Science.gov

Sample records for exonuclease structure molecular

  1. WRN Exonuclease Structure, Molecular Mechanism, and DNA EndProcessing Role

    SciTech Connect

    Perry, J. Jefferson P.; Yannone, Steven M.; Holden, Lauren G.; Hitomi, Chiharu; Asaithamby, Aroumougame; Han, Seungil; Cooper, PriscillaK.; Chen, David J.; Tainer, John A.

    2006-02-15

    WRN is unique among the five human RecQ DNA helicases by having a functional exonuclease domain (WRN-exo) and being defective in the premature aging and cancer-related disorder Werner syndrome. Here, we characterize WRN-exo crystal structures, biochemical activity and participation in DNA end-joining. Metal ion complex structures, active site mutations and activity assays reveal a two-metal-ion mediated nuclease mechanism. The DNA end-binding Ku70/80 complex specifically stimulates WRN-exo activity, and structure-based mutational inactivation of WRN-exo alters DNA end-joining in human cells. We furthermore establish structural and biochemical similarities of WRN-exo to DnaQ family replicative proofreading exonucleases, with WRN-specific adaptations consistent with dsDNA specificity and functionally important conformational changes. These results indicate WRN-exo is a human DnaQ family member and support analogous proof-reading activities that are stimulated by Ku70/80 with implications for WRN functions in age related pathologies and maintenance of genomic integrity.

  2. Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes.

    PubMed

    Xie, Ping

    2009-09-16

    A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

  3. Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.

    PubMed

    Kovall, R A; Matthews, B W

    1998-07-07

    lambda-exonuclease participates in DNA recombination and repair. It binds a free end of double-stranded DNA and degrades one strand in the 5' to 3' direction. The primary sequence does not appear to be related to any other protein, but the crystal structure shows part of lambda-exonuclease to be similar to the type II restriction endonucleases PvuII and EcoRV. There is also a weaker correspondence with EcoRI, BamHI, and Cfr10I. The structure comparisons not only suggest that these enzymes all share a similar catalytic mechanism and a common structural ancestor but also provide strong evidence that the toroidal structure of lambda-exonuclease encircles its DNA substrate during hydrolysis.

  4. Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease.

    PubMed

    Hastie, Kathryn M; King, Liam B; Zandonatti, Michelle A; Saphire, Erica Ollmann

    2012-01-01

    Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA). dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by "relocation" of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.

  5. Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis

    PubMed Central

    Yang, Wen; Chen, Wen-yang; Wang, Hui; Ho, John W. S.; Huang, Jian-Dong; Woo, Patrick C. Y.; Lau, Susanna K.P.; Yuen, Kwok-Yung; Zhang, Qionglin; Zhou, Weihong; Bartlam, Mark; Watt, Rory M.; Rao, Zihe

    2011-01-01

    Alkaline exonuclease and single-strand DNA (ssDNA) annealing proteins (SSAPs) are key components of DNA recombination and repair systems within many prokaryotes, bacteriophages and virus-like genetic elements. The recently sequenced β-proteobacterium Laribacter hongkongensis (strain HLHK9) encodes putative homologs of alkaline exonuclease (LHK-Exo) and SSAP (LHK-Bet) proteins on its 3.17 Mb genome. Here, we report the biophysical, biochemical and structural characterization of recombinant LHK-Exo protein. LHK-Exo digests linear double-stranded DNA molecules from their 5′-termini in a highly processive manner. Exonuclease activities are optimum at pH 8.2 and essentially require Mg2+ or Mn2+ ions. 5′-phosphorylated DNA substrates are preferred over dephosphorylated ones. The crystal structure of LHK-Exo was resolved to 1.9 Å, revealing a ‘doughnut-shaped’ toroidal trimeric arrangement with a central tapered channel, analogous to that of λ-exonuclease (Exo) from bacteriophage-λ. Active sites containing two bound Mg2+ ions on each of the three monomers were located in clefts exposed to this central channel. Crystal structures of LHK-Exo in complex with dAMP and ssDNA were determined to elucidate the structural basis for substrate recognition and binding. Through structure-guided mutational analysis, we discuss the roles played by various active site residues. A conserved two metal ion catalytic mechanism is proposed for this class of alkaline exonucleases. PMID:21893587

  6. Multiplex detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

    PubMed

    Liu, Yacui; Zhang, Jiangyan; Tian, Jingxiao; Fan, Xiaofei; Geng, Hao; Cheng, Yongqiang

    2017-01-01

    A simple, highly sensitive, and specific assay was developed for the homogeneous and multiplex detection of microRNAs (miRNAs) by combining molecular beacon (MB) probes and T7 exonuclease-assisted cyclic amplification. An MB probe with five base pairs in the stem region without special modification can effectively prevent the digestion by T7 exonuclease. Only in the presence of target miRNA is the MB probe hybridized with the target miRNA, and then digested by T7 exonuclease in the 5' to 3' direction. At the same time, the target miRNA is released and subsequently initiates the nuclease-assisted cyclic digestion process, generating enhanced fluorescence signal significantly. The results show that the combination of T7 exonuclease-assisted cyclic amplification reaction and MB probe possesses higher sensitivity for miRNA detection. Moreover, multiplex detection of miRNAs was successfully achieved by designing two MB probes labeled with FAM and Cy3, respectively. As a result, the method opens a new pathway for the sensitive and multiplex detection of miRNAs as well as clinical diagnosis. Graphical Abstract A simple, highly sensitive, and specific assay was developed for the detection of microRNAs by combining molecular beacon probes with T7 exonuclease-assisted cyclic amplification reaction.

  7. Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII

    PubMed Central

    Poleszak, Katarzyna; Kaminska, Katarzyna H.; Dunin-Horkawicz, Stanislaw; Lupas, Andrei; Skowronek, Krzysztof J.; Bujnicki, Janusz M.

    2012-01-01

    Exonuclease VII (ExoVII) is a bacterial nuclease involved in DNA repair and recombination that hydrolyses single-stranded DNA. ExoVII is composed of two subunits: large XseA and small XseB. Thus far, little was known about the molecular structure of ExoVII, the interactions between XseA and XseB, the architecture of the nuclease active site or its mechanism of action. We used bioinformatics methods to predict the structure of XseA, which revealed four domains: an N-terminal OB-fold domain, a middle putatively catalytic domain, a coiled-coil domain and a short C-terminal segment. By series of deletion and site-directed mutagenesis experiments on XseA from Escherichia coli, we determined that the OB-fold domain is responsible for DNA binding, the coiled-coil domain is involved in binding multiple copies of the XseB subunit and residues D155, R205, H238 and D241 of the middle domain are important for the catalytic activity but not for DNA binding. Altogether, we propose a model of sequence–structure–function relationships in ExoVII. PMID:22718974

  8. Crystal structures of [lamda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

    SciTech Connect

    Zhang, Jinjin; McCabe, Kimberly A.; Bell, Charles E.

    2011-07-19

    The {lambda} exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of {lambda} exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of {lambda} exonuclease in complex with DNA at 1.88-{angstrom} resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg{sup 2+} ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of {lambda} exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

  9. Structured RNAs that evade or confound exonucleases: function follows form

    PubMed Central

    Akiyama, Benjamin M.; Eiler, Daniel; Kieft, Jeffrey S.

    2016-01-01

    Cells contain powerful RNA decay machinery to eliminate unneeded RNA from the cell, and this process is an important and regulated part of controlling gene expression. However, certain structured RNAs have been found that can robustly resist degradation and extend the lifetime of an RNA. In this review, we present three RNA structures that use a specific three-dimensional fold to provide protection from RNA degradation, and discuss how the recently-solved structures of these RNAs explain their function. Specifically, we describe the Xrn1-resistant RNAs from arthropod-borne flaviviruses, exosome-resistant long non-coding RNAs associated with lung cancer metastasis and found in Kaposi’s Sarcoma-associated herpesvirus, and tRNA-like sequences occurring in certain plant viruses. These three structures reveal three different mechanisms to protect RNAs from decay and suggest RNA structure-based nuclease resistance may be a widespread mechanism of regulation. PMID:26797676

  10. Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES).

    PubMed

    Huang, Kuan-Wei; Hsu, Kai-Cheng; Chu, Lee-Ya; Yang, Jinn-Moon; Yuan, Hanna S; Hsiao, Yu-Yuan

    2016-09-08

    The DEDDh family of exonucleases plays essential roles in DNA and RNA metabolism in all kingdoms of life. Several viral and human DEDDh exonucleases can serve as antiviral drug targets due to their critical roles in virus replication. Here using RNase T and CRN-4 as the model systems, we identify potential inhibitors for DEDDh exonucleases. We further show that two of the inhibitors, ATA and PV6R, indeed inhibit the exonuclease activity of the viral protein NP exonuclease of Lassa fever virus in vitro. Moreover, we determine the crystal structure of CRN-4 in complex with MES that reveals a unique inhibition mechanism by inducing the general base His179 to shift out of the active site. Our results not only provide the structural basis for the inhibition mechanism but also suggest potential lead inhibitors for the DEDDh exonucleases that may pave the way for designing nuclease inhibitors for biochemical and biomedical applications.

  11. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    SciTech Connect

    Ahn, Byungchan; Bohr, Vilhelm A.

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  12. Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases

    PubMed Central

    Brucet, Marina; Querol-Audí, Jordi; Bertlik, Kamila; Lloberas, Jorge; Fita, Ignacio; Celada, Antonio

    2008-01-01

    TREX1 is the major exonuclease in mammalian cells, exhibiting the highest level of activity with a 3′→5′ activity. This exonuclease is responsible in humans for Aicardi-Goutières syndrome and for an autosomal dominant retinal vasculopathy with cerebral leukodystrophy. In addition, this enzyme is associated with systemic lupus erythematosus. TREX1 belongs to the exonuclease DEDDh family, whose members display low levels of sequence identity, while possessing a common fold and active site organization. For these exonucleases, a catalytic mechanism has been proposed that involves two divalent metal ions bound to the DEDD motif. Here we studied the interaction of TREX1 with the monovalent cations lithium and sodium. We demonstrate that these metals inhibit the exonucleolytic activity of TREX1, as measured by the classical gel method, as well as by a new technique developed for monitoring the real-time exonuclease reaction. The X-ray structures of the enzyme in complex with these two cations and with a nucleotide, a product of the exonuclease reaction, were determined at 2.1 Å and 2.3 Å, respectively. A comparison with the structures of the active complexes (in the presence of magnesium or manganese) explains that the inhibition mechanism is caused by the noncatalytic metals competing with distinct affinities for the two metal-binding sites and inducing subtle rearrangements in active centers. Our analysis also reveals that a histidine residue (His124), highly conserved in the DEDDh family, is involved in the activity of TREX1, as confirmed by mutational studies. Our results shed further light on the mechanism of activity of the DEDEh family of exonucleases. PMID:18780819

  13. Target-protecting dumbbell molecular probe against exonucleases digestion for sensitive detection of ATP and streptavidin.

    PubMed

    Chen, Jinyang; Liu, Yucheng; Ji, Xinghu; He, Zhike

    2016-09-15

    In this work, a versatile dumbbell molecular (DM) probe was designed and employed in the sensitively homogeneous bioassay. In the presence of target molecule, the DM probe was protected from the digestion of exonucleases. Subsequently, the protected DM probe specifically bound to the intercalation dye and resulted in obvious fluorescence signal which was used to determine the target molecule in return. This design allows specific and versatile detection of diverse targets with easy operation and no sophisticated fluorescence labeling. Integrating the idea of target-protecting DM probe with adenosine triphosphate (ATP) involved ligation reaction, the DM probe with 5'-end phosphorylation was successfully constructed for ATP detection, and the limitation of detection was found to be 4.8 pM. Thanks to its excellent selectivity and sensitivity, this sensing strategy was used to detect ATP spiked in human serum as well as cellular ATP. Moreover, the proposed strategy was also applied in the visual detection of ATP in droplet-based microfluidic platform with satisfactory results. Similarly, combining the principle of target-protecting DM probe with streptavidin (SA)-biotin interaction, the DM probe with 3'-end biotinylation was developed for selective and sensitive SA determination, which demonstrated the robustness and versatility of this design.

  14. Crystal structure of the protein from Arabidopsis thaliana gene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly.

    PubMed

    Smith, David W; Han, Mi Ra; Park, Joon Sung; Kim, Kyung Rok; Yeom, Taeho; Lee, Ji Yeon; Kim, Do Jin; Bingman, Craig A; Kim, Hyun-Jung; Jo, Kyubong; Han, Byung Woo; Phillips, George N

    2013-09-01

    Arabidopsis thaliana gene At5g06450 encodes a putative DnaQ-like 3'-5' exonuclease domain-containing protein (AtDECP). The DnaQ-like 3'-5' exonuclease domain is often found as a proofreading domain of DNA polymerases. The overall structure of AtDECP adopts an RNase H fold that consists of a mixed β-sheet flanked by α-helices. Interestingly, AtDECP forms a homohexameric assembly with a central six fold symmetry, generating a central cavity. The ring-shaped structure and comparison with WRN-exo, the best structural homologue of AtDECP, suggest a possible mechanism for implementing its exonuclease activity using positively charged patch on the N-terminal side of the homohexameric assembly. The homohexameric structure of AtDECP provides unique information about the interaction between the DnaQ-like 3'-5' exonuclease and its substrate nucleic acids.

  15. Crystal structure of the protein from Arabidopsis thaliana gene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly

    PubMed Central

    Park, Joon Sung; Kim, Kyung Rok; Yeom, Taeho; Lee, Ji Yeon; Kim, Do Jin; Bingman, Craig A.; Kim, Hyun-Jung; Jo, Kyubong; Han, Byung Woo; Phillips, George N.

    2015-01-01

    Arabidopsis thaliana gene At5g06450 encodes a putative DnaQ-like 3′-5′ exonuclease domain-containing protein (AtDECP). The DnaQ-like 3′-5′ exonuclease domain is often found as a proofreading domain of DNA polymerases. The overall structure of AtDECP adopts an RNase H fold that consists of a mixed β-sheet flanked by α-helices. Interestingly, AtDECP forms a homohexameric assembly with a central 6-fold symmetry, generating a central cavity. The ring-shaped structure and comparison with WRN-exo, the best structural homologue of AtDECP, suggest a possible mechanism for implementing its exonuclease activity using positively charged patch on the N-terminal side of the homohexameric assembly. The homohexameric structure of AtDECP provides unique information about the interaction between the DnaQ-like 3′-5′ exonuclease and its substrate nucleic acids. PMID:23616405

  16. Structural and Biochemical Studies of a Moderately Thermophilic Exonuclease I from Methylocaldum szegediense

    PubMed Central

    Fei, Li; Tian, SiSi; Moysey, Ruth; Misca, Mihaela; Barker, John J.; Smith, Myron A.; McEwan, Paul A.; Pilka, Ewa S.; Crawley, Lauren; Evans, Tom; Sun, Dapeng

    2015-01-01

    A novel exonuclease, designated as MszExo I, was cloned from Methylocaldum szegediense, a moderately thermophilic methanotroph. It specifically digests single-stranded DNA in the 3ʹ to 5ʹ direction. The protein is composed of 479 amino acids, and it shares 47% sequence identity with E. coli Exo I. The crystal structure of MszExo I was determined to a resolution of 2.2 Å and it aligns well with that of E. coli Exo I. Comparative studies revealed that MszExo I and E. coli Exo I have similar metal ion binding affinity and similar activity at mesophilic temperatures (25–47°C). However, the optimum working temperature of MszExo I is 10°C higher, and the melting temperature is more than 4°C higher as evaluated by both thermal inactivation assays and DSC measurements. More importantly, two thermal transitions during unfolding of MszExo I were monitored by DSC while only one transition was found in E. coli Exo I. Further analyses showed that magnesium ions not only confer structural stability, but also affect the unfolding of MszExo I. MszExo I is the first reported enzyme in the DNA repair systems of moderately thermophilic bacteria, which are predicted to have more efficient DNA repair systems than mesophilic ones. PMID:25658953

  17. A Structure-Activity Analysis for Probing the Mechanism of Processive Double-Stranded DNA Digestion by λ Exonuclease Trimers.

    PubMed

    Pan, Xinlei; Smith, Christopher E; Zhang, Jinjin; McCabe, Kimberly A; Fu, Jun; Bell, Charles E

    2015-10-06

    λ exonuclease (λexo) is an ATP-independent 5'-to-3' exonuclease that binds to double-stranded DNA (dsDNA) ends and processively digests the 5'-strand into mononucleotides. The crystal structure of λexo revealed that the enzyme forms a ring-shaped homotrimer with a central funnel-shaped channel for tracking along the DNA. On the basis of this structure, it was proposed that dsDNA enters the open end of the channel, the 5'-strand is digested at one of the three active sites, and the 3'-strand passes through the narrow end of the channel to emerge out the back. This model was largely confirmed by the structure of the λexo-DNA complex, which further revealed that the enzyme unwinds the DNA by 2 bp prior to cleavage, to thread the 5'-end of the DNA into the active site. On the basis of this structure, an "electrostatic ratchet" model was proposed, in which the enzyme uses a hydrophobic wedge to insert into the base pairs to unwind the DNA, a two-metal mechanism for nucleotide hydrolysis, a positively charged pocket to bind to the terminal 5'-phosphate generated after each round of cleavage, and an arginine residue (Arg-45) to bind to the minor groove of the downstream end of the DNA. To test this model, in this study we have determined the effects of 11 structure-based mutations in λexo on DNA binding and exonuclease activities in vitro, and on DNA recombination in vivo. The results are largely consistent with the model for the mechanism that was proposed on the basis of the structure and provide new insights into the roles of particular residues of the protein in promoting the reaction. In particular, a key role for Arg-45 in DNA binding is revealed.

  18. Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex

    PubMed Central

    Nishida, Hirokazu; Mayanagi, Kouta; Kiyonari, Shinichi; Sato, Yuichi; Oyama, Takuji; Ishino, Yoshizumi; Morikawa, Kosuke

    2009-01-01

    Proliferating cell nuclear antigen (PCNA) is responsible for the processivity of DNA polymerase. We determined the crystal structure of Pyrococcus furiosus DNA polymerase (PfuPol) complexed with the cognate monomeric PCNA, which allowed us to construct a convincing model of the polymerase-PCNA ring interaction, with unprecedented configurations of the two molecules. Electron microscopic analyses indicated that this complex structure exists in solution. Our structural study revealed that an interaction occurs between a stretched loop of PCNA and the PfuPol Thumb domain, in addition to the authentic PCNA-polymerase recognition site (PIP box). Comparisons of the present structure with the previously reported structures of polymerases complexed with DNA, suggested that the second interaction plays a crucial role in switching between the polymerase and exonuclease modes, by inducing a PCNA-polymerase complex configuration that favors synthesis over editing. This putative mechanism for fidelity control of replicative DNA polymerases is supported by experiments, in which mutations at the second interaction site caused enhancements in the exonuclease activity in the presence of PCNA. PMID:19934045

  19. Structural Determinant for Switching between the Polymerase and Exonuclease Modes in the PCNA-Replicative DNA Polymerase Complex

    NASA Astrophysics Data System (ADS)

    Nishida, Hirokazu; Mayanagi, Kouta; Ishino, Yoshizumi; Morikawa, Kosuke

    Proliferating cell nuclear antigen (PCNA) is responsible for the processivity of DNA polymerase. We determined the crystal structure of Pyrococcus furiosus DNA polymerase (PfuPol) complexed with a cognate monomeric PCNA, which allowed us to construct a convincing model of the polymerase-PCNA ring interaction. Electron microscopy analyses confirmed that this complex structure exists among the multiple functional configurations in solution. Together with data from mutational analyses, this structural study indicated that the novel interaction between a stretched loop of PCNA and the PfuPol Thumb domain is quite important, in addition to the authentic PCNA-polymerase recognition site (PIP box). A comparison of the present structures with the previously reported structures of polymerases complexed with DNA suggested that the second interaction site plays a crucial role in switching between the polymerase and exonuclease modes, by stabilizing only the polymerase mode. This proposed mechanism of fidelity control of replicative DNA polymerases was supported by experiments, in which a mutation within the second interaction site caused an enhancement in the exonuclease activity in the presence of PCNA.

  20. Exonuclease IX of Escherichia coli.

    PubMed Central

    Shafritz, K M; Sandigursky, M; Franklin, W A

    1998-01-01

    The bacteria Escherichia coli contains several exonucleases acting on both double- and single-stranded DNA and in both a 5'-->3' and 3'-->5' direction. These enzymes are involved in replicative, repair and recombination functions. We have identified a new exonuclease found in E.coli, termed exonuclease IX, that acts preferentially on single-stranded DNA as a 3'-->5' exonuclease and also functions as a 3'-phosphodiesterase on DNA containing 3'-incised apurinic/apyrimidinic (AP) sites to remove the product trans -4-hydroxy-2-pentenal 5-phosphate. The enzyme showed essentially no activity as a deoxyribophosphodiesterase acting on 5'-incised AP sites. The activity was isolated as a glutathione S-transferase fusion protein from a sequence of the E.coli genome that was 60% identical to a 260 bp region of the small fragment of the DNA polymerase I gene. The protein has a molecular weight of 28 kDa and is free of AP endonuclease and phosphatase activities. Exonuclease IX is expressed in E.coli , as demonstrated by reverse transcription-PCR, and it may function in the DNA base excision repair and other pathways. PMID:9592142

  1. Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways

    PubMed Central

    Hsiao, Yu-Yuan; Fang, Woei-Horng; Lee, Chia-Chia; Chen, Yi-Ping; Yuan, Hanna S.

    2014-01-01

    DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V–dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3′-end processing. PMID:24594808

  2. The DNA exonucleases of Escherichia coli

    PubMed Central

    Lovett, Susan T.

    2014-01-01

    DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB) and III (dnaQ/mutD), Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG) and X (exoX), the RecBCD, RecJ, and RecE exonucleases, SbcCD endo/exonuclease, the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo) and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life. PMID:26442508

  3. Homogeneous Electrochemical Biosensor for Melamine Based on DNA Triplex Structure and Exonuclease III-Assisted Recycling Amplification.

    PubMed

    Fu, Caili; Liu, Chang; Li, Ying; Guo, Yajing; Luo, Fang; Wang, Peilong; Guo, Longhua; Qiu, Bin; Lin, Zhenyu

    2016-10-03

    Abasic site (AP site) in the triplex structure can recognize specific target with high selectivity. In this study, this character was first applied to develop a simple, sensitive, and selective homogeneous electrochemical biosensor for melamine determination. The assay combines the advantage of the high selectivity of the DNA triplex structure containing an AP site to melamine and high efficiency of exonuclease (Exo) III-assisted recycling amplification. DNA-1 (T1), DNA-2 (T2), poly[dA] probe containing an AP site (8A) and methylene blue-labeled DNA probe (dMB probe) were carefully designed. Melamine can specifically locate in the AP site through hydrogen bonding interaction between thymine and melamine to make T1, T2, and 8A close to each other, therefore, forming a stable T-melamine-T DNA triplex structure. Under the optimal conditions, the differential pulse voltammetric (DPV) response had a linear relationship with the logarithm of melamine concentration in the range of 1 nM∼0.5 μM. The developed biosensor has been successfully applied to detect the migration of melamine from melamine bowl. Result showed that the migration in 4% acetic acid solvent was the largest, which is similar to that detected by high performance liquid chromatography. This homogeneous electrochemical sensor may have a potential prospect in detecting melamine in dairy products and migration of melamine from multicategory food packaging or application materials.

  4. Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.

    PubMed

    Brucet, Marina; Querol-Audí, Jordi; Serra, Maria; Ramirez-Espain, Ximena; Bertlik, Kamila; Ruiz, Lidia; Lloberas, Jorge; Macias, Maria J; Fita, Ignacio; Celada, Antonio

    2007-05-11

    TREX1 is the most abundant mammalian 3' --> 5' DNA exonuclease. It has been described to form part of the SET complex and is responsible for the Aicardi-Goutières syndrome in humans. Here we show that the exonuclease activity is correlated to the binding preferences toward certain DNA sequences. In particular, we have found three motifs that are selected, GAG, ACA, and CTGC. To elucidate how the discrimination occurs, we determined the crystal structures of two murine TREX1 complexes, with a nucleotide product of the exonuclease reaction, and with a single-stranded DNA substrate. Using confocal microscopy, we observed TREX1 both in nuclear and cytoplasmic subcellular compartments. Remarkably, the presence of TREX1 in the nucleus requires the loss of a C-terminal segment, which we named leucine-rich repeat 3. Furthermore, we detected the presence of a conserved proline-rich region on the surface of TREX1. This observation points to interactions with proline-binding domains. The potential interacting motif "PPPVPRPP" does not contain aromatic residues and thus resembles other sequences that select SH3 and/or Group 2 WW domains. By means of nuclear magnetic resonance titration experiments, we show that, indeed, a polyproline peptide derived from the murine TREX1 sequence interacted with the WW2 domain of the elongation transcription factor CA150. Co-immunoprecipitation studies confirmed this interaction with the full-length TREX1 protein, thereby suggesting that TREX1 participates in more functional complexes than previously thought.

  5. Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.

    PubMed

    Redrejo-Rodríguez, Modesto; Vigouroux, Armelle; Mursalimov, Aibek; Grin, Inga; Alili, Doria; Koshenov, Zhanat; Akishev, Zhiger; Maksimenko, Andrei; Bissenbaev, Amangeldy K; Matkarimov, Bakhyt T; Saparbaev, Murat; Ishchenko, Alexander A; Moréra, Solange

    2016-01-01

    Oxidatively damaged DNA bases are substrates for two overlapping repair pathways: DNA glycosylase-initiated base excision repair (BER) and apurinic/apyrimidinic (AP) endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, an AP endonuclease cleaves DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in the NIR pathway, the same AP endonuclease incises DNA 5' to an oxidized base. The majority of characterized AP endonucleases possess classic BER activities, and approximately a half of them can also have a NIR activity. At present, the molecular mechanism underlying DNA substrate specificity of AP endonucleases remains unclear mainly due to the absence of a published structure of the enzyme in complex with a damaged base. To identify critical residues involved in the NIR function, we performed biochemical and structural characterization of Bacillus subtilis AP endonuclease ExoA and compared its crystal structure with the structures of other AP endonucleases: Escherichia coli exonuclease III (Xth), human APE1, and archaeal Mth212. We found conserved amino acid residues in the NIR-specific enzymes APE1, Mth212, and ExoA. Four of these positions were studied by means of point mutations in APE1: we applied substitution with the corresponding residue found in NIR-deficient E. coli Xth (Y128H, N174Q, G231S, and T268D). The APE1-T268D mutant showed a drastically decreased NIR activity and an inverted Mg(2+) dependence of the AP site cleavage activity, which is in line with the presence of an aspartic residue at the equivalent position among other known NIR-deficient AP endonucleases. Taken together, these data show that NIR is an evolutionarily conserved function in the Xth family of AP endonucleases.

  6. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication

    PubMed Central

    Oyama, Takuji; Ishino, Sonoko; Shirai, Tsuyoshi; Yamagami, Takeshi; Nagata, Mariko; Ogino, Hiromi; Kusunoki, Masami; Ishino, Yoshizumi

    2016-01-01

    In eukaryotic DNA replication initiation, hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins, Cdc45 and GINS, which constitute the ‘CMG’ unwindosome complex together with the MCM core. The archaeal DNA replication system is quite similar to that of eukaryotes, but only limited knowledge about the DNA unwinding mechanism is available, from a structural point of view. Here, we describe the crystal structure of an archaeal GAN (GINS-associated nuclease) from Thermococcus kodakaraensis, the homolog of eukaryotic Cdc45, in both the free form and the complex with the C-terminal domain of the cognate Gins51 subunit (Gins51C). This first archaeal GAN structure exhibits a unique, ‘hybrid’ structure between the bacterial RecJ and the eukaryotic Cdc45. GAN possesses the conserved DHH and DHH1 domains responsible for the exonuclease activity, and an inserted CID (CMG interacting domain)-like domain structurally comparable to that in Cdc45, suggesting its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. A structural comparison of the GAN–Gins51C complex with the GINS tetramer suggests that GINS uses the mobile Gins51C as a hook to bind GAN for CMG formation. PMID:27599844

  7. The 3'-5' exonuclease site of DNA polymerase III from gram-positive bacteria: definition of a novel motif structure.

    PubMed

    Barnes, M H; Spacciapoli, P; Li, D H; Brown, N C

    1995-11-07

    The primary structure of the 3'-5' exonuclease (Exo) site of the Gram+ bacterial DNA polymerase III (Pol III) was examined by site-directed mutagenesis of Bacillus subtilis Pol III (BsPol III). It was found to differ significantly from the conventional three-motif substructure established for the Exo site of DNA polymerase I of Escherichia coli (EcPol I) and the majority of other DNA polymerase-exonucleases. Motifs I and II were conventionally organized and anchored functionally by the predicted carboxylate residues. However, the conventional downstream motif, motif III, was replaced by motif III epsilon, a novel 55-amino-acid (aa) segment incorporating three essential aa (His565, Asp533 and Asp570) which are strictly conserved in three Gram+ Pol III and in the Ec Exo epsilon (epsilon). Despite its unique substructure, the Gram+ Pol III-specific Exo site was conventionally independent of Pol, the site of 2'-deoxyribonucleoside 5-triphosphate (dNTP) binding and polymerization. The entire Exo site, including motif III epsilon, could be deleted without profoundly affecting the enzyme's capacity to polymerize dNTPs. Conversely, Pol and all other sequences downstream of the Exo site could be deleted with little apparent effect on Exo activity. Whether the three essential aa within the unique motif III epsilon substructure participate in the conventional two-metal-ion mechanism elucidated for the model Exo site of EcPol I, remains to be established.

  8. The Drosophila Werner Exonuclease Participates in an Exonuclease-Independent Response to Replication Stress

    PubMed Central

    Bolterstein, Elyse; Rivero, Rachel; Marquez, Melissa; McVey, Mitch

    2014-01-01

    Members of the RecQ family of helicases are known for their roles in DNA repair, replication, and recombination. Mutations in the human RecQ helicases, WRN and BLM, cause Werner and Bloom syndromes, which are diseases characterized by genome instability and an increased risk of cancer. While WRN contains both a helicase and an exonuclease domain, the Drosophila melanogaster homolog, WRNexo, contains only the exonuclease domain. Therefore the Drosophila model system provides a unique opportunity to study the exonuclease functions of WRN separate from the helicase. We created a null allele of WRNexo via imprecise P-element excision. The null WRNexo mutants are not sensitive to double-strand break-inducing reagents, suggesting that the exonuclease does not play a key role in homologous recombination-mediated repair of DSBs. However, WRNexo mutant embryos have a reduced hatching frequency and larvae are sensitive to the replication fork-stalling reagent, hydroxyurea (HU), suggesting that WRNexo is important in responding to replication stress. The role of WRNexo in the HU-induced stress response is independent of Rad51. Interestingly, the hatching defect and HU sensitivity of WRNexo mutants do not occur in flies containing an exonuclease-dead copy of WRNexo, suggesting that the role of WRNexo in replication is independent of exonuclease activity. Additionally, WRNexo and Blm mutants exhibit similar sensitivity to HU and synthetic lethality in combination with mutations in structure-selective endonucleases. We propose that WRNexo and BLM interact to promote fork reversal following replication fork stalling and in their absence regressed forks are restarted through a Rad51-mediated process. PMID:24709634

  9. Identification of a new motif required for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): the RRRY motif is necessary for the binding of single-stranded DNA substrate and the template strand of the mismatched duplex.

    PubMed

    Kukreti, Pinky; Singh, Kamalendra; Ketkar, Amit; Modak, Mukund J

    2008-06-27

    The Klenow fragment of Escherichia coli DNA polymerase I houses catalytic centers for both polymerase and 3'-5' exonuclease activities that are separated by about 35 A. Upon the incorporation of a mismatched nucleotide, the primer terminus is transferred from the polymerase site to an exonuclease site designed for excision of the mismatched nucleotides. The structural comparison of the binary complexes of DNA polymerases in the polymerase and the exonuclease modes, together with a molecular modeling of the template strand overhang in Klenow fragment, indicated its binding in the region spanning residues 821-824. Since these residues are conserved in the "A" family DNA polymerases, we have designated this region as the RRRY motif. The alanine substitution of individual amino acid residues of this motif did not change the polymerase activity; however, the 3'-5' exonuclease activity was reduced 2-29-fold, depending upon the site of mutation. The R821A and R822A/Y824A mutant enzymes showed maximum cleavage defect with single-stranded DNA, mainly due to a large decrease in the ssDNA binding affinity of these enzymes. Mismatch removal by these enzymes was only moderately affected. However, data from the exonuclease-polymerase balance assays with mismatched template-primer suggest that the mutant enzymes are defective in switching mismatched primer from the polymerase to the exonuclease site. Thus, the RRRY motif provides a binding track for substrate ssDNA and for nonsubstrate single-stranded template overhang, in a polarity-dependent manner. This binding then facilitates cleavage of the substrate at the exonuclease site.

  10. Lambda Exonuclease Digestion of CGG Trinucleotide Repeats

    PubMed Central

    Conroy, R.S.; Koretsky, A.P.; Moreland, J.

    2011-01-01

    Fragile X syndrome and other triplet repeat diseases are characterized by an elongation of a repeating DNA triplet. The ensemble-averaged lambda exonuclease digestion rate of different substrates, including one with an elongated FMR1 gene containing 120 CGG repeats, was measured using absorption and fluorescence spectroscopy. Using magnetic tweezers sequence-dependent digestion rates and pausing was measured for individual lambda exonucleases. Within the triplet repeats a lower average and narrower distribution of rates and a higher frequency of pausing was observed. PMID:19562332

  11. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  12. Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA

    PubMed Central

    Yoda, Takuya; Tanabe, Maiko; Tsuji, Toshiyuki; Yoda, Takao; Ishino, Sonoko; Shirai, Tsuyoshi; Ishino, Yoshizumi; Takeyama, Haruko; Nishida, Hirokazu

    2017-01-01

    Family B DNA polymerases comprise polymerase and 3′ −>5′ exonuclease domains, and detect a mismatch in a newly synthesized strand to remove it in cooperation with Proliferating cell nuclear antigen (PCNA), which encircles the DNA to provide a molecular platform for efficient protein–protein and protein–DNA interactions during DNA replication and repair. Once the repair is completed, the enzyme must stop the exonucleolytic process and switch to the polymerase mode. However, the cue to stop the degradation is unclear. We constructed several PCNA mutants and found that the exonuclease reaction was enhanced in the mutants lacking the conserved basic patch, located on the inside surface of PCNA. These mutants may mimic the Pol/PCNA complex processing the mismatched DNA, in which PCNA cannot interact rigidly with the irregularly distributed phosphate groups outside the dsDNA. Indeed, the exonuclease reaction with the wild type PCNA was facilitated by mismatched DNA substrates. PCNA may suppress the exonuclease reaction after the removal of the mismatched nucleotide. PCNA seems to act as a “brake” that stops the exonuclease mode of the DNA polymerase after the removal of a mismatched nucleotide from the substrate DNA, for the prompt switch to the DNA polymerase mode. PMID:28300173

  13. Purification and characterization of DNase VII, a 3'. -->. 5'-directed exonuclease from human placenta

    SciTech Connect

    Hollis, G.F.; Grossman, L.

    1981-01-01

    An exonuclease, DNase VII, has been purified 6000-fold from human placenta. The enzyme has an apparent molecular weight of 43,000, requires Mg/sup 2 +/ for activity, and has a pH optimum of 7.8. The enzyme hydrolyzes single-stranded and nicked duplex DNA at the same rate proceeding in a 3' ..-->.. 5' direction liberating 5'-mononucleotides. It does not measurably hydrolyze polyribonucleotides.

  14. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.

    PubMed

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2009-04-01

    The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.

  15. Human Exonuclease 5 Is a Novel Sliding Exonuclease Required for Genome Stability*

    PubMed Central

    Sparks, Justin L.; Kumar, Rakesh; Singh, Mayank; Wold, Marc S.; Pandita, Tej K.; Burgers, Peter M.

    2012-01-01

    Previously, we characterized Saccharomyces cerevisiae exonuclease 5 (EXO5), which is required for mitochondrial genome maintenance. Here, we identify the human homolog (C1orf176; EXO5) that functions in the repair of nuclear DNA damage. Human EXO5 (hEXO5) contains an iron-sulfur cluster. It is a single-stranded DNA (ssDNA)-specific bidirectional exonuclease with a strong preference for 5′-ends. After loading at an ssDNA end, hEXO5 slides extensively along the ssDNA prior to cutting, hence the designation sliding exonuclease. However, the single-stranded binding protein human replication protein A (hRPA) restricts sliding and enforces a unique, species-specific 5′-directionality onto hEXO5. This specificity is lost with a mutant form of hRPA (hRPA-t11) that fails to interact with hEXO5. hEXO5 localizes to nuclear repair foci in response to DNA damage, and its depletion in human cells leads to an increased sensitivity to DNA-damaging agents, in particular interstrand cross-linking-inducing agents. Depletion of hEXO5 also results in an increase in spontaneous and damage-induced chromosome abnormalities including the frequency of triradial chromosomes, suggesting an additional defect in the resolution of stalled DNA replication forks in hEXO5-depleted cells. PMID:23095756

  16. Dynamic molecular graphs: "hopping" structures.

    PubMed

    Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

    2014-05-05

    This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the η(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the FeCH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions.

  17. Nucleotide Specificity versus Complex Heterogeneity in Exonuclease Activity Measurements

    PubMed Central

    Enderlein, Jörg

    2007-01-01

    A recent publication reported on measurements of Exonuclease I activity using a real-time fluorescence method that measures the time required by molecules of Exonuclease I to hydrolyze single-stranded DNA that was synthesized to have two fluorescently labeled nucleotides. The observed fluorescence-intensity curves were interpreted as a sign of strong heterogeneity of the activity of Exonuclease I. Here, I propose a different model, which assumes that Exonuclease I activity is nucleotide-dependent, and that a fluorescent label bound to a nucleotide significantly slows its cleavage rate. The presented model fits the observed data equally well, but can be used to make specific predictions upon observable sequence dependence of measured fluorescence-intensity curves. PMID:17142274

  18. Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading

    NASA Astrophysics Data System (ADS)

    Gaspard, Pierre

    2016-04-01

    Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorporated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a 100-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

  19. Nanogap structures for molecular nanoelectronics.

    PubMed

    Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

    2012-02-09

    This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

  20. Nanogap structures for molecular nanoelectronics

    PubMed Central

    2012-01-01

    This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

  1. Domain Structure of the Redβ Single-Strand Annealing Protein: the C-terminal Domain is Required for Fine-Tuning DNA-binding Properties, Interaction with the Exonuclease Partner, and Recombination in vivo.

    PubMed

    Smith, Christopher E; Bell, Charles E

    2016-02-13

    Redβ is a component of the Red recombination system of bacteriophage λ that promotes a single strand annealing (SSA) reaction to generate end-to-end concatemers of the phage genome for packaging. Redβ interacts with λ exonuclease (λexo), the other component of the Red system, to form a "synaptosome" complex that somehow integrates the end resection and annealing steps of the reaction. Previous work using limited proteolysis and chemical modification revealed that Redβ consists of an N-terminal DNA binding domain, residues 1-177, and a flexible C-terminal "tail", residues 178-261. Here, we quantitatively compare the binding of the full-length protein (Redβ(FL)) and the N-terminal domain (Redβ(177)) to different lengths of ssDNA substrate and annealed duplex product. We find that in general, Redβ(FL) binds more tightly to annealed duplex product than to ssDNA substrate, while Redβ(177) binds more tightly to ssDNA. In addition, the C-terminal region of Redβ corresponding to residues 182-261 was purified and found to fold into an α-helical domain that is required for the interaction with λexo to form the synaptosome complex. Deletion analysis of Redβ revealed that removal of just eleven residues from the C-terminus disrupts the interaction with λexo as well as ssDNA and dsDNA recombination in vivo. By contrast, the determinants for self-oligomerization of Redβ appear to reside solely within the N-terminal domain. The subtle but significant differences in the relative binding of Redβ(FL) and Redβ(177) to ssDNA substrate and annealed duplex product may be important for Redβ to function as a SSA protein in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3′–5′ exonuclease activity

    PubMed Central

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2009-01-01

    The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3′–5′ exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg2+/Mn2+-dependent DNA/RNA polymerase, Mn2+-dependent 3′–5′ exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn2+-dependent 3′–5′ exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3′–5′ exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3′–5′ exonuclease activity. PMID:19211662

  3. Selective Elimination of the Exonuclease Activity of the Deoxyribonucleic Acid Polymerase from Escherichia coli B by Limited Proteolysis*

    PubMed Central

    Klenow, H.; Henningsen, I.

    1970-01-01

    Purification of DNA polymerase from E. coli B has in two cases each time led to the isolation of two separate polymerase activities, enzyme A and enzyme B. Enzyme A was in contrast to enzyme B almost completely devoid of exonuclease activity. Each of the two enzymes yielded a single symmetrical activity peak in gel filtration chromatograms. From the elution volumes the molecular weights were estimated to be about 70,000 for enzyme A and about 150,000 for enzyme B. Treatment of enzyme B with subtilisin led to an increase of about 30 per cent of the polymerase activity while the exonuclease activity almost completely disappeared. The product of the subtilisin treatment (enzyme C) gave rise to a single symmetrical polymerase activity peak in a gel filtration chromatogram. The elution volume was identical to that obtained with enzyme A. It is concluded that enzyme A and enzyme C are formed by limited proteolysis of enzyme B. PMID:4905667

  4. Sequence-Dependent Pausing of Single Lambda Exonuclease Molecules

    NASA Astrophysics Data System (ADS)

    Perkins, Thomas T.; Dalal, Ravindra V.; Mitsis, Paul G.; Block, Steven M.

    2003-09-01

    Lambda exonuclease processively degrades one strand of duplex DNA, moving 5'-to-3' in an ATP-independent fashion. When examined at the single-molecule level, the speeds of digestion were nearly constant at 4 nanometers per second (12 nucleotides per second), interspersed with pauses of variable duration. Long pauses, occurring at stereotypical locations, were strand-specific and sequence-dependent. Pause duration and probability varied widely. The strongest pause, GGCGATTCT, was identified by gel electrophoresis. Correlating single-molecule dwell positions with sequence independently identified the motif GGCGA. This sequence is found in the left lambda cohesive end, where exonuclease inhibition may contribute to the reduced recombination efficiency at that end.

  5. Molecular events during translocation and proofreading extracted from 200 static structures of DNA polymerase

    PubMed Central

    Ren, Zhong

    2016-01-01

    DNA polymerases in family B are workhorses of DNA replication that carry out the bulk of the job at a high speed with high accuracy. A polymerase in this family relies on a built-in exonuclease for proofreading. It has not been observed at the atomic resolution how the polymerase advances one nucleotide space on the DNA template strand after a correct nucleotide is incorporated, that is, a process known as translocation. It is even more puzzling how translocation is avoided after the primer strand is excised by the exonuclease and returned back to the polymerase active site once an error occurs. The structural events along the bifurcate pathways of translocation and proofreading have been unwittingly captured by hundreds of structures in Protein Data Bank. This study analyzes all available structures of a representative member in family B and reveals the orchestrated event sequence during translocation and proofreading. PMID:27325739

  6. Critical determinants for substrate recognition and catalysis in the M. tuberculosis class II AP-endonuclease/3'-5' exonuclease III.

    PubMed

    Khanam, Taran; Shukla, Ankita; Rai, Niyati; Ramachandran, Ravishankar

    2015-05-01

    The Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair (BER). We demonstrate that the enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5'-exonuclease activity is predominant at low ionic environments. Our molecular modelling and mutational experiments show that E57 and D251 are critical for catalysis. Although nicked DNA and gapped DNA are fair substrates of MtbXthA, the gap-size did not affect the excision activity and furthermore, a substrate with a recessed 3'-end is preferred. To understand the determinants of abasic-site recognition, we examined the possible roles of (i) the base opposite the abasic site, (ii) the abasic ribose ring itself, (iii) local distortions in the AP-site, and (iv) conserved residues located near the active site. Our experiments demonstrate that the first three determinants do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. We therefore, used a combination of mutational analysis, kinetic assays, and structure-based modelling, to identify that Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision.

  7. Contribution of polar residues of the J-helix in the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): Q677 regulates the removal of terminal mismatch.

    PubMed

    Singh, Kamalendra; Modak, Mukund J

    2005-06-07

    Previous structural and biochemical data indicate a participation of the J-helix of Escherichia coli pol I in primer positioning at the polymerase and exonuclease sites. The J-helix contains three polar residues: N675, Q677, and N678. Preliminary characterization of alanine substitutions of these residues showed that only Q677A DNA polymerase has substantially decreased polymerase and increased exonuclease activity. The Q677A enzyme had approximately 2- and approximately 5-fold greater exonuclease activity than the wild type (WT) with mismatched and matched template-primers (TPs), respectively. N675A and N678A DNA polymerases did not differ significantly from the WT in these activities, despite the fact that both residues are seen to interact with the TP in various pol I-DNA complexes. Pre-steady-state kinetic measurements for the exonuclease activity of WT and mutant enzymes indicated nearly identical DNA binding affinity for ssDNA and mismatched TPs. However, with a matched TP, Q677A DNA polymerase exhibited increased exonuclease site affinity. The most important characteristic of Q677A DNA polymerase was its ability to continue cleavage into the matched region of the TP after mismatch excision, in contrast to the WT and other mutant enzymes. The increase in the exonuclease activity of Q677A DNA polymerase was further determined not to be solely due to the weakened binding at the polymerase site, by comparison with another polymerase-defective mutant enzyme, namely, R668A DNA polymerase. These enzymes have significantly decreased DNA binding affinity at the polymerase site, yet the exonuclease activity parameters of R668A DNA polymerase remain similar to those of the WT. These results strongly suggest that participation of Q677 is required for positioning the primer terminus (a) in the polymerase site for continued nucleotide addition and (b) in the 3'-exonuclease site for the controlled removal of mismatched nucleotides.

  8. Single molecule analysis reveals three phases of DNA degradation by an exonuclease

    PubMed Central

    Lee, Gwangrog; Yoo, Jungmin; Leslie, Benjamin J.; Ha, Taekjip

    2011-01-01

    λ exonuclease degrades one strand of duplex DNA in the 5’-3’ direction to generate a 3’ overhang required for recombination. Its ability to hydrolyze thousands of nucleotides processively is attributed to its ring structure and most studies have focused on the processive phase. Here, we use single molecule FRET to reveal three phases of λ exonuclease reactions: initiation, distributive and processive phases. The distributive phase occurs at early reactions where the 3’ overhang is too short for a stable engagement with the enzyme. A mismatched base is digested five times slower than a Watson-Crick paired base and concatenating multiple mismatches has a cooperatively negative effect, highlighting the crucial role of basepairing in aligning the 5’ end toward the active site. The rate-limiting step during processive degradation appears to be the post-cleavage melting of the terminal base pair. We also found that an escape from a known pausing sequence requires enzyme backtracking. PMID:21552271

  9. Structure parameters in molecular tunneling ionization theory

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Ping; Li, Wei; Zhao, Song-Feng

    2014-04-01

    We extracted the accurate structure parameters in molecular tunneling ionization theory (so called MO-ADK theory) for 22 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model.

  10. Molecular modeling of nucleic acid structure

    PubMed Central

    Galindo-Murillo, Rodrigo; Bergonzo, Christina

    2013-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure. PMID:18428873

  11. The Molecular Structure of Penicillin

    NASA Astrophysics Data System (ADS)

    Bentley, Ronald

    2004-10-01

    The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

  12. Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

    NASA Astrophysics Data System (ADS)

    Gaspard, Pierre

    2016-04-01

    A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependencies on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production are calculated analytically in terms of the rate constants and the concentrations. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

  13. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  14. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  15. Blinded histopathological characterisation of POLE exonuclease domain-mutant endometrial cancers: sheep in wolf's clothing.

    PubMed

    Van Gool, Inge C; Ubachs, Jef E H; Stelloo, Ellen; de Kroon, Cor D; Goeman, Jelle J; Smit, Vincent T H B M; Creutzberg, Carien L; Bosse, Tjalling

    2017-08-10

    POLE exonuclease domain mutations identify a subset of endometrial cancer (EC) patients with an excellent prognosis. Implementation of this biomarker has been suggested to refine adjuvant treatment decisions, but the necessary sequencing is not widely performed and relatively expensive. Therefore, we aimed to identify histopathological and immunohistochemical characteristics to aid the detection of POLE-mutant ECs. Fifty-one POLE-mutant endometrioid, 67 POLE-wild-type endometrioid and 15 POLE-wild-type serous ECs were included (total N=133). An expert gynaecopathologist, blinded for molecular features, evaluated each case (≥2 slides) for 16 morphological characteristics. Immunohistochemistry was performed for p53, p16, MLH1, MSH2, MSH6, PMS2. POLE-mutant ECs were characterised by a prominent immune infiltrate: 80% showed peritumoural lymphocytes and 59% tumour-infiltrating lymphocytes, compared to 43% and 28% of POLE-wild-type endometrioid and 27% and 13% of serous counterparts (P<0.01, all comparisons). Of POLE-mutants, 33% contained tumour giant cells, which was significantly higher than in POLE-wild-type endometrioid (10%; P=0.003), but not significantly different from serous cancers (53%). Serous-like features were as often (focally) present in POLE-mutant as in POLE-wild-type endometrioid cases (6-24% depending on the feature). The majority of POLE-mutant ECs showed wild-type p53 (86%), negative/focal p16 (82%) and normal mismatch repair protein expression (90%). A simple combination of morphological and immunohistochemical characteristics (tumour type, grade, peritumoural lymphocytes, MLH1, p53 expression) can assist in pre-screening for POLE exonuclease domain mutations in EC, increasing the probability of a mutation being present from 7% to 33%. This facilitates the implementation of this important prognostic biomarker in routine pathology. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights

  16. DNA polymerase ɛ and δ exonuclease domain mutations in endometrial cancer

    PubMed Central

    Church, David N.; Briggs, Sarah E.W.; Palles, Claire; Domingo, Enric; Kearsey, Stephen J.; Grimes, Jonathon M.; Gorman, Maggie; Martin, Lynn; Howarth, Kimberley M.; Hodgson, Shirley V.; Kaur, Kulvinder; Taylor, Jenny; Tomlinson, Ian P.M.

    2013-01-01

    Accurate duplication of DNA prior to cell division is essential to suppress mutagenesis and tumour development. The high fidelity of eukaryotic DNA replication is due to a combination of accurate incorporation of nucleotides into the nascent DNA strand by DNA polymerases, the recognition and removal of mispaired nucleotides (proofreading) by the exonuclease activity of DNA polymerases δ and ɛ, and post-replication surveillance and repair of newly synthesized DNA by the mismatch repair (MMR) apparatus. While the contribution of defective MMR to neoplasia is well recognized, evidence that faulty DNA polymerase activity is important in cancer development has been limited. We have recently shown that germline POLE and POLD1 exonuclease domain mutations (EDMs) predispose to colorectal cancer (CRC) and, in the latter case, to endometrial cancer (EC). Somatic POLE mutations also occur in 5–10% of sporadic CRCs and underlie a hypermutator, microsatellite-stable molecular phenotype. We hypothesized that sporadic ECs might also acquire somatic POLE and/or POLD1 mutations. Here, we have found that missense POLE EDMs with good evidence of pathogenic effects are present in 7% of a set of 173 endometrial cancers, although POLD1 EDMs are uncommon. The POLE mutations localized to highly conserved residues and were strongly predicted to affect proofreading. Consistent with this, POLE-mutant tumours were hypermutated, with a high frequency of base substitutions, and an especially large relative excess of G:C>T:A transversions. All POLE EDM tumours were microsatellite stable, suggesting that defects in either DNA proofreading or MMR provide alternative mechanisms to achieve genomic instability and tumourigenesis. PMID:23528559

  17. Characterization of 3'----5' exonuclease associated with DNA polymerase of silkworm nuclear polyhedrosis virus.

    PubMed Central

    Mikhailov, V S; Marlyev, K A; Ataeva, J O; Kullyev, P K; Atrazhev, A M

    1986-01-01

    3'----5' Exonuclease specific for single-stranded DNA copurified with DNA polymerase of nuclear polyhedrosis virus of silkworm Bombyx mori (BmNPV Pol). BmNPV Pol has no detectable 5'----3' exonuclease activity on single-stranded or duplex DNA. Analysis of the products of 3'----5' exonucleolytic reaction showed that deoxynucleoside monophosphates were released during the hydrolysis of single-stranded DNA. The exonuclease activity cosedimented with the polymerase activity during ultracentrifugation of BmNPV Pol in glycerol gradient. The polymerase and the exonuclease activities of BmNPV Pol were inactivated by heat with nearly identical kinetics. The mode of the hydrolysis of single-stranded DNA by BmNPV Pol-associated exonuclease was strictly distributive. The enzyme dissociated from single-stranded DNA after the release of a single dNMP and then reassociated with a next polynucleotide being degradated. Images PMID:3012482

  18. Structured Molecular Gas Reveals Galactic Spiral Arms

    NASA Astrophysics Data System (ADS)

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory 13CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  19. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  20. Choristoneura fumiferana nucleopolyhedrovirus encodes a functional 3'-5' exonuclease.

    PubMed

    Yang, Dan-Hui; de Jong, Jondavid G; Makhmoudova, Amina; Arif, Basil M; Krell, Peter J

    2004-12-01

    The Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) encodes an ORF homologous to type III 3'-5' exonucleases. The CfMNPV v-trex ORF was cloned into the Bac-to-Bac baculovirus expression-vector system, expressed in insect Sf21 cells with an N-terminal His tag and purified to homogeneity by using Ni-NTA affinity chromatography. Biochemical characterization of the purified V-TREX confirmed that this viral protein is a functional 3'-5' exonuclease that cleaves oligonucleotides from the 3' end in a stepwise, distributive manner, suggesting a role in proofreading during viral DNA replication and DNA repair. Enhanced degradation of a 5'-digoxigenin- or 5'-(32)P-labelled oligo(dT)(30) substrate was observed at increasing incubation times or increased amounts of V-TREX. The 3'-excision activity of V-TREX was maximal at alkaline pH (9.5) in the presence of 5 mM MgCl(2), 2 mM dithiothreitol and 0.1 mg BSA ml(-1).

  1. ExoMeg1: a new exonuclease from metagenomic library

    PubMed Central

    Silva-Portela, Rita C. B.; Carvalho, Fabíola M.; Pereira, Carolina P. M.; de Souza-Pinto, Nadja C.; Modesti, Mauro; Fuchs, Robert P.; Agnez-Lima, Lucymara F.

    2016-01-01

    DNA repair mechanisms are responsible for maintaining the integrity of DNA and are essential to life. However, our knowledge of DNA repair mechanisms is based on model organisms such as Escherichia coli, and little is known about free living and uncultured microorganisms. In this study, a functional screening was applied in a metagenomic library with the goal of discovering new genes involved in the maintenance of genomic integrity. One clone was identified and the sequence analysis showed an open reading frame homolog to a hypothetical protein annotated as a member of the Exo_Endo_Phos superfamily. This novel enzyme shows 3′-5′ exonuclease activity on single and double strand DNA substrates and it is divalent metal-dependent, EDTA-sensitive and salt resistant. The clone carrying the hypothetical ORF was able to complement strains deficient in recombination or base excision repair, suggesting that the new enzyme may be acting on the repair of single strand breaks with 3′ blockers, which are substrates for these repair pathways. Because this is the first report of an enzyme obtained from a metagenomic approach showing exonuclease activity, it was named ExoMeg1. The metagenomic approach has proved to be a useful tool for identifying new genes of uncultured microorganisms. PMID:26815639

  2. Structures in Molecular Clouds: Modeling

    SciTech Connect

    Kane, J O; Mizuta, A; Pound, M W; Remington, B A; Ryutov, D D

    2006-04-20

    We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

  3. Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease.

    PubMed

    Grieves, Jessica L; Fye, Jason M; Harvey, Scott; Grayson, Jason M; Hollis, Thomas; Perrino, Fred W

    2015-04-21

    The TREX1 gene encodes a potent DNA exonuclease, and mutations in TREX1 cause a spectrum of lupus-like autoimmune diseases. Most lupus patients develop autoantibodies to double-stranded DNA (dsDNA), but the source of DNA antigen is unknown. The TREX1 D18N mutation causes a monogenic, cutaneous form of lupus called familial chilblain lupus, and the TREX1 D18N enzyme exhibits dysfunctional dsDNA-degrading activity, providing a link between dsDNA degradation and nucleic acid-mediated autoimmune disease. We determined the structure of the TREX1 D18N protein in complex with dsDNA, revealing how this exonuclease uses a novel DNA-unwinding mechanism to separate the polynucleotide strands for single-stranded DNA (ssDNA) loading into the active site. The TREX1 D18N dsDNA interactions coupled with catalytic deficiency explain how this mutant nuclease prevents dsDNA degradation. We tested the effects of TREX1 D18N in vivo by replacing the TREX1 WT gene in mice with the TREX1 D18N allele. The TREX1 D18N mice exhibit systemic inflammation, lymphoid hyperplasia, vasculitis, and kidney disease. The observed lupus-like inflammatory disease is associated with immune activation, production of autoantibodies to dsDNA, and deposition of immune complexes in the kidney. Thus, dysfunctional dsDNA degradation by TREX1 D18N induces disease in mice that recapitulates many characteristics of human lupus. Failure to clear DNA has long been linked to lupus in humans, and these data point to dsDNA as a key substrate for TREX1 and a major antigen source in mice with dysfunctional TREX1 enzyme.

  4. The Molecular Structure of Monofluorobenzaldehydes

    NASA Astrophysics Data System (ADS)

    Lozada, Issiah Byen; Sun, Wenhao; van Wijngaarden, Jennifer

    2017-06-01

    The pure rotational spectra of 2- and 3-fluorobenzaldehyde have been investigated using a chirped pulse Fourier transform microwave (FTMW) spectrometer in the range of 8-18 GHz and a Balle-Flygare FTMW spectrometer in the range of 4-26 GHz. As in a previous study of monofluorobenzaldehydes, only transitions due to a single planar conformer were observed for 2-fluorobenzaldehyde (O-trans) whereas two planar conformers (O-trans and O-cis) of 3-fluorobenzaldehydes were confirmed. Transitions due to the seven unique ^{13}C isotopologues of each of the three molecules have been observed for the first time. Their rotational constants were used to derive the effective ground state (r_{0}) and substitution (r_{s}) structures. The results compare favourably with the equilibrium (r_{e}) geometries which were determined following geometry optimization at the MP2/aug-cc-pVTZ level of theory. José L. Alonso and Rosa M. Villamañán, J. Chem. Soc., Faraday Trans. 2, 1989, 85(2), 137-149

  5. Evidence that the DNA endonuclease ARTEMIS also has intrinsic 5'-exonuclease activity.

    PubMed

    Li, Sicong; Chang, Howard H; Niewolik, Doris; Hedrick, Michael P; Pinkerton, Anthony B; Hassig, Christian A; Schwarz, Klaus; Lieber, Michael R

    2014-03-14

    ARTEMIS is a member of the metallo-β-lactamase protein family. ARTEMIS has endonuclease activity at DNA hairpins and at 5'- and 3'-DNA overhangs of duplex DNA, and this endonucleolytic activity is dependent upon DNA-PKcs. There has been uncertainty about whether ARTEMIS also has 5'-exonuclease activity on single-stranded DNA and 5'-overhangs, because this 5'-exonuclease is not dependent upon DNA-PKcs. Here, we show that the 5'-exonuclease and the endonuclease activities co-purify. Second, we show that a point mutant of ARTEMIS at a putative active site residue (H115A) markedly reduces both the endonuclease activity and the 5'-exonuclease activity. Third, divalent cation effects on the 5'-exonuclease and the endonuclease parallel one another. Fourth, both the endonuclease activity and 5'-exonuclease activity of ARTEMIS can be blocked in parallel by small molecule inhibitors, which do not block unrelated nucleases. We conclude that the 5'-exonuclease is intrinsic to ARTEMIS, making it relevant to the role of ARTEMIS in nonhomologous DNA end joining.

  6. Evidence That the DNA Endonuclease ARTEMIS also Has Intrinsic 5′-Exonuclease Activity*

    PubMed Central

    Li, Sicong; Chang, Howard H.; Niewolik, Doris; Hedrick, Michael P.; Pinkerton, Anthony B.; Hassig, Christian A.; Schwarz, Klaus; Lieber, Michael R.

    2014-01-01

    ARTEMIS is a member of the metallo-β-lactamase protein family. ARTEMIS has endonuclease activity at DNA hairpins and at 5′- and 3′-DNA overhangs of duplex DNA, and this endonucleolytic activity is dependent upon DNA-PKcs. There has been uncertainty about whether ARTEMIS also has 5′-exonuclease activity on single-stranded DNA and 5′-overhangs, because this 5′-exonuclease is not dependent upon DNA-PKcs. Here, we show that the 5′-exonuclease and the endonuclease activities co-purify. Second, we show that a point mutant of ARTEMIS at a putative active site residue (H115A) markedly reduces both the endonuclease activity and the 5′-exonuclease activity. Third, divalent cation effects on the 5′-exonuclease and the endonuclease parallel one another. Fourth, both the endonuclease activity and 5′-exonuclease activity of ARTEMIS can be blocked in parallel by small molecule inhibitors, which do not block unrelated nucleases. We conclude that the 5′-exonuclease is intrinsic to ARTEMIS, making it relevant to the role of ARTEMIS in nonhomologous DNA end joining. PMID:24500713

  7. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  8. Molecular docking to ensembles of protein structures.

    PubMed

    Knegtel, R M; Kuntz, I D; Oshiro, C M

    1997-02-21

    Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an "energy-weighted average" of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a "geometry-weighted average" of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.

  9. Directed evolution of nucleotide-based libraries using lambda exonuclease.

    PubMed

    Lim, Bee Nar; Choong, Yee Siew; Ismail, Asma; Glökler, Jörn; Konthur, Zoltán; Lim, Theam Soon

    2012-12-01

    Directed evolution of nucleotide libraries using recombination or mutagenesis is an important technique for customizing catalytic or biophysical traits of proteins. Conventional directed evolution methods, however, suffer from cumbersome digestion and ligation steps. Here, we describe a simple method to increase nucleotide diversity using single-stranded DNA (ssDNA) as a starting template. An initial PCR amplification using phosphorylated primers with overlapping regions followed by treatment with lambda exonuclease generates ssDNA templates that can then be annealed via the overlap regions. Double-stranded DNA (dsDNA) is then generated through extension with Klenow fragment. To demonstrate the applicability of this methodology for directed evolution of nucleotide libraries, we generated both gene shuffled and regional mutagenesis synthetic antibody libraries with titers of 2×108 and 6×107, respectively. We conclude that our method is an efficient and convenient approach to generate diversity in nucleic acid based libraries, especially recombinant antibody libraries.

  10. Learning surface molecular structures via machine vision

    NASA Astrophysics Data System (ADS)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  11. Learning surface molecular structures via machine vision

    DOE PAGES

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-10

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

  12. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  13. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  14. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  15. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  16. How We Teach Molecular Structure to Freshmen.

    ERIC Educational Resources Information Center

    Hurst, Michael O.

    2002-01-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  17. A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

    PubMed Central

    Mason, Penelope A.; Boubriak, Ivan; Cox, Lynne S.

    2013-01-01

    WRN exonuclease is involved in resolving DNA damage that occurs either during DNA replication or following exposure to endogenous or exogenous genotoxins. It is likely to play a role in preventing accumulation of recombinogenic intermediates that would otherwise accumulate at transiently stalled replication forks, consistent with a hyper-recombinant phenotype of cells lacking WRN. In humans, the exonuclease domain comprises an N-terminal portion of a much larger protein that also possesses helicase activity, together with additional sites important for DNA and protein interaction. By contrast, in Drosophila, the exonuclease activity of WRN (DmWRNexo) is encoded by a distinct genetic locus from the presumptive helicase, allowing biochemical (and genetic) dissection of the role of the exonuclease activity in genome stability mechanisms. Here, we demonstrate a fluorescent method to determine WRN exonuclease activity using purified recombinant DmWRNexo and end-labeled fluorescent oligonucleotides. This system allows greater reproducibility than radioactive assays as the substrate oligonucleotides remain stable for months, and provides a safer and relatively rapid method for detailed analysis of nuclease activity, permitting determination of nuclease polarity, processivity, and substrate preferences. PMID:24378758

  18. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Cohen, R. S.; Cong, H.; Dame, T. M.; Thaddeus, P.

    1980-01-01

    Two large-scale 2.6 mm CO surveys of the galactic plane, one in the first quadrant (l = 12 to 60 deg, b = -1 to +1 deg), the other in the second (l = 105 to 139 deg, b = -3 to +3 deg), have provided evidence that, contrary to previous findings, molecular clouds constitute a highly specific tracer of spiral structure. Molecular counterparts of five of the classical 21-cm spiral arms have been identified: the Perseus arm, the local arm (including Lindblad's local expanding ring), the Sagittarius arm, the Scutum arm, and the 4-kpc arm. The region between the local arm and the Perseus arm is apparently devoid of molecular clouds, and the interarm regions of the inner Galaxy appear largely so. CO spiral structure implies that the mean lifetime of molecular clouds cannot be greater than 100 million years, the time required for interstellar matter to cross a spiral arm. Conservation of mass then sets a limit on the fraction of the interstellar medium in the form of molecular clouds: it cannot exceed one-half at any distance from the galactic center in the range 4-12 kpc.

  19. Expansion of CAG Repeats in Escherichia coli Is Controlled by Single-Strand DNA Exonucleases of Both Polarities

    PubMed Central

    Jackson, Adam; Okely, Ewa A.

    2014-01-01

    The expansion of CAG·CTG repeat tracts is responsible for several neurodegenerative diseases, including Huntington disease and myotonic dystrophy. Understanding the molecular mechanism of CAG·CTG repeat tract expansion is therefore important if we are to develop medical interventions limiting expansion rates. Escherichia coli provides a simple and tractable model system to understand the fundamental properties of these DNA sequences, with the potential to suggest pathways that might be conserved in humans or to highlight differences in behavior that could signal the existence of human-specific factors affecting repeat array processing. We have addressed the genetics of CAG·CTG repeat expansion in E. coli and shown that these repeat arrays expand via an orientation-independent mechanism that contrasts with the orientation dependence of CAG·CTG repeat tract contraction. The helicase Rep contributes to the orientation dependence of repeat tract contraction and limits repeat tract expansion in both orientations. However, RuvAB-dependent fork reversal, which occurs in a rep mutant, is not responsible for the observed increase in expansions. The frequency of repeat tract expansion is controlled by both the 5′–3′ exonuclease RecJ and the 3′–5′ exonuclease ExoI, observations that suggest the importance of both 3′and 5′ single-strand ends in the pathway of CAG·CTG repeat tract expansion. We discuss the relevance of our results to two competing models of repeat tract expansion. PMID:25081568

  20. How We Teach Molecular Structure to Freshmen

    NASA Astrophysics Data System (ADS)

    Hurst, Michael O.

    2002-06-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Explaining bond type with electronegativity is also done poorly. Teaching of valence bond theory and molecular orbital theory should be left to upper-level classes where it will be used. Currently, valence bond theory and VSEPR are used together in a way that often confuses the students about the difference between the different theories.

  1. Structural effects in molecular metal halides.

    PubMed

    Hargittai, Magdolna

    2009-03-17

    Metal halides are a relatively large class of inorganic compounds that participate in many industrial processes, from halogen metallurgy to the production of semiconductors. Because most metal halides are ionic crystals at ambient conditions, the term "molecular metal halides" usually refers to vapor-phase species. These gas-phase molecules have a special place in basic research because they exhibit the widest range of chemical bonding from the purely ionic to mostly covalent bonding through to weakly interacting systems. Although our focus is basic research, knowledge of the structural and thermodynamic properties of gas-phase metal halides is also important in industrial processes. In this Account, we review our most recent work on metal halide molecular structures. Our studies are based on electron diffraction and vibrational spectroscopy, and increasingly, we have augmented our experimental work with quantum chemical computations. Using both experimental and computational techniques has enabled us to determine intriguing structural effects with better accuracy than using either technique alone. We loosely group our discussion based on structural effects including "floppiness", relativistic effects, vibronic interactions, and finally, undiscovered molecules with computational thermodynamic stability. Floppiness, or serious "nonrigidity", is a typical characteristic of metal halides and makes their study challenging for both experimentalists and theoreticians. Relativistic effects are mostly responsible for the unique structure of gold and mercury halides. These molecules have shorter-than-expected bonds and often have unusual geometrical configurations. The gold monohalide and mercury dihalide dimers and the molecular-type crystal structure of HgCl(2) are examples. We also examined spin-orbit coupling and the possible effect of the 4f electrons on the structure of lanthanide trihalides. Unexpectedly, we found that the geometry of their dimers depends on the f

  2. An exonuclease I-based label-free fluorometric aptasensor for adenosine triphosphate (ATP) detection with a wide concentration range.

    PubMed

    Wei, Yanli; Chen, Yanxia; Li, Huanhuan; Shuang, Shaomin; Dong, Chuan; Wang, Gufeng

    2015-01-15

    A novel aptamer-based label-free assay for sensitive and selective detection of ATP was developed. This assay employs a new aptamer/fluorescent probe system that shows resistance to exonuclease I (Exo I) digestion upon binding to ATP molecules. In the absence of ATP, the complex between the ATP-binding aptamer (ATP-aptamer) and a DNA binding dye, berberine, is digested upon the addition of exonuclease I, leading to the release of berberine into solution and consequently, quenched berberine fluorescence. In the presence of ATP, the ATP-binding aptamer folds into a G-quadruplex structure that is resistant to Exo I digestion. Accordingly, berberine is protected in the G-quadruplex structure and high fluorescence intensity is observed. As such, based on the fluorescence signal change, a label-free fluorescence assay for ATP was developed. Factors affecting the analysis of ATP including the concentration of ATP-binding aptamer, reaction time, temperature and the concentration of Exo I were comprehensively investigated. Under optimal conditions, the fluorescence intensity of the sensing system displayed a response for ATP in a wide range up to 17.5 mM with a detection limit of 140 nM.

  3. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  4. 8B structure in Fermionic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Henninger, K. R.; Neff, T.; Feldmeier, H.

    2015-04-01

    The structure of the light exotic nucleus 8B is investigated in the Fermionic Molecular Dynamics (FMD) model. The decay of 8B is responsible for almost the entire high- energy solar-neutrino flux, making structure calculations of 8B important for determining the solar core temperature. 8B is a proton halo candidate thought to exhibit clustering. FMD uses a wave-packet basis and is well-suited for modelling clustering and halos. For a multiconfiguration treatment we construct the many-body Hilbert space from antisymmetrised angular-momentum projected 8-particle states. First results show formation of a proton halo.

  5. A general fluorescent sensor design strategy for "turn-on" activity detection of exonucleases and restriction endonucleases based on graphene oxide.

    PubMed

    Zhang, Qi; Kong, De-Ming

    2013-11-07

    Using graphene oxide (GO) as a nanoquencher, a universal sensor design strategy was developed on the basis of significantly different binding affinities of GO to single-stranded DNAs (ss-DNAs) with different lengths. The proposed sensors could be used for the activity detection of both exonucleases and restriction endonucleases. To achieve this, a single-labeled fluorescent oligonucleotide probe, which had a single-stranded structure or a hairpin structure with a long single-stranded loop, was used. Such a probe could be efficiently absorbed on the surface of GO, resulting in the quenching of the fluorescent signal. Excision of the single-stranded probe by exonucleases or site-specific cleavage at the double-stranded stem of the hairpin probe by restriction endonuclease released fluorophore-labeled nucleotide, which could not be efficiently absorbed by GO, thus leading to increase in fluorescence of the corresponding sensing system. As examples, three sensors, which were used for activity detection of the exonuclease Exo 1 and the restriction endonucleases EcoR I and Hind III, were developed. These three sensors could specifically and sensitively detect the activities of Exo 1, EcoR I and Hind III with detection limits of 0.03 U mL(-1), 0.06 U mL(-1) and 0.04 U mL(-1), respectively. Visual detection was also possible.

  6. The Drosophila prage Gene, Required for Maternal Transcript Destabilization in Embryos, Encodes a Predicted RNA Exonuclease

    PubMed Central

    Cui, Jun; Lai, Yun Wei; Sartain, Caroline V.; Zuckerman, Rebecca M.; Wolfner, Mariana F.

    2016-01-01

    Egg activation, the transition of mature oocytes into developing embryos, is critical for the initiation of embryogenesis. This process is characterized by resumption of meiosis, changes in the egg’s coverings and by alterations in the transcriptome and proteome of the egg; all of these occur in the absence of new transcription. Activation of the egg is prompted by ionic changes in the cytoplasm (usually a rise in cytosolic calcium levels) that are triggered by fertilization in some animals and by mechanosensitive cues in others. The egg’s transcriptome is dramatically altered during the process, including by the removal of many maternal mRNAs that are not needed for embryogenesis. However, the mechanisms and regulators of this selective RNA degradation are not yet fully known. Forward genetic approaches in Drosophila have identified maternal-effect genes whose mutations prevent the transcriptome changes. One of these genes, prage (prg), was identified by Tadros et al. in a screen for mutants that fail to destabilize maternal transcripts. We identified the molecular nature of the prg gene through a combination of deficiency mapping, complementation analysis, and DNA sequencing of both extant prg mutant alleles. We find that prg encodes a ubiquitously expressed predicted exonuclease, consistent with its role in maternal mRNA destabilization during egg activation. PMID:27172196

  7. The Exonuclease Trex2 Shapes Psoriatic Phenotype.

    PubMed

    Manils, Joan; Casas, Eduard; Viña-Vilaseca, Arnau; López-Cano, Marc; Díez-Villanueva, Anna; Gómez, Diana; Marruecos, Laura; Ferran, Marta; Benito, Carmen; Perrino, Fred W; Vavouri, Tanya; de Anta, Josep Maria; Ciruela, Francisco; Soler, Concepció

    2016-12-01

    Trex2 is a keratinocyte-specific 3'-deoxyribonuclease that participates in the maintenance of skin homeostasis after DNA damage. Here, we show that this exonuclease is strongly upregulated in human psoriasis, a hyperproliferative and inflammatory skin disease. Similarly, the imiquimod (IMQ)- and Il23-induced mouse psoriasis was associated with a substantial upregulation of Trex2, which was recruited into fragmented chromatin in keratinocytes that were undergoing impaired proliferation, differentiation, and cell death, indicating an important role in DNA processing. Using Trex2 knockout mice, we have found that Trex2 deficiency attenuated IMQ-induced psoriasis-like skin inflammation and enhanced IMQ-induced parakeratosis. Also, Il23-induced ear swelling was diminished in Trex2 knockout mice in comparison with wild-type (wt) mice. Transcriptome analysis identified multiple genes that were deregulated by Trex2 loss after treatment with IMQ. Specifically, immune response genes and pathways normally associated with inflammation were downregulated, whereas those related to skin differentiation and chromatin biology showed increased expression. Interestingly, Trex2 deficiency led to decreased IMQ-induced keratinocyte death via both cell autonomous and noncell autonomous mechanisms. Hence, our data indicate that Trex2 acts as a critical factor in the pathogenesis of psoriasis by promoting keratinocyte apoptosis and enucleation and thereby influencing skin immune responses. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Molecular Structure of a Functional Drosophila Centromere

    PubMed Central

    Sun, Xiaoping; Wahlstrom, Janice

    2011-01-01

    Summary Centromeres play a critical role in chromosome inheritance but are among the most difficult genomic components to analyze in multicellular eukaryotes. Here, we present a highly detailed molecular structure of a functional centromere in a multicellular organism. The centromere of the Drosophila minichromosome Dp1187 is contained within a 420 kb region of centric heterochromatin. We have used a new approach to characterize the detailed structure of this centromere and found that it is primarily composed of satellites and single, complete transposable elements. In the rest of the Drosophila genome, these satellites and transposable elements are neither unique to the centromeres nor present at all centromeres. We discuss the impact of these results on our understanding of heterochromatin structure and on the determinants of centromere identity and function. PMID:9428523

  9. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    DTIC Science & Technology

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  10. [Novel mechanism of 3' exonuclease of polymerase in maintenance of DNA replication fidelity and its application in SNP assay].

    PubMed

    Chen, Lin-Ling; Zhang, Jia; Peng, Cui-Ying; Liao, Duan-Fang; Li, Hong-Jian; Gao, Han-Lin; Li, Kai

    2005-03-01

    Polymerase with 3' to 5'exonulcease plays an important role in the maintenance of in vivo DNA replication fidelity. In order to develop more reliable SNP assays, we revisit the underlying molecular mechanisms by which DNA polymerases with 3' exonucleases maintain high fidelity of DNA replication. In addition to mismatch removal by proofreading, we recently discovered a premature termination of polymerization by a new mechanism of OFF-switch. This novel ON/OFF switch turns off DNA polymerization from mismatched primers and turns on DNA polymerization from matched primers. Two SNP assays were developed based on the proofreading and the newly identified OFF-switch respectively: terminal labeled primer extension and the ON/OFF switch operated SNP assay. These two new methods are well adapted to conventional techniques such as electrophoresis, real time PCR, microplates, and microarray. Application of these reliable SNP assays will greatly facilitate genetic and biomedical studies in the post-genome era.

  11. [Molecular structure and fractal analysis of oligosaccharide].

    PubMed

    Liu, Wen-long; Wang, Lu-man; He, Dong-qi; Zhang, Tian-lan; Gou, Bao-di; Li, Qing

    2014-10-18

    To propose a calculation method of oligosaccharides' fractal dimension, and to provide a new approach to studying the drug molecular design and activity. By using the principle of energy optimization and computer simulation technology, the steady structures of oligosaccharides were found, and an effective way of oligosaccharides fractal dimension's calculation was further established by applying the theory of box dimension to the chemical compounds. By using the proposed method, 22 oligosaccharides' fractal dimensions were calculated, with the mean 1.518 8 ± 0.107 2; in addition, the fractal dimensions of the two activity multivalent oligosaccharides which were confirmed by experiments, An-2 and Gu-4, were about 1.478 8 and 1.516 0 respectively, while C-type lectin-like receptor Dectin-1's fractal dimension was about 1.541 2. The experimental and computational results were expected to help to find a class of glycoside drugs whose target receptor was Dectin-1. Fractal dimension, differing from other known macro parameters, is a useful tool to characterize the compound molecules' microscopic structure and function, which may play an important role in the molecular design and biological activity study. In the process of oligosaccharides drug screening, the fractal dimension of receptor and designed oligosaccharides or glycoclusters can be calculated respectively. The oligosaccharides with fractal dimension close to that of target receptor should then take priority compared with others, to get the drug molecules with latent activity.

  12. Viewpoint 9--molecular structure of aqueous interfaces

    NASA Technical Reports Server (NTRS)

    Pohorille, A.; Wilson, M. A.

    1993-01-01

    In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the

  13. Viewpoint 9--molecular structure of aqueous interfaces.

    PubMed

    Pohorille, A; Wilson, M A

    1993-01-01

    In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the

  14. Molecular structure of the collagen triple helix.

    PubMed

    Brodsky, Barbara; Persikov, Anton V

    2005-01-01

    The molecular conformation of the collagen triple helix confers strict amino acid sequence constraints, requiring a (Gly-X-Y)(n) repeating pattern and a high content of imino acids. The increasing family of collagens and proteins with collagenous domains shows the collagen triple helix to be a basic motif adaptable to a range of proteins and functions. Its rodlike domain has the potential for various modes of self-association and the capacity to bind receptors, other proteins, GAGs, and nucleic acids. High-resolution crystal structures obtained for collagen model peptides confirm the supercoiled triple helix conformation, and provide new information on hydrogen bonding patterns, hydration, sidechain interactions, and ligand binding. For several peptides, the helix twist was found to be sequence dependent, and such variation in helix twist may serve as recognition features or to orient the triple helix for binding. Mutations in the collagen triple-helix domain lead to a variety of human disorders. The most common mutations are single-base substitutions that lead to the replacement of one Gly residue, breaking the Gly-X-Y repeating pattern. A single Gly substitution destabilizes the triple helix through a local disruption in hydrogen bonding and produces a discontinuity in the register of the helix. Molecular information about the collagen triple helix and the effect of mutations will lead to a better understanding of function and pathology.

  15. Algorithmic dimensionality reduction for molecular structure analysis.

    PubMed

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul

    2008-08-14

    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  16. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  17. The exonuclease activity of the yeast mitochondrial DNA polymerase γ suppresses mitochondrial DNA deletions between short direct repeats in Saccharomyces cerevisiae.

    PubMed

    Stumpf, Jeffrey D; Copeland, William C

    2013-06-01

    The importance of mitochondrial DNA (mtDNA) deletions in the progeroid phenotype of exonuclease-deficient DNA polymerase γ mice has been intensely debated. We show that disruption of Mip1 exonuclease activity increases mtDNA deletions 160-fold, whereas disease-associated polymerase variants were mostly unaffected, suggesting that exonuclease activity is vital to avoid deletions during mtDNA replication.

  18. Speculations on the molecular structure of eumelanin.

    PubMed

    Swift, J A

    2009-04-01

    Eumelanin is the polymeric black pigment commonly found in hair and skin. Its chemical intractability, to all but vigorous oxidizing agents, has hindered satisfactory understanding of its molecular structure. It is well-established that the immediate precursor to polymerization, indole-5,6-quinone (IQ), is biosynthesized from the amino acid tyrosine. Current views are that the polymer consists of single bond connections between random indole and degraded indole units. In this paper, an alternative chemical scheme for the polymerization of IQ is proposed based upon the original suggestion by Horner in 1949 that a Diels-Alder (D-A) reaction might be involved. The proposed basic chemical scheme for eumelanin formation is that D-A addition occurs specifically between the 2- and 3-positions of one IQ molecule and the 7- and 4- positions respectively of a second IQ molecule, that the ensuing diketo bridge is oxidized to carboxyl groups and that, by decarboxylation and aromatization, a fused indole dimer is produced. It is envisaged that, by further D-A addition of more IQ molecules, oligomers of greater molecular mass are produced. Calculations based on published bond lengths and angles for the indole nucleus show that oligomeric units containing a total of up to 11 fused indoles could be packed into a flat circular disc of 20 A diameter. The discs of the extensively conjugated polymer are envisaged to be stacked above each other by pi-pi interaction and with a spacing of 3.4 A to produce cylindrical units, the mass density of which is calculated to be 1.54 gm cm(-3); approximating with actual physical measurements. The size and shape of the predicted cylinders are in concordance with those observed in atomic force microscope investigations of eumelanin proto-particles. The model is also in agreement with published experimental data that 2/3rds of the carbon dioxide liberated during eumelanin formation derives from positions 5- and 6- of the IQ molecule.

  19. A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

    SciTech Connect

    Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.; Doublié, Sylvie

    2012-06-27

    Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.

  20. Tungsten disulfide nanosheet and exonuclease III co-assisted amplification strategy for highly sensitive fluorescence polarization detection of DNA glycosylase activity.

    PubMed

    Zhao, Jingjin; Ma, Yefei; Kong, Rongmei; Zhang, Liangliang; Yang, Wen; Zhao, Shulin

    2015-08-05

    Herein, we introduced a tungsten disulfide (WS2) nanosheet and exonuclease III (Exo III) co-assisted signal amplification strategy for highly sensitive fluorescent polarization (FP) assay of DNA glycosylase activity. Two DNA glycosylases, uracil-DNA glycosylase (UDG) and human 8-oxoG DNA glycosylase 1 (hOGG1), were tested. A hairpin-structured probe (HP) which contained damaged bases in the stem was used as the substrate. The removal of damaged bases from substrate by DNA glycosylase would lower the melting temperature of HP. The HP was then opened and hybridized with a FAM dye-labeled single strand DNA (DP), generating a duplex with a recessed 3'-terminal of DP. This design facilitated the Exo III-assisted amplification by repeating the hybridization and digestion of DP, liberating numerous FAM fluorophores which could not be adsorbed on WS2 nanosheet. Thus, the final system exhibited a small FP signal. However, in the absence of DNA glycosylases, no hybridization between DP and HP was occurred, hampering the hydrolysis of DP by Exo III. The intact DP was then adsorbed on the surface of WS2 nanosheet that greatly amplified the mass of the labeled-FAM fluorophore, resulting in a large FP value. With the co-assisted amplification strategy, the sensitivity was substantially improved. In addition, this method was applied to detect UDG activity in cell extracts. The study of the inhibition of UDG was also performed. Furthermore, this method is simple in design, easy in implementation, and selective, which holds potential applications in the DNA glycosylase related mechanism research and molecular diagnostics.

  1. The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication

    PubMed Central

    Macao, Bertil; Uhler, Jay P.; Siibak, Triinu; Zhu, Xuefeng; Shi, Yonghong; Sheng, Wenwen; Olsson, Monica; Stewart, James B.; Gustafsson, Claes M.; Falkenberg, Maria

    2015-01-01

    Mitochondrial DNA (mtDNA) polymerase γ (POLγ) harbours a 3′–5′ exonuclease proofreading activity. Here we demonstrate that this activity is required for the creation of ligatable ends during mtDNA replication. Exonuclease-deficient POLγ fails to pause on reaching a downstream 5′-end. Instead, the enzyme continues to polymerize into double-stranded DNA, creating an unligatable 5′-flap. Disease-associated mutations can both increase and decrease exonuclease activity and consequently impair DNA ligation. In mice, inactivation of the exonuclease activity causes an increase in mtDNA mutations and premature ageing phenotypes. These mutator mice also contain high levels of truncated, linear fragments of mtDNA. We demonstrate that the formation of these fragments is due to impaired ligation, causing nicks near the origin of heavy-strand DNA replication. In the subsequent round of replication, the nicks lead to double-strand breaks and linear fragment formation. PMID:26095671

  2. Adenovirus terminal protein protects single stranded DNA from digestion by a cellular exonuclease.

    PubMed Central

    Dunsworth-Browne, M; Schell, R E; Berk, A J

    1980-01-01

    Adenovirus 5 DNA-protein complex is isolated from virions as a duplex DNA molecule covalently attached by the 5' termini of each strand to virion protein of unknown function. The DNA-protein complex can be digested with E. coli exonuclease III to generate molecules analogous to DNA replication intermediates in that they contain long single stranded regions ending in 5' termini bound to terminal protein. The infectivity of pronase digested Adenovirus 5 DNA is greatly diminished by exonuclease III digestion. However, the infectivity of the DNA-protein complex is not significantly altered when up to at least 2400 nucleotides are removed from the 3' ends of each strand. This indicates that the terminal protein protects 5' terminated single stranded regions from digestion by a cellular exonuclease. DNA-protein complex prepared from a host range mutant with a mutation mapping in the left 4% of the genome was digested with exonuclease III, hybridized to a wild type restriction fragment comprising the left 8% of the genome, and transfected into HeLa cells. Virus with wild type phenotype was recovered at high frequency. Images PMID:6255444

  3. Analyzing Exonuclease-Induced Hyperchromicity by Uv Spectroscopy: An Undergraduate Biochemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Ackerman, Megan M.; Ricciardi, Christopher; Weiss, David; Chant, Alan; Kraemer-Chant, Christina M.

    2016-01-01

    An undergraduate biochemistry laboratory experiment is described that utilizes free online bioinformatics tools along with readily available exonucleases to study the effects of base stacking and hydrogen bonding on the UV absorbance of DNA samples. UV absorbance of double-stranded DNA at the ?[subscript max] is decreased when the DNA bases are…

  4. The WRN exonuclease domain protects nascent strands from pathological MRE11/EXO1-dependent degradation

    PubMed Central

    Iannascoli, Chiara; Palermo, Valentina; Murfuni, Ivana; Franchitto, Annapaola; Pichierri, Pietro

    2015-01-01

    The WRN helicase/exonuclease protein is required for proper replication fork recovery and maintenance of genome stability. However, whether the different catalytic activities of WRN cooperate to recover replication forks in vivo is unknown. Here, we show that, in response to replication perturbation induced by low doses of the TOP1 inhibitor camptothecin, loss of the WRN exonuclease resulted in enhanced degradation and ssDNA formation at nascent strands by the combined action of MRE11 and EXO1, as opposed to the limited processing of nascent strands performed by DNA2 in wild-type cells. Nascent strand degradation by MRE11/EXO1 took place downstream of RAD51 and affected the ability to resume replication, which correlated with slow replication rates in WRN exonuclease-deficient cells. In contrast, loss of the WRN helicase reduced exonucleolytic processing at nascent strands and led to severe genome instability. Our findings identify a novel role of the WRN exonuclease at perturbed forks, thus providing the first in vivo evidence for a distinct action of the two WRN enzymatic activities upon fork stalling and providing insights into the pathological mechanisms underlying the processing of perturbed forks. PMID:26275776

  5. Ultrasensitive fluorescence polarization DNA detection by target assisted exonuclease III-catalyzed signal amplification.

    PubMed

    Zhang, Min; Guan, Yi-Meng; Ye, Bang-Ce

    2011-03-28

    Single stranded DNA sequences can be detected by target assisted exonuclease III-catalyzed signal amplification fluorescence polarization (TAECA-FP). The method offers an impressive detection limit of 83 aM within one hour for DNA detection and exhibits high discrimination ability even against a single base mismatch.

  6. Analyzing Exonuclease-Induced Hyperchromicity by Uv Spectroscopy: An Undergraduate Biochemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Ackerman, Megan M.; Ricciardi, Christopher; Weiss, David; Chant, Alan; Kraemer-Chant, Christina M.

    2016-01-01

    An undergraduate biochemistry laboratory experiment is described that utilizes free online bioinformatics tools along with readily available exonucleases to study the effects of base stacking and hydrogen bonding on the UV absorbance of DNA samples. UV absorbance of double-stranded DNA at the ?[subscript max] is decreased when the DNA bases are…

  7. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  8. Filamentary structure in the Orion molecular cloud

    NASA Technical Reports Server (NTRS)

    Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.; Bally, J.; Langer, W. D.

    1986-01-01

    A large scale 13CO map (containing 33,000 spectra) of the giant molecular cloud located in the southern part of Orion is presented which contains the Orion Nebula, NGC1977, and the LI641 dark cloud complex. The overall structure of the cloud is filamentary, with individual features having a length up to 40 times their width. This morphology may result from the effects of star formation in the region or embedded magnetic fields in the cloud. We suggest a simple picture for the evolution of the Orion-A cloud and the formation of the major filament. A rotating proto-cloud (counter rotating with respect to the galaxy) contians a b-field aligned with the galaxtic plane. The northern protion of this cloud collapsed first, perhaps triggered by the pressure of the Ori I OB association. The magnetic field combined with the anisotropic pressure produced by the OB-association breaks the symmetry of the pancake instability, a filament rather than a disc is produced. The growth of instabilities in the filament formed sub-condensations which are recent sites of star formation.

  9. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  10. A 3′-5′ exonuclease activity embedded in the helicase core domain of Candida albicans Pif1 helicase

    PubMed Central

    Wei, Xiao-Bin; Zhang, Bo; Bazeille, Nicolas; Yu, Ying; Liu, Na-Nv; René, Brigitte; Mauffret, Olivier; Xi, Xu-Guang

    2017-01-01

    3′-5′ exonucleases are frequently found to be associated to polymerases or helicases domains in the same enzyme or could function as autonomous entities. Here we uncovered that Candida albicans Pif1 (CaPif1) displays a 3′-5′ exonuclease activity besides its main helicase activity. These two latter activities appear to reside on the same polypeptide and the new exonuclease activity could be mapped to the helicase core domain. We clearly show that CaPif1 displays exclusively exonuclease activity and unambiguously establish the directionality of the exonuclease activity as the 3′-to-5′ polarity. The enzyme appears to follow the two-metal-ion driven hydrolyzing activity exhibited by most of the nucleases, as shown by its dependence of magnesium and also by the identification of aspartic residues. Interestingly, an excellent correlation could be found between the presence of the conserved residues and the exonuclease activity when testing activities on Pif1 enzymes from eight fungal organisms. In contrast to others proteins endowed with the double helicase/exonuclease functionality, CaPif1 differs in the fact that the two activities are embedded in the same helicase domain and not located on separated domains. Our findings may suggest a biochemical basis for mechanistic studies of Pif1 family helicases. PMID:28216645

  11. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  12. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  13. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

  14. Similarity Measure for Molecular Structure: A Brief Review

    NASA Astrophysics Data System (ADS)

    Bero, S. A.; Muda, A. K.; Choo, Y. H.; Muda, N. A.; Pratama, S. F.

    2017-09-01

    Similarity or distance measures have been used widely to calculate the similarity or dissimilarity between two samples of dataset. Cheminformatics is known as the domain that dealing with chemical information and both similarity and distance coefficient have been an important role for matching, searching and classification of chemical information. There are various types of similarity/distance coefficient used in molecular structure similarity searching. Generally, the calculation using similarity/distance coefficient is focusing more on 2-dimensional (2D) rather than 3-dimensional (3D) structure. In this paper, the popular similarity/distance coefficients for molecular structure will be reviewed together with the review on 3D molecular structure.

  15. A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus.

    PubMed

    Couvillion, Mary T; Bounova, Gergana; Purdom, Elizabeth; Speed, Terence P; Collins, Kathleen

    2012-11-30

    Emerging evidence suggests that Argonaute (Ago)/Piwi proteins have diverse functions in the nucleus and cytoplasm, but the molecular mechanisms employed in the nucleus remain poorly defined. The Tetrahymena thermophila Ago/Piwi protein Twi12 is essential for growth and functions in the nucleus. Twi12-bound small RNAs (sRNAs) are 3' tRNA fragments that contain modified bases and thus are attenuated for base pairing to targets. We show that Twi12 assembles an unexpected complex with the nuclear exonuclease Xrn2. Twi12 functions to stabilize and localize Xrn2, as well as to stimulate its exonuclease activity. Twi12 function depends on sRNA binding, which is required for its nuclear import. Depletion of Twi12 or Xrn2 induces a cellular ribosomal RNA processing defect known to result from limiting Xrn2 activity in other organisms. Our findings suggest a role for an Ago/Piwi protein and 3' tRNA fragments in nuclear RNA metabolism. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Lewis Structures Are Models for Predicting Molecular Structure, Not Electronic Structure

    NASA Astrophysics Data System (ADS)

    Purser, Gordon H.

    1999-07-01

    This article argues against a close relationship between Lewis dot structures and electron structure obtained from quantum mechanical calculations. Lewis structures are a powerful tool for structure prediction, though they are classical models of bonding and do not predict electronic structure. The "best" Lewis structures are those that, when combined with the VSEPR model, allow the accurate prediction of molecular properties, such as polarity, bond length, bond angle, and bond strength. These structures are achieved by minimizing formal charges within the molecule, even if it requires an expanded octet on atoms beyond the second period. Lewis structures that show an expanded octet do not imply full d-orbital involvement in the bonding. They suggest that the presence of low-lying d-orbitals is important in producing observed molecular structures. Based on this work, the presence of electron density, not a large separation in charge, is responsible for the short bond lengths and large angles in species containing nonmetal atoms from beyond the second period. This result contradicts results obtained from natural population analysis, a method that attempts to derive Lewis structures from molecular orbital calculations.

  17. A Survey of Quantitative Descriptions of Molecular Structure

    PubMed Central

    Guha, Rajarshi; Willighagen, Egon

    2013-01-01

    Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems. PMID:23110530

  18. A survey of quantitative descriptions of molecular structure.

    PubMed

    Guha, Rajarshi; Willighagen, Egon

    2012-01-01

    Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems.

  19. Realizing directional cloning using sticky ends produced by 3'-5' exonuclease of Klenow fragment.

    PubMed

    Zhao, Guojie; Li, Jun; Hu, Tianyu; Wei, Hua; Guan, Yifu

    2013-12-01

    The Klenow fragment (KF) has been used to make the blunt end as a tool enzyme. Its 5'-3' polymerase activity can extend the 5' overhanging sticky end to the blunt end, and 3'-5' exonuclease activity can cleave the 3' overhanging sticky end to the blunt end. The blunt end is useful for cloning. Here, we for the first time determined that a sticky end can be made by using the 3'-5' exonuclease activity of KF. We found that KF can cleave the blunt end into certain sticky ends under controlled conditions. We optimized enzyme cleavage conditions, and characterized the cleaved sticky ends to be mainly 2 nt 5' overhang. By using these sticky ends, we realized ligation reaction in vitro, and accomplished cloning short oligonucleotides directionally with high cloning efficiency. In some cases, this method can provide sticky end fragments in large scale for subsequent convenient cloning at low cost.

  20. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  1. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  2. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  3. Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures

    DTIC Science & Technology

    2010-05-10

    REPORT Final Report on " Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New Molecular Structures" (Agreement...Beratan, Weitao Yang, Michael J. Therien, Koen Clays Duke University Office of Research Support Duke University Durham, NC 27705 - REPORT...Prescribed by ANSI Std. Z39.18 - 31-Jul-2009 Final Report on " Sculpting Molecular Potentials to Design Optimized Materials: The Inverse Design of New

  4. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  5. Smart DNA Machine for Carcinoembryonic Antigen Detection by Exonuclease III-Assisted Target Recycling and DNA Walker Cascade Amplification.

    PubMed

    He, Meng-Qi; Wang, Kun; Wang, Wen-Jing; Yu, Yong-Liang; Wang, Jian-Hua

    2017-09-05

    A synthetic DNA machine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA walker biosensor for label-free detection of carcinoembryonic antigen (CEA) is developed for the first time by a novel cascade amplification strategy of exonuclease (Exo) III-assisted target recycling amplification (ERA) and DNA walker. ERA as the first stage of amplification generates the walker DNA, while the autonomous traveling of the walker DNA on the substrate-modified silica microspheres as the second stage of amplification produces an ultrasensitive fluorescent signal with the help of N-methylmesoporphyrin IX (NMM). The DNA machine as a biosensor could be applied for transducing and quantifying signals from isothermal molecular amplifications, avoiding the complicated reporter elements and thermal cycling. The present biosensor achieves a detection limit of 1.2 pg·mL(-1) within a linear range of 10 pg·mL(-1) to 100 ng·mL(-1) for CEA, along with a favorable specificity. The practical applicability of the biosensor is demonstrated by the detection of CEA in human serum with satisfactory results; thus, it shows great potential in clinical diagnosis.

  6. Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo).

    PubMed

    Matteau, Dominick; Rodrigue, Sébastien

    2015-01-01

    DNA-binding proteins play a crucial role in all living organisms by interacting with various DNA sequences across the genome. While several methods have been used to study the interaction between DNA and proteins in vitro, chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard technique for identifying the genome-wide location of DNA-binding proteins in vivo. However, the resolution of standard ChIP-seq methodology is limited by the DNA fragmentation process and presence of contaminating DNA. A significant improvement of the ChIP-seq technique results from the addition of an exonuclease treatment during the immunoprecipitation step (ChIP-exo) that lowers background noise and more importantly increases the identification of binding sites to a level near to single-base resolution by effectively footprinting DNA-bound proteins. By doing so, ChIP-exo offers new opportunities for a better characterization of the complex and fascinating architecture that resides in DNA-proteins interactions and provides new insights for the comprehension of important molecular mechanisms.

  7. Molecular structure of the lecithin ripple phase.

    PubMed

    de Vries, Alex H; Yefimov, Serge; Mark, Alan E; Marrink, Siewert J

    2005-04-12

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments.

  8. Molecular structure of the lecithin ripple phase

    PubMed Central

    de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

    2005-01-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. PMID:15809443

  9. Exonuclease-Catalyzed Target Recycling Amplification and Immobilization-free Electrochemical Aptasensor.

    PubMed

    Tan, Yue; Wei, Xiaofeng; Zhang, Ying; Wang, Peilong; Qiu, Bin; Guo, Longhua; Lin, Zhenyu; Yang, Huang-Hao

    2015-12-01

    A simple, sensitive, and selective immobilization-free electrochemical aptasensor had been developed which combines the advantages of the discrimination of the aggregation of long and short DNA on a negatively charged indium tin oxide (ITO) electrode, high selectivity of the aptamer, and high efficiency of exonuclease-catalyzed target recycling amplification. Ochratoxin A (OTA), a type of mycotoxin, has been chosen as the model target. Methylene blue (MB) labeled probe DNA had been hybridized with the OTA aptamer first, which cannot diffuse freely to the negative charged ITO electrode surface due to the repulsion of the negative charges, since the hybridized DNA contains large negative charges. In the presence of target (OTA), the aptamer prefers to form an OTA-aptamer complex in lieu of an aptamer-DNA duplex, which results in the dissociation of probe DNA from the probe DNA-aptamer complex. The released probe DNA could be digested into mononucleotides, including a MB-labeled electroactive mononucleotide (eT), due to the employment of the RecJf exonuclease, a single-stranded DNA specific exonuclease. Since the eT contains little negative charge, it can diffuse easily to the negative charged ITO electrode surface, which results in the enhanced electrochemical response detected. At the same time, the aptamer in the OTA-aptamer complex can be digested by RecJf exonuclease also to liberate the target, which can participate in the next reaction cycling and realize the electrochemical signal amplification. Based on this strategy, an ultrasensitive homogeneous immobilization-free electrochemical aptasensor for OTA can be developed with a low detection limit (LOD) of 0.004 ng mL(-1) (S/N = 3). The proposed biosensor combines the advantages of the simplicity of immobilization-free homogeneous ITO based electrochemical determination, high efficiency of exonuclease-catalyzed target recycling, and high selectivity of the aptamer. The fabricated biosensor has been applied to

  10. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  11. Structural Studies of DNA End Detection and Resection in Homologous Recombination

    PubMed Central

    Schiller, Christian Bernd; Seifert, Florian Ulrich; Linke-Winnebeck, Christian; Hopfner, Karl-Peter

    2014-01-01

    DNA double-strand breaks are repaired by two major pathways, homologous recombination or nonhomologous end joining. The commitment to one or the other pathway proceeds via different steps of resection of the DNA ends, which is controlled and executed by a set of DNA double-strand break sensors, endo- and exonucleases, helicases, and DNA damage response factors. The molecular choreography of the underlying protein machinery is beginning to emerge. In this review, we discuss the early steps of genetic recombination and double-strand break sensing with an emphasis on structural and molecular studies. PMID:25081516

  12. Hygrothermal aging effects on buried molecular structures at epoxy interfaces.

    PubMed

    Myers, John N; Zhang, Chi; Lee, Kang-Wook; Williamson, Jaimal; Chen, Zhan

    2014-01-14

    Interfacial properties such as adhesion are determined by interfacial molecular structures. Adhesive interfaces in microelectronic packages that include organic polymers such as epoxy are susceptible to delamination during accelerated stress testing. Infrared-visible sum frequency generation vibrational spectroscopy (SFG) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) were used to study molecular structures at buried epoxy interfaces during hygrothermal aging to relate molecular structural changes at buried interfaces to decreases in macroscopic adhesion strength. SFG peaks associated with strongly hydrogen bonded water were detected at hydrophilic epoxy interfaces. Ordered interfacial water was also correlated to large decreases in interfacial adhesion strength that occurred as a result of hygrothermal aging, which suggests that water diffused to the interface and replaced original hydrogen bond networks. No water peaks were observed at hydrophobic epoxy interfaces, which was correlated with a much smaller decrease in adhesion strength from the same aging process. ATR-FTIR water signals observed in the epoxy bulk were mainly contributed by relatively weakly hydrogen bonded water molecules, which suggests that the bulk and interfacial water structure was different. Changes in interfacial methyl structures were observed regardless of the interfacial hydrophobicity which could be due to water acting as a plasticizer that restructured both the bulk and interfacial molecular structure. This research demonstrates that SFG studies of molecular structural changes at buried epoxy interfaces during hygrothermal aging can contribute to the understanding of moisture-induced failure mechanisms in electronic packages that contain organic adhesives.

  13. Fluorescence detection of telomerase activity in cancer cell extracts based on autonomous exonuclease III-assisted isothermal cycling signal amplification.

    PubMed

    Ding, Caifeng; Li, Xiaoqian; Wang, Wei; Chen, Yaoyao

    2016-09-15

    Based on the extension reaction of a telomerase substrate (TS) primer in the presence of the telomerase, strand-displacement process to perform more stable longer duplex chain, and stepwise hydrolysis of mononucleotides from the blunt or the recessed 3'-hydroxyl termini of duplex DNA in the presence of Exonuclease III (Exo III), an amplified fluorescence detection of telomerase activity in the cancer cells was described in this manuscript. A fluorescence probe DNA, a quencher DNA, and a TS primer were mixed to construct a three-chain DNA structure and a two-chain DNA structure because the amount of the TS primer was less than the other two DNA. In the presence of the telomerase, the quencher DNA was replaced from the probe DNA and the telomerase activity could be determined with the fluorescence enhancement. The telomerase activity in HeLa extracts equivalent to 6-2000 cells was detected by this method. Moreover, the strategy was further proved by using telomerase extracted from Romas cells. With the multiple rounds of isothermal strand displacement and the hydrolysis process, constituted consecutive of signal amplification for the novel detection paradigm that allowed measuring of telomerase activity in crude cancer cell extracts confirmed the reliability and practicality of the protocol, which reveal this platform holds great promise in the biochemical assay for the telomerase activity in early diagnosis for cancers. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Marine Toxins Origin, Structure, and Molecular Pharmacology

    DTIC Science & Technology

    1990-01-01

    thin-layer chromatography (TLC) were instrumental in the initial isolation and purification processes. Mass spectrometry (MS), infrared spectroscopy ...Frederick, MD 21701-5011 Methods of detection, metabolism, and pathophysiology of the brevetoxins, PbTx-2 and PbTx-3, are summarized. Infrared spectros...1R), circular dichroism (CD), nuclear magnetic resonance spectroscopy (NMR), and X-ray crystal- lography all played important roles in structure

  15. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  16. Prediction of chemical carcinogenicity from molecular structure.

    PubMed

    Sun, Hongmao

    2004-01-01

    Carcinogens represent a serious threat to human health. In vivo determination of carcinogenicity is time-consuming and expensive, thus in silico models to predict chemical carcinogenicity are highly desirable for virtual screening of compound libraries of both pharmaceutically and other commercially interesting molecules. In the present study, a PLS-DA (partial least squares discriminant analysis) model was developed to predict carcinogenicities in each of four rodent models: male mouse (MM), female mouse (FM), male rat (MR), and female rat (FR). The data set that was used contained over 520 compounds from both the NTP and the FDA databases. All the models were built from the same molecular descriptor system, which is based on atom typing [Sun, H. J. Chem. Inf. Comput. Sci. 2004, 44, 748-757], enabling the comparison of atomic contributions to carcinogenicity with respect to species and gender. Using four components, the models were able to achieve excellent fitting and prediction, with r(2) = 0.987 and q(2) = 0.944 for MM, r(2) = 0.985 and q(2) = 0.950 for FM, r(2) = 0.989 and q(2) = 0.962 for MR, and r(2) = 0.990 and q(2) = 0.965 for FR. The models were further validated by response permutation testing and external validation, and the results indicated that the models were both statistically significant and predictive. Variable influence on projection (VIP) analysis identified the key atom types and fragments that contributed to carcinogenicities and response differences across species and gender.

  17. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  18. Complementary molecular information changes our perception of food web structure.

    PubMed

    Wirta, Helena K; Hebert, Paul D N; Kaartinen, Riikka; Prosser, Sean W; Várkonyi, Gergely; Roslin, Tomas

    2014-02-04

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host-parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them.

  19. Complementary molecular information changes our perception of food web structure

    PubMed Central

    Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

    2014-01-01

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

  20. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  1. Syntheses and molecular structures of new cali.

    PubMed

    Attner, J; Radius, U

    2001-01-01

    An unusual disproportionation reaction of the molybdenum(IV) and tungsten(IV) chlorides [MCl4L2] (M=Mo, L=Et2S, Et2O; M=W; L= Et2S) in the presence of p-tBu-calix[4]arene (Cax(OH)4) and triethylamine leads to d0 complexes [(CaxO4)[CaxO2(OH)2]M] (1) and d3 compounds (HNEt3)2[(CaxO4)2M2] (2). Complexes la (M = Mo), 1b (M = W), and the HCl adduct of 2a (M = Mo) have been structurally characterized. Compound 1a represents one of the few examples of a well-characterized molybdenum(VI) hexa-alkoxide complex of the type [Mo(OR)6]. Isolation and structural characterization of the side product [(CaxO4W)[kappa2(O)-kappa1(O)-CaxO3(OH)](CaxO4WCl)] (3) suggests the intermediacy of chloro-containing calix[4]arene complexes in these reaction mixtures. The reaction of 1a with HCI provides [CaxO4MoCl2] (4a), the first well-defined example of a mixed molybdenum(VI) alkoxide halide compound of the general formula [MoClx(OR)6-x].

  2. Role of the 5' --> 3' exonuclease and Klenow fragment of Escherichia coli DNA polymerase I in base mismatch repair.

    PubMed

    Imai, Masaru; Tago, Yu-ichiro; Ihara, Makoto; Kawata, Masakado; Yamamoto, Kazuo

    2007-08-01

    We have previously demonstrated that the Escherichia coli strain mutS DeltapolA had a higher rate of transition and minus frameshift mutations than mutS or DeltapolA strains. We argued that DNA polymerase I (PolI) corrects transition mismatches. PolI, encoded by the polA gene, possesses Klenow and 5' --> 3' exonuclease domains. In the present study, rates of mutation were found to be higher in Klenow-defective mutS strains and 5' --> 3' exonuclease-defective mutS strains than mutS or polA strains. The Klenow-defective or 5' --> 3' exonuclease-defective mutS strains showed a marked increase in transition mutations. Sites of transition mutations in mutS, Klenow-defective mutS and 5' --> 3' exonuclease-defective mutS strains are different. Thus, it is suggested that, in addition to mutS function, both the Klenow and 5' --> 3' exonuclease domains are involved in the decrease of transition mutations. Transition hot and warm spots in mutS+ polA+ strains were found to differ from those in mutS and mutS DeltapolA strains. We thus argue that all the spontaneous transition mutations in the wild-type strain do not arise from transition mismatches left unrepaired by the MutS system or MutS PolI system.

  3. Microwave spectrum and molecular structure of PNO

    NASA Astrophysics Data System (ADS)

    Okabayashi, Toshiaki; Yamazaki, Emi; Tanimoto, Mitsutoshi

    1999-08-01

    The microwave spectra of P14N16O and its isotopomers P15N16O and P14N18O were observed in a dc glow discharge plasma of a mixture of nitric oxide and hydrogen gases over solid red phosphorus placed on the stainless steel electrode. Rotational transitions of the parent P14N16O species were measured in the ground state as well as in the vibrationally excited ν1 (PN str.), ν2 (bend), and 2ν2 states. The l=0 substate of the 2ν2 state interacts with the ν1 state through a Fermi resonance. The rotational constants determined for the ground states of the three isotopomers yield the substitution structure, rs(PN)=151.6516(87) pm and rs(NO)=119.5025(80) pm.

  4. Molecular structures and properties of starches of Australian wild rice.

    PubMed

    Tikapunya, Tiparat; Zou, Wei; Yu, Wenwen; Powell, Prudence O; Fox, Glen P; Furtado, Agnelo; Henry, Robert J; Gilbert, Robert G

    2017-09-15

    Australian wild rices have significant genetic differences from domesticated rices, which might provide rices with different starch molecular structure and thus different functional properties. Molecular structure, gelatinization properties, and pasting behaviours of starch of three Australian wild rices (Oryza australiensis, taxa A (O. rufipogon like) and taxa B (O. meridionalis like)) were determined and compared to domesticated indica and japonica rice. These had higher amylose content, more shorter amylose chains and fewer short amylopectin chains, resulted in a high gelatinization temperature in these wild rices. Compared to domesticated japonica rice, taxa A had a lower pasting viscosity; taxa B had a similar pasting viscosity but lower final viscosity. The significantly different starch molecular structure from that of normal domesticated rices, and concomitantly different properties, suggest advantageous uses in products such as rice crackers or rice pudding, and a source of nutritionally-desirable slowly digestible starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  6. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  7. Comprehensive Molecular Structure of the Eukaryotic Ribosome

    PubMed Central

    Taylor, Derek J.; Devkota, Batsal; Huang, Andrew D.; Topf, Maya; Narayanan, Eswar; Sali, Andrej; Harvey, Stephen C.; Frank, Joachim

    2009-01-01

    Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than bacterial ribosomes, which are implicated in extra-ribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial and novel interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2. PMID:20004163

  8. Molecular Evolution, Structure, and Function of Peroxidasins

    PubMed Central

    Soudi, Monika; Zamocky, Marcel; Jakopitsch, Christa; Furtmüller, Paul G; Obinger, Christian

    2012-01-01

    Peroxidasins represent the subfamily 2 of the peroxidase-cyclooxygenase superfamily and are closely related to chordata peroxidases (subfamily 1) and peroxinectins (subfamily 3). They are multidomain proteins containing a heme peroxidase domain with high homology to human lactoperoxidase that mediates one- and two-electron oxidation reactions. Additional domains of the secreted and glycosylated metalloproteins are type C-like immunoglobulin domains, typical leucine-rich repeats, as well as a von Willebrand factor C module. These are typical motifs of extracellular proteins that mediate protein–protein interactions. We have reconstructed the phylogeny of this new family of oxidoreductases and show the presence of four invertebrate clades as well as one vertebrate clade that includes also two different human representatives. The variability of domain assembly in the various clades was analyzed, as was the occurrence of relevant catalytic residues in the peroxidase domain based on the knowledge of catalysis of the mammalian homologues. Finally, the few reports on expression, localization, enzymatic activity, and physiological roles in the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens are critically reviewed. Roles attributed to peroxidasins include antimicrobial defense, extracellular matrix formation, and consolidation at various developmental stages. Many research questions need to be solved in future, including detailed biochemical/physical studies and elucidation of the three dimensional structure of a model peroxidasin as well as the relation and interplay of the domains and the in vivo functions in various organisms including man. PMID:22976969

  9. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    PubMed

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  10. Sensitive detection of DNA methyltransferase activity based on exonuclease-mediated target recycling.

    PubMed

    Xing, Xi-Wen; Tang, Feng; Wu, Jun; Chu, Jie-Mei; Feng, Yu-Qi; Zhou, Xiang; Yuan, Bi-Feng

    2014-11-18

    DNA methylation plays vital roles in various biological processes in both prokaryotes and eukaryotes. In bacteria, modification of adenine at N6 can protect bacterial DNA against cleavage by restriction enzymes, and bacterial DNA adenine methyltransferases are essential for bacterial virulence and viability. DNA adenine methyltransferase (DAM) targets the sequence of 5'-GATC-3' and can convert adenine into N(6)-methyladenine (m(6)A). Because mammals do not methylate DNA at adenine, bacterial DAM represents an excellent candidate for antibiotic development. Here, we developed an exonuclease III-aided target recycling strategy to sensitively assay activity of DAM. In this method, a hairpin probe labeled with a donor fluorophore (FAM) at the 5' end and a quencher (BHQ) close to the 3' end (FQ probe) was employed as reporter. Another hairpin substrate containing sequence of GATC was used as the methylation substrate of DAM. Once the hairpin substrate was methylated by DAM, it could be recognized and cleaved by Dpn I, which allows the release of a single-stranded oligodeoxynucleotide (ssODN). The ssODN can then hybridize to the 3' protruding terminus of FQ probe, which subsequently triggers the exonuclease III-mediated target recycling reaction and therefore can significantly improve the detection sensitivity of DAM. The exonuclease-mediated target recycling strategy is extremely sensitive and as low as 0.01 U/mL DAM can be distinctly determined. Using this developed method, we evaluated DAM activity in different growth stages of E. coli cells, and we also demonstrated that the assay has the potential to screen suitable inhibitor drugs for DAM for disease(s) treatment.

  11. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

    PubMed Central

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît

    2015-01-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  12. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  13. Structural properties of CHAPS micelles, studied by molecular dynamics simulations.

    PubMed

    Herrera, Fernando E; Garay, A Sergio; Rodrigues, Daniel E

    2014-04-10

    Detergents are essential tools to study biological membranes, and they are frequently used to solubilize lipids and integral membrane proteins. Particularly the nondenaturing zwitterionic detergent usually named CHAPS was designed for membrane biochemistry and integrates the characteristics of the sulfobetaine-type detergents and bile salts. Despite the available experimental data little is known about the molecular structure of its micelles. In this work, molecular dynamics simulations were performed to study the aggregation in micelles of several numbers of CHAPS (≤ 18) starting from a homogeneous water dilution. The force field parameters to describe the interactions of the molecule were developed and validated. After 50 ns of simulation almost all the systems result in the formation of stable micelles. The molecular shape (gyration radii, volume, surface) and the molecular structure (RDF, salt bridges, H-bonds, SAS) of the micelles were characterized. It was found that the main interactions that lead to the stability of the micelles are the electrostatic ones among the polar groups of the tails and the OH's from the ring moiety. Unlike micelles of other compounds, CHAPS show a grainlike heterogeneity with hydrophobic micropockets. The results are in complete agreement with the available experimental information from NMR, TEM, and SAXS studies, allowing the modeling of the molecular structure of CHAPS micelles. Finally, we hope that the new force field parameters for this detergent will be a significant contribution to the knowledge of such an interesting molecule.

  14. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  15. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  16. Determination of structure parameters in molecular tunnelling ionisation model

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Ping; Zhao, Song-Feng; Zhang, Cai-Rong; Li, Wei; Zhou, Xiao-Xin

    2014-04-01

    We extracted the accurate structure parameters in a molecular tunnelling ionisation model (the so-called MO-ADK model) for 23 selected linear molecules including some inner orbitals. The molecular wave functions with the correct asymptotic behaviour are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials numerically constructed using the modified Leeuwen-Baerends (LBα) model. We show that the orientation-dependent ionisation rate reflects the shape of the ionising orbitals in general. The influences of the Stark shifts of the energy levels on the orientation-dependent ionisation rates of the polar molecules are studied. We also examine the angle-dependent ionisation rates (or probabilities) based on the MO-ADK model by comparing with the molecular strong-field approximation calculations and with recent experimental measurements.

  17. ALMA Reveals Internal Structure of Molecular Clouds in the LMC

    NASA Astrophysics Data System (ADS)

    Sawada, T.; Hasegawa, T.; Koda, J.

    2015-12-01

    We carried out high-resolution (0.7 pc) CO J=1-0 mosaic observations of five giant molecular clouds, which cover a wide range of evolutionary stages based on their associations to recent star formation, in the Large Magellanic Cloud with ALMA. The observations revealed a variety of spatial structures of the gas, from faint and diffuse emission to bright and compact structures. The variation of structures, which is similar to that seen in the Milky Way, is quantified by the brightness distribution function (BDF) and brightness distribution index (BDI) established in our prior studies. The structured molecular gas may indicate the readiness for, rather than the outcome of, star formation.

  18. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  19. The Oligomeric Structure of High Molecular Weight Adiponectin

    PubMed Central

    Suzuki, Shinji; Wilson-Kubalek, Elizabeth M.; Wert, David; Tsao, Tsu-Shuen; Lee, David H.

    2007-01-01

    There is great interest in the structure of adiponectin as its oligomeric state may specify its biological activities. It occurs as a trimer, a hexamer and a high molecular weight complex. Epidemiological data indicates that the high molecular weight form is significant with low serum levels in type 2 diabetics but to date, has not been well-defined. To resolve this issue, characterization of this oligomer from bovine serum and 3T3-L1 adipocytes by sedimentation equilibrium centrifugation and gel electrophoresis respectively, was carried out, revealing that it is octadecameric. Further studies by dynamic light scattering and electron microscopy established that bovine and possibly mouse high molecular weight adiponectin is C1q-like in structure. PMID:17292892

  20. Molecular structure of DNA by scanning tunneling microscopy.

    PubMed

    Cricenti, A; Selci, S; Felici, A C; Generosi, R; Gori, E; Djaczenko, W; Chiarotti, G

    1989-09-15

    Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  1. Molecular Structure of DNA by Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Cricenti, A.; Selci, S.; Felici, A. C.; Generosi, R.; Gori, E.; Djaczenko, W.; Chiarotti, G.

    1989-09-01

    Uncoated DNA molecules marked with an activated tris(1-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 and 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.

  2. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1992-09-10

    Aird, S. D., and Kaiser, I. I. (1988) Physiological and immunological properties of small myotoxins from -Zhe venom of the midget faded rattlesnake ...AD-A258 669 AD RATTLESNAKE NEUROTOXIN STRUCTURE, MECHANISM OF ACTION, IMMUNOLOGY AND MOLECULAR BIOLOGY FINAL REPORT D TIC IVAN I. KAISER ELECTE S DEC...u m_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 6 2 7 8 7 A I 6 2 7 8 7 A 8 7 7 I A A [ ~A 3 1 7 8 2 1 (u) Rattlesnake neurotoxin structure

  3. Molecular structure and elastic properties of thermotropic liquid crystals: integrated molecular dynamics--statistical mechanical theory vs molecular field approach.

    PubMed

    Ilk Capar, M; Nar, A; Ferrarini, A; Frezza, E; Greco, C; Zakharov, A V; Vakulenko, A A

    2013-03-21

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  4. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    NASA Astrophysics Data System (ADS)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  5. Connecting molecular structure and exciton diffusion length in rubrene derivatives.

    PubMed

    Mullenbach, Tyler K; McGarry, Kathryn A; Luhman, Wade A; Douglas, Christopher J; Holmes, Russell J

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene.

  6. Crystal and molecular structure of lancerodiol–p–hydroxybenzoate

    PubMed Central

    Abd El–Razek, Mohamed H.; Hegazy, Mohamed–Elamir F.; Mohamed, Abou El–Hamd H.

    2010-01-01

    Lancerodiol–p–hydroxybenzoate was isolated from the leaves of Ferula sinaica L. (Apiaceae) as light needle crystals. This work reports for the first time the molecular structure and relative configuration of compound 1, established by X-ray analysis. PMID:21808543

  7. HoLaMa: A Klenow sub-fragment lacking the 3'-5' exonuclease domain.

    PubMed

    Martina, Cristina Elisa; Lapenta, Fabio; Montón Silva, Alejandro; Hochkoeppler, Alejandro

    2015-06-01

    The design, construction, overexpression, and purification of a Klenow sub-fragment lacking the 3'-5' exonuclease domain is presented here. In particular, a synthetic gene coding for the residues 515-928 of Escherichia coli DNA polymerase I was constructed. To improve the solubility and stability of the corresponding protein, the synthetic gene was designed to contain 11 site-specific substitutions. The gene was inserted into the pBADHis expression vector, generating 2 identical Klenow sub-fragments, bearing or not a hexahistidine tag. Both these Klenow sub-fragments, denominated HoLaMa and HoLaMaHis, were purified, and their catalytic properties were compared to those of Klenow enzyme. When DNA polymerase activity was assayed under processive conditions, the Klenow enzyme performed much better than HoLaMa and HoLaMaHis. However, when DNA polymerase activity was assayed under distributive conditions, the initial velocity of the reaction catalyzed by HoLaMa was comparable to that observed in the presence of Klenow enzyme. In particular, under distributive conditions HoLaMa was found to strongly prefer dsDNAs bearing a short template overhang, to the length of which the Klenow enzyme was relatively insensitive. Overall, our observations indicate that the exonuclease domain of the Klenow enzyme, besides its proofreading activity, does significantly contribute to the catalytic efficiency of DNA elongation. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.

    PubMed

    Serandour, Aurelien A; Brown, Gordon D; Cohen, Joshua D; Carroll, Jason S

    2013-12-27

    ChIP-exonuclease (ChIP-exo) is a modified ChIP-seq approach for high resolution mapping of transcription factor DNA sites. We describe an Illumina-based ChIP-exo method which provides a global improvement of the data quality of estrogen receptor (ER) ChIP and insights into the motif structure for key ER-associated factors. ChIP-exo of the ER pioneer factor FoxA1 identifies protected DNA with a predictable 8 bp overhang from the Forkhead motif, which we term mesas. We show that mesas occur in multiple cellular contexts and exist as single or overlapping motifs. Our Illumina-based ChIP-exo provides high resolution mapping of transcription factor binding sites.

  9. Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties

    PubMed Central

    2013-01-01

    ChIP-exonuclease (ChIP-exo) is a modified ChIP-seq approach for high resolution mapping of transcription factor DNA sites. We describe an Illumina-based ChIP-exo method which provides a global improvement of the data quality of estrogen receptor (ER) ChIP and insights into the motif structure for key ER-associated factors. ChIP-exo of the ER pioneer factor FoxA1 identifies protected DNA with a predictable 8 bp overhang from the Forkhead motif, which we term mesas. We show that mesas occur in multiple cellular contexts and exist as single or overlapping motifs. Our Illumina-based ChIP-exo provides high resolution mapping of transcription factor binding sites. PMID:24373287

  10. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    NASA Astrophysics Data System (ADS)

    Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  11. Molecular design for growth of supramolecular membranes with hierarchical structure.

    PubMed

    Zha, R Helen; Velichko, Yuri S; Bitton, Ronit; Stupp, Samuel I

    2016-02-07

    Membranes with hierarchical structure exist in biological systems, and bio-inspired building blocks have been used to grow synthetic analogues in the laboratory through self-assembly. The formation of these synthetic membranes is initiated at the interface of two aqueous solutions, one containing cationic peptide amphiphiles (PA) and the other containing the anionic biopolymer hyaluronic acid (HA). The membrane growth process starts within milliseconds of interface formation and continues over much longer timescales to generate robust membranes with supramolecular PA-HA nanofibers oriented orthogonal to the interface. Computer simulation indicates that formation of these hierarchically structured membranes requires strong interactions between molecular components at early time points in order to generate a diffusion barrier between both solutions. Experimental studies using structurally designed PAs confirm simulation results by showing that only PAs with high ζ potential are able to yield hierarchically structured membranes. Furthermore, the chemical structure of such PAs must incorporate residues that form β-sheets, which facilitates self-assembly of long nanofibers. In contrast, PAs that form low aspect ratio nanostructures interact weakly with HA and yield membranes that exhibit non-fibrous fingering protrusions. Furthermore, experimental results show that increasing HA molecular weight decreases the growth rate of orthogonal nanofibers. This result is supported by simulation results suggesting that the thickness of the interfacial contact layer generated immediately after initiation of self-assembly increases with polymer molecular weight.

  12. Molecular, Functional, and Structural Imaging of Major Depressive Disorder.

    PubMed

    Zhang, Kai; Zhu, Yunqi; Zhu, Yuankai; Wu, Shuang; Liu, Hao; Zhang, Wei; Xu, Caiyun; Zhang, Hong; Hayashi, Takuya; Tian, Mei

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD.

  13. Photoelectron Angular Distribution and Molecular Structure in Multiply Charged Anions

    SciTech Connect

    Xing, Xiaopeng; Wang, Xue B.; Wang, Lai S.

    2009-02-12

    Photoelectrons emitted from multiply charged anions (MCAs) carry information of the intramolecular Coulomb repulsion (ICR), which is dependent on molecular structures. Using photoelectron imaging, we observed the effects of ICR on photoelectron angular distributions (PAD) of the three isomers of benzene dicarboxylate dianions C6H4(CO2)22– (o-, m- and p-BDC2–). Photoelectrons were observed to peak along the laser polarization due to the ICR, but the anisotropy was the largest for p-BDC2–, followed by the m- and o-isomer. The observed anisotropy is related to the direction of the ICR or the detailed molecular structures, suggesting that photoelectron imaging may allow structural information to be obtained for complex multiply charged anions.

  14. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  15. Building bridges between cellular and molecular structural biology.

    PubMed

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  16. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  17. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  18. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    PubMed

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  19. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  20. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron

    PubMed Central

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons. PMID:27570482

  1. Three-dimensional depth profiling of molecular structures.

    PubMed

    Wucher, A; Cheng, J; Zheng, L; Winograd, N

    2009-04-01

    Molecular time of flight secondary ion mass spectrometry (ToF-SIMS) imaging and cluster ion beam erosion are combined to perform a three-dimensional chemical analysis of molecular films. The resulting dataset allows a number of artifacts inherent in sputter depth profiling to be assessed. These artifacts arise from lateral inhomogeneities of either the erosion rate or the sample itself. Using a test structure based on a trehalose film deposited on Si, we demonstrate that the "local" depth resolution may approach values which are close to the physical limit introduced by the information depth of the (static) ToF-SIMS method itself.

  2. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  3. Molecular structures in the charmonium spectrum: the XYZ puzzle

    NASA Astrophysics Data System (ADS)

    Ortega, P. G.; Entem, D. R.; Fernández, F.

    2013-06-01

    We study in the framework of a constituent quark model the possible contributions of molecular structures to the XYZ charmonium-like states. We analyze simultaneously the c\\bar{c} structures and the possible molecular components in the coupled channel formalism. In the 1++ sector two states appear which could be identified with X(3872) and X(3940). The recently confirmed X(3915) state appears as a mixture of c\\bar{c} and D\\bar{D} components as a JPC = 0++ state in agreement with the new measurements. A second broad resonance which may correspond with the so-called Y(3940) state is found with these quantum numbers. In the JPC = 1-- sector we also found significant contributions of the molecular structures which may affect the phenomenology. In particular the study allows us to understand the G(3900) state recently observed in Belle and BaBar. All these resonances together with the prediction of the model of a c\\bar{c} structure for Z(3930) provide a reasonable scenario for the so-called XYZ states with masses near 3.9 GeV.

  4. Molecular structure in soil humic substances: The new view

    SciTech Connect

    Sutton, Rebecca; Sposito, Garrison

    2005-04-21

    A critical examination of published data obtained primarily from recent nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies reveals an evolving new view of the molecular structure of soil humic substances. According to the new view, humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules intimately associated with a humic substance, such that they cannot be separated effectively by chemical or physical methods. Thus biomolecules strongly bound within humic fractions are by definition humic components, a conclusion that necessarily calls into question key biogeochemical pathways traditionally thought to be required for the formation of humic substances. Further research is needed to elucidate the intermolecular interactions that link humic components into supramolecular associations and to establish the pathways by which these associations emerge from the degradation of organic litter.

  5. Enhanced Molecular Mobility of Ordinarily Structured Regions Drives Polyglutamine Disease*

    PubMed Central

    Lupton, Christopher J.; Steer, David L.; Wintrode, Patrick L.; Bottomley, Stephen P.; Hughes, Victoria A.; Ellisdon, Andrew M.

    2015-01-01

    Polyglutamine expansion is a hallmark of nine neurodegenerative diseases, with protein aggregation intrinsically linked to disease progression. Although polyglutamine expansion accelerates protein aggregation, the misfolding process is frequently instigated by flanking domains. For example, polyglutamine expansion in ataxin-3 allosterically triggers the aggregation of the catalytic Josephin domain. The molecular mechanism that underpins this allosteric aggregation trigger remains to be determined. Here, we establish that polyglutamine expansion increases the molecular mobility of two juxtaposed helices critical to ataxin-3 deubiquitinase activity. Within one of these helices, we identified a highly amyloidogenic sequence motif that instigates aggregation and forms the core of the growing fibril. Critically, by mutating residues within this key region, we decrease local structural fluctuations to slow ataxin-3 aggregation. This provides significant insight, down to the molecular level, into how polyglutamine expansion drives aggregation and explains the positive correlation between polyglutamine tract length, protein aggregation, and disease severity. PMID:26260925

  6. Study of the structuring of pure molecular liquids

    NASA Astrophysics Data System (ADS)

    Letamendia, L.; Duplessix, R.; Nouchi, G.; Vaucamps, C.

    Recent experiments have shown that changes in the slope of specific heat variation as a function of temperature in liquids are not always regular. In this study, the authors consider the possibility that fluid structure can change with temperature, by shifting from one form to another. They study such molecular liquids as benzene, hexafluorobenzene, and quinoleine using Rayleigh-Brillouin and depolarized Rayleigh diffusion, and total intensity diffusion. The authors clearly found anomalies for all collective properties of the medium in the liquids studied, though purely molecular properties were undisturbed. The accidents observed occurred at the same temperatures, whatever the collective or intermolecular property under study. But it took some time (several hours) for them to manifest themselves, which suggests that molecular liquids are characterized by a long thermodynamic equilibrium. Results also show a disturbance in hydrodynamic state at accident temperatures, which are similar to those generated by long spatial correlation processes.

  7. Molecular docking and structure-based drug design strategies.

    PubMed

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  8. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  9. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  10. Structural and Molecular Modeling Features of P2X Receptors

    PubMed Central

    Alves, Luiz Anastacio; da Silva, João Herminio Martins; Ferreira, Dinarte Neto Moreira; Fidalgo-Neto, Antonio Augusto; Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; Caffarena, Ernesto Raúl; de Freitas, Mônica Santos

    2014-01-01

    Currently, adenosine 5′-triphosphate (ATP) is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors. PMID:24637936

  11. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  12. Nucleotide sequence of polypyrimidines from cloned mouse DNA as determined by base-specific blockage of exonuclease action

    SciTech Connect

    Deugau, K.V.; Mitchel, R.E.J.; Birnboim, H.C.

    1983-01-01

    Cloned fragments of mouse DNA have been screened for the presence of long polypyrimidine/polypurine segments. The polypyrimidine portion of one such segment (about 2000 nucleotides in length) has been isolated by acidic depurination of the entire cloned fragment and plasmid vector followed by selective precipitation and 5'-/sup 32/P labeling. This polypyrimidine has been used to demonstrate a new procedure for sequencing. Covalent modification of thymine with a water-soluble carbodiimide, or cytosine with glutaric anhydride, at low levels blocked in the action of snake venom exonuclease. After deblocking, separation of the products of digestion by polyacrylamide gel electrophoresis yields a sequence ladder which can be used to determine the position of C and T residues as in other sequencing methods. A sequence of 72 residues adjacent to the 5' end had been established, consisting principally of the repeating tetranucleotide (CCTT)n. A low ratio of endonuclease to exonuclease is essential for application of this method to sequences of this size. Accordingly, a very sensitive modification of a fluorometric endonuclease assay was developed and used to optimize pH and Mg/sup 2 +/ conditions to favor exonuclease activity over the accompanying endonuclease activity. The results clearly indicate that long polypyrimidine tracts can be efficiently prepared and their sequences determined with this method using commercially available exonuclease preparations without additional purification. 26 references, 5 figures.

  13. Structures of polycyclic aromatic hydrocarbon adducts by molecular mechanics and molecular dynamics simulations

    SciTech Connect

    Singh, S.B.

    1992-01-01

    The structures of the adducts of (+)- and (-)trans-7,8,dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo (a)pyrene (anti-BPDE) formed by trans addition to N[sup 2] of guanine have been of great interest because the high biological activity of BPDE in mammalian mutagenesis and tumorigenesis has been attributed to the predominant (+)-adduct, while the (-)-adduct is inactive. Molecular mechanics and dynamics calculations have been employed to elucidate the structural difference between this mirror image adduct pair in a duplex dodecamer, d(5' GCGCGCG-(BPDE)CGCGC3') [center dot] d(5'GCGCGCGCGCGC3'). Minimized potential energy calculations using the program DUPLEX were employed to locate starting structures for the dynamics. Three types of structures were found in the energy minimized conformation space searches for each enantiomer: pyrenyl moiety in the minor groove of a Watson-Crick base paired B-DNA duplex, pyrenyl moiety in the major groove of a B-DNA duplex with syn guanine and Hoogsteen base pairs at the modification site, and intercalation type structures. The minor groove structure is energetically preferred for the (+) enantiomer while both minor groove and major groove structures are favored and of comparable energy in the (-) enantiomer. These energy-minimized duplex dodecamers, as well as an unmodified B-DNA control of the same sequence, were subjected to 100 ps molecular dynamics simulations with solvent and salt with the program AMBER. The duplex dodecamer, d(CGCGAATTCGCG)[sub 2], was subjected to a similar simulation using the crystal structure as starting coordinates. Detailed analysis of the dynamic evolution of the conformational and the helical parameters of all the dodecamer simulations were carried out with Molecular Dynamics Analysis Toolchest.

  14. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ: Novel Mechanisms of Function and Pathogenesis.

    PubMed

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz; Vattulainen, Ilpo; Suomalainen, Anu; Sharma, Vivek

    2017-03-07

    DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform in the "intrinsic processivity" subdomain of the enzyme. Our data indicate that noncatalytic mutations may disrupt replisomal interactions, thereby causing Pol γ-associated neurodegenerative disorders.

  15. Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

    PubMed Central

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand the structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the multiple minima or conformational sampling problems—and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These are discussed in detail in this unit. PMID:18428877

  16. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    PubMed

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  17. Exonuclease VII is involved in "reckless" DNA degradation in UV-irradiated Escherichia coli.

    PubMed

    Repar, Jelena; Briški, Nina; Buljubašić, Maja; Zahradka, Ksenija; Zahradka, Davor

    2013-01-20

    The recA mutants of Escherichia coli exhibit an abnormal DNA degradation that starts at sites of double-strand DNA breaks (DSBs), and is mediated by RecBCD exonuclease (ExoV). This "reckless" DNA degradation occurs spontaneously in exponentially growing recA cells, and is stimulated by DNA-damaging agents. We have previously found that the xonA and sbcD mutations, which inactivate exonuclease I (ExoI) and SbcCD nuclease, respectively, markedly suppress "reckless" DNA degradation in UV-irradiated recA cells. In the present work, we show that inactivation of exonuclease VII (ExoVII) by an xseA mutation contributes to attenuation of DNA degradation in UV-irradiated recA mutants. The xseA mutation itself has only a weak effect, however, it acts synergistically with the xonA or sbcD mutations in suppressing "reckless" DNA degradation. The quadruple xseA xonA sbcD recA mutants show no sign of DNA degradation during post-irradiation incubation, suggesting that ExoVII, together with ExoI and SbcCD, plays a crucial role in regulating RecBCD-catalyzed chromosome degradation. We propose that these nucleases act on DSBs to create blunt DNA ends, the preferred substrates for the RecBCD enzyme. In addition, our results show that in UV-irradiated recF recA(+) cells, the xseA, xonA, and sbcD mutations do not affect RecBCD-mediated DNA repair, suggesting that ExoVII, ExoI and SbcCD nucleases are not essential for the initial targeting of RecBCD to DSBs. It is possible that the DNA-blunting activity provided by ExoVII, ExoI and SbcCD is required for an exchange of RecBCD molecules on dsDNA ends during ongoing "reckless" DNA degradation.

  18. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.

  19. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance.

  20. Toxicological implications of esterases-From molecular structures to functions

    SciTech Connect

    Satoh, Tetsuo . E-mail: satohbri@peach.ifnet.or.jp

    2005-09-01

    This article reports on a keynote lecture at the 10th International Congress of Toxicology sponsored by the International Union of Toxicology and held on July 2004. Current developments in molecular-based studies into the structure and function of cholinesterases, carboxylesterases, and paraoxonases are described. This article covers mechanisms of regulation of gene expression of the various esterases by developmental factors and xenobiotics, as well as the interplay between physiological and chemical regulation of the enzyme activity.

  1. Rattlesnake Neurotoxin Structure, Mechanism of Action, Immunology and Molecular Biology

    DTIC Science & Technology

    1990-09-01

    from the venom of the midget faded . rattlesnake (Crotalus viridis concolor . Toxicon 2&, 319- 323. Rehm, H. and Betz, H. (1982) Binding of B...8217determined. It was shown to have great similarity to the basic subunits of related toxins from the venoms of the South American and midget faded ...AD-A228 003 CONTRACT NO.: DAMD17-89-C-9007 TITLE: RATTLESNAKE NEUROTOXIN STRUCTURE, MECHANISM OF ACTION, IMMUNOLOGY AND MOLECULAR BIOLOGY PRINCIPAL

  2. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems.

  3. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  4. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  5. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  6. Functional cooperation between exonucleases and endonucleases—basis for the evolution of restriction enzymes

    PubMed Central

    Raghavendra, Nidhanapathi K.; Rao, Desirazu N.

    2003-01-01

    Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25–27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed. PMID:12655005

  7. New spectrophotometric method for continuous recording of the spleen exonuclease activity.

    PubMed

    Dolapchiev, L B; Bakalova, A T

    1988-11-01

    Some of the synthetic chromophoric substrates of various enzymes cannot be used for direct spectrophotometric recording of the reactions, when a difference between the pH optimum of the enzyme reaction and the pH of maximum absorption of the released chromophore exists. In the present paper we describe a new method for following the time course of the spleen exonuclease-catalyzed reaction with thymidine 3'-monophospho-p-nitrophenyl ester as a substrate, based on the difference obtained in the absorbency of the substrate and its products in the far UV (at 330 nm). This difference, not published before, permits direct spectrophotometric recording of the amount of the hydrolyzed chromophoric substrate in acidic pH, whereas the maximum absorption of the product as accepted in the literature, is in alkaline pH. The molar absorption coefficient of the measurement at pH 5.7 is determined to be epsilon = 522 M-1.mm-1.

  8. Molecular structures of amyloid and prion fibrils: consensus versus controversy.

    PubMed

    Tycko, Robert; Wickner, Reed B

    2013-07-16

    Many peptides and proteins self-assemble into amyloid fibrils. Examples include mammalian and fungal prion proteins, polypeptides associated with human amyloid diseases, and proteins that may have biologically functional amyloid states. To understand the propensity for polypeptides to form amyloid fibrils and to facilitate rational design of amyloid inhibitors and imaging agents, it is necessary to elucidate the molecular structures of these fibrils. Although fibril structures were largely mysterious 15 years ago, a considerable body of reliable structural information about amyloid fibril structures now exists, with essential contributions from solid state nuclear magnetic resonance (NMR) measurements. This Account reviews results from our laboratories and discusses several structural issues that have been controversial. In many cases, the amino acid sequences of amyloid fibrils do not uniquely determine their molecular structures. Self-propagating, molecular-level polymorphism complicates the structure determination problem and can lead to apparent disagreements between results from different laboratories, particularly when different laboratories study different polymorphs. For 40-residue β-amyloid (Aβ₁₋₄₀) fibrils associated with Alzheimer's disease, we have developed detailed structural models from solid state NMR and electron microscopy data for two polymorphs. These polymorphs have similar peptide conformations, identical in-register parallel β-sheet organizations, but different overall symmetry. Other polymorphs have also been partially characterized by solid state NMR and appear to have similar structures. In contrast, cryo-electron microscopy studies that use significantly different fibril growth conditions have identified structures that appear (at low resolution) to be different from those examined by solid state NMR. Based on solid state NMR and electron paramagnetic resonance (EPR) measurements, the in-register parallel β-sheet organization

  9. Local structure in anisotropic systems determined by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Komolkin, Andrei V.; Maliniak, Arnold

    In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4'-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, gm2(z1 2, d1 2) and g12(Z1 2, D1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the motional amplitude in the chain. Absence of long range order was confirmed, a feature typical for a nematic liquid crystal.

  10. Structural characterization of polymorphs and molecular complexes of finasteride

    NASA Astrophysics Data System (ADS)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

    1999-01-01

    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  11. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  12. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  13. Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, ε, θ and β reveals a highly flexible arrangement of the proofreading domain

    PubMed Central

    Ozawa, Kiyoshi; Horan, Nicholas P.; Robinson, Andrew; Yagi, Hiromasa; Hill, Flynn R.; Jergic, Slobodan; Xu, Zhi-Qiang; Loscha, Karin V.; Li, Nan; Tehei, Moeava; Oakley, Aaron J.; Otting, Gottfried; Huber, Thomas; Dixon, Nicholas E.

    2013-01-01

    A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data. PMID:23580545

  14. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  15. Discovering structural alerts for mutagenicity using stable emerging molecular patterns.

    PubMed

    Métivier, Jean-Philippe; Lepailleur, Alban; Buzmakov, Aleksey; Poezevara, Guillaume; Crémilleux, Bruno; Kuznetsov, Sergei O; Le Goff, Jérémie; Napoli, Amedeo; Bureau, Ronan; Cuissart, Bertrand

    2015-05-26

    This study is dedicated to the introduction of a novel method that automatically extracts potential structural alerts from a data set of molecules. These triggering structures can be further used for knowledge discovery and classification purposes. Computation of the structural alerts results from an implementation of a sophisticated workflow that integrates a graph mining tool guided by growth rate and stability. The growth rate is a well-established measurement of contrast between classes. Moreover, the extracted patterns correspond to formal concepts; the most robust patterns, named the stable emerging patterns (SEPs), can then be identified thanks to their stability, a new notion originating from the domain of formal concept analysis. All of these elements are explained in the paper from the point of view of computation. The method was applied to a molecular data set on mutagenicity. The experimental results demonstrate its efficiency: it automatically outputs a manageable number of structural patterns that are strongly related to mutagenicity. Moreover, a part of the resulting structures corresponds to already known structural alerts. Finally, an in-depth chemical analysis relying on these structures demonstrates how the method can initiate promising processes of chemical knowledge discovery.

  16. Biological spectra analysis: Linking biological activity profiles to molecular structure

    PubMed Central

    Fliri, Anton F.; Loging, William T.; Thadeio, Peter F.; Volkmann, Robert A.

    2005-01-01

    Establishing quantitative relationships between molecular structure and broad biological effects has been a longstanding challenge in science. Currently, no method exists for forecasting broad biological activity profiles of medicinal agents even within narrow boundaries of structurally similar molecules. Starting from the premise that biological activity results from the capacity of small organic molecules to modulate the activity of the proteome, we set out to investigate whether descriptor sets could be developed for measuring and quantifying this molecular property. Using a 1,567-compound database, we show that percent inhibition values, determined at single high drug concentration in a battery of in vitro assays representing a cross section of the proteome, provide precise molecular property descriptors that identify the structure of molecules. When broad biological activity of molecules is represented in spectra form, organic molecules can be sorted by quantifying differences between biological spectra. Unlike traditional structure–activity relationship methods, sorting of molecules by using biospectra comparisons does not require knowledge of a molecule's putative drug targets. To illustrate this finding, we selected as starting point the biological activity spectra of clotrimazole and tioconazole because their putative target, lanosterol demethylase (CYP51), was not included in the bioassay array. Spectra similarity obtained through profile similarity measurements and hierarchical clustering provided an unbiased means for establishing quantitative relationships between chemical structures and biological activity spectra. This methodology, which we have termed biological spectra analysis, provides the capability not only of sorting molecules on the basis of biospectra similarity but also of predicting simultaneous interactions of new molecules with multiple proteins. PMID:15625110

  17. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  18. State of water, molecular structure, and cytotoxicity of silk hydrogels.

    PubMed

    Numata, Keiji; Katashima, Takuya; Sakai, Takamasa

    2011-06-13

    A novel technique was developed to regulate the bulk water content of silk hydrogels by adjusting the concentrations of silk proteins, which is helpful to investigate the effects of the state of water in polymeric hydrogel on its biological functions, such as cytotoxicity. Gelation of the silk hydrogel was induced with ethanol and its gelation behavior was analyzed by rheometry. The silk hydrogels prepared at various silk concentrations were characterized with respect to their water content, molecular and network structures, state of water, mechanical properties, and cytotoxicity to human mesenchymal stem cells. The network structure of silk hydrogel was heterogeneous with β-sheet and fibrillar structures. The influence of the state of water in the silk hydrogel on the cytotoxicity was recognized by means of differential scanning calorimetry and cell proliferation assay, which revealed that the bound water will support cell-adhesion proteins in the cellular matrix to interact with the surface of the silk hydrogels.

  19. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

  20. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  1. On calculating the equilibrium structure of molecular crystals

    NASA Astrophysics Data System (ADS)

    Mattsson, Ann E.; Wixom, Ryan R.; Mattsson, Thomas R.

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  2. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  3. Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'–5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch

    PubMed Central

    Zhang, Dapeng; Xiong, Huiling; Shan, Jufang; Xia, Xuhua; Trudeau, Vance L

    2008-01-01

    Abstract Maelstrom (MAEL) plays a crucial role in a recently-discovered piRNA pathway; however its specific function remains unknown. Here a novel MAEL-specific domain characterized by a set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC) was identified in a broad range of species including vertebrates, sea squirts, insects, nematodes, and protists. It exhibits ancient lineage-specific expansions in several species, however, appears to be lost in all examined teleost fish species. Functional involvement of MAEL domains in DNA- and RNA-related processes was further revealed by its association with HMG, SR-25-like and HDAC_interact domains. A distant similarity to the DnaQ-H 3'–5' exonuclease family with the RNase H fold was discovered based on the evidence that all MAEL domains adopt the canonical RNase H fold; and several protist MAEL domains contain the conserved 3'–5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). This evolutionary link together with structural examinations leads to a hypothesis that MAEL domains may have a potential nuclease activity or RNA-binding ability that may be implicated in piRNA biogenesis. The observed transition of two sets of characteristic residues between the ancestral DnaQ-H and the descendent MAEL domains may suggest a new mode for protein function evolution called "active site switch", in which the protist MAEL homologues are the likely evolutionary intermediates due to harboring the specific characteristics of both 3'–5' exonuclease and MAEL domains. Reviewers This article was reviewed by L Aravind, Wing-Cheong Wong and Frank Eisenhaber. For the full reviews, please go to the Reviewers' Comments section. PMID:19032786

  4. Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch.

    PubMed

    Zhang, Dapeng; Xiong, Huiling; Shan, Jufang; Xia, Xuhua; Trudeau, Vance L

    2008-11-25

    Maelstrom (MAEL) plays a crucial role in a recently-discovered piRNA pathway; however its specific function remains unknown. Here a novel MAEL-specific domain characterized by a set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC) was identified in a broad range of species including vertebrates, sea squirts, insects, nematodes, and protists. It exhibits ancient lineage-specific expansions in several species, however, appears to be lost in all examined teleost fish species. Functional involvement of MAEL domains in DNA- and RNA-related processes was further revealed by its association with HMG, SR-25-like and HDAC_interact domains. A distant similarity to the DnaQ-H 3'-5' exonuclease family with the RNase H fold was discovered based on the evidence that all MAEL domains adopt the canonical RNase H fold; and several protist MAEL domains contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). This evolutionary link together with structural examinations leads to a hypothesis that MAEL domains may have a potential nuclease activity or RNA-binding ability that may be implicated in piRNA biogenesis. The observed transition of two sets of characteristic residues between the ancestral DnaQ-H and the descendent MAEL domains may suggest a new mode for protein function evolution called "active site switch", in which the protist MAEL homologues are the likely evolutionary intermediates due to harboring the specific characteristics of both 3'-5' exonuclease and MAEL domains.

  5. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  6. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

    NASA Astrophysics Data System (ADS)

    Myasnikov, Alexander G.; Afonina, Zhanna A.; Ménétret, Jean-François; Shirokov, Vladimir A.; Spirin, Alexander S.; Klaholz, Bruno P.

    2014-11-01

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  7. Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

    2002-02-01

    Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

  8. Label-free and ultrasensitive electrochemical detection of nucleic acids based on autocatalytic and exonuclease III-assisted target recycling strategy.

    PubMed

    Liu, Shufeng; Wang, Chunfeng; Zhang, Chengxin; Wang, Ying; Tang, Bo

    2013-02-19

    In this work, a very simple, label-free, isothermal, and ultrasensitive electrochemical DNA biosensor has been developed on the basis of an autocatalytic and exonuclease III (Exo III)-assisted target recycling amplification strategy. A duplex DNA probe constructed by the hybridization of a quadruplex-forming oligomer with a molecular beacon is ingeniously designed and assembled on the electrode as recognition element. Upon sensing of the analyte nucleic acid, the strand of molecular beacon in the duplex DNA probe could be stepwise removed by Exo III accompanied by the releasing of target DNA and autonomous generation of new secondary target DNA fragment for the successive hybridization and cleavage process. Simultaneously, numerous quadruplex-forming oligomers are liberated and folded into G-quadruplex-hemin complexes with the help of K(+) and hemin on the electrode surface to give a remarkable electrochemical response. Because of this autocatalytic target recycling amplification and the specifically catalyzed formation of G-quadruplex-hemin complexes, this newly designed protocol provides an ultrasensitive electrochemical detection of DNA down to the 10 fM level, can discriminate mismatched DNA from perfectly matched target DNA, and holds a great potential for early diagnosis in gene-related diseases. It further could be developed as a universal protocol for the detection of various DNA sequences and may be extended for the detection of aptamer-binding molecules.

  9. Insights into molecular structure and digestion rate of oat starch.

    PubMed

    Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

    2017-04-01

    The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Structure-based molecular modeling approaches to GPCR oligomerization.

    PubMed

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  11. Molecular Conductance: Effects of Contact Atomic Structure and Anchoring Group

    NASA Astrophysics Data System (ADS)

    Ke, S.-H.; Baranger, H. U.; Yang, Weitao

    2004-03-01

    The nature of the molecule-lead contact is of crucial importance in molecular transport. As an example, we study the molecular conductance of benzene connected to two Au leads through three different anchoring groups (S, Se, and Te). Our calculations proceed from first-principles by using a density functional theory calculation for the electronic structure and a Green function method for the electron transport. We analyze systematically the effects of contact atomic relaxation, lead orientation, absorption site, chemical trends in the anchoring group, and atomic structure around the contact. Different lead orientations, absorption sites, and anchoring groups can cause a change of several times in conductance. Most significantly, adding an additional Au atom at each contact can increase the conductance by two orders of magnitude because of a LUMO-like resonance peak around the Fermi energy. This also leads to a large negative differential conductance. Finally, the equilibrium conductance decreases with increasing atomic number of the anchoring group. This is opposite to the conclusion of previous work using the jellium model for the leads in which the contact atomic structure cannot be taken into account. Supported in part by the NSF (DMR-0103003).

  12. Optical investigation of molecular structure of sophisticated materials for photonics

    NASA Astrophysics Data System (ADS)

    Gnyba, Marcin; Keraenen, Mikko

    2003-10-01

    Permanent development of photonics stimulates a searching for new materials, which have better optical, mechanical and electrical properties. One of the new classes of materials with large application and development potential are hybrid polymers, synthesized in sol-gel technology. Thanks to incorporation of organic components into an in organic network, a combination of advantages of both class of materials became available. Properties of hybrids may be formed in wide range. These materials can be used in photonics to produce planar waveguides, lenses, Bragg gratings and components for integrated optics. Moreover, dielectric layers, coatings and packaging are made from hybrids. Additionally, research to apply them in optical fiber sensors (including bio-sensors) and solid state lasers is underway. However, to obtain a high quality product, a strict control of its molecular structure must be ensured. This is a very difficult task, because of a sophisticated structure of hybrid polymers. To address these problems, optical, non-destructive measurement techniques such as Raman and infrared spectroscopy were used. They are compementary methods, so their simultaneous application, as it was shown in this paper, can significantly increase the amoung of information about molecular structure of materials and process of their synthesis.

  13. Kinetic Effects of Aromatic Molecular Structures on Diffusion Flame Extinction

    SciTech Connect

    Won, Sang Hee; Dooley, S.; Dryer, F. L.; Ju, Yiguang

    2011-01-01

    Kinetic effects of aromatic molecular structures for jet fuel surrogates on the extinction of diffusion flames have been investigated experimentally and numerically in the counterflow configuration for toluene, n-propylbenzene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. Quantitative measurement of OH concentration for aromatic fuels was conducted by directly measuring the quenching rate from the emission lifetimes of OH planar laser induced fluorescence (LIF). The kinetic models for toluene and 1,2,4-trimethylbenzene were validated against the measurements of extinction strain rates and LIF measurements. A semi-detailed n-propylbenzene kinetic model was developed and tested. The experimental results showed that the extinction limits are ranked from highest to lowest as n-propylbenzene, toluene, 1,2,4-trimethylbenzene, and 1,3,5-trimethylbenzene. The present models for toluene and n-propylbenzene agree reasonably well with the measurements, whereas the model for 1,2,4-trimethylbenzene under-estimates extinction limits. Kinetic pathways of OH production and consumption were analyzed to investigate the impact of fuel fragmentation on OH formation. It was found that, for fuels with different molecular structures, the fuel decomposition pathways and their propagation into the formation of radical pool play an important role to determine the extinction limits of diffusion flames. Furthermore, OH concentrations were found to be representative of the entire radical pool concentration, the balance between chain branching and propagation/termination reactions and the balance between heat production from the reaction zone and heat losses to the fuel and oxidizer sides. Finally, a proposed “OH index,” was defined to demonstrate a linear correlation between extinction strain rate and OH index and fuel mole fraction, suggesting that the diffusion flame extinctions for the tested aromatic fuels can be determined by the capability of a fuel to establish a radical pool

  14. Relationship between antimold activity and molecular structure of cinnamaldehyde analogues.

    PubMed

    Zhang, Yuanyuan; Li, Shujun; Kong, Xianchao

    2013-03-01

    A quantitative structure-activity relationship (QSAR) modeling of the antimold activity of cinnamaldehyde analogues against of Aspergillus niger and Paecilomyces variotii was presented. The molecular descriptors of cinnamaldehyde analogues were calculated by the CODESSA program, and these descriptors were selected by best multi-linear regression method (BMLR). Satisfactory multilinear regression models of Aspergillus niger and Paecilomyces variotii were obtained with R(2)=0.9099 and 0.9444, respectively. The models were also satisfactorily validated using internal validation and leave one out validation. The QSAR models provide the guidance for further synthetic work. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  16. Structural Organization of {pi} Conjugated Highly Luminescent Molecular Material

    SciTech Connect

    Toudic, B.; Limelette, P.; Le Gac, F.; Moreac, A.; Rabiller, P.; Froyer, G.

    2005-11-18

    We report on striking evidence for a room temperature structural phase instability in p-hexaphenyl, inducing a nonplanar conformation of the molecules. Solid state proton NMR and single crystal x-ray diffraction allow the analysis of the organization, the individual dynamics and the involved symmetry breaking. The analysis of Raman spectra above and below room temperature reveals a singular behavior suggesting a modification of the overlap between the electronic wave function induced by the nonplanarity. These results provide a new basis to answer fundamental issues related to molecular and electronic materials and, in particular, luminescent organic devices.

  17. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  18. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  19. Vibrational spectroscopic studies of 3-hydroxyphenylboronic acid: molecular structure

    NASA Astrophysics Data System (ADS)

    Sert, Y.; Ucun, F.; Böyükata, M.

    2013-02-01

    In this work, optimized molecular structure, vibrational frequencies and corresponding vibrational assignments, HOMO-LUMO energy values and electron density clouds of 3-hydroxyphenylboