus-like particles (PPV-VLPs) formed by the self-assembly of the VP2 protein of PPV carrying a foreign epitope at its N terminus. In this study, different constructs were made containing a CD8(+) T-cell epitope of chicken ovalbumin (OVA) to analyse the influence of the sequence inserted into VP2 on the correct processing of VLPs by antigen-presenting cells. We analysed the presentation of the OVA epitope inserted without flanking sequences or with either different natural flanking sequences or with the natural flanking sequences of a CD8(+) T-cell epitope from the lymphocytic choriomeningitis virus nucleoprotein, and as a dimer with or without linker sequences. All constructs were studied in terms of level of expression, assembly of VLPs and ability to deliver the inserted epitope into the MHC I pathway. The presentation of the OVA epitope was considerably improved by insertion of short natural flanking sequences, which indicated the relevance of the flanking sequences on the processing of PPV-VLPs. Only PPV-VLPs carrying two copies of the OVA epitope linked by two glycines were able to be properly processed, suggesting that the introduction of flexible residues between the two consecutive OVA epitopes may be necessary for the correct presentation of these dimers by PPV-VLPs. These results provide information to improve the insertion of epitopes into PPV-VLPs to facilitate their processing and presentation by MHC class I molecules. PMID:14993639

  18. 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. PMID:25464315

  19. 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…

  20. D-dimer test

    MedlinePlus

    D-dimer tests are used to check for blood clotting problems. Blood clots can cause health problems, such ... that you probably do not have problems with blood clotting. If you are getting the D-dimer test ...

  1. ALGAL METABOLITE INFLUENCE ON BLOOM SEQUENCE IN EUTROPHIED FRESHWATER PONDS

    EPA Science Inventory

    The extracellular metabolites of planktonic bloom dominant algae play a most significant role in the determination of bloom sequence in a eutrophied freshwater pond. Certain extracellular metabolites of planktonic blue-green algae substantially inhibit the growth of planktonic di...

  2. Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT).

    PubMed

    Ferreira, Rubén; Marchand, Adrien; Gabelica, Valérie

    2012-05-01

    We survey here state of the art mass spectrometry methodologies for investigating G-quadruplexes, and will illustrate them with a new study on a simple model system: the dimeric G-quadruplex of the 12-mer telomeric DNA sequence d(TAGGGTTAGGGT), which can adopt either a parallel or an antiparallel structure. We will discuss the solution conditions compatible with electrospray ionisation, the quantification of complexes using ESI-MS, the interpretation of ammonium ion preservation in the complexes in the gas phase, and the use of ion mobility spectrometry to resolve ambiguities regarding the strand stoichiometry, or separate and characterise different structural isomers. We also describe that adding electrospray-compatible organic co-solvents (methanol, ethanol, isopropanol or acetonitrile) to aqueous ammonium acetate increases the stability and rate of formation of dimeric G-quadruplexes, and causes structural transitions to parallel structures. Structural changes were probed by circular dichroism and ion mobility spectrometry, and the excellent correlation between the two techniques validates the use of ion mobility to investigate G-quadruplex folding. We also demonstrate that parallel G-quadruplex structures are easier to preserve in the gas phase than antiparallel structures. PMID:22465284

  3. Dimerization of an immunoactivating peptide derived from mycobacterial hsp65 using N-hydroxysuccinimide based bifunctional reagents is critical for its antitumor properties.

    PubMed

    Bezouška, Karel; Kubínková, Zuzana; Stříbný, Jiří; Volfová, Barbora; Pompach, Petr; Kuzma, Marek; Šírová, Milada; Říhová, Blanka

    2012-10-17

    We have shown previously that a short pentapeptide derived from the mycobacterial heat shock protein hsp65 can be highly activating for the immune system based on its strong reactivity with the early activation antigen of lymphocytes CD69. Here, we investigated an optimal form of presentation of this antigen to the cells of the immune system. Four different forms of the dimerized heptapeptide LELTEGY, and of the control inactive dimerized heptapeptide LELLEGY that both contained an extra UV active glycine-tyrosine sequence, were prepared using dihydroxysuccinimidyl oxalate (DSO), dihydroxysuccinimidyl tartarate (DST), dihydroxysuccinimidyl glutarate (DSG), and dihydroxysuccinimidyl suberate (DSS), respectively. Heptapeptides dimerized through DST and DSG linkers had optimal activity in CD69 precipitation assay. Moreover, dimerization of active heptapeptide resulted in a remarkable increase in its proliferation activity and production of cytokines in vitro. Furthermore, while DST and DSG dimerized heptapeptides both significantly enhanced the cytotoxicity of natural killer cells in vitro, only the DSG dimerized compound was active in suppressing growth of melanoma tumors in mice and in enhancing the cytotoxic activity of tumor infiltrating lymphocytes ex vivo. Thus, while the dimerization of the immunoactive peptide caused a dramatic increase in its immunoactivating properties, its in vivo anticancer properties were influenced by the chemical nature of linker used for its dimerization. PMID:22988810

  4. 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.

  5. Hydrolysis of oligoribonucleotides: influence of sequence and length.

    PubMed Central

    Kierzek, R

    1992-01-01

    The chemical stability of phosphodiester bonds of some oligoribonucleotides in the presence of a cofactor like polyvinylpyrolidine (PVP) is sequence dependent. It was found that pyrimidine-A (YA) and pyrimidine-C (YC) are especially susceptible to hydrolysis. The hydrolyzability of this same phosphodiester bond is dependent on its position in the oligomer. The presence of 3' and 5'-adjacent nucleotides enhances hydrolysis of the UA phosphodiester bond. The acceleration of the hydrolysis of UA by a 5'-adjacent nucleotide is not base dependent. However, a 3'-adjacent purine increases hydrolysis of a UA phosphodiester bond more than a 3'-pyrimidine. The presence of the exoamino group on the 3'-side base (on 6 and 4 position for adenosine and cytidine, respectively) of YA or YZ phosphodiester bond is required for hydrolysis. Images PMID:1408823

  6. Dimeric Cinchona alkaloids.

    PubMed

    Boratyński, Przemysław J

    2015-05-01

    Nature is full of dimeric alkaloids of various types from many plant families, some of them with interesting biological properties. However, dimeric Cinchona alkaloids were not isolated from any species but were products of designed partial chemical synthesis. Although the Cinchona bark is amongst the sources of oldest efficient medicines, the synthetic dimers found most use in the field of asymmetric synthesis. Prominent examples include the Sharpless dihydroxylation and aminohydroxylation ligands, and dimeric phase transfer catalysts. In this article the syntheses of Cinchona alkaloid dimers and oligomers are reviewed, and their structure and applications are outlined. Various synthetic routes exploit reactivity of the alkaloids at the central 9-hydroxyl group, quinuclidine, and quinoline rings, as well as 3-vinyl group. This availability of reactive sites, in combination with a plethora of linker molecules, contributes to the diversity of the products obtained. PMID:25586655

  7. Environment assisted energy transfer in dimer system

    SciTech Connect

    Khan, Salman; Ibrahim, M.; Khan, M.K.

    2014-02-15

    The influence of collective and multilocal environments on the energy transfer between the levels of a dimer is studied. The dynamics of energy transfer are investigated by considering coupling of collective environment with the levels of the dimer in the presence of both two individuals and mutually correlated multilocal environments. It is shown that every way of coupling we consider assists, though differently, the probability of transition between the levels of dimer. The probability of transition is strongly enhanced when the two local environments are mutually correlated. -- Highlights: • The dynamics of energy transfer between the levels of a dimer are studied. • Coupling of collective as well as individual environments are considered. • The environments are in spin star configurations. • The environment assists the energy transfer between the levels. • For correlated multilocal environments, the transition probability is almost 100%.

  8. 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. PMID:27592487

  9. Peptides Interfering 3A Protein Dimerization Decrease FMDV Multiplication

    PubMed Central

    de la Torre, Beatriz G.; Valle, Javier; Andreu, David; Sobrino, Francisco

    2015-01-01

    Nonstructural protein 3A is involved in relevant functions in foot-and-mouth disease virus (FMDV) replication. FMDV 3A can form homodimers and preservation of the two hydrophobic α-helices (α1 and α2) that stabilize the dimer interface is essential for virus replication. In this work, small peptides mimicking residues involved in the dimer interface were used to interfere with dimerization and thus gain insight on its biological function. The dimer interface peptides α1, α2 and that spanning the two hydrophobic α-helices, α12, impaired in vitro dimer formation of a peptide containing the two α-helices, this effect being higher with peptide α12. To assess the effect of dimer inhibition in cultured cells, the interfering peptides were N-terminally fused to a heptaarginine (R7) sequence to favor their intracellular translocation. Thus, when fused to R7, interference peptides (100 μM) were able to inhibit dimerization of transiently expressed 3A, the higher inhibitions being found with peptides α1 and α12. The 3A dimerization impairment exerted by the peptides correlated with significant, specific reductions in the viral yield recovered from peptide-treated FMDV infected cells. In this case, α2 was the only peptide producing significant reductions at concentrations lower than 100 μM. Thus, dimer interface peptides constitute a tool to understand the structure-function relationship of this viral protein and point to 3A dimerization as a potential antiviral target. PMID:26505190

  10. Dimerization of lipocalin allergens

    PubMed Central

    Niemi, Merja H.; Rytkönen-Nissinen, Marja; Miettinen, Ilja; Jänis, Janne; Virtanen, Tuomas; Rouvinen, Juha

    2015-01-01

    Lipocalins are one of the most important groups of inhalant animal allergens. The analysis of structural features of these proteins is important to get insights into their allergenicity. We have determined two different dimeric crystal structures for bovine dander lipocalin Bos d 2, which was earlier described as a monomeric allergen. The crystal structure analysis of all other determined lipocalin allergens also revealed oligomeric structures which broadly utilize inherent structural features of the β-sheet in dimer formation. According to the moderate size of monomer-monomer interfaces, most of these dimers would be transient in solution. Native mass spectrometry was employed to characterize quantitatively transient dimerization of two lipocalin allergens, Bos d 2 and Bos d 5, in solution. PMID:26346541

  11. Dimeric 3-phosphoglycerate kinases from hyperthermophilic Archaea. Cloning, sequencing and expression of the 3-phosphoglycerate kinase gene of Pyrococcus woesei in Escherichia coli and characterization of the protein. Structural and functional comparison with the 3-phosphoglycerate kinase of Methanothermus fervidus.

    PubMed

    Hess, D; Krüger, K; Knappik, A; Palm, P; Hensel, R

    1995-10-01

    The gene coding for the 3-phosphoglycerate kinase (EC 2.7.2.3) of Pyrococcus woesei was cloned and sequenced. The gene sequence comprises 1230 bp coding for a polypeptide with the theoretical M(r) of 46,195. The deduced protein sequence exhibits a high similarity (46.1% and 46.6% identity) to the other known archaeal 3-phosphoglycerate kinases of Methanobacterium bryantii and Methanothermus fervidus [Fabry, S., Heppner, P., Dietmaier, W. & Hensel, R. (1990) Gene 91, 19-25]. By comparing the 3-phosphoglycerate kinase sequences of the mesophilic and the two thermophilic Archaea, trends in thermoadaptation were confirmed that could be deduced from comparisons of glyceraldehyde-3-phosphate dehydrogenase sequences from the same organisms [Zwickl, P., Fabry, S., Bogedain, C., Haas, A. & Hensel, R. (1990) J. Bacteriol. 172, 4329-4338]. With increasing temperature the average hydrophobicity and the portion of aromatic residues increases, whereas the chain flexibility as well as the content in chemically labile residues (Asn, Cys) decreases. To study the phenotypic properties of the 3-phosphoglycerate kinases from thermophilic Archaea in more detail, the 3-phosphoglycerate kinase genes from P. woesei and M. fervidus were expressed in Escherichia coli. Comparisons of kinetic and molecular properties of the enzymes from the original organisms and from E. coli indicate that the proteins expressed in the mesophilic host are folded correctly. Besides their higher thermostability according to their origin from hyperthermophilic organisms, both enzymes differ from their bacterial and eucaryotic homologues mainly in two respects. (a) The 3-phosphoglycerate kinases from P. woesei and M. fervidus are homomeric dimers in their native state contrary to all other known 3-phosphoglycerate kinases, which are monomers including the enzyme from the mesophilic Archaeum M. bryantii. (b) Monovalent cations are essential for the activity of both archaeal enzymes with K+ being significantly more

  12. Sequence Effect on the Topology of 3 + 1 Interlocked Bimolecular DNA G-Quadruplexes.

    PubMed

    Gao, Shang; Cao, Yanwei; Yan, Yuting; Guo, Xinhua

    2016-05-17

    Electrospray ionization mass spectrometry (ESI-MS) combined with fluorescence, circular dichroism, UV spectrophotometer, and native polyacrylamide gel electrophoresis techniques are used to study structural features of interlocked dimers formed by DNA sequence 93del (GGGGTGGGAGGAGGGT) and its derivatives. Herein, we demonstrate that the interlocked dimers can be distinguished from stacked dimers formed by sequences T30923 (GGGTGGGTGGGTGGGT) and T30177 (GTGGTGGGTGGGTGGGT). In addition, loop length, the base at 5'-end, and the isolation of T and TT to the first 4G tract do significantly influence the formation and topologies of interlocked dimers. Furthermore, our results suggest that the 4G tract and the 2G tract in various locations in the 93del derivative sequence can form interlocked structure. This work not only provides new insight into the assembly of 3 + 1 interlocked DNA conformations but also demonstrates that ESI-MS combined with other analytical methods is rapid and useful for DNA structural studies. PMID:27027538

  13. Dryland crop sequence and tillage influences on soil water storage: First 15 years

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Management practices and cropping systems have greatly changed over the past half century. In the northern Great Plains, soil water storage during the non-crop period of annual cropping systems helps to stabilize crop yields. Our objectives were to determine the influences of six crop sequences an...

  14. 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

  15. Binding of the UvrB dimer to non-damaged and damaged DNA: residues Y92 and Y93 influence the stability of both subunits.

    PubMed

    Moolenaar, Geri F; Schut, Menno; Goosen, Nora

    2005-06-01

    UvrB is the ultimate damage-binding protein in bacterial nucleotide excision repair. Previous AFM experiments have indicated that UvrB binds to a damage as a dimer. In this paper we visualize for the first time a UvrB dimer in a gel retardation assay, with the second subunit (B2) more loosely bound than the subunit (B1) that interacts with the damage. A beta-hairpin motif in UvrB plays an important role in damage specific binding. Alanine substitutions of Y92 or Y93 in the beta-hairpin result in proteins that kill E. coli cells as a consequence of incision in non-damaged DNA. Apparently, both residues are needed to prevent binding of UvrB to non-damaged DNA. The lethality of Y93A results from UvrC-mediated incisions, whereas that of Y92A is due to incisions by Cho. This difference could be ascribed to a difference in stability of the B2 subunit in the mutant UvrB-DNA complexes. We show that for 3' incision UvrC needs to displace this second UvrB subunit from the complex, whereas Cho seems capable to incise the dimer-complex. Footprint analysis of the contacts of UvrB with damaged DNA revealed that the B2 subunit interacts with the flanking DNA at the 3' side of the lesion. The B2 subunit of mutant Y92A appeared to be more firmly associated with the DNA, indicating that even when B1 is bound to a lesion, the B2 subunit probes the adjacent DNA for presence of damage. We propose this to be a reflection of the process that the UvrB dimer uses to find lesions in the DNA. In addition to preventing binding to non-damaged DNA, the Y92 and Y93 residues appear also important for making specific contacts (of B1) with the damaged site. We show that the concerted action of the two tyrosines lead to a conformational change in the DNA surrounding the lesion, which is required for the 3' incision reaction. PMID:15886069

  16. The influence of protein coding sequences on protein folding rates of all-β proteins.

    PubMed

    Li, Rui Fang; Li, Hong

    2011-06-01

    It is currently believed that the protein folding rate is related to the protein structures and its amino acid sequence. However, few studies have been done on the problem that whether the protein folding rate is influenced by its corresponding mRNA sequence. In this paper, we analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding rates to inspect its effect in protein folding process. The multiple linear regression analysis and jack-knife test show that the new parameter is significant. The linear correlation coefficient between the experimental and the predicted values of the protein folding rates increased significantly from 0.96 to 0.99, and the population variance decreased from 0.50 to 0.24 compared with Gromiha's results. The results show that the GC content of palindromes in the corresponding protein coding sequence really influences the protein folding rate. Further analysis indicates that this kind of effect mostly comes from the synonymous codon usage and from the information of palindrome structure itself, but not from the translation information from codons to amino acids. PMID:21613670

  17. Mesoscale elucidation of the influence of mixing sequence in electrode processing.

    PubMed

    Liu, Zhixiao; Battaglia, Vincent; Mukherjee, Partha P

    2014-12-23

    Mixing sequence during electrode processing affects the internal microstructure and resultant performance of a lithium-ion battery. In order to fundamentally understand the microstructure evolution during electrode processing, a mesoscale model is presented, which investigates the influence of mixing sequence for different evaporation conditions. Our results demonstrate that a stepwise mixing sequence can produce larger conductive interfacial area ratios than that via a one-step mixing sequence. Small-sized cubical nanoparticles are beneficial for achieving a high conductive interfacial area ratio when a stepwise mixing sequence is employed. Two variants of multistep mixing have been investigated with constant temperature and linearly increasing temperature conditions. It is found that the temperature condition does not significantly affect the conductive interfacial area ratio. The homogeneity of binder distribution in the electrode is also studied, which plays an important role along with the solvent evaporation condition. This study suggests that an appropriate combination of mixing sequence and active particle size and morphology plays a critical role in the formation of electrode microstructures with improved performance. PMID:25470770

  18. Quantification and compensation of the influence of pulse transients on symmetry-based recoupling sequences.

    PubMed

    Wittmann, Johannes J; Mertens, Valerie; Takeda, Kazuyuki; Meier, Beat H; Ernst, Matthias

    2016-02-01

    Deviations of amplitude and phase of radio-frequency pulses from the desired values, can have a severe impact on the performance of multiple-pulse sequences in NMR spectroscopy. A particular problem are pulse transients that appear every time there is a discontinuity in amplitude or phase. Based on a Floquet description using pulses with arbitrarily shaped amplitudes and phases we present a systematic study of the influence of pulse transients on symmetry-based pulse sequences in solid-state NMR under magic-angle spinning. This treatment explains the dependence of the experimentally observed transfer efficiency on the details of experimental setups. In addition, three approaches are compared which have the aim to re-establish highly efficient recoupling. We demonstrate that the application of transient-compensated pulses as basic elements of symmetry-based sequences leads to a significantly improved robustness of the experiments with respect to variations in the experimental setup. PMID:26766289

  19. 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

  20. 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. PMID:15230544

  1. A monomer-dimer equilibrium modulates the interaction of the sunflower homeodomain leucine-zipper protein Hahb-4 with DNA.

    PubMed Central

    Palena, C M; Gonzalez, D H; Chan, R L

    1999-01-01

    We have analysed the interaction of the sunflower homeodomain leucine-zipper (Hd-Zip) protein Hahb-4 with DNA. The complete Hd-Zip domain from Hahb-4 was able to select specific sequences from a random oligonucleotide mixture that contained a 9-bp core with four fixed and five degenerate positions. Analysis of the binding of some of the selected sequences suggests that Hahb-4 preferentially binds the dyad-symmetrical sequence CAAT(A/T)ATTG. Single-nucleotide replacements at positions 1, 5 or 9 of this sequence produced a decrease in binding of 2-4-fold. DNA binding as a function of protein concentration was non-hyperbolic. This behaviour could be explained by an equation in which dimer formation is a pre-requisite for DNA binding. A global dissociation constant (Kd) of 1.31x10(-14) M2 could be calculated. The removal of the leucine zipper promoted a change in specificity and a decrease in binding affinity (Kd=5. 03x10(-5) M). Mutation of Phe-20 of the homeodomain into Leu completely abolished DNA binding. The mutant protein, however, was able to inhibit DNA binding by the non-mutant form, presumably through the formation of heterodimers. The analysis of this inhibitory effect at different mutant concentrations allowed the estimation of the Kd for the dimer-monomer equilibrium [about (2-4)x10(-6) M]; from this, a Kd of 3-6x10(-9) M for the dimer-DNA complex could be estimated. The results obtained indicate that the formation of dimers is the main factor influencing the interaction of Hahb-4 with DNA. It is proposed that shifts in a dimer-monomer equilibrium could be used within the cell to modulate the interaction of this protein with target genes. PMID:10377247

  2. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes

    PubMed Central

    Nelson, Jonathan W.; Das, Anjali J.; Barnes, Anthony P.; Alkayed, Nabil J.

    2016-01-01

    The epoxyeicosatrienoic acid (EET) neutralizing enzyme soluble epoxide hydrolase (sEH) is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS). Recently, a missense polymorphism was identified in human sEH (R287Q) that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP) fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson’s correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization. PMID:27203283

  3. 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.

  4. 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.

  5. 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.

  6. 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. PMID:25481659

  7. Metalloporphines: Dimers and Trimers.

    PubMed

    Jentzen, Walter; Shelnutt, John A; Scheidt, W Robert

    2016-06-20

    Procedures for the purification and subsequent crystallization of the slightly soluble four-coordinate metallporphines, the simplest possible porphyrin derivatives, are described. Crystals of the porphine derivatives of cobalt(II), copper(II), platinum(II), and two polymorphs of zinc(II) were obtained. Analysis of the crystal and molecular structures shows that all except the platinum(II) derivative form an unusual trimeric species in the solid state. The isomorphous cobalt(II), copper(II), and one zinc(II) polymorph pack in the unit cell to form dimers as well as the trimers. Interplanar spacings between porphine rings are similar in both the dimers and trimers and range between 3.24 and 3.37 Å. Porphine rings are strongly overlapped with lateral shifts between ring centers in both the dimers and trimers with values between 1.52 and 1.70 Å or in Category S as originally defined by Scheidt and Lee. Periodic trends in the M-Np bond distances parallel those observed previously for tetraphenyl- and octaethylporphyrin derivatives. PMID:27276239

  8. 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.

    PubMed

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

    2016-07-01

    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. PMID:27315020

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

    PubMed

    Moon, Sunjin; Akey, Joshua M

    2016-06-01

    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

  10. Sequence and domain arrangements influence mechanical properties of elastin-like polymeric elastomers.

    PubMed

    Miao, Ming; Sitarz, Eva; Bellingham, Catherine M; Won, Emily; Muiznieks, Lisa D; Keeley, Fred W

    2013-06-01

    Elastin is the polymeric, extracellular matrix protein that provides properties of extensibility and elastic recoil to large arteries, lung parenchyma, and other tissues. Elastin assembles by crosslinking through lysine residues of its monomeric precursor, tropoelastin. Tropoelastin, as well as polypeptides based on tropoelastin sequences, undergo a process of self-assembly that aligns lysine residues for crosslinking. As a result, both the full-length monomer as well as elastin-like polypeptides (ELPs) can be made into biomaterials whose properties resemble those of native polymeric elastin. Using both full-length human tropoelastin (hTE) as well as ELPs, we and others have previously reported on the influence of sequence and domain arrangements on self-assembly properties. Here we investigate the role of domain sequence and organization on the tensile mechanical properties of crosslinked biomaterials fabricated from ELP variants. In general, substitutions in ELPs involving similiar domain types (hydrophobic or crosslinking) had little effect on mechanical properties. However, modifications altering either the structure or the characteristic sequence style of these domains had significant effects on such properties. In addition, using a series of deletion and replacement constructs for full-length hTE, we provide new insights into the role of conserved domains of tropoelastin in determining mechanical properties. PMID:23529691

  11. Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

    PubMed Central

    Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

    1991-01-01

    The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process. Images PMID:1645868

  12. 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.

  13. MspA Nanopores from Subunit Dimers

    PubMed Central

    Pavlenok, Mikhail; Derrington, Ian M.; Gundlach, Jens H.; Niederweis, Michael

    2012-01-01

    Mycobacterium smegmatis porin A (MspA) forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore sequencing of DNA. PMID

  14. MspA nanopores from subunit dimers.

    PubMed

    Pavlenok, Mikhail; Derrington, Ian M; Gundlach, Jens H; Niederweis, Michael

    2012-01-01

    Mycobacterium smegmatis porin A (MspA) forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore sequencing of DNA. PMID

  15. 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. PMID:24607271

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

    PubMed

    Eftekharzadeh, Bahareh; Piai, Alessandro; Chiesa, Giulio; Mungianu, Daniele; García, Jesús; Pierattelli, Roberta; Felli, Isabella C; Salvatella, Xavier

    2016-06-01

    Expansions of polyglutamine (polyQ) tracts in nine different proteins cause a family of neurodegenerative disorders called polyQ diseases. Because 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 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, to our knowledge, 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

  17. HIV-1 gp140 epitope recognition is influenced by immunoglobulin DH gene segment sequence.

    PubMed

    Wang, Yuge; Kapoor, Pratibha; Parks, Robert; Silva-Sanchez, Aaron; Alam, S Munir; Verkoczy, Laurent; Liao, Hua-Xin; Zhuang, Yingxin; Burrows, Peter; Levinson, Michael; Elgavish, Ada; Cui, Xiangqin; Haynes, Barton F; Schroeder, Harry

    2016-02-01

    Complementarity Determining Region 3 of the immunoglobulin (Ig) H chain (CDR-H3) lies at the center of the antigen-binding site where it often plays a decisive role in antigen recognition and binding. Amino acids encoded by the diversity (DH) gene segment are the main component of CDR-H3. Each DH has the potential to rearrange into one of six DH reading frames (RFs), each of which exhibits a characteristic amino acid hydrophobicity signature that has been conserved among jawed vertebrates by natural selection. A preference for use of RF1 promotes the incorporation of tyrosine into CDR-H3 while suppressing the inclusion of hydrophobic or charged amino acids. To test the hypothesis that these evolutionary constraints on DH sequence influence epitope recognition, we used mice with a single DH that has been altered to preferentially use RF2 or inverted RF1. B cells in these mice produce a CDR-H3 repertoire that is enriched for valine or arginine in place of tyrosine. We serially immunized this panel of mice with gp140 from HIV-1 JR-FL isolate and then used enzyme-linked immunosorbent assay (ELISA) or peptide microarray to assess antibody binding to key or overlapping HIV-1 envelope epitopes. By ELISA, serum reactivity to key epitopes varied by DH sequence. By microarray, sera with Ig CDR-H3s enriched for arginine bound to linear peptides with a greater range of hydrophobicity but had a lower intensity of binding than sera containing Ig CDR-H3s enriched for tyrosine or valine. We conclude that patterns of epitope recognition and binding can be heavily influenced by DH germ line sequence. This may help explain why antibodies in HIV-infected patients must undergo extensive somatic mutation in order to bind to specific viral epitopes and achieve neutralization. PMID:26687685

  18. The hnRNPs F and H2 bind to similar sequences to influence gene expression

    PubMed Central

    Alkan, Serkan A.; Martincic, Kathleen; Milcarek, Christine

    2005-01-01

    The hnRNPs (heterogeneous nuclear ribonucleoproteins) F and H2 share a similar protein structure. Both have been implicated as regulating polyadenylation, but hnRNP H2 had a positive effect, whereas hnRNP F acted negatively. We therefore carried out side-by-side comparisons of their RNA-binding and in vivo actions. The binding of the CstF2 (64 kDa cleavage stimulatory factor) to SV40 (simian virus 40) late pre-mRNA substrates containing a downstream GRS (guanine-rich sequence) was reduced by hnRNP F, but not by hnRNP H2, in a UV-cross-linking assay. Point mutations of the 14-nt GRS influenced the binding of purified hnRNP F or H2 in parallel. Co-operative binding of the individual proteins to RNA was lost with mutations of the GRS in the G1−5 or G12−14 regions; both regions seem to be necessary for optimal interactions. Using a reporter green fluorescent protein assay with the GRS inserted downstream of the poly(A) (polyadenine) signal, expression in vivo was diminished by a mutant G1−5 sequence which decreased binding of both hnRNPs (SAA20) and was enhanced by a 12–14-nt mutant that showed enhanced hnRNP F or H2 binding (SAA10). Using small interfering RNA, down-regulation of hnRNP H2 levels diminished reporter expression, confirming that hnRNP H2 confers a positive influence; in contrast, decreasing hnRNP F levels had a negligible influence on reporter expression with the intact GRS. A pronounced diminution in reporter expression was seen with the SAA20 mutant for both. Thus the relative levels of hnRNP F and H2 in cells, as well as the target sequences in the downstream GRS on pre-mRNA, influence gene expression. PMID:16171461

  19. A dimeric form of prothrombin on membrane surfaces.

    PubMed Central

    Anderson, P J

    1998-01-01

    Blood coagulation requires the conversion of zymogens to active enzymes. These reactions are facilitated by Ca2+-dependent protein binding to membrane surfaces containing anionic phospholipids. Here it is shown that only in the presence of both Ca2+ and phospholipid vesicles composed of phosphatidylcholine and phosphatidylserine can a prothrombin dimer be chemically cross-linked. A cross-linker containing evenly spaced reactive groups was prepared by activating the carboxy groups of a ten-residue glutamic acid peptide and allowed to react with physiological concentrations of prothrombin. When Ca2+ and anionic phospholipids were both present during exposure to the cross-linker, it was found that more than 50% of the prothrombin was trapped as a chemically defined dimer with reaction times of the order of 1 min. The dimer yield remained high even when reactions were performed at high phospholipid-to-protein ratios at protein concentrations an order of magnitude less than physiological. Amino acid sequencing of a CNBr peptide produced from the purified dimer localized the cross-link to residues Lys341 and Lys427 of prothrombin. The specificity and high yield under mild conditions of the cross-linking suggest that dimeric membrane bound prothrombin might be a physiologically relevant substrate for the formation of thrombin. Prothrombinase converts this modified protein to an enzyme that catalyses the hydrolysis of a thrombin chromogenic substrate as efficiently as thrombin and is inhibited by a thrombin active-site directed inhibitor, but is a thrombin dimer. The thrombin dimer has impaired activity compared with thrombin with respect to physiological functions requiring binding to exosite I. A model based on the known structure of thrombin is presented that can account for the prothrombin dimer and the properties of the dimeric thrombin formed from it. PMID:9841875

  20. 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

  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

    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. PMID:26152461

  3. Acoustic markers of prominence influence infants' and adults' segmentation of speech sequences.

    PubMed

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

    2011-03-01

    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 of syllables with constant pitch and duration and were asked whether the syllables had appeared adjacently during familiarization. Adults were better at remembering pairs of syllables that during familiarization had short syllables preceding long syllables, or high-pitched syllables preceding low-pitched syllables. In the second experiment, infants were familiarized and tested with similar stimuli as in the first experiment, and their preference for pairs of syllables was accessed using the head-turn preference paradigm.When familiarized with syllables alternating in pitch, infants showed a preference to listen to pairs of syllables that had high pitch in the first syllable. However, no preference was found when the familiarization stream alternated in duration. It is proposed that these perceptual biases help infants and adults find linguistic units in the continuous speech stream.While the bias for grouping based on pitch appears early in development, biases for durational grouping might rely on more extensive linguistic experience. PMID:21524015

  4. 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.

  5. 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. PMID:27250126

  6. Mechanically Stabilized Tetrathiafulvalene Radical Dimers

    SciTech Connect

    Coskun, Ali; Spruell, Jason M.; Barin, Gokhan; Fahrenbach, Albert C.; Forgan, Ross S.; Colvin, Michael T.; Carmieli, Raanan; Benitez, Diego; Tkatchouk, Ekaterina; Friedman, Douglas C.; Sarjeant, Amy A.; Wasielewski, Michael R.; Goddard, William A.; Stoddart, J. Fraser

    2011-01-01

    Two donor-acceptor [3]catenanes—composed of a tetracationic molecular square, cyclobis(paraquat-4,4'-biphenylene), as the π-electron deficient ring and either two tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) containing macrocycles or two TTF-butadiyne-containing macrocycles as the π-electron rich components—have been investigated in order to study their ability to form TTF radical dimers. It has been proven that the mechanically interlocked nature of the [3]catenanes facilitates the formation of the TTF radical dimers under redox control, allowing an investigation to be performed on these intermolecular interactions in a so-called “molecular flask” under ambient conditions in considerable detail. In addition, it has also been shown that the stability of the TTF radical-cation dimers can be tuned by varying the secondary binding motifs in the [3]catenanes. By replacing the DNP station with a butadiyne group, the distribution of the TTF radical-cation dimer can be changed from 60% to 100%. These findings have been established by several techniques including cyclic voltammetry, spectroelectrochemistry and UV-vis-NIR and EPR spectroscopies, as well as with X-ray diffraction analysis which has provided a range of solid-state crystal structures. The experimental data are also supported by high-level DFT calculations. The results contribute significantly to our fundamental understanding of the interactions within the TTF radical dimers.

  7. Influence of transcriptional and translational control sequences on the expression of foreign genes in Caulobacter crescentus.

    PubMed Central

    Yap, W H; Thanabalu, T; Porter, A G

    1994-01-01

    The influence of expression control sequences (ECSs; promoters and ribosome-binding sites [RBSs]), transcriptional terminators, and gene orientation on the expression of the Escherichia coli lacZ gene in the gram-negative microorganisms Caulobacter crescentus and E. coli was investigated. A series of broad-host-range expression vectors, based on the RK2 plasmid derivative pRK248, were constructed. The ECSs included the tac promoter, the promoter for the surface layer protein of C. crescentus, and promoters from a number of gram-positive bacteria together with their associated RBSs. In addition, synthetic ECSs were constructed by using different combinations of promoters and RBSs. lacZ expression was found to be dependent on the nature of the promoter and RBS and, to a lesser extent, on the presence of a transcriptional terminator and the orientation of the promoter-lacZ construct in pRK248. The relative efficiencies of the various ECSs in driving lacZ expression differed markedly in C. crescentus and E. coli. In C. crescentus, the ECS ptac1 (tac promoter and consensus RBS for C. crescentus mRNAs) appeared to be the most efficient, producing 12-fold-higher activity than did pSL (promoter for the surface layer protein of C. crescentus and its putative RBS). pSL was not transcribed in E. coli, whereas various promoters from gram-positive microorganisms were transcribed in both C. crescentus and E. coli. A number of ECSs were also used to drive mosquitocidal toxin gene expression in C. crescentus, and a correlation between toxin expression and lacZ expression was observed. PMID:8169208

  8. Temperature influences on the expression of GFP promoted by the upstream sequence of cpcB from Arthrospira platensis

    NASA Astrophysics Data System (ADS)

    Lu, Yongzhong; Zhang, Xuecheng

    2007-07-01

    In order to investigate the regulation mechanism of the phycocyanin gene, a series of functional analyses of the upstream sequence of cpcB gene from Arthrospira platensis were conducted in E. coli with green fluorescent protein encoding gene (gfp) as the reporter. Results showed that the gfp gene could express at a high level under the promotion of the upstream sequence, suggesting the existence of some strong promoter elements in it. The expression of GFP was influenced by temperature. Higher temperature led to higher expression level. The bioinformatics analyses followed by mutation analyses on the secondary structure of translation initiation region (TIR) revealed that RNA thermosensor might account for the temperature regulation.

  9. Dimerization of the 3'UTR of bicoid mRNA involves a two-step mechanism.

    PubMed

    Wagner, C; Palacios, I; Jaeger, L; St Johnston, D; Ehresmann, B; Ehresmann, C; Brunel, C

    2001-10-26

    The proper localization of bicoid (bcd) mRNA requires cis-acting signals within its 3' untranslated region (UTR) and trans-acting factors such as Staufen. Dimerization of bcd mRNA through intermolecular base-pairing between two complementary loops of domain III of the 3'UTR was proposed to be important for particle formation in the embryo. The participation in the dimerization process of each domain building the 3'UTR was evaluated by thermodynamic and kinetic analysis of various mutated and truncated RNAs. Although sequence complementarity between the two loops of domain III is required for initiating mRNA dimerization, the initial reversible loop-loop complex is converted rapidly into an almost irreversible complex. This conversion involves parts of RNA outside of domain III that promote initial recognition, and dimerization can be inhibited by sense or antisense oligonucleotides only before conversion has proceeded. Injection of the different bcd RNA variants into living Drosophila embryos shows that all elements that inhibit RNA dimerization in vitro prevent formation of localized particles containing Staufen. Particle formation appeared to be dependent on both mRNA dimerization and other element(s) in domains IV and V. Domain III of bcd mRNA could be substituted by heterologous dimerization motifs of different geometry. The resulting dimers were converted into stable forms, independently of the dimerization module used. Moreover, these chimeric RNAs were competent in forming localized particles and recruiting Staufen. The finding that the dimerization domain of bcd mRNA is interchangeable suggests that dimerization by itself, and not the precise geometry of the intermolecular interactions, is essential for the localization process. This suggests that the stabilizing interactions that are formed during the second step of the dimerization process might represent crucial elements for Staufen recognition and localization. PMID:11676536

  10. Adventures in Holographic Dimer Models

    SciTech Connect

    Kachru, Shamit; Karch, Andreas; Yaida, Sho; /Stanford U., Phys. Dept.

    2011-08-12

    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.

  11. The nucleotide composition of the spacer sequence influences the expression yield of heterologously expressed genes in Bacillus subtilis.

    PubMed

    Liebeton, Klaus; Lengefeld, Jette; Eck, Jürgen

    2014-12-10

    Bacillus subtilis is a commonly used host for the heterologous expression of genes in academia and industry. Many factors are known to influence the expression yield in this organism e.g. the complementarity between the Shine-Dalgarno sequence (SD) and the 16S-rRNA or secondary structures in the translation initiation region of the transcript. In this study, we analysed the impact of the nucleotide composition between the SD sequence and the start codon (the spacer sequence) on the expression yield. We demonstrated that a polyadenylate-moiety spacer sequence moderately increases the expression level of laccase CotA from B. subtilis. By screening a library of artificially generated spacer variants, we identified clones with greatly increased expression levels of two model enzymes, the laccase CotA from B. subtilis (11 fold) and the metagenome derived protease H149 (30 fold). Furthermore, we demonstrated that the effect of the spacer sequence is specific to the gene of interest. These results prove the high impact of the spacer sequence on the expression yield in B. subtilis. PMID:24997355

  12. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

    PubMed Central

    Philippe, Nicolas; Boureux, Anthony; Bréhélin, Laurent; Tarhio, Jorma; Commes, Thérèse; Rivals, Éric

    2009-01-01

    Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on a genome sequence to predict putatively transcribed or protein-interacting regions. We argue that factors such as background distribution, sequence errors, and read length impact on the prediction capacity of sequence census experiments. Here we suggest a computational approach to measure these factors and analyse their influence on both transcriptomic and epigenomic assays. This investigation provides new clues on both methodological and biological issues. For instance, by analysing chromatin immunoprecipitation read sets, we estimate that 4.6% of reads are affected by SNPs. We show that, although the nucleotide error probability is low, it significantly increases with the position in the sequence. Choosing a read length above 19 bp practically eliminates the risk of finding irrelevant positions, while above 20 bp the number of uniquely mapped reads decreases. With our procedure, we obtain 0.6% false positives among genomic locations. Hence, even rare signatures should identify biologically relevant regions, if they are mapped on the genome. This indicates that digital transcriptomics may help to characterize the wealth of yet undiscovered, low-abundance transcripts. PMID:19531739

  13. Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity.

    PubMed

    Philippe, Nicolas; Boureux, Anthony; Bréhélin, Laurent; Tarhio, Jorma; Commes, Thérèse; Rivals, Eric

    2009-08-01

    Ultra high-throughput sequencing is used to analyse the transcriptome or interactome at unprecedented depth on a genome-wide scale. These techniques yield short sequence reads that are then mapped on a genome sequence to predict putatively transcribed or protein-interacting regions. We argue that factors such as background distribution, sequence errors, and read length impact on the prediction capacity of sequence census experiments. Here we suggest a computational approach to measure these factors and analyse their influence on both transcriptomic and epigenomic assays. This investigation provides new clues on both methodological and biological issues. For instance, by analysing chromatin immunoprecipitation read sets, we estimate that 4.6% of reads are affected by SNPs. We show that, although the nucleotide error probability is low, it significantly increases with the position in the sequence. Choosing a read length above 19 bp practically eliminates the risk of finding irrelevant positions, while above 20 bp the number of uniquely mapped reads decreases. With our procedure, we obtain 0.6% false positives among genomic locations. Hence, even rare signatures should identify biologically relevant regions, if they are mapped on the genome. This indicates that digital transcriptomics may help to characterize the wealth of yet undiscovered, low-abundance transcripts. PMID:19531739

  14. Benchmarking of optical dimerizer systems.

    PubMed

    Pathak, Gopal P; Strickland, Devin; Vrana, Justin D; Tucker, Chandra L

    2014-11-21

    Optical dimerizers are a powerful new class of optogenetic tools that allow light-inducible control of protein-protein interactions. Such tools have been useful for regulating cellular pathways and processes with high spatiotemporal resolution in live cells, and a growing number of dimerizer systems are available. As these systems have been characterized by different groups using different methods, it has been difficult for users to compare their properties. Here, we set about to systematically benchmark the properties of four optical dimerizer systems, CRY2/CIB1, TULIPs, phyB/PIF3, and phyB/PIF6. Using a yeast transcriptional assay, we find significant differences in light sensitivity and fold-activation levels between the red light regulated systems but similar responses between the CRY2/CIB and TULIP systems. Further comparison of the ability of the CRY2/CIB1 and TULIP systems to regulate a yeast MAPK signaling pathway also showed similar responses, with slightly less background activity in the dark observed with CRY2/CIB. In the process of developing this work, we also generated an improved blue-light-regulated transcriptional system using CRY2/CIB in yeast. In addition, we demonstrate successful application of the CRY2/CIB dimerizers using a membrane-tethered CRY2, which may allow for better local control of protein interactions. Taken together, this work allows for a better understanding of the capacities of these different dimerization systems and demonstrates new uses of these dimerizers to control signaling and transcription in yeast. PMID:25350266

  15. The dimer of unsubstituted silole

    SciTech Connect

    Lei, Deqing; Chen, Yue-Shen; Gaspar, P.P.

    1992-02-01

    Gas-phase flow pyrolysis of 1-(trimethylsilyl)-1-silacyclopent-3-ene and 1-methoxy-1-(trimethylsilyl)-1-silacyclopent-3-ene leads to the formation of the dimer of silole, 3,8-disila-3a, 4,7,7a-tetrahydro-4,7-methano-1H-indene. Attempts to isolate or trap the silole monomer by means other than self-reaction have failed. It is suggested that the initially formed intermediate silylene, 1-silacyclopent-3-enylidene, undergoes rearrangement to silole and that silole is not very reactive in 2 + 4 cycloadditions, but does undergo dimerization. 19 refs., 1 fig.

  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. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

    PubMed

    Das, Rahul K; Pappu, Rohit V

    2013-08-13

    The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequence-ensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyampholytes. Using atomistic simulations, we show that weak polyampholytes form globules, whereas the conformational preferences of strong polyampholytes are determined by a combination of fraction of charged residues values and the linear sequence distributions of oppositely charged residues. We quantify the latter using a patterning parameter κ that lies between zero and one. The value of κ is low for well-mixed sequences, and in these sequences, intrachain electrostatic repulsions and attractions are counterbalanced, leading to the unmasking of preferences for conformations that resemble either self-avoiding random walks or generic Flory random coils. Segregation of oppositely charged residues within linear sequences leads to high κ-values and preferences for hairpin-like conformations caused by long-range electrostatic attractions induced by conformational fluctuations. We propose a scaling theory to explain the sequence-encoded conformational properties of strong polyampholytes. We show that naturally occurring strong polyampholytes have low κ-values, and this feature implies a selection for random coil ensembles. The design of sequences with different κ-values demonstrably alters the conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for enabling direct inquiries into connections between sequence-ensemble relationships and functions of IDPs. PMID:23901099

  18. Gold(I) and silver(I) complexes containing a tripodal tetraphosphine ligand: influence of the halogen and stoichiometry on the properties. The X-ray crystal structure of two gold(I) dimeric aggregates.

    PubMed

    Fernández, D; García-Seijo, M I; Bardají, M; Laguna, A; García-Fernández, M E

    2008-05-21

    Complexes of the type [Au2(micro-PP3)2]X2 [X=Cl (), Br (), I ()], [Ag2(micro-PP3)2](NO3)2 (), Ag(PP3)Cl (), M3(micro-PP3)X3 [M=Au, X=Cl (), Br (), I (); M=Ag, X=NO3 ()] and Au4(micro-PP3)X4 [X=Cl (), Br (), I ()] have been prepared by interaction between gold(I) or silver(I) salts and the ligand tris[2-(diphenylphosphino)ethyl]phosphine (PP3) in the appropriate molar ratio. Microanalysis, mass spectrometry, IR and NMR spectroscopies and conductivity measurements were used for characterization. and are ionic dinuclear species containing four-coordinate gold(i) and four/three coordinate silver(i), respectively. Solutions of behave as mixtures of complexes in a 2:1 [Au2(micro-PP3)X2; X=Cl(), Br(), I()] and 4:1 () metal to ligand ratio. and react with free PP(3) in solution to generate the ionic compounds and , respectively. Complexes and , with four linear PAuX fragments per molecule, were shown by X-ray diffraction to consist of dimeric aggregates via close intermolecular gold(I)gold(I) contacts of 3.270 A () and 3.184 A (). The resultant octanuclear systems have an inversion center with two symmetry-related gold(I) atoms being totally out of the aurophilic area and represent a new form of aggregation compared to that found in other halo complexes of gold(I) containing polyphosphines. The luminescence properties of the ligand and complexes, in the solid state, have been studied. Most of the gold systems display intense luminescent emission at room and low temperature. The influence of the halogen on the aurophilic contacts of compounds with a 4:1 metal to ligand ratio results in different photophysical properties, while and are luminescent complex is nonemissive. The luminescence increases with increasing the phosphine/metal ratio affording for complexes , without aurophilic contacts, the stronger emissions. Silver complexes and are nonemissive at room temperature and show weaker emissions than gold(I) species at 77 K. PMID:18443708

  19. Influence of tacking sequence on residual stress and distortion of single sided fillet submerged arc welded joint

    NASA Astrophysics Data System (ADS)

    Mondal, Arpan Kumar; Biswas, Pankaj; Bag, Swarup

    2015-07-01

    Submerged arc welding (SAW) is advantageous for joining high thickness materials in large structure due to high material deposition rate. The non-uniform heating and cooling generates the thermal stresses and subsequently the residual stresses and distortion. The longitudinal and transverse residual stresses and angular distortion are generally measured in large panel structure of submerged arc welded fillet joints. Hence, the objective of this present work is to quantify the amount of residual stress and distortion in and around the weld joint due to positioning of stiffeners tack. The tacking sequence influences the level of residual stress and proper controlling of tacking sequences is required to minimize the stress. In present study, an elasto-plastic material behavior is considered to develop the thermo mechanical model which predicts the residual stress and angular distortion with varying tacking sequences. The simulated result reveals that the tacking sequence heavily influences the residual stress and deformation pattern of the single sided fillet joint. The finite element based numerical model is calibrated by comparing the experimental data from published literature. Henceforth, the angular distortions are measured from an in-house developed experimental set-up. A fair agreement between the predicted and experimental results indicates the robustness of the developed numerical model. However, the most significant conclusion from present study states that tack weld position should be placed opposite to the fillet weld side to minimize the residual stress.

  20. Influence of time and length size feature selections for human activity sequences recognition.

    PubMed

    Fang, Hongqing; Chen, Long; Srinivasan, Raghavendiran

    2014-01-01

    In this paper, Viterbi algorithm based on a hidden Markov model is applied to recognize activity sequences from observed sensors events. Alternative features selections of time feature values of sensors events and activity length size feature values are tested, respectively, and then the results of activity sequences recognition performances of Viterbi algorithm are evaluated. The results show that the selection of larger time feature values of sensor events and/or smaller activity length size feature values will generate relatively better results on the activity sequences recognition performances. PMID:24075148

  1. Photochemical dimerization of organic compounds

    SciTech Connect

    Crabtree, R.H.; Brown, S.H.; Muedas, C.A.; Ferguson, R.R.

    1992-04-14

    This patent describes improvement in a Group IIb photosensitized vapor phase dimerization of an organic compound in which a gaseous mixture of a Group IIB metal and the organic compound is irradiated in a reaction zone with a photosensitizing amount of radiant energy. The improvement comprises: a continuous stream of the gaseous mixture is passed as a vapor phase in a single pass through the reaction zone at a temperature at which the thus-produced dimer condenses immediately upon the formation thereof; the starting gaseous mixture comprises hydrogen and two ethylenically unsaturated compounds selected from the group consisting of alkenes of at least six carbon atoms, unsaturated nitriles, unsaturated epoxides, unsaturated silanes, unsaturated amines, unsaturated phosphines, and fluorinated alkenes; the gaseous mixture comprises nitrous oxide and the organic compound is a saturated compound with C-H bond strengths greater than 100 kcal/mol or a mixture of the saturated compound and an alkene; or the starting gaseous comprises an activating amount of hydrogen and the dimerization is a dehydrodimerization or cross-dimerization of a saturated hydrocarbon.

  2. 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. PMID:24794259

  3. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

    PubMed Central

    Das, Rahul K.; Pappu, Rohit V.

    2013-01-01

    The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequence–ensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyampholytes. Using atomistic simulations, we show that weak polyampholytes form globules, whereas the conformational preferences of strong polyampholytes are determined by a combination of fraction of charged residues values and the linear sequence distributions of oppositely charged residues. We quantify the latter using a patterning parameter κ that lies between zero and one. The value of κ is low for well-mixed sequences, and in these sequences, intrachain electrostatic repulsions and attractions are counterbalanced, leading to the unmasking of preferences for conformations that resemble either self-avoiding random walks or generic Flory random coils. Segregation of oppositely charged residues within linear sequences leads to high κ-values and preferences for hairpin-like conformations caused by long-range electrostatic attractions induced by conformational fluctuations. We propose a scaling theory to explain the sequence-encoded conformational properties of strong polyampholytes. We show that naturally occurring strong polyampholytes have low κ-values, and this feature implies a selection for random coil ensembles. The design of sequences with different κ-values demonstrably alters the conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for enabling direct inquiries into connections between sequence–ensemble relationships and functions of IDPs. PMID:23901099

  4. Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures

    PubMed Central

    Hunt, Rebecca A.; Munde, Manoj; Kumar, Arvind; Ismail, Mohamed A.; Farahat, Abdelbasset A.; Arafa, Reem K.; Say, Martial; Batista-Parra, Adalgisa; Tevis, Denise; Boykin, David W.; Wilson, W. David

    2011-01-01

    Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and ATATA. The AAAAA and AAATT sequences have the largest intrinsic bend, whereas the TTTAA and ATATA sequences are relatively straight. The changes caused by binding of the compounds are sequence dependent, but generally the topological effects on AAAAA and AAATT are similar as are the effects on TTTAA and ATATA. A total of 13 compounds with a variety of structural differences were evaluated for topological changes to DNA. All compounds decrease the mobility of the ATATA sequence that is consistent with decreased minor groove width and bending of the relatively straight DNA into the minor groove. Similar, but generally smaller, effects are seen with TTTAA. The intrinsically bent AAAAA and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding that are consistent with increased or decreased bending depending on compound structure. PMID:21266485

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

    PubMed

    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

    2016-07-01

    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

  6. Single residue modification of only one dimer within the hemoglobin tetramer reveals autonomous dimer function

    NASA Astrophysics Data System (ADS)

    Ackers, Gary K.; Dalessio, Paula M.; Lew, George H.; Daugherty, Margaret A.; Holt, Jo M.

    2002-07-01

    The mechanism of cooperativity in the human hemoglobin tetramer (a dimer of dimers) has historically been modeled as a simple two-state system in which a low-affinity structural form (T) switches, on ligation, to a high-affinity form (R), yielding a net loss of hydrogen bonds and salt bridges in the dimer-dimer interface. Modifications that weaken these cross-dimer contacts destabilize the quaternary T tetramer, leading to decreased cooperativity and enhanced ligand affinity, as demonstrated in many studies on symmetric double modifications, i.e., a residue site modified in both - or both -subunits. In this work, hybrid tetramers have been prepared with only one modified residue, yielding molecules composed of a wild-type dimer and a modified dimer. It is observed that the cooperative free energy of ligation to the modified dimer is perturbed to the same extent whether in the hybrid tetramer or in the doubly modified tetramer. The cooperative free energy of ligation to the wild-type dimer is unperturbed, even in the hybrid tetramer, and despite the overall destabilization of the T tetramer by the modification. This asymmetric response by the two dimers within the same tetramer shows that loss of dimer-dimer contacts is not communicated across the dimer-dimer interface, but is transmitted through the dimer that bears the modified residue. These observations are interpreted in terms of a previously proposed dimer-based model of cooperativity with an additional quaternary (T/R) component.

  7. Influences on the variability of eruption sequences and style transitions in the Auckland Volcanic Field, New Zealand

    NASA Astrophysics Data System (ADS)

    Kereszturi, Gábor; Németh, Károly; Cronin, Shane J.; Procter, Jonathan; Agustín-Flores, Javier

    2014-10-01

    Monogenetic basaltic volcanism is characterised by a complex array of eruptive behaviours, reflecting spatial and temporal variability of the magmatic properties (e.g. composition, eruptive volume, magma flux) as well as environmental factors at the vent site (e.g. availability of water, country rock geology, faulting). These combine to produce changes in eruption style over brief periods (minutes to days) in many eruption episodes. Monogenetic eruptions in some volcanic fields often start with a phreatomagmatic vent-opening phase that later transforms into "dry" magmatic explosive or effusive activity, with a strong variation in the duration and importance of this first phase. Such an eruption sequence pattern occurred in 83% of the known eruption in the 0.25 My-old Auckland Volcanic Field (AVF), New Zealand. In this investigation, the eruptive volumes were compared with the sequences of eruption styles preserved in the pyroclastic record at each volcano of the AVF, as well as environmental influencing factors, such as distribution and thickness of water-saturated semi- to unconsolidated sediments, topographic position, distances from known fault lines. The AVF showed that there is no correlation between ejecta ring volumes and environmental influencing factors that is valid for the entire AVF. In contrary, using a set of comparisons of single volcanoes with well-known and documented sequences, resultant eruption sequences could be explained by predominant patterns of the environment in which these volcanoes were erupted. Based on the spatial variability of these environmental factors, a first-order susceptibility hazard map was constructed for the AVF that forecasts areas of largest likelihood for phreatomagmatic eruptions by overlaying topographical and shallow geological information. Combining detailed phase-by-phase breakdowns of eruptive volumes and the event sequences of the AVF, along with the new susceptibility map, more realistic eruption scenarios can be

  8. Analysis of hepatitis C virus RNA dimerization and core–RNA interactions

    PubMed Central

    Ivanyi-Nagy, Roland; Kanevsky, Igor; Gabus, Caroline; Lavergne, Jean-Pierre; Ficheux, Damien; Penin, François; Fossé, Philippe; Darlix, Jean-Luc

    2006-01-01

    The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus. PMID:16707664

  9. A Model for Dimerization of the SOX Group E Transcription Factor Family

    PubMed Central

    Ramsook, Sarah N.; Ni, Joyce; Shahangian, Shokofeh; Vakiloroayaei, Ana; Khan, Naveen; Kwan, Jamie J.

    2016-01-01

    Group E members of the SOX transcription factor family include SOX8, SOX9, and SOX10. Preceding the high mobility group (HMG) domain in each of these proteins is a thirty-eight amino acid region that supports the formation of dimers on promoters containing tandemly inverted sites. The purpose of this study was to obtain new structural insights into how the dimerization region functions with the HMG domain. From a mutagenic scan of the dimerization region, the most essential amino acids of the dimerization region were clustered on the hydrophobic face of a single, predicted amphipathic helix. Consistent with our hypothesis that the dimerization region directly contacts the HMG domain, a peptide corresponding to the dimerization region bound a preassembled HMG-DNA complex. Sequence conservation among Group E members served as a basis to identify two surface exposed amino acids in the HMG domain of SOX9 that were necessary for dimerization. These data were combined to make a molecular model that places the dimerization region of one SOX9 protein onto the HMG domain of another SOX9 protein situated at the opposing site of a tandem promoter. The model provides a detailed foundation for assessing the impact of mutations on SOX Group E transcription factors. PMID:27532129

  10. Influence of next-generation sequencing and storage conditions on miRNA patterns generated from PAXgene blood.

    PubMed

    Backes, Christina; Leidinger, Petra; Altmann, Gabriela; Wuerstle, Maximilian; Meder, Benjamin; Galata, Valentina; Mueller, Sabine C; Sickert, Daniel; Stähler, Cord; Meese, Eckart; Keller, Andreas

    2015-09-01

    Whole blood derived miRNA signatures determined by Next-Generation Sequencing (NGS) offer themselves as future minimally invasive biomarkers for various human diseases. The PAXgene system is a commonly used blood storage system for miRNA analysis. Central to all miRNA analyses that aim to identify disease specific miRNA signatures, is the question of stability and variability of the miRNA profiles that are generated by NGS. We characterized the influence of five different conditions on the genome wide miRNA expression pattern of human blood isolated in PAXgene RNA tubes. In detail, we analyzed 15 miRNomes from three individuals. The blood was subjected to different numbers of freeze/thaw cycles and analyzed for the influence of storage at -80 or 8 °C. We also determined the influence of blood collection and NGS preparations on the miRNA pattern isolated from a single individual, which has been sequenced 10 times. Here, five PAXGene tubes were consecutively collected that have been split in two replicates, representing two experimental batches. All samples were analyzed by Illumina NGS. For each sample, approximately 20 million NGS reads have been generated. Hierarchical clustering and Principal Component Analysis (PCA) showed an influence of the different conditions on the miRNA patterns. The effects of the different conditions on miRNA abundance are, however, smaller than the differences that are due to interindividual variability. We also found evidence for an influence of the NGS measurement on the miRNA pattern. Specifically, hsa-miR-1271-5p and hsa-miR-182-5p showed coefficients of variation above 100% indicating a strong influence of the NGS protocol on the abundance of these miRNAs. PMID:26207298

  11. 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

  12. The influence of tightening sequence and method on screw preload in implant superstructures.

    PubMed

    Al-Sahan, Maha M; Al Maflehi, Nassr S; Akeel, Riyadh F

    2014-01-01

    This study evaluated the effect of six screw-tightening sequences and two tightening methods on the screw preload in implant-supported superstructures. The preload was measured using strain gauges following the screw tightening of a metal framework connected to four implants. The experiment included six sequences ([1] 1-2-3-4, [2] 4-2-3-1, [3] 4-3-1-2, [4] 1-4-2-3, [5] 2-3-4-1, and [6] 3-2-4-1), two methods (onestep, three-step), and five replications. Significant differences were found between tightening sequences and methods. In the three-step method, a higher total preload was found in sequences 2 (312 ± 85 N), 3 (246 ± 54 N), and 4 (310 ± 96 N). In the one-step method, a higher total preload was found in sequences 1 (286 ± 94 N), 5 (764 ± 142 N), and 6 (350 ± 69 N). It is concluded that the highest total screw preload was achieved when anterior implants of the superstructure were first tightened in one step, followed by posterior implants. PMID:24392482

  13. 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

  14. 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

    2014-07-01

    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

  15. Influence of the sequence on elastic properties of long DNA chains

    NASA Astrophysics Data System (ADS)

    Vaillant, C.; Audit, B.; Thermes, C.; Arnéodo, A.

    2003-03-01

    We revisit the results of single-molecule DNA stretching experiments using a rodlike chain (RLC) model that explicitly includes some intrinsic structural disorder induced by the sequence. The investigation of artificial and real genomic sequences shows that the wormlike chain model reproduces quite well the data but with an effective bend stiffness Aeff, which underestimates the true elastic bend stiffness A, independently of the elastic twist stiffness C. Mainly dominated by the amplitude of the structural disorder, this correction seems rather insensitive to the presence of long-range correlations. This RLC model is shown to remarkably fit the experimental data for λ-DNA when considering A≃70±10 nm (>Aeff≃50 nm), in good agreement with previous experimental estimates of the “dynamic” persistent length. From the analysis of large human contigs, we speculate about the possible dependence of Aeff and/or A upon the (G+C) content of the considered sequence.

  16. Matching Measure, Benjamini-Schramm Convergence and the Monomer-Dimer Free Energy

    NASA Astrophysics Data System (ADS)

    Abért, Miklós; Csikvári, Péter; Hubai, Tamás

    2015-10-01

    We define the matching measure of a lattice L as the spectral measure of the tree of self-avoiding walks in L. We connect this invariant to the monomer-dimer partition function of a sequence of finite graphs converging to L. This allows us to express the monomer-dimer free energy of L in terms of the matching measure. Exploiting an analytic advantage of the matching measure over the Mayer series then leads to new, rigorous bounds on the monomer-dimer free energies of various Euclidean lattices. While our estimates use only the computational data given in previous papers, they improve the known bounds significantly.

  17. 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.

  18. A fractographic investigation of the influence of stacking sequence on the strength of notched laminated composites

    NASA Technical Reports Server (NTRS)

    Harris, Charles E.; Morris, Don H.

    1987-01-01

    The fracture behavior of T300/5208 CFRP laminate panels with 12 different combinations of ply orientation and stacking sequence is investigated experimentally, using optical microscopy, SEM, and X-ray radiography to characterize the notch-tip damage zones and fracture surfaces of center-cracked tension specimens subjected to tensile loading at constant crosshead displacement rate 20 micron/s. The results are presented graphically and analyzed in detail. Significant differences in notched strength are found for different ply fiber orientations and stacking sequences; the laminates with few major delaminations had a greater percentage of fracture due to broken fibers and also higher notched strength.

  19. Functional analysis of mouse Hoxa-7 in Saccharomyces cerevisiae: sequences outside the homeodomain base contact zone influence binding and activation.

    PubMed Central

    Gross, M K; Gruss, P

    1994-01-01

    The murine developmental control gene product, Hoxa-7, was shown to function as a DNA-binding transactivator in Saccharomyces cerevisiae. The importance of the ATTA core, the preference for antp class flanking nucleotides, the importance of Asn-51 of the homeodomain (HD), and the synergism of multiple binding sites all reflect properties that have previously been described for HOM or Hox proteins in tissue culture systems. A comparison of contact positions among genes of paralog groups and classes of mammalian HDs points to a lack of diversity in positions that make base contact, suggesting that besides the combination of HD amino acid-base pair contacts, another means of recognizing differences between targets must exist if Hox genes select different targets. The HD of antennapedia is identical to the Hoxa-7 HD. The interaction of Hoxa-7 with the exact sequence used in the nuclear magnetic resonance three-dimensional structural analysis on the antennapedia HD was studied. Hoxa-7 binding and transactivation was influenced by sequences outside of the known base contact zone of this site. We conclude that Hoxa-7 protein has a second means to interact with DNA or/and that the sequences flanking the base contact zone influence HD interactions by distorting DNA within the contact zone (base or backbone). This result is discussed in terms of DNA flexure and two modes of transcription used in S. cerevisiae. Images PMID:8264592

  20. The influence of viral coding sequences on pestivirus IRES activity reveals further parallels with translation initiation in prokaryotes.

    PubMed Central

    Fletcher, Simon P; Ali, Iraj K; Kaminski, Ann; Digard, Paul; Jackson, Richard J

    2002-01-01

    Classical swine fever virus (CSFV) is a member of the pestivirus family, which shares many features in common with hepatitis C virus (HCV). It is shown here that CSFV has an exceptionally efficient cis-acting internal ribosome entry segment (IRES), which, like that of HCV, is strongly influenced by the sequences immediately downstream of the initiation codon, and is optimal with viral coding sequences in this position. Constructs that retained 17 or more codons of viral coding sequence exhibited full IRES activity, but with only 12 codons, activity was approximately 66% of maximum in vitro (though close to maximum in transfected BHK cells), whereas with just 3 codons or fewer, the activity was only approximately 15% of maximum. The minimal coding region elements required for high activity were exchanged between HCV and CSFV. Although maximum activity was observed in each case with the homologous combination of coding region and 5' UTR, the heterologous combinations were sufficiently active to rule out a highly specific functional interplay between the 5' UTR and coding sequences. On the other hand, inversion of the coding sequences resulted in low IRES activity, particularly with the HCV coding sequences. RNA structure probing showed that the efficiency of internal initiation of these chimeric constructs correlated most closely with the degree of single-strandedness of the region around and immediately downstream of the initiation codon. The low activity IRESs could not be rescued by addition of supplementary eIF4A (the initiation factor with ATP-dependent RNA helicase activity). The extreme sensitivity to secondary structure around the initiation codon is likely to be due to the fact that the eIF4F complex (which has eIF4A as one of its subunits) is not required for and does not participate in initiation on these IRESs. PMID:12515388

  1. [Cooperative mechanism of phosphorylation of the monomeric and dimeric forms of inorganic pyrophosphatase from baker's yeast].

    PubMed

    Bakulevá, N P; Kasho, V N; Baĭkov, A A; Nazarova, T I; Avaeva, S M

    1982-07-01

    A comparative study of phosphorylation of native dimeric and artificial monomeric forms of inorganic pyrophosphatase and its fluoride-stabilized complex with PPi has been carried out. The maximal incorporation of Pi for the dimeric and monomeric proteins is 0.5 and 1 mole per mole of subunit, respectively. The saturation kinetic curves are suggestive of strong positive cooperative interactions. The value of the Hill coefficient (5.5) for the free dimeric enzyme drastically changes upon the active center blockage and/or transition to the monomeric enzyme. Acceleration of dephosphorylation induced by Pi in the presence of Mg2+ is observed only in the case of the dimeric protein. The data obtained indicate that phosphorylation of native dimeric pyrophosphatase occurs according to a "flip-flop" mechanism; the Pi binding in the active center exerts a strong influence on individual steps of the reaction. PMID:6126224

  2. Long-term tillage and cropping sequence influence on dryland soil aggregate-carbon dynamics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sequestration and transformation of soil C as a result of long-term management practices occur mainly in aggregates. This study evaluated the 21-yr effect of tillage and cropping sequence combinations on dryland soil C sequestration and transformation into various C fractions in aggregates at the 0-...

  3. Children's Imitation of Causal Action Sequences Is Influenced by Statistical and Pedagogical Evidence

    ERIC Educational Resources Information Center

    Buchsbaum, Daphna; Gopnik, Alison; Griffiths, Thomas L.; Shafto, Patrick

    2011-01-01

    Children are ubiquitous imitators, but how do they decide which actions to imitate? One possibility is that children rationally combine multiple sources of information about which actions are necessary to cause a particular outcome. For instance, children might learn from contingencies between action sequences and outcomes across repeated…

  4. Mechanism of FGF receptor dimerization and activation.

    PubMed

    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. PMID:26725515

  5. 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.

  6. Mechanism of FGF receptor dimerization and activation

    PubMed Central

    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. PMID:26725515

  7. Singlet fission in pentacene dimers.

    PubMed

    Zirzlmeier, Johannes; Lehnherr, Dan; Coto, Pedro B; Chernick, Erin T; Casillas, Rubén; Basel, Bettina S; Thoss, Michael; Tykwinski, Rik R; Guldi, Dirk M

    2015-04-28

    Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley-Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

  8. Singlet fission in pentacene dimers

    PubMed Central

    Zirzlmeier, Johannes; Lehnherr, Dan; Coto, Pedro B.; Chernick, Erin T.; Casillas, Rubén; Basel, Bettina S.; Thoss, Michael; Tykwinski, Rik R.; Guldi, Dirk M.

    2015-01-01

    Singlet fission (SF) has the potential to supersede the traditional solar energy conversion scheme by means of boosting the photon-to-current conversion efficiencies beyond the 30% Shockley–Queisser limit. Here, we show unambiguous and compelling evidence for unprecedented intramolecular SF within regioisomeric pentacene dimers in room-temperature solutions, with observed triplet quantum yields reaching as high as 156 ± 5%. Whereas previous studies have shown that the collision of a photoexcited chromophore with a ground-state chromophore can give rise to SF, here we demonstrate that the proximity and sufficient coupling through bond or space in pentacene dimers is enough to induce intramolecular SF where two triplets are generated on one molecule. PMID:25858954

  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. Entanglement and bifurcation in the integrable dimer

    SciTech Connect

    Hou Xiwen; Chen Jinghua; Hu Bambi

    2005-03-01

    In this Brief Report the properties of both dynamical and static entanglement in the integrable quantum dimer are studied in terms of the reduced-density linear entropy and von Neumann entropy with various coupling parameters, total boson numbers, and initial states. The mean entanglement, which is defined to be averaged over time, is used to describe the influence of the classical separatrix on the behavior of entanglement. It is shown that the mean entanglement exhibits a maximum near the position of the corresponding classical separatrix energy and that the static entanglement of the state with the largest eigenvalue of the quantum spectrum displays a maximum near the bifurcation point. For weak coupling and larger total boson number the maximum entanglement state is exactly at the position of the classical separatrix and bifurcation. In strong coupling all initial states have nearly the same mean entanglement.

  12. An RSA study of dimers

    NASA Astrophysics Data System (ADS)

    Ciesla, Michal; Barbasz, Jakub

    2012-03-01

    The first theoretical study of a dimer adsorption process at a homogeneous surface is presented. By using the RSA algorithm, we show example monolayers, discuss estimations of random jamming coverages and measure the surface blocking function, which could be used for calculating real systems kinetics. We also find the correlation function for coverages generated and analyse the orientational ordering inside the adsorbed monolayer. The results are compared with theoretical and experimental data.

  13. Redox properties of metalloporphyrin dimers

    SciTech Connect

    Collman, J.P.; Prodolliet, J.W.; Leidner, C.R.

    1986-05-28

    Cyclic and rotated disk voltammetry of two metalloporphyrin dimers, (Ru(OEP))/sub 2/ and (Os(OEP))/sub 2/, exhibit four oxidations and two reductions for each compound which are all chemically and electrochemically reversible on the voltammetric time scale. Comparison of the formal potentials of the six couples suggests that the first two oxidations are metal-centered redox processes; the remaining four couples are likely to be ligand centered. Controlled chemical oxidations using ferricinium hexafluorophosphate, silver tetrafluoroborate, and tris(4-bromophenyl)ammonium hexachloroantimonate cleanly generate the monocations (M(OEP))/sub 2//sup +/ and the dications (M(OEP))/sub 2//sup 2 +/. NMR, ESR, and electronic spectroscopy of these dimeric, cationic products support the assignment of the two oxidations as metal centered. These oxidations permit the preparation of the two series of metalloporphyrin dimers: paramagnetic (M(OEP))/sub 2/ with bond order = 2, paramagnetic (M(OEP))/sub 2//sup +/ with bond order = 2.5, and diamagnetic (M(OEP))/sub 2//sup 2 +/ with bond order = 3.

  14. LEF-1 recognition of platinated GG sequences within double-stranded DNA. Influence of flanking bases.

    PubMed

    Chválová, Katerina; Sari, Marie-Agnès; Bombard, Sophie; Kozelka, Jirí

    2008-02-01

    The lymphoid enhancer-binding factor 1 (LEF-1) recognizes a double-stranded 9 base-pairs (bp) long motif in DNA which is significantly bent upon binding. This bend is centered at two destacked adenines whose geometry closely resembles that of two adjacent guanines crosslinked by the antitumor drug cisplatin. It has been proposed that cisplatin-GG crosslinks could hijack high mobility group (HMG) box containing transcription factors such as LEF-1. In order to examine such a possibility, we used electrophoretic mobility shift assays to determine the affinity of the HMG box of LEF-1 for a series of 25 oligonucleotides containing a central GG sequence, free or site-specifically modified by cisplatin. The binding affinity of the GG-platinated oligonucleotides was 3-6-fold higher than that determined for the corresponding unplatinated oligonucleotides, however, the binding to all cisplatin-modified oligonucleotides was at least 1 order of magnitude weaker than that to the 25 bp oligonucleotide containing the recognition 9 bp motif. The binding affinity was dependent on the nature of bases flanking the cisplatin-crosslinked G(*)G(*) dinucleotide, the AG(*)G(*)T sequence displaying the strongest affinity and CG(*)G(*)T showing the strongest binding enhancement upon platination. In contrast, modification of the AGGT sequence with the third-generation platinum antitumor drug oxaliplatin did not enhance the affinity significantly. These results suggest that the cisplatin-caused bending of DNA does produce a target for LEF-1 binding, however, the cisplatinated DNA does not appear to be a strong competitor for the LEF-1 recognition sequence. PMID:17961652

  15. Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins.

    PubMed

    Tiana, G; Provasi, D; Broglia, R A

    2003-05-01

    Some dimeric proteins first fold and then dimerize (three-state dimers) while others first dimerize and then fold (two-state dimers). Within the framework of a minimal lattice model, we can distinguish between sequences following one or the other mechanism on the basis of the distribution of the ground state energy between bulk and interface contacts. The topology of contacts is very different for the bulk than for the interface: while the bulk displays a rich network of interactions, the dimer interface is built up of a set of essentially independent contacts. Consequently, the two sets of interactions play very different roles both, in the folding and in the evolutionary history of the protein. Three-state dimers, where a large fraction of energy is concentrated in few contacts buried in the bulk, and where the relative contact energy of interface contacts is considerably smaller than that associated with bulk contacts, fold according to a hierarchical pathway controlled by local elementary structures, as also happens in the folding of single-domain monomeric proteins. On the other hand, two-state dimers display a relative contact energy of interface contacts, which is larger than the corresponding quantity associated with the bulk. In this case, the assembly of the interface stabilizes the system and leads the two chains to fold. The specific properties of three-state dimers acquired through evolution are expected to be more robust than those of two-state dimers; a fact that has consequences on proteins connected with viral diseases. PMID:12786180

  16. 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

  17. CLEC-2 activates Syk through dimerization.

    PubMed

    Hughes, Craig E; Pollitt, Alice Y; Mori, Jun; Eble, Johannes A; Tomlinson, Michael G; Hartwig, John H; O'Callaghan, Christopher A; Fütterer, Klaus; Watson, Steve P

    2010-04-01

    The C-type lectin receptor CLEC-2 activates platelets through Src and Syk tyrosine kinases, leading to tyrosine phosphorylation of downstream adapter proteins and effector enzymes, including phospholipase-C gamma2. Signaling is initiated through phosphorylation of a single conserved tyrosine located in a YxxL sequence in the CLEC-2 cytosolic tail. The signaling pathway used by CLEC-2 shares many similarities with that used by receptors that have 1 or more copies of an immunoreceptor tyrosine-based activation motif, defined by the sequence Yxx(L/I)x(6-12)Yxx(L/I), in their cytosolic tails or associated receptor chains. Phosphorylation of the conserved immunoreceptor tyrosine-based activation motif tyrosines promotes Syk binding and activation through binding of the Syk tandem SH2 domains. In this report, we present evidence using peptide pull-down studies, surface plasmon resonance, quantitative Western blotting, tryptophan fluorescence measurements, and competition experiments that Syk activation by CLEC-2 is mediated by the cross-linking through the tandem SH2 domains with a stoichiometry of 2:1. In support of this model, cross-linking and electron microscopy demonstrate that CLEC-2 is present as a dimer in resting platelets and converted to larger complexes on activation. This is a unique mode of activation of Syk by a single YxxL-containing receptor. PMID:20154219

  18. 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.…

  19. Frequency of the first feature in action sequences influences feature binding.

    PubMed

    Mattson, Paul S; Fournier, Lisa R; Behmer, Lawrence P

    2012-10-01

    We investigated whether binding among perception and action feature codes is a preliminary step toward creating a more durable memory trace of an action event. If so, increasing the frequency of a particular event (e.g., a stimulus requiring a movement with the left or right hand in an up or down direction) should increase the strength and speed of feature binding for this event. The results from two experiments, using a partial-repetition paradigm, confirmed that feature binding increased in strength and/or occurred earlier for a high-frequency (e.g., left hand moving up) than for a low-frequency (e.g., right hand moving down) event. Moreover, increasing the frequency of the first-specified feature in the action sequence alone (e.g., "left" hand) increased the strength and/or speed of action feature binding (e.g., between the "left" hand and movement in an "up" or "down" direction). The latter finding suggests an update to the theory of event coding, as not all features in the action sequence equally determine binding strength. We conclude that action planning involves serial binding of features in the order of action feature execution (i.e., associations among features are not bidirectional but are directional), which can lead to a more durable memory trace. This is consistent with physiological evidence suggesting that serial order is preserved in an action plan executed from memory and that the first feature in the action sequence may be critical in preserving this serial order. PMID:22777733

  20. 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.

  1. 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).

  2. T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

    PubMed Central

    Fauzi, Hamid; Agyeman, Akwasi; Hines, Jennifer V.

    2008-01-01

    Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5′-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation. PMID:19152843

  3. Influence of atom termination and stacking sequence on the θ‧/Al interfaces from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Sun, Dongqiang; Wang, Yongxin; Lu, Yanli; Chen, Zheng; Rao, Qinglei

    2016-06-01

    First-principles calculations was used to explore the influence of atom termination and stacking sequence on the interface strength and stability between θ‧(Al2Cu) precipitate and Al matrix along experimentally observed orientations, (001)θ‧/(001)Al and (010)θ‧/(010)Al interfaces. Six interfacial structures were modeled, and work of adhesion, bonding characters, number of valence electrons and thermal stability had been studied. Calculated results revealed that the Cu-terminated interface has larger work of adhesion than Al-terminated interface, and hollow site stacking sequence, with stronger bonding, is superior to top site stacking sequence, adhesion strength for coherent (001)θ‧/(001)Al interface is better than that for semi-coherent (010)θ‧/(010)Al interface. These differences are attributed to the bonding feature and number of valence electrons. Among the six interface models, the Cu-terminated (001)θ‧/(001)Al interface with hollow site stacking has the largest work of adhesion and the smallest interface energy, indicating that it has the best mechanical and thermodynamic properties.

  4. Bifilar enzyme-sensitive sites in ultraviolet-irradiated DNA are indicative of closely opposed cyclobutyl pyrimidine dimers.

    PubMed Central

    Lam, L H; Reynolds, R J

    1986-01-01

    Incubation of UV-irradiated DNA with pyrimidine dimer-DNA glycosylase in cell-free lysates prepared from Micrococcus luteus results in the appearance of double-strand breaks. It has previously been assumed that such double-strand breaks result from cleavage at closely opposed dimers. We have used hybrid molecules of bacteriophage T7 DNA comprised of two unirradiated strands, two UV-irradiated strands, or one unirradiated and one UV-irradiated strand to test this hypothesis. Bifilar cleavage was observed only with molecules consisting of two irradiated strands and no bifilar cleavage was observed after the monomerization of pyrimidine dimers by enzymatic photoreactivation. Our results indicate that at least 80% of the double-strand breaks result from cleavage at closely opposed dimers and that the induction of dimers in one strand does not influence the induction of dimers at closely opposed positions in the complementary strand of a DNA double helix. PMID:3527288

  5. Functional Significance of Serotonin Receptor Dimerization

    PubMed Central

    Herrick-Davis, Katharine

    2013-01-01

    The original model of G protein activation by a single G-protein-coupled receptor (GPCR) is giving way to a new model wherein two protomers of a GPCR dimer interact with a single G protein. This article will review the evidence suggesting that 5-HT receptors form dimers/oligomers and will compare the findings with results obtained from studies with other biogenic amine receptors. Topics to be covered include the origin or biogenesis of dimer formation, potential dimer interface(s), and oligomer size (dimer versus tetramer or higher order). The functional significance will be discussed in terms of G-protein activation following ligand binding to one or two protomers in a dimeric structure, the formation of heterodimers and the development of bivalent ligands. PMID:23811735

  6. 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.

  7. Quantum criticality in dimerized spin ladders

    NASA Astrophysics Data System (ADS)

    Chitov, Gennady Y.; Ramakko, Brandon W.; Azzouz, Mohamed

    2008-06-01

    We analyze the possibility of quantum criticality (gaplessness) in dimerized antiferromagnetic two- and three-leg spin- (1)/(2) ladders. Contrary to earlier studies of these models, we examine different dimerization patterns in the ladder. We find that ladders with the columnar dimerization order have lower zero-temperature energies, and they are always gapped. For the staggered dimerization order, we find the quantum critical lines, in agreement with earlier analyses. The bond mean-field theory we apply demonstrates its quantitative accuracy and agrees with available numerical results. We conclude that unless some mechanism for locking dimerization into the energetically less favorable staggered configuration is provided, the dimerized ladders do not order into the phase where the quantum criticality occurs.

  8. Molecular Mechanisms in the Repair of the Cyclobutane Pyrimidine Dimer

    NASA Astrophysics Data System (ADS)

    Hassanali, Ali A.; Zhong, Dongping; Singer, Sherwin J.

    2009-06-01

    Exposure to far UV radiation induces DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Cyclobutane dimer lesions can be repaired by the enzyme photolyase, in which the absorption of a blue light photon initiates a sequence of photochemical events leading to the injection of an electron at the site of the CPD lesion in DNA. The electron catalyzes the repair of the cyclobutane dimer, splitting the CPD to is original pyrimidine units, and is subsequently recaptured by the photolyase protein. In this work we investigate the molecular mechanism of the repair of the cyclobutane dimer radical anion in aqueous solution using ab initio MD simulations. Umbrella sampling is used to determine a two-dimensional free energy surface as a function of the C5-C5-4 and C6-C6-4 distances. The neutral dimer is unable to surmount a large free energy barrier for repair. Upon addition of an electron, the splitting of the C5-C5-4 coordinate is virtually barrier less. Transition state theory predicts that the splitting of the C6-C6-4 bond is complete on a picosecond timescale. The free energy surface suggests that the splitting of the two bonds is asynchronously concerted. Our work is the first to explicitly include the electronic degrees of freedom for both the cyclobutane dimer and the surrounding water pocket. The ab initio simulations show that at least 30% of the electron density is delocalized onto the surrounding solvent during the splitting process. Simulations on the neutral surface show that back electron transfer from the dimer is critical for the completion of splitting: splitting of the C5-C5' and C6-C6' bonds can be reversed or enhanced depending on when electron return occurs. To maximize splitting yield, the back electron transfer should occur beyond the transition state along the splitting coordinate. Non-equilibrium trajectories are also conducted that begin with the electron added to a neutral unrepaired solvated CPD. Our results indicate that there are two

  9. STIM1 dimers undergo unimolecular coupling to activate Orai1 channels

    NASA Astrophysics Data System (ADS)

    Zhou, Yandong; Wang, Xizhuo; Wang, Xianming; Loktionova, Natalia A.; Cai, Xiangyu; Nwokonko, Robert M.; Vrana, Erin; Wang, Youjun; Rothberg, Brad S.; Gill, Donald L.

    2015-09-01

    The endoplasmic reticulum (ER) Ca2+ sensor, STIM1, becomes activated when ER-stored Ca2+ is depleted and translocates into ER-plasma membrane junctions where it tethers and activates Orai1 Ca2+ entry channels. The dimeric STIM1 protein contains a small STIM-Orai-activating region (SOAR)--the minimal sequence sufficient to activate Orai1 channels. Since SOAR itself is a dimer, we constructed SOAR concatemer-dimers and introduced mutations at F394, which is critical for Orai1 coupling and activation. The F394H mutation in both SOAR monomers completely blocks dimer function, but F394H introduced in only one of the dimeric SOAR monomers has no effect on Orai1 binding or activation. This reveals an unexpected unimolecular coupling between STIM1 and Orai1 and argues against recent evidence suggesting dimeric interaction between STIM1 and two adjacent Orai1 channel subunits. The model predicts that STIM1 dimers may be involved in crosslinking between Orai1 channels with implications for the kinetics and localization of Orai1 channel opening.

  10. 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.

  11. 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.

  12. Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity.

    PubMed

    Rizzo, V; Battistini, C; Vigevani, A; Sacchi, N; Razzano, G; Arcamone, F; Garbesi, A; Colonna, F P; Capobianco, M; Tondelli, L

    1989-11-01

    The equilibrium and kinetic aspects of the interaction between four anthracyclines and two synthetic self-complementary hexanucleotides was investigated by fluorescence detection. Two of the studied anthracyclines are widely used antitumor drugs: doxorubicin (1, formerly adriamycin) and daunorubicin (2, formerly daunomycin). The other two, 9-deoxydoxorubicin (3) and 3'-deamino-3'-hydroxy-4'-epidoxorubicin (4), are doxorubicin analogues with modifications of the chemical groups that have been proposed as responsible for sequence specificity (Chen, K.-X., Gresh, N. and Pullman, B. (1985). J. Biomol. Struct. Dyn. 3, 445-466). One of the oligonucleotides, d(CGTACG), is identical to that used in the high resolution x-ray structure determination of the daunorubicin intercalative complex (Wang, A. H.-J., Ughetto, G., Quigley, G. J. & Rich, A. (1987). Biochemistry 26, 1152-1163). Binding to this hexanucleotide is compared with intercalation into the d(CGCGCG) duplex, revealing sequence preferences of the four anthracyclines. Taking into account the anthracycline aggregation and the dissociation of the hexanucleotide double standard form, results can be interpreted with a model that assumes complete fluorescence quenching at intercalative sites containing the CG base pair, and a large residual fluorescence after intercalation within the TpA fragment. All four anthracyclines show preferential intercalation at sites near the ends of both hexanucleotide duplexes, partly as a result of positive cooperativity in the formation of di-intercalated species at these sites. Within the limits of experimental error, complete site specificity for the CpG fragment is found in the intercalation of 1 and 2 into d(CGTACG) duplex, whereas analogues 3 and 4 give increasing evidence of intercalation at other sites including the fluorescence-preserving TpA fragment. Site specificity is less pronounced in the association with d(CGCGCG), when cooperativity is taken into account. Kinetic data

  13. 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. PMID:22419802

  14. Sputtering of dimers off a silicon surface

    NASA Astrophysics Data System (ADS)

    Nietiadi, Maureen L.; Rosandi, Yudi; Kopnarski, Michael; Urbassek, Herbert M.

    2012-10-01

    We present experimental and molecular-dynamics simulation results of the sputtering of a Si surface by 2 keV Ar ions. Results on both the monomer and dimer distributions are presented. In simulation, these distributions follow a generalized Thompson law with power exponent n=2 and n=3, respectively. The experimental data, obtained via plasma post-ionization in an SNMS (secondary neutral mass spectrometry) apparatus, show good agreement with respect to the dimer fraction, and the relative energy distributions of dimers and monomers. The consequences for the dimer sputtering mechanism are discussed.

  15. Experimental separation of virtual photon exchange and electron transfer in interatomic coulombic decay of neon dimers.

    PubMed

    Jahnke, T; Czasch, A; Schöffler, M; Schössler, S; Käsz, M; Titze, J; Kreidi, K; Grisenti, R E; Staudte, A; Jagutzki, O; Schmidt, L Ph H; Weber, Th; Schmidt-Böcking, H; Ueda, K; Dörner, R

    2007-10-12

    We investigate the interatomic Coulombic decay (ICD) of neon dimers following photoionization with simultaneous excitation of the ionized atom (shakeup) in a multiparticle coincidence experiment. We find that, depending on the parity of the excited state, which determines whether ICD takes place via virtual dipole photon emission or overlap of the wave functions, the decay happens at different internuclear distances, illustrating that nuclear dynamics heavily influence the electronic decay in the neon dimer. PMID:17995162

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

    PubMed

    Goffinont, S; Davidkova, M; Spotheim-Maurizot, 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. PMID:19520056

  17. Polypyrimidine tract sequences direct selection of alternative branch sites and influence protein binding.

    PubMed Central

    Norton, P A

    1994-01-01

    IVS1, an intron derived from the rat fibronectin gene, is spliced inefficiently in vitro, involving the use of three alternative branch sites. Mutation of one branch point site, BP3, so as to increase complementarity to U2 snRNA resulted in exclusive use of that site and improved splicing efficiency, indicating that the wild type BP3 site is one determinant of poor IVS1 splicing. Deletions within the polypyrimidine tract had a variable effect on splicing efficiency and altered the pattern of branch site usage. Selection of each branch site was influenced negatively by purine substitutions ca. 20 nucleotides downstream. It is proposed that all three IVS1 branch sites are pyrimidine tract-dependent. Pyrimidine tract deletions also influenced the crosslinking of PTB (the polypyrimidine tract-binding protein), hnRNP C, and splicing factor U2AF65. All three proteins bound preferentially to distinct regions within the polypyrimidine tract and thus are candidates for mediating pyrimidine tract-dependent branch site selection. The findings indicate the complexity of the IVS1 polypyrimidine tract and suggest a crucial role for this region in modulating branch site selection and IVS1 splicing. Images PMID:7937104

  18. 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

  19. Structural requirements for nucleocapsid protein-mediated dimerization of avian leukosis virus RNA.

    PubMed

    Ali, Moez Ben; Chaminade, Françoise; Kanevsky, Igor; Ennifar, Eric; Josset, Laurence; Ficheux, Damien; Darlix, Jean-Luc; Fossé, Philippe

    2007-09-28

    The avian leukosis virus (ALV) belongs to the alpha group of retroviruses that are widespread in nature. The 5'-untranslated region of ALV genome contains the L3 element that is important for virus infectivity and the formation of an unstable RNA dimer in vitro. The L3 sequence is predicted to fold into a long stem-loop structure with two internal loops and an apical one. Phylogenetic analysis predicts that the L3 stem-loop is conserved in alpharetroviruses. Furthermore, a significant selection mechanism maintains a palindrome in the apical loop. The nucleocapsid protein of the alpharetroviruses (NCp12) is required for RNA dimer formation and replication in vivo. It is not known whether L3 can be an NCp12-mediated RNA dimerization site able to bind NCp12 with high affinity. Here, we report that NCp12 chaperones formation of a stable ALV RNA dimer through L3. To investigate the NCp12-mediated L3 dimerization reaction, we performed site-directed mutagenesis, gel retardation and heterodimerization assays and analysis of thermostability of dimeric RNAs. We show that the affinity of NCp12 for L3 is lower than its affinity for the microPsi RNA packaging signal. Results show that conservation of a long stem-loop structure and a loop-loop interaction are not required for NCp12-mediated L3 dimerization. We show that the L3 apical stem-loop is sufficient to form an extended duplex and the whole stem-loop L3 cannot be converted by NCp12 into a duplex extending throughout L3. Three-dimensional modelling of the stable L3 dimer supports the notion that the extended duplex may represent the minimal dimer linkage structure found in the genomic RNA. PMID:17706668

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

    PubMed

    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

    2016-03-01

    Mycobacterium tuberculosis infections cause 9 million new tuberculosis cases and 1.5 million deaths annually. To identify variants conferring risk of tuberculosis, we tested 28.3 million variants identified through whole-genome sequencing of 2,636 Icelanders for association with tuberculosis (8,162 cases and 277,643 controls), pulmonary tuberculosis (PTB) and M. tuberculosis infection. We found association of three variants in the region harboring genes encoding the class II human leukocyte antigens (HLAs): rs557011[T] (minor allele frequency (MAF) = 40.2%), associated with M. tuberculosis infection (odds ratio (OR) = 1.14, P = 3.1 × 10(-13)) and PTB (OR = 1.25, P = 5.8 × 10(-12)), and rs9271378[G] (MAF = 32.5%), associated with PTB (OR = 0.78, P = 2.5 × 10(-12))--both located between HLA-DQA1 and HLA-DRB1--and a missense variant encoding p.Ala210Thr in HLA-DQA1 (MAF = 19.1%, rs9272785), associated with M. tuberculosis infection (P = 9.3 × 10(-9), OR = 1.14). We replicated association of these variants with PTB in samples of European ancestry from Russia and Croatia (P < 5.9 × 10(-4)). These findings show that the HLA class II region contributes to genetic risk of tuberculosis, possibly through reduced presentation of protective M. tuberculosis antigens to T cells. PMID:26829749

  1. 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.

  2. Dithiothreitol causes HIV-1 integrase dimer dissociation while agents interacting with the integrase dimer interface promote dimer formation.

    PubMed

    Tsiang, Manuel; Jones, Gregg S; Hung, Magdeleine; Samuel, Dharmaraj; Novikov, Nikolai; Mukund, Susmith; Brendza, Katherine M; Niedziela-Majka, Anita; Jin, Debi; Liu, Xiaohong; Mitchell, Michael; Sakowicz, Roman; Geleziunas, Romas

    2011-03-15

    We have developed a homogeneous time-resolved fluorescence resonance energy transfer (FRET)-based assay that detects the formation of HIV-1 integrase (IN) dimers. The assay utilizes IN monomers that express two different epitope tags that are recognized by their respective antibodies, coupled to distinct fluorophores. Surprisingly, we found that dithiothreitol (DTT), a reducing agent essential for in vitro enzymatic activity of IN, weakened the interaction between IN monomers. This effect of DTT on IN is dependent on its thiol groups, since the related chemical threitol, which contains hydroxyls in place of thiols, had no effect on IN dimer formation. By studying mutants of IN, we determined that cysteines in IN appear to be dispensable for the dimer dissociation effect of DTT. Peptides derived from the IN binding domain (IBD) of lens epithelium derived growth factor/transcriptional coactivator p75 (LEDGF), a cellular cofactor that interacts with the IN dimer interface, were tested in this IN dimerization assay. These peptides, which compete with LEDGF for binding to IN, displayed an intriguing equilibrium binding dose-response curve characterized by a plateau rising to a peak, then descending to a second plateau. Mathematical modeling of this binding system revealed that these LEDGF-derived peptides promote IN dimerization and block subunit exchange between IN dimers. This dose-response behavior was also observed with a small molecule that interacts with the IN dimer interface and inhibits LEDGF binding to IN. In conclusion, this novel IN dimerization assay revealed that peptide and small molecule inhibitors of the IN-LEDGF interaction also stabilize IN dimers and promote their formation. PMID:21222490

  3. 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

  4. Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding.

    PubMed Central

    Jossinet, F; Paillart, J C; Westhof, E; Hermann, T; Skripkin, E; Lodmell, J S; Ehresmann, C; Ehresmann, B; Marquet, R

    1999-01-01

    Retroviruses encapsidate their genome as a dimer of homologous RNA molecules noncovalently linked close to their 5' ends. The dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1) RNA is a hairpin structure that contains in the loop a 6-nt self-complementary sequence flanked by two 5' and one 3' purines. The self-complementary sequence, as well as the flanking purines, are crucial for dimerization of HIV-1 RNA, which is mediated by formation of a "kissing-loop" complex between the DIS of each monomer. Here, we used chemical modification interference, lead-induced cleavage, and three-dimensional modeling to compare dimerization of subtype A and B HIV-1 RNAs. The DIS loop sequences of these RNAs are AGGUGCACA and AAGCGCGCA, respectively. In both RNAs, ethylation of most but not all phosphate groups in the loop and methylation of the N7 position of the G residues in the self-complementary sequence inhibited dimerization. These results demonstrate that small perturbations of the loop structure are detrimental to dimerization. Conversely, methylation of the N1 position of the first and last As in the loop were neutral or enhanced dimerization, a result consistent with these residues forming a noncanonical sheared base pair. Phosphorothioate interference, lead-induced cleavage, and Brownian-dynamics simulation revealed an unexpected difference in the dimerization mechanism of these RNAs. Unlike subtype B, subtype A requires binding of a divalent cation in the loop to promote RNA dimerization. This difference should be taken into consideration in the design of antidimerization molecules aimed at inhibiting HIV-1 replication. PMID:10496223

  5. Influence of the agitation rate on the treatment of partially soluble wastewater in anaerobic sequencing batch biofilm reactor.

    PubMed

    Pinho, Samantha Cristina; Ratusznei, Suzana Maria; Rodrigues, José Alberto Domingues; Foresti, Eugenio; Zaiat, Marcelo

    2004-11-01

    This work reports on the influence of the agitation rate on the organic matter degradation in an anaerobic sequencing batch reactor, containing biomass immobilized on 3 cm cubic polyurethane matrices, stirred mechanically and fed with partially soluble soymilk substrate with mean chemical oxygen demand (COD) of 974+/-70 mg l(-1). Hydrodynamic studies informed on the homogenization time under agitagion rates from 500 to 1100 rpm provided by three propeller impellers. It occurred very quickly compared to the total cycle time. The results showed that agitation provided good mixing and improved the overall organic matter consumption rates. A modified first-order kinetic model represented adequately the data in the entire range of agitation rate. The apparent first-order kinetic constant for suspended COD rose approximately 360% when the agitation rate was changed from 500 to 900 rpm, whereas the apparent first-order kinetic constant for soluble COD did not vary significantly. PMID:15491659

  6. Long-term tillage and cropping sequence influence on dryland soil aggregate-carbon dynam

    NASA Astrophysics Data System (ADS)

    Sainju, U.; Tonthat, T.-C.; Jabro, J. D.

    2009-04-01

    Sequestration and transformation of soil C as a result of long-term management practices occur mainly in aggregates. This study evaluated the 21-yr effect of tillage and cropping sequence combinations on dryland soil C sequestration and transformation into various C fractions in aggregates at the 0-20 cm depth in eastern Montana, USA. Tillage and cropping sequences were no-tilled continuous spring wheat (NTCW), spring-tilled continuous spring wheat (STCW), fall- and spring-tilled continuous spring wheat (FSTCW), fall- and spring-tilled spring wheat-barley (1984-1999) followed by spring wheat-pea (2000-2004) (FSTW-B/P), and spring-tilled spring wheat-fallow (STW-F). Carbon fractions were soil organic C (SOC), particulate organic C (POC), microbial biomass C (MBC), and potential C mineralization (PCM). Total amount of crop biomass (stems + leaves) residue returned to soil from 1984 to 2004 was lower in STW-F than in other treatments. Aggregate proportion was greater in NTCW than in FSTCW in 4.75-2.00 mm aggregate-size class at 0-5 cm but was greater in STW-F than in STCW in 2.00-0.25 mm size class at 5-20 cm. The SOC and POC were greater in NTCW and STCW than in STW-F in all aggregate-size classes at 0-5 cm and greater in NTCW than in STW-F in 4.75-2.00 mm and <0.25 mm size classes at 5-20 cm. The PCM was greater in STCW and FSTCW than in STW-F in all aggregate-size classes at 0-5 cm and greater in STCW than in NTCW, FSTCW, and STW-F in 4.75-2.00 mm size class at 5-20 cm. Similarly, MBC was greater in NTCW and STCW than in STW-F in <2.00 mm size class at 0-5 cm and greater in STCW and FSTCW than in STW-F in 4.75-0.25 mm class size at 5-20 cm. No-till increased aggregate proportion and POC but reduced PCM and MBC compared with tilled practices in the continuous spring wheat system in 4.75-2.00 mm size class. Aggregate proportion was greater in 2.00-0.25 mm size class than in other aggregate-size classes. The SOC, POC, and PCM were greater in 4.75-2.00 mm than in <0

  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. 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. PMID:26505635

  9. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

    PubMed Central

    Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis

    2016-01-01

    Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal

  10. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference.

    PubMed

    Shen, Xing-Xing; Salichos, Leonidas; Rokas, Antonis

    2016-01-01

    Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal

  11. The water dimer I: Experimental characterization

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Anamika; Cole, William T. S.; Saykally, Richard J.

    2015-07-01

    As the archetype of water hydrogen bonding, the water dimer has been studied extensively by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the experimental dimer studies and the insights into the complex nature of water and hydrogen bonding gained from them. A subsequent letter will review the corresponding theoretical advances.

  12. 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

    2015-01-01

    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. PMID:26694345

  13. Statistical transmutation in doped quantum dimer models.

    PubMed

    Lamas, C A; Ralko, A; Cabra, D C; Poilblanc, D; Pujol, P

    2012-07-01

    We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families. PMID:23031119

  14. The amyloid precursor protein C-terminal fragment C100 occurs in monomeric and dimeric stable conformations and binds γ-secretase modulators.

    PubMed

    Botev, Anne; Munter, Lisa-Marie; Wenzel, Ringo; Richter, Luise; Althoff, Veit; Ismer, Jochen; Gerling, Ulla; Weise, Christoph; Koksch, Beate; Hildebrand, Peter W; Bittl, Robert; Multhaup, Gerd

    2011-02-01

    The amyloid-β (Aβ) peptide is contained within the C-terminal fragment (β-CTF) of the amyloid precursor protein (APP) and is intimately linked to Alzheimer's disease. In vivo, Aβ is generated by sequential cleavage of β-CTF within the γ-secretase module. To investigate γ-secretase function, in vitro assays are in widespread use which require a recombinant β-CTF substrate expressed in bacteria and purified from inclusion bodies, termed C100. So far, little is known about the conformation of C100 under different conditions of purification and refolding. Since C100 dimerization influences the efficiency and specificity of γ-secretase cleavage, it is also of great interest to determine the secondary structure and the oligomeric state of the synthetic substrate as well as the binding properties of small molecules named γ-secretase modulators (GSMs) which we could previously show to modulate APP transmembrane sequence interactions [Richter et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 14597-14602]. Here, we use circular dichroism and continuous-wave electron spin resonance measurements to show that C100 purified in a buffer containing SDS at micelle-forming concentrations adopts a highly stable α-helical conformation, in which it shows little tendency to aggregate or to form higher oligomers than dimers. By surface plasmon resonance analysis and molecular modeling we show that the GSM sulindac sulfide binds to C100 and has a preference for C100 dimers. PMID:21186781

  15. 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}.

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

    PubMed

    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

  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. Evolutionary patterns of carbohydrate transport and metabolism in Halomonas boliviensis as derived from its genome sequence: influences on polyester production

    PubMed Central

    2012-01-01

    Background Halomonas boliviensis is a halophilic bacterium that is included in the γ-Proteobacteria sub-group, and is able to assimilate different types of carbohydrates. H. boliviensis is also able to produce poly(3-hydroxybutyrate) (PHB) in high yields using glucose as the carbon precursor. Accumulation of PHB by microorganisms is induced by excess of intracellular NADH. The genome sequences and organization in microorganisms should be the result of evolution and adaptation influenced by mutation, gene duplication, horizontal gen transfer (HGT) and recombination. Furthermore, the nearly neutral theory of evolution sustains that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions. Results This article reports the genome sequence of H. boliviensis. The chromosome size of H. boliviensis was 4 119 979 bp, and contained 3 863 genes. A total of 160 genes of H. boliviensis were related to carbohydrate transport and metabolism, and were organized as: 70 genes for metabolism of carbohydrates; 47 genes for ABC transport systems and 43 genes for TRAP-type C4-dicarboxylate transport systems. Protein sequences of H. boliviensis related to carbohydrate transport and metabolism were selected from clusters of orthologous proteins (COGs). Similar proteins derived from the genome sequences of other 41 archaea and 59 bacteria were used as reference. We found that most of the 160 genes in H. boliviensis, c.a. 44%, were obtained from other bacteria by horizontal gene transfer, while 13% of the genes were acquired from haloarchaea and thermophilic archaea, only 34% of the genes evolved among Proteobacteria and the remaining genes encoded proteins that did not cluster with any of the proteins obtained from the reference strains. Furthermore, the diversity of the enzymes derived from these genes

  19. Ratchet rotation of a 3D dimer on a vibrating plate.

    PubMed

    Wang, Jiao; Liu, Caishan; Jia, Yan-Bin; Ma, Daolin

    2014-01-01

    This work studies the dynamics of a 3D dimer bouncing upon a horizontal plate undergoing a vertical harmonic vibration. Despite complex interactions within the system due to impacts and friction, numerical simulation shows that, under certain conditions prescribed for the dynamics, the center of mass of the dimer, when projected onto a horizontal plane, will follow a circular orbit. The phenomenon is like a particle under Coulomb friction performing a ratchet motion that rotates around. Investigations further reveal that the dimer dynamics bear some typical characteristics of a nonlinear system, including sensitivity to the initial conditions and bifurcation behaviors related to the physical parameters of the dynamics. Our results indicate that the coefficient of restitution and the plate's vibration intensity play critical roles in exciting the circular orbit, while the dimer's geometry and the vibration frequency mainly influence the trajectory characteristics. These findings may help understand transport mechanisms underlying systems of granular matter with anisotropic particles. PMID:24458553

  20. Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

    PubMed Central

    2011-01-01

    Background During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, dif. Results To study the evolution of the dif/XerCD system and its relationship with replication termination, we report the comprehensive prediction of dif sequences in silico using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, dif sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The dif sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted dif sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures. Conclusions The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between dif position and the degree of GC skew suggests that replication termination does not occur strictly at dif sites. PMID:21223577

  1. dimerization and DNA binding alter phosphorylation of Fos and Jun

    SciTech Connect

    Abate, C.; Baker, S.J.; Curran, T. ); Lees-Miller, S.P.; Anderson, C.W. ); Marshak, D.R. )

    1993-07-15

    Fos and Jun form dimeric complexes that bind to activator protein 1 (AP-1) DNA sequences and regulate gene expression. The levels of expression and activities of these proteins are regulated by a variety of extracellular stimuli. They are thought to function in nuclear signal transduction processes in many different cell types. The role of Fos and Jun in gene transcription is complex and may be regulated in several ways including association with different dimerization partners, interactions with other transcription factors, effects on DNA topology, and reduction/oxidation of a conserved cysteine residue in the DNA-binding domain. In addition, phosphorylation has been suggested to control the activity of Fos and Jun. Here the authors show that phosphorylation of Fos and Jun by several protein kinases is affected by dimerization and binding to DNA. Jun homodimers are phosphorylated efficiently by casein kinase II, whereas Fos-Jun heterodimers are not. DNA binding also reduces phosphorylation of Jun by casein kinase II, p34[sup cdc2] (cdc2) kinase, and protein kinase C. Phosphorylation of Fos by cAMP-dependent protein kinase and cdc2 is relatively insensitive to dimerization and DNA binding, whereas phosphorylation of Fos and Jun by DNA-dependent protein kinase is dramatically stimulated by binding to the AP-1 site. These results imply that different protein kinases can distinguish among Fos and Jun proteins in the form of monomers, homodimers, and heterodimers and between DNA-bound and non-DNA-bound proteins. Thus, potentially, these different states of Fos and Jun can be recognized and regulated independently by phosphorylation. 44 refs., 4 figs.

  2. Dimeric calixarenes: a new family of major-groove binders.

    PubMed

    Hu, Wenbin; Blecking, Caroline; Kralj, Marijeta; Šuman, Lidija; Piantanida, Ivo; Schrader, Thomas

    2012-03-19

    A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl-protected calix[4]arene tetramines in relatively short synthetic sequences (3-5 steps). The compounds attach themselves to double-stranded nucleic acids in a noncovalent fashion, with micro- to nanomolar affinities. Guanidinium headgroups with their extended hydrogen-bonding "fingers" are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K(d))dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye-loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A-form to a perfect B-signature, providing further experimental evidence for major-groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte-Carlo simulations on 1:1 complexes in water. PMID:22336964

  3. The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

    PubMed Central

    Purzycka, Katarzyna J.; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W.

    2011-01-01

    RNA dimerization is an essential step in the retroviral life cycle. Dimerization and encapsidation signals, closely linked in HIV-2, are located in the leader RNA region. The SL1 motif and nucleocapsid protein are considered important for both processes. In this study, we show the structure of the HIV-2 leader RNA (+1–560) captured as a loose dimer. Potential structural rearrangements within the leader RNA were studied. In the loose dimer form, the HIV-2 leader RNA strand exists in vitro as a single global fold. Two kissing loop interfaces within the loose dimer were identified: SL1/SL1 and TAR/TAR. Evidence for these findings is provided by RNA probing using SHAPE, chemical reagents, enzymes, non-denaturing PAGE mobility assays, antisense oligonucleotides hybridization and analysis of an RNA mutant. Both TAR and SL1 as isolated domains are bound by recombinant NCp8 protein with high affinity, contrary to the hairpins downstream of SL1. Foot-printing of the SL1/NCp8 complex indicates that the major binding site maps to the SL1 upper stem. Taken together, these data suggest a model in which TAR hairpin III, the segment of SL1 proximal to the loop and the PAL palindromic sequence play specific roles in the initiation of dimerization. PMID:21622659

  4. Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions.

    PubMed

    McKim, Mikeal; Buxton, Alexander; Johnson, Courtney; Metz, Amanda; Sheardy, Richard D

    2016-08-11

    The structure and stability of DNA is highly dependent upon the sequence context of the bases (A, G, C, and T) and the environment under which the DNA is prepared (e.g., buffer, temperature, pH, ionic strength). Understanding the factors that influence structure and stability of the i-motif conformation can lead to the design of DNA sequences with highly tunable properties. We have been investigating the influence of pH and temperature on the conformations and stabilities for all permutations of the DNA sequence (CCCXXX)4, where X = A and/or T, using spectroscopic approaches. All oligomers undergo transitions from single-stranded structures at pH 7.0 to i-motif conformations at pH 5.0 as evidenced by circular dichroism (CD) studies. These folded structures possess stacked C:CH(+) base pairs joined by loops of 5'-XXX-3'. Although the pH at the midpoint of the transition (pHmp) varies slightly with loop sequence, the linkage between pH and log K for the proton induced transition is highly loop sequence dependent. All oligomers also undergo the thermally induced i-motif to single-strand transition at pH 5.0 as the temperature is increased from 25 to 95 °C. The temperature at the midpoint of this transition (Tm) is also highly dependent on loop sequence context effects. For seven of eight possible permutations, the pH induced, and thermally induced transitions appear to be highly cooperative and two state. Analysis of the CD optical melting profiles via a van't Hoff approach reveals sequence-dependent thermodynamic parameters for the unfolding as well. Together, these data reveal that the i-motif conformation exhibits exquisite sensitivity to loop sequence context with respect to formation and stability. PMID:27438583

  5. A Sequence-Independent Study of the Influence of Short Loop Lengths on the Stability and Topology of Intramolecular DNA G-Quadruplexes†

    PubMed Central

    Bugaut, Anthony; Balasubramanian, Shankar

    2008-01-01

    G-Rich sequences found within biologically important regions of the genome have been shown to form intramolecular G-quadruplexes with varied loop lengths and sequences. Many of these quadruplexes will be distinguishable from each other on the basis of their thermodynamic stabilities and folded conformations. It has been proposed that loop lengths can strongly influence the topology and stability of intramolecular G-quadruplexes. Previous studies have been limited to the analysis of quadruplex sequences with particular loop sequences, making it difficult to make generalizations. Here, we describe an original study that aimed to elucidate the effect of loop length on the biophysical properties of G-quadruplexes in a sequence-independent context. We employed UV melting and circular dichroism spectroscopy to examine and compare the properties of 21 DNA quadruplex libraries, each comprising partially randomized loop sequences with lengths ranging from one to three nucleotides. Our work supports a number of general predictions that can be made solely on the basis of loop lengths. In particular, the results emphasize the strong influence of single-nucleotide loops on quadruplex properties. This study provides a predictive framework that may help identify or classify biologically relevant G-quadruplex-forming sequences. PMID:18092816

  6. Single residue modification of only one dimer within the hemoglobin tetramer reveals autonomous dimer function

    PubMed Central

    Ackers, Gary K.; Dalessio, Paula M.; Lew, George H.; Daugherty, Margaret A.; Holt, Jo M.

    2002-01-01

    The mechanism of cooperativity in the human hemoglobin tetramer (a dimer of αβ dimers) has historically been modeled as a simple two-state system in which a low-affinity structural form (T) switches, on ligation, to a high-affinity form (R), yielding a net loss of hydrogen bonds and salt bridges in the dimer–dimer interface. Modifications that weaken these cross-dimer contacts destabilize the quaternary T tetramer, leading to decreased cooperativity and enhanced ligand affinity, as demonstrated in many studies on symmetric double modifications, i.e., a residue site modified in both α- or both β-subunits. In this work, hybrid tetramers have been prepared with only one modified residue, yielding molecules composed of a wild-type dimer and a modified dimer. It is observed that the cooperative free energy of ligation to the modified dimer is perturbed to the same extent whether in the hybrid tetramer or in the doubly modified tetramer. The cooperative free energy of ligation to the wild-type dimer is unperturbed, even in the hybrid tetramer, and despite the overall destabilization of the T tetramer by the modification. This asymmetric response by the two dimers within the same tetramer shows that loss of dimer–dimer contacts is not communicated across the dimer–dimer interface, but is transmitted through the dimer that bears the modified residue. These observations are interpreted in terms of a previously proposed dimer-based model of cooperativity with an additional quaternary (T/R) component. PMID:12119405

  7. 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

  8. 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

    2014-09-01

    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

  9. Molecular evolution of dimeric α-amylase inhibitor genes in wild emmer wheat and its ecological association

    PubMed Central

    2008-01-01

    Background α-Amylase inhibitors are attractive candidates for the control of seed weevils, as these insects are highly dependent on starch as an energy source. In this study, we aimed to reveal the structure and diversity of dimeric α-amylase inhibitor genes in wild emmer wheat from Israel and to elucidate the relationship between the emmer wheat genes and ecological factors using single nucleotide polymorphism (SNP) markers. Another objective of this study was to find out whether there were any correlations between SNPs in functional protein-coding genes and the environment. Results The influence of ecological factors on the genetic structure of dimeric α-amylase inhibitor genes was evaluated by specific SNP markers. A total of 244 dimeric α-amylase inhibitor genes were obtained from 13 accessions in 10 populations. Seventy-five polymorphic positions and 74 haplotypes were defined by sequence analysis. Sixteen out of the 75 SNP markers were designed to detect SNP variations in wild emmer wheat accessions from different populations in Israel. The proportion of polymorphic loci P (5%), the expected heterozygosity He, and Shannon's information index in the 16 populations were 0.887, 0.404, and 0.589, respectively. The populations of wild emmer wheat showed great diversity in gene loci both between and within populations. Based on the SNP marker data, the genetic distance of pair-wise comparisons of the 16 populations displayed a sharp genetic differentiation over long geographic distances. The values of P, He, and Shannon's information index were negatively correlated with three climatic moisture factors, whereas the same values were positively correlated by Spearman rank correlation coefficients' analysis with some of the other ecological factors. Conclusion The populations of wild emmer wheat showed a wide range of diversity in dimeric α-amylase inhibitors, both between and within populations. We suggested that SNP markers are useful for the estimation of

  10. The influence of radiative core growth on coronal X-ray emission from pre-main-sequence stars

    NASA Astrophysics Data System (ADS)

    Gregory, Scott G.; Adams, Fred C.; Davies, Claire L.

    2016-04-01

    Pre-main-sequence (PMS) stars of mass ≳0.35 M⊙ transition from hosting fully convective interiors to configurations with a radiative core and outer convective envelope during their gravitational contraction. This stellar structure change influences the external magnetic field topology and, as we demonstrate herein, affects the coronal X-ray emission as a stellar analogue of the solar tachocline develops. We have combined archival X-ray, spectroscopic, and photometric data for ˜1000 PMS stars from five of the best studied star-forming regions: the Orion Nebula Cluster, NGC 2264, IC 348, NGC 2362, and NGC 6530. Using a modern, PMS calibrated, spectral type-to-effective temperature and intrinsic colour scale, we de-redden the photometry using colours appropriate for each spectral type, and determine the stellar mass, age, and internal structure consistently for the entire sample. We find that PMS stars on Henyey tracks have, on average, lower fractional X-ray luminosities (LX/L*) than those on Hayashi tracks, where this effect is driven by changes in LX. X-ray emission decays faster with age for higher mass PMS stars. There is a strong correlation between L* and LX for Hayashi track stars but no correlation for Henyey track stars. There is no correlation between LX and radiative core mass or radius. However, the longer stars have spent with radiative cores, the less X-ray luminous they become. The decay of coronal X-ray emission from young early K to late G-type PMS stars, the progenitors of main-sequence A-type stars, is consistent with the dearth of X-ray detections of the latter.

  11. SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

    PubMed Central

    Huang, Yong-Heng; Jankowski, Aleksander; Cheah, Kathryn S. E.; Prabhakar, Shyam; Jauch, Ralf

    2015-01-01

    The SOXE transcription factors SOX8, SOX9 and SOX10 are master regulators of mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. We identified a set of palindromic SOX binding sites specifically enriched in regulatory regions of melanoma cells. SOXE proteins homodimerize on these sequences with high cooperativity. In contrast to other transcription factor dimers, which are typically rigidly spaced, SOXE group proteins can bind cooperatively at a wide range of dimer spacings. Using truncated forms of SOXE proteins, we show that a single dimerization (DIM) domain, that precedes the DNA binding high mobility group (HMG) domain, is sufficient for dimer formation, suggesting that DIM : HMG rather than DIM:DIM interactions mediate the dimerization. All SOXE members can also heterodimerize in this fashion, whereas SOXE heterodimers with SOX2, SOX4, SOX6 and SOX18 are not supported. We propose a structural model where SOXE-specific intramolecular DIM:HMG interactions are allosterically communicated to the HMG of juxtaposed molecules. Collectively, SOXE factors evolved a unique mode to combinatorially regulate their target genes that relies on a multifaceted interplay between the HMG and DIM domains. This property potentially extends further the diversity of target genes and cell-specific functions that are regulated by SOXE proteins. PMID:26013289

  12. 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

  13. Biomimetic synthesis: discovery of xanthanolide dimers.

    PubMed

    Shang, Hai; Liu, Junhua; Bao, Ruiyang; Cao, Yu; Zhao, Kun; Xiao, Chengqian; Zhou, Bing; Hu, Lihong; Tang, Yefeng

    2014-12-22

    Starting from xanthatin, the biomimetic synthesis of 4β,5β-epoxyxanthatin-1α,4α-endoperoxide, a novel monomeric xanthanolide, has been achieved. Moreover, four unprecedented xanthanolide dimers were synthesized by three different dimerizations of xanthatin, either in a head-to-head or head-to-tail fashion. Notably, these dimeric compounds were firstly identified as artifacts in the laboratory, and two of them, mogolides A and B, proved to be natural products present in the Xanthium mogolium Kitag plant. PMID:25430055

  14. Spin 3/2 dimer model

    NASA Astrophysics Data System (ADS)

    Rachel, S.

    2009-05-01

    We present a parent Hamiltonian for weakly dimerized valence bond solid states for arbitrary half-integral S. While the model reduces for S=1/2 to the Majumdar-Ghosh Hamiltonian, we discuss this model and its properties for S=3/2. Its degenerate ground state is the most popular toy model state for discussing dimerization in spin 3/2 chains. In particular, it describes the impurity-induced dimer phase in Cr8Ni as proposed recently. We point out that the explicit construction of the Hamiltonian and its main features apply to arbitrary half-integral spin S.

  15. The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State

    PubMed Central

    Oshaben, Kaylyn M.; Salari, Reza; McCaslin, Darrell R.; Chong, Lillian T.; Horne, W. Seth

    2012-01-01

    The dimerization domain of the yeast transcription factor GCN4, one of the first coiled-coil proteins to be structurally characterized at high resolution, has served as the basis for numerous fundamental studies on α-helical folding. Mutations in the GCN4 leucine zipper are known to change its preferred oligomerization state from dimeric to trimeric or tetrameric; however, the wild-type sequence has been assumed to encode a two-chain assembly exclusively. Here we demonstrate that the GCN4 coiled-coil domain can populate either a dimer or trimer fold, depending on environment. We report high-resolution crystal structures of the wild-type sequence in dimeric and trimeric assemblies. Biophysical measurements suggest populations of both oligomerization states under certain experimental conditions in solution. We use parallel tempering molecular dynamics simulations on the microsecond timescale to compare the stability of the dimer and trimer folded states in isolation. In total, our results suggest that the folding behavior of the well-studied GCN4 leucine-zipper domain is more complex than was previously appreciated. Our results have implications in ongoing efforts to establish predictive algorithms for coiled-coil folds and the selection of coiled-coil model systems for design and mutational studies where oligomerization state specificity is an important consideration. PMID:23116373

  16. 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.

  17. Formation of cystine slipknots in dimeric proteins.

    PubMed

    Sikora, Mateusz; Cieplak, Marek

    2013-01-01

    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher. PMID:23520470

  18. Formation of Cystine Slipknots in Dimeric Proteins

    PubMed Central

    Sikora, Mateusz; Cieplak, Marek

    2013-01-01

    We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher. PMID:23520470

  19. 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. PMID:22988630

  20. Distance within colloidal dimers probed by rotation-induced oscillations of scattered light.

    PubMed

    van Vliembergen, Roland W L; van IJzendoorn, Leo J; Prins, Menno W J

    2016-01-25

    Aggregation processes of colloidal particles are of broad scientific and technological relevance. The earliest stage of aggregation, when dimers appear in an ensemble of single particles, is very important to characterize because it opens routes for further aggregation processes. Furthermore, it represents the most sensitive phase of diagnostic aggregation assays. Here, we characterize dimers by rotating them in a magnetic field and by recording the angle dependence of light scattering. At small scattering angles, the scattering cross section can be approximated by the total cross-sectional area of the dimer. In contrast, at scattering angles around 90 degrees, we reveal that the dependence of the scattering cross section on the dimer angle shows a series of peaks per single 2π rotation of the dimers. These characteristics originate from optical interactions between the two particles, as we have verified with two-particle Mie scattering simulations. We have studied in detail the angular positions of the peaks. It appears from simulations that the influence of particle size polydispersity, Brownian rotation and refractive index on the angular positions of the peaks is relatively small. However, the angular positions of the peaks strongly depend on the distance between the particles. We find a good correspondence between measured data and calculations for a gap of 180 nm between particles having a diameter of 1 micrometer. The experiment and simulations pave the way for extracting distance-specific data from ensembles of dimerizing colloidal particles, with application for sensitive diagnostic aggregation assays. PMID:26832566

  1. Dimerization of truncated melittin analogues results in cytolytic peptides.

    PubMed Central

    Rivett, D E; Kirkpatrick, A; Hewish, D R; Reilly, W; Werkmeister, J A

    1996-01-01

    A synthetic peptide with the sequence of the first 20 residues of melittin and terminating with an additional cysteine amide was found to have cytolytic activity similar to that of melittin. It was apparent from MS data that the cysteine-terminating peptides had formed disulphide dimers. A peptide in which the thiol was blocked by iodoacetate showed no activity, whereas the same peptide blocked by acetamidomethyl showed activity marginally less haemolytic than that of melittin. Cytolytic activity of melittin analogues comprising the full 26 residues could be obtained with wide sequence permutations providing that a general amphipathic helical structure was preserved. In contrast, the activity of the dimers was dependent not only on retention of an amphipathic helix but also on certain individual residues and a free positive charge. A free N-terminus was essential for haemolytic activity. In addition, a lysine or arginine residue at position 7 and a proline at position 14 were found to be necessary for activity, although it was apparent that additional residues are important for retention of the full lytic potential. PMID:8687396

  2. A dimeric form of lipocortin-1 in human placenta.

    PubMed Central

    Pepinsky, R B; Sinclair, L K; Chow, E P; O'Brine-Greco, B

    1989-01-01

    We have characterized a 68 kDa lipocortin from human placenta that was identified as a covalently linked homodimer of lipocortin-1 by peptide mapping and sequence analysis. The site of cross-linking was localized within the 3 kDa N-terminal tail region, an exposed domain that contains the phosphorylation sites for protein tyrosine kinase and protein kinase C and is sensitive to proteolysis. Sequence analysis of the corresponding peptide revealed that glutamine-18 was modified, suggesting that the cross-link may be generated by a transglutaminase. By incubating lipocortin-1 with placental membranes and with labelled glycine ethyl ester we observed a Ca2+-dependent labelling of lipocortin-1 within the tail region, supporting this notion. Like lipocortin-1, the dimer inhibits phospholipase Ad2 activity, is a substrate for the epidermal-growth-factor (EGF) receptor/kinase, and display Ca2+-dependent binding to phosphatidylserine-containing vesicles. In preparations from human placenta the dimer is particularly abundant, accounting for approx. 20% of the lipocortin-1. Images Fig. 1. Fig. 2. Fig. 3. Fig. 5. Fig. 7. PMID:2532504

  3. Dissection of the Dimerization Modes in the DJ-1 Superfamily

    PubMed Central

    Jung, Hoi Jong; Kim, Sangok; Kim, Yun Jae; Kim, Min-Kyu; Kang, Sung Gyun; Lee, Jung-Hyun; Kim, Wankyu; Cha, Sun-Shin

    2012-01-01

    The DJ-1 superfamily (DJ-1/ThiJ/PfpI superfamily) is distributed across all three kingdoms of life. These proteins are involved in a highly diverse range of cellular functions, including chaperone and protease activity. DJ-1 proteins usually form dimers or hexamers in vivo and show at least four different binding orientations via distinct interface patches. Abnormal oligomerization of human DJ-1 is related to neurodegenerative disorders including Parkinson’s disease, suggesting important functional roles of quaternary structures. However, the quaternary structures of the DJ-1 superfamily have not been extensively studied. Here, we focus on the diverse oligomerization modes among the DJ-1 superfamily proteins and investigate the functional roles of quaternary structures both computationally and experimentally. The oligomerization modes are classified into 4 types (DJ-1, YhbO, Hsp, and YDR types) depending on the distinct interface patches (I–IV) upon dimerization. A unique, rotated interface via patch I is reported, which may potentially be related to higher order oligomerization. In general, the groups based on sequence similarity are consistent with the quaternary structural classes, but their biochemical functions cannot be directly inferred using sequence information alone. The observed phyletic pattern suggests the dynamic nature of quaternary structures in the course of evolution. The amino acid residues at the interfaces tend to show lower mutation rates than those of non-interfacial surfaces. PMID:22228183

  4. 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

  5. Comparability of D-dimer assays in clinical samples.

    PubMed

    Freyburger, Geneviève; Labrouche, Sylvie

    2005-11-01

    D-dimers (DD) have shown sufficient proof of their efficiency in the last 10 years to play an important role in hemostasis laboratories for excluding thromboembolic events. Numerous reagents are available on the market but their performances differ. This overview takes stock of the methods used to evaluate the performances of DD assays, the results published in the literature, the technical parameters influencing assay performance, the difficulties caused by the lack of harmonization of DD units, and the attempts to tackle this problem. It raises the issue of the potential optimization of their use with regard to better adaptation to multidisciplinary diagnostic strategies and to target patient populations. PMID:16302154

  6. 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. PMID:25605536

  7. Identification of Specific Transmembrane Residues and Ligand-Induced Interface Changes Involved In Homo-Dimer Formation of A Yeast G Protein-Coupled Receptor

    PubMed Central

    Kim, Heejung; Lee, Byung-Kwon; Naider, Fred; Becker, Jeffrey M.

    2009-01-01

    The S. cerevisiae α-factor pheromone receptor, Ste2p, has been studied as a model for G protein-coupled receptor (GPCR) structure and function. Dimerization has been demonstrated for many GPCRs, although the role(s) of dimerization in receptor function is disputed. Transmembrane domains one (TM1) and four (TM4) of Ste2p were shown previously to play a role in dimerization. In this study, single cysteine substitutions were introduced into a Cys-less Ste2p, and disulfide-mediated dimerization was assessed. Six residues in TM1 (L64 to M69) that had not been previously investigated and nineteen residues in TM7 (T278 to A296) of which fifteen were not previously investigated were mutated to create 25 single Cys-containing Ste2p molecules. Ste2p mutants V68C in TM1 and nine mutants in TM7 (cysteine substituted into residues 278, 285, 289, and 291 to 296) showed increased dimerization upon addition of an oxidizing agent in comparison to the background dimers formed by the Cys-less receptor. The formation of dimers was decreased for TM7 mutant receptors in the presence of α-factor indicating that ligand binding resulted in a conformational change that influenced dimerization. The effect of ligand on dimer formation suggests that dimers are formed in the resting state and the activated state of the receptor by different TM interactions. PMID:19839649

  8. Hydrogen bonding inside and outside carbon nanotubes: HF dimer as a case study.

    PubMed

    Roztoczyńska, Agnieszka; Kozłowska, Justyna; Lipkowski, Paweł; Bartkowiak, Wojciech

    2016-01-28

    In this theoretical work we analyze the noncovalent interactions of molecular complexes formed between the hydrogen bonded HF dimer and single-walled carbon nanotubes (SWCNTs) of different diameters. In particular, the interaction energies of: (i) spatially confined hydrogen fluoride molecules and (ii) HF dimer and the exterior or interior of SWCNTs are investigated. The computations are carried out in a supermolecular manner using the M06-2X exchange-correlation functional. In order to establish the influence of mutual orientation of the hydrogen fluoride dimer and molecular carbon cages on the analyzed energetic parameters energy scans are performed. Furthermore, changes in the charge distribution of the investigated endo- and exohedral complexes are studied employing the Natural Bond Orbital analysis. Among others, the position of the HF dimer with respect to the carbon cages proves to have a significant influence on the analyzed quantities. The results of our study also indicate that the HF dimer interacts stronger with the interior rather than the exterior of SWCNTs. Moreover, a substantial enhancement of the basis set superposition error is disclosed. PMID:26701220

  9. Chiral and Achiral Nanodumbbell Dimers: The Effect of Geometry on Plasmonic Properties.

    PubMed

    Smith, Kyle W; Zhao, Hangqi; Zhang, Hui; Sánchez-Iglesias, Ana; Grzelczak, Marek; Wang, Yumin; Chang, Wei-Shun; Nordlander, Peter; Liz-Marzán, Luis M; Link, Stephan

    2016-06-28

    Metal nanoparticles with a dumbbell-like geometry have plasmonic properties similar to those of their nanorod counterparts, but the unique steric constraints induced by their enlarged tips result in distinct geometries when self-assembled. Here, we investigate gold dumbbells that are assembled into dimers within polymeric micelles. A single-particle approach with correlated scanning electron microscopy and dark-field scattering spectroscopy reveals the effects of dimer geometry variation on the scattering properties. The dimers are prepared using exclusively achiral reagents, and the resulting dimer solution produces no detectable ensemble circular dichroism response. However, single-particle circular differential scattering measurements uncover that this dimer sample is a racemic mixture of individual nanostructures with significant positive and negative chiroptical signals. These measurements are complemented with detailed simulations that confirm the influence of various symmetry elements on the overall peak resonance energy, spectral line shape, and circular differential scattering response. This work expands the current understanding of the influence self-assembled geometries have on plasmonic properties, particularly with regard to chiral and/or racemic samples which may have significant optical activity that may be overlooked when using exclusively ensemble characterization techniques. PMID:27172606

  10. Neonatal Mandibular Distraction Osteogenesis Reduces Cleft Palate Width and Lengthens Soft Palate, Influencing Palatoplasty in Patients With Pierre Robin Sequence.

    PubMed

    Collares, Marcus V M; Duarte, Daniele W; Sobral, Davi S; Portinho, Ciro P; Faller, Gustavo J; Fraga, Mariana M

    2016-07-01

    The aim of this study was to evaluate the influence of neonatal mandibular distraction osteogenesis (MDO) on cleft dimensions and on early palatoplasty outcomes in patients with Pierre Robin Sequence (PRS). In a prospective cohort study that enrolled 24 nonsyndromic patients with PRS, 12 submitted to the MDO group and 12 patients not treated (non-MDO group), the authors compared patients for cleft palate dimensions through 7 morphometric measurements at the moment of palatoplasty and for early palatoplasty outcomes. At palatoplasty, the MDO group presented a significant shorter distance between the posterior nasal spines (PNS-PNS, P < 0.001) and between uvular bases (UB-UB, P < 0.001), representing a reduction in cleft palate width. They also had significant soft palate lengthening represented by a larger distance between UB and retromolar space (UB-RM, P < 0.001) and UB and PNS (UB-PNS, P = 0.014). Their UB moved away from the posterior wall of the nasopharynx (UB-NPH, P < 0.001). The MDO group had a length of operative time significantly shorter (P < 0.001) and no early palatoplasty complications compared with the non-MDO group. In conclusion, MDO acted as an orthopedic procedure that reduced cleft palate width and elongated the soft palate in patients with PRS. These modifications enabled a reduction of around 11% in the length of operative time of palatoplasty (P < 0.001). PMID:27315309

  11. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro)

    PubMed Central

    Tomar, Sakshi; Johnston, Melanie L.; St. John, Sarah E.; Osswald, Heather L.; Nyalapatla, Prasanth R.; Paul, Lake N.; Ghosh, Arun K.; Denison, Mark R.; Mesecar, Andrew D.

    2015-01-01

    All coronaviruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the proteolytic activity of the nsp5 protease (also known as 3C-like protease, 3CLpro) during virus replication, making it a high value target for the development of anti-coronavirus therapeutics. Kinetic studies indicate that in contrast to 3CLpro from other β-CoV 2c members, including HKU4 and HKU5, MERS-CoV 3CLpro is less efficient at processing a peptide substrate due to MERS-CoV 3CLpro being a weakly associated dimer. Conversely, HKU4, HKU5, and SARS-CoV 3CLpro enzymes are tightly associated dimers. Analytical ultracentrifugation studies support that MERS-CoV 3CLpro is a weakly associated dimer (Kd ∼52 μm) with a slow off-rate. Peptidomimetic inhibitors of MERS-CoV 3CLpro were synthesized and utilized in analytical ultracentrifugation experiments and demonstrate that MERS-CoV 3CLpro undergoes significant ligand-induced dimerization. Kinetic studies also revealed that designed reversible inhibitors act as activators at a low compound concentration as a result of induced dimerization. Primary sequence comparisons and x-ray structural analyses of two MERS-CoV 3CLpro and inhibitor complexes, determined to 1.6 Å, reveal remarkable structural similarity of the dimer interface with 3CLpro from HKU4-CoV and HKU5-CoV. Despite this structural similarity, substantial differences in the dimerization ability suggest that long range interactions by the nonconserved amino acids distant from the dimer interface may control MERS-CoV 3CLpro dimerization. Activation of MERS-CoV 3CLpro through ligand-induced dimerization appears to be unique within the genogroup 2c and may potentially increase the complexity in the development of MERS-CoV 3CLpro inhibitors as antiviral agents. PMID:26055715

  12. A structure-based approach for targeting the HIV-1 genomic RNA dimerization initiation site.

    PubMed

    Ennifar, Eric; Paillart, Jean-Christophe; Bernacchi, Serena; Walter, Philippe; Pale, Patrick; Decout, Jean-Luc; Marquet, Roland; Dumas, Philippe

    2007-10-01

    Dimerization of the genomic RNA is an important step of the HIV-1 replication cycle. The Dimerization Initiation Site (DIS) promotes dimerization of the viral genome by forming a loop-loop complex between two DIS hairpins. Crystal structures of the DIS loop-loop complex revealed an unexpected and strong similitude with the bacterial 16S ribosomal aminoacyl-tRNA site (A site), which is the target of aminoglycoside antibiotics. As a consequence of these structural and sequence similarities, the HIV-1 DIS also binds some aminoglycosides, not only in vitro, but also ex vivo, in lymphoid cells and in viral particles. Crystal structures of the DIS loop-loop in complex with several aminoglycoside antibiotics provide a detailed-view of the DIS/drug interaction and reveal some hints about possible modifications to increase the drug affinity and/or specificity. PMID:17434658

  13. 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. PMID:18562638

  14. A dominant negative inhibitor indicates that monocyte chemoattractant protein 1 functions as a dimer.

    PubMed Central

    Zhang, Y; Rollins, B J

    1995-01-01

    Monocyte chemoattractant protein 1 (MCP-1) is a member of the chemokine family of proinflammatory cytokines, all of which share a high degree of amino acid sequence similarity. Aberrant expression of chemokines occurs in a variety of diseases that have an inflammatory component, such as atherosclerosis. Although structural analyses indicate that chemokines form homodimers, there is controversy about whether dimerization is necessary for activity. To address this question for MCP-1, we obtained evidence in four steps. First, coprecipitation experiments demonstrated that MCP-1 forms dimers at physiological concentrations. Second, chemically cross-linked MCP-1 dimers attract monocytes in vitro with a 50% effective concentration of 400 pM, identical to the activity of non-cross-linked MCP-1. Third, an N-terminal deletion variant of MCP-1 (called 7ND) that inhibits MCP-1-mediated monocyte chemotaxis specifically forms heterodimers with wild-type MCP-1. Finally, although 7ND inhibits wild-type MCP-1 activity, it has no effect on cross-linked MCP-1. These results indicate that 7ND is a dominant negative inhibitor, implying that MCP-1 activates its receptor as a dimer. In addition, chemical cross-linking restores activity to an inactive N-terminal insertional variant of MCP-1, further supporting the need for dimerization. Since the reported Kd for MCP-1 monomer dissociation is much higher than its 50% effective concentration or Kd for receptor binding, active dimer formation may require high local concentrations of MCP-1. Our data further suggest that the dimer interface can be a target for MCP-1 inhibitory drugs. PMID:7651403

  15. Structural and functional characterization of α-isopropylmalate synthase and citramalate synthase, members of the LeuA dimer superfamily.

    PubMed

    Frantom, Patrick A

    2012-03-15

    The manipulation of modular regulatory domains from allosteric enzymes represents a possible mechanism to engineer allostery into non-allosteric systems. Currently, there is insufficient understanding of the structure/function relationships in modular regulatory domains to rationally implement this methodology. The LeuA dimer regulatory domain represents a well-conserved, novel fold responsible for the regulation of two enzymes involved in branched chain amino acid biosynthesis, α-isopropylmalate synthase and citramalate synthase. The LeuA dimer regulatory domain is responsible for the feedback inhibition of these enzymes by their respective downstream products. Both enzymes display multidomain architecture with a conserved N-terminal TIM barrel catalytic domain and a C-terminal (βββα)2 LeuA dimer domain joined by a flexible linker region. Due to the similarity of three-dimensional structure and catalytic mechanism combined with low sequence similarity, we propose these enzymes can be classified as members of the LeuA dimer superfamily. Despite their similarity, members of the LeuA dimer superfamily display diversity in their allosteric mechanisms. In this review, structural aspects of the LeuA dimer superfamily are discussed followed by three examples highlighting the diversity of allosteric mechanisms in the LeuA dimer superfamily. PMID:22033339

  16. 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

  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. Structural model for an AxxxG-mediated dimer of surfactant-associated protein C.

    PubMed

    Kairys, Visvaldas; Gilson, Michael K; Luy, Burkhard

    2004-06-01

    The pulmonary surfactant prevents alveolar collapse and is required for normal pulmonary function. One of the important components of the surfactant besides phospholipids is surfactant-associated protein C (SP-C). SP-C shows complex oligomerization behavior and a transition to beta-amyloid-like fibril structures, which are not yet fully understood. Besides this nonspecific oligomerization, MS and chemical cross-linking data combined with CD spectra provide evidence of a specific, mainly alpha-helical, dimer at low to neutral pH. Furthermore, resistance to CNBr cleavage and dual NMR resonances of porcine and human recombinant SP-C with Met32 replaced by isoleucine point to a dimerization site located at the C-terminus of the hydrophobic alpha-helix of SP-C, where a strictly conserved heptapeptide sequence is found. Computational docking of two SP-C helices, described here, reveals a dimer with a helix-helix interface that strikingly resembles that of glycophorin A and is mediated by an AxxxG motif similar to the experimentally determined GxxxG pattern of glycophorin A. It is highly likely that mature SP-C adopts such a dimeric structure in the lamellar bilayer systems found in the surfactant. Dimerization has been shown in previous studies to have a role in sorting and trafficking of SP-C and may also be important to the surfactant function of this protein. PMID:15153098

  19. Dimeric tRNA gene arrangement in Schizosaccharomyces pombe allows increased expression of the downstream gene.

    PubMed Central

    Hottinger-Werlen, A; Schaack, J; Lapointe, J; Mao, J; Nichols, M; Söll, D

    1985-01-01

    Three Schizosaccharomyces pombe dimeric tRNA genes, consisting of a tRNASer gene encoding a minor species with an intervening sequence followed by a tRNAMeti gene, have been described [Mao et al. (1980) Cell 21, 509-516; Hottinger et al. (1982) Mol. Gen. Genet. 188, 219-224; Willis et al. (1984) EMBO J. 3, 1573-1580]. We have examined the reason for the dimeric structure by comparing the transcriptional efficiencies and competitive abilities of the genes subcloned from the dimeric arrangement. Both of the subcloned genes are active in vivo in Saccharomyces cerevisiae, but only the tRNASer gene is efficiently transcribed in vitro. The tRNASer gene competes efficiently for transcription factors, while the tRNAMeti gene does so only weakly. Thus, it appears that the dimeric arrangement is required to support expression of the tRNAMeti gene. S. pombe genes encoding major species of tRNASer are transcribed considerably less efficiently than are the minor genes from the dimers, so coupling of the tRNAMeti gene to the minor species genes should lead to efficient production of tRNAMeti. Images PMID:3936021

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

    PubMed

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

    2016-03-01

    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 (Me(2+))-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

  1. Helix packing and orientation in the transmembrane dimer of gp55-P of the spleen focus forming virus.

    PubMed

    Liu, Wei; Crocker, Evan; Constantinescu, Stefan N; Smith, Steven O

    2005-08-01

    gp55-P is a dimeric membrane protein with a single transmembrane helix that is coded by the env gene of the polycythemic strain of the spleen focus forming virus. gp55-P activates the erythropoietin (Epo) receptor through specific transmembrane helix interactions, leading to Epo-independent growth of erythroid progenitors and eventually promoting erythroleukemia. We describe the use of magic angle spinning deuterium NMR to establish the structure of the transmembrane dimer of gp55-P in model membranes. Comparison of the deuterium lineshapes of leucines in the center (Leu(396-399)) and at the ends (Leu(385), Leu(407)) of the transmembrane sequence shows that gp55-P has a right-handed crossing angle with Leu(399) packed in the dimer interface. We discuss the implications of the structure of the gp55-P transmembrane dimer for activation of the Epo receptor. PMID:15894629

  2. Structure of the human dimeric ATM kinase

    PubMed Central

    Lau, Wilson C. Y.; Li, Yinyin; Liu, Zhe; Gao, Yuanzhu; Zhang, Qinfen; Huen, Michael S. Y.

    2016-01-01

    ABSTRACT DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. PMID:27097373

  3. 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.

  4. Structure of the human dimeric ATM kinase.

    PubMed

    Lau, Wilson C Y; Li, Yinyin; Liu, Zhe; Gao, Yuanzhu; Zhang, Qinfen; Huen, Michael S Y

    2016-01-01

    DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. PMID:27097373

  5. Thermodynamics of porphyrin dimerization in aqueous solutions.

    PubMed Central

    Margalit, R; Rotenberg, M

    1984-01-01

    The dimerization equilibrium of deuteroporphyrin IX and of mesoporphyrin IX in aqueous solutions were studied by fluorimetric techniques over the 0.01-1 microM concentration range, where dimerization is the dominant aggregation process. Deuteroporphyrin IX was studied at several temperatures over the range 22-37 degrees C, and mesoporphyrin at 25 and 37 degrees C. The magnitudes determined for the dimerization equilibrium constants (25 degrees C, neutral pH, phosphate-buffered saline) are 2.3 X 10(6)M-1 and 5.4 X 10(6)M-1 for the deutero and meso derivatives respectively. The meso, deutero and haemato species tested show a similar temperature effect, namely dimerization decreasing with increasing temperature, indicating the involvement of a negative enthalpy change. Van't Hoff isochore of the dimerization constants determined for deuteroporphyrin IX was linear within the temperature range of 22-37 degrees C, allowing the calculation of the thermodynamic parameters. For deuteroporphyrin dimerization, those were found to be delta G0 = -36. 4kJ X mol-1; delta H0 = -46. 0kJ X mol-1 and delta S0 = -32.2J X K-1 X mol-1 (at neutral pH, 25 degrees C, phosphate-buffered saline), showing the process to be enthalpy-driven. Similar trends have been found for porphyrin species other than those studied here. Our data fit with a hypothesis giving a major role to the solvent in driving porphyrins to aggregate in aqueous solution. The magnitudes and directions of the energetic changes fit better with the expectation of the ' solvophobic force' theory predicting enthalpy-driven association, than with the classic hydrophobic bonding, predicting the association to be entropy-driven. PMID:6743228

  6. 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.

  7. Temperature measurement of sputtered metal dimers

    SciTech Connect

    Fayet, P.; Wolf, J.P.; Woeste, L.

    1986-05-15

    The temperatures of sputtered alkali-metal dimers have been measured using one- and two-photon ionization spectroscopy. They are estimated to be 1470 +- 300 K, 1025 +- 200 K, and 1000 +- 200 K for Cs/sub 2/, K/sub 2/, and Na/sub 2/, respectively. The vibrational and rotational temperatures are found to be very similar. No dependence of the dimer excitation is found, neither on target temperature nor on the primary-ion energy. The results are compared with some currently used models to explain cluster formation in sputtering experiments.

  8. Dimeric Structure of the Bacterial Extracellular Foldase PrsA*

    PubMed Central

    Jakob, Roman P.; Koch, Johanna R.; Burmann, Björn M.; Schmidpeter, Philipp A. M.; Hunkeler, Moritz; Hiller, Sebastian; Schmid, Franz X.; Maier, Timm

    2015-01-01

    Secretion of proteins into the membrane-cell wall space is essential for cell wall biosynthesis and pathogenicity in Gram-positive bacteria. Folding and maturation of many secreted proteins depend on a single extracellular foldase, the PrsA protein. PrsA is a 30-kDa protein, lipid anchored to the outer leaflet of the cell membrane. The crystal structure of Bacillus subtilis PrsA reveals a central catalytic parvulin-type prolyl isomerase domain, which is inserted into a larger composite NC domain formed by the N- and C-terminal regions. This domain architecture resembles, despite a lack of sequence conservation, both trigger factor, a ribosome-binding bacterial chaperone, and SurA, a periplasmic chaperone in Gram-negative bacteria. Two main structural differences are observed in that the N-terminal arm of PrsA is substantially shortened relative to the trigger factor and SurA and in that PrsA is found to dimerize in a unique fashion via its NC domain. Dimerization leads to a large, bowl-shaped crevice, which might be involved in vivo in protecting substrate proteins from aggregation. NMR experiments reveal a direct, dynamic interaction of both the parvulin and the NC domain with secretion propeptides, which have been implicated in substrate targeting to PrsA. PMID:25525259

  9. The influence of action possibility and end-state comfort on motor imagery of manual action sequences.

    PubMed

    Seegelke, Christian; Hughes, Charmayne M L

    2015-12-01

    It has been proposed that the preparation of goal-direct actions involves internal movement simulation, or motor imagery. Evidence suggests that motor imagery is critically involved in the prediction of action consequences and contributes heavily to movement planning processes. The present study examined whether the sensitivity towards end-state comfort and the possibility/impossibility to perform an action sequence are considered during motor imagery. Participants performed a mental rotation task in which two images were simultaneously presented. The image on the left depicted the start posture of a right hand when grasping a bar, while the right image depicted the hand posture at the end of the action sequence. The right image displayed the bar in a vertical orientation with the hand in a comfortable (thumb-up) or in an uncomfortable (thumb-down) posture, while the bar in the left image was rotated in picture plane in steps of 45°. Crucially, the two images formed either a physically possible or physically impossible to perform action sequence. Results revealed strikingly different response time patterns for the two action sequence conditions. In general, response times increased almost monotonically with increasing angular disparity for the possible to perform action sequences. However, slight deviations from this monotonicity were apparent when the sequences contained an uncomfortable as opposed to a comfortable final posture. In contrast, for the impossible sequences, response times did not follow a typical mental rotation function, but instead were uniformly very slow. These findings suggest that both biomechanical constraints (i.e., end-state comfort) and the awareness of the possibility/impossibility to perform an action sequence are considered during motor imagery. We conclude that motor representations contain information about the spatiotemporal movement organization and the possibility of performing an action, which are crucially involved in

  10. Synthesis and biological properties of caffeic acid-PNA dimers containing guanine.

    PubMed

    Gaglione, Maria; Malgieri, Gaetano; Pacifico, Severina; Severino, Valeria; D'Abrosca, Brigida; Russo, Luigi; Fiorentino, Antonio; Messere, Anna

    2013-01-01

    Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is endowed with high antioxidant activity. CA derivatives (such as amides) have gained a lot of attention due to their antioxidative, antitumor and antimicrobial properties as well as stable characteristics. Caffeoyl-peptide derivatives showed different antioxidant activity depending on the type and the sequence of amino acid used. For these reasons, we decided to combine CA with Peptide Nucleic Acid (PNA) to test whether the new PNA-CA amide derivatives would result in an improvement or gain of CA's biological (i.e., antioxidant, cytotoxic, cytoprotective) properties. We performed the synthesis and characterization of seven dimer conjugates with various combinations of nucleic acid bases and focused NMR studies on the model compound ga-CA dimer. We demonstrate that PNA dimers containing guanine conjugated to CA exhibited different biological activities depending on composition and sequence of the nucleobases. The dimer ag-CA protected HepG2, SK-B-NE(2), and C6 cells from a cytotoxic dose of hydrogen peroxide (H₂O₂). PMID:23912270

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

    PubMed Central

    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

    2013-01-01

    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. PMID:23275571

  12. 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. PMID:26864532

  13. Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics.

    PubMed

    Marchand, Adrien; Ferreira, Rubén; Tateishi-Karimata, Hisae; Miyoshi, Daisuke; Sugimoto, Naoki; Gabelica, Valérie

    2013-10-17

    Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely sensitive to the sequence and to the chemical environment, for example, solvation. Dehydrating conditions are known to stabilize G-quadruplex structures, but information on how solvation influences the individual rates of folding and unfolding of G-quadruplexes remains scarce. Here, we used electrospray mass spectrometry for the first time to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands, in the presence of common organic cosolvents (methanol, ethanol, isopropanol, and acetonitrile). Based on the ammonium ion distribution, the total dimer signal was decomposed into contributions from the parallel and antiparallel structures to obtain individual reaction rates, and the antiparallel G-quadruplex structure was found to form faster than the parallel one. A dimeric reaction intermediate, in rapid equilibrium with the single strands, was also identified. Organic cosolvents increase the stability of the final structures mainly by increasing the folding rates. Our quantitative analysis of reaction rate dependence on cosolvent percentage shows that organic cosolvent molecules can be captured or released upon G-quadruplex formation, highlighting that they are not inert with DNA. In contrast to the folding rates, the G-quadruplex unfolding rates are almost insensitive to solvation effects, but are instead governed by the sequence and by the final structure: parallel dimers dissociate slower than antiparallel dimers only when thymine bases are present at the 5'-end. These results contribute unraveling the folding pathways of telomeric G-quadruplexes. The solvent effects revealed here enlighten that G-quadruplex structure in dehydrated, and molecularly crowded environments are modulated by the nature of cosolvent (e.g., methanol favors antiparallel structures) due to direct interactions, and by the time scale of the reaction, with >200-fold acceleration of

  14. 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.

  15. 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

  16. 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.

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

    PubMed Central

    Urbic, Tomaz; Dias, Cristiano L.

    2014-01-01

    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. PMID:24606372

  18. Transport properties of the H2O@C60-dimer-based junction.

    PubMed

    Zhu, Chengbo; Wang, Xiaolin

    2015-09-23

    Theoretical predictions play an important role in finding potential applications in molecular electronics. Fullerenes have a number of potential applications, and the charge flow from a single C60 molecule to another becomes more versatile and more interesting after doping. Here, we report the conductance of two H2O@C60 molecules in series order and how the number of encapsulated water molecules influences the transport properties of the junction. Encapsulating an H2O molecule into one of the C60 cages increases the conductance of the dimer. Negative differential resistance is found in the dimer systems, and its peak-to-valley current ratio depends on the number of encapsulated H2O molecules. The conductance of the C60 dimer and the H2O@C60 dimer is two orders of magnitude smaller than that of the C60 monomer. Furthermore, we demonstrate that the conductance of the molecular junctions based on the H2O@C60 dimer can be tuned by moving the encapsulated H2O molecules. The conductance is H2O-position dependent. Our findings indicate that H2O@C60 can be used as a building block in C60-based molecular electronic devices and sensors. PMID:26325223

  19. Transport properties of the H2O@C60-dimer-based junction

    NASA Astrophysics Data System (ADS)

    Zhu, Chengbo; Wang, Xiaolin

    2015-09-01

    Theoretical predictions play an important role in finding potential applications in molecular electronics. Fullerenes have a number of potential applications, and the charge flow from a single C60 molecule to another becomes more versatile and more interesting after doping. Here, we report the conductance of two H2O@C60 molecules in series order and how the number of encapsulated water molecules influences the transport properties of the junction. Encapsulating an H2O molecule into one of the C60 cages increases the conductance of the dimer. Negative differential resistance is found in the dimer systems, and its peak-to-valley current ratio depends on the number of encapsulated H2O molecules. The conductance of the C60 dimer and the H2O@C60 dimer is two orders of magnitude smaller than that of the C60 monomer. Furthermore, we demonstrate that the conductance of the molecular junctions based on the H2O@C60 dimer can be tuned by moving the encapsulated H2O molecules. The conductance is H2O-position dependent. Our findings indicate that H2O@C60 can be used as a building block in C60-based molecular electronic devices and sensors.

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

    PubMed

    Błoński, Piotr; Hafner, Jürgen

    2014-04-01

    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

  1. Ligand regulation of a constitutively dimeric EGF receptor.

    PubMed

    Freed, Daniel M; Alvarado, Diego; Lemmon, Mark A

    2015-01-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers. PMID:26060020

  2. Thymine Dimer Formation probed by Time-Resolved Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schreier, Wolfgang J.; Schrader, Tobias E.; Roller, Florian O.; Gilch, Peter; Zinth, Wolfgang; Kohler, Bern

    Cyclobutane pyrimidine dimers are the major photoproducts formed when DNA is exposed to UV light. Femtosecond time-resolved vibrational spectroscopy reveals that thymine dimers are formed in thymidine oligonucleotides in an ultrafast photoreaction.

  3. Ligand regulation of a constitutively dimeric EGF receptor

    NASA Astrophysics Data System (ADS)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.

    2015-06-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  4. Molecular mechanisms of asymmetric RAF dimer activation.

    PubMed

    Jambrina, Pablo G; Bohuszewicz, Olga; Buchete, Nicolae-Viorel; Kolch, Walter; Rosta, Edina

    2014-08-01

    Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms. PMID:25109958

  5. Dimers on the 33 .42 lattice

    NASA Astrophysics Data System (ADS)

    Li, Shuli; Yan, Weigen

    2016-06-01

    In this work, we obtain explicit expression of the number of close-packed dimers (perfect matchings) of the 33 .42 lattice with cylindrical boundary condition. Particularly, we show that the entropy of 33 .42 lattice is the same for cylindrical and toroidal boundary conditions.

  6. 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

  7. Dimerization of visual pigments in vivo.

    PubMed

    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

    2016-08-01

    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

  8. The influence of aging, environmental exposures and local sequence features on the variation of DNA methylation in blood

    PubMed Central

    Langevin, Scott M; Houseman, E Andres; Christensen, Brock C; Wiencke, John K; Nelson, Heather H; Karagas, Margaret R; Marsit, Carmen J

    2011-01-01

    In order to properly comprehend the epigenetic dysregulation that occurs during the course of disease, there is a need to characterize the epigenetic variability in healthy individuals that arises in response to aging and exposures, and to understand such variation within the biological context of the DNA sequence. We analyzed the methylation of 26,486 autosomal CpG loci in blood from 205 healthy subjects, using three complementary approaches to assess the association between methylation, age or exposures and local sequence features, such as CpG island status, repeat sequences, location within a polycomb target gene or proximity to a transcription factor binding site. We clustered CpGs (1) using unsupervised recursively partitioned mixture modeling (RPMM) and (2) bioinformatically-informed methods and (3) also employed a marginal model-based (non-clustering) approach. We observed associations between age and methylation and hair dye use and methylation, where the direction and magnitude was contingent on the local sequence features of the CpGs. Our results demonstrate that CpGs are differentially methylated dependent upon the genomic features of the sequence in which they are embedded, and that CpG methylation is associated with age and hair dye use in a CpG context-dependent manner in healthy individuals. PMID:21617368

  9. Path Forward for RAF Therapies: Inhibition of Monomers and Dimers.

    PubMed

    Kortum, Robert L; Morrison, Deborah K

    2015-09-14

    Current BRAF inhibitors block signaling from monomeric BRAF(V600E), but not from oncogenic RAS, which requires RAF dimerization. In this issue of Cancer Cell, Yao and colleagues investigate why current drugs are ineffective against RAF dimers, while Peng and colleagues describe a pan-RAF inhibitor targeting both monomeric and dimeric RAF. PMID:26373275

  10. Dimerization mediated through a leucine zipper activates the oncogenic potential of the met receptor tyrosine kinase.

    PubMed Central

    Rodrigues, G A; Park, M

    1993-01-01

    Oncogenic activation of the met (hepatocyte growth factor/scatter factor) receptor tyrosine kinase involves a genomic rearrangement that generates a hybrid protein containing tpr-encoded sequences at its amino terminus fused directly to the met-encoded receptor kinase domain. Deletion of Tpr sequences abolishes the transforming ability of this protein, implicating this region in oncogenic activation. We demonstrate, by site-directed mutagenesis and coimmunoprecipitation experiments, that a leucine zipper motif within Tpr mediates dimerization of the tpr-met product and is essential for the transforming activity of the met oncogene. By analogy with ligand-stimulated activation of receptor tyrosine kinases, we propose that constitutive dimerization mediated by a leucine zipper motif within Tpr is responsible for oncogenic activation of the Met kinase. The possibility that this mechanism of activation represents a paradigm for a class of receptor tyrosine kinase oncogenes activated by DNA rearrangement is discussed. Images PMID:8413267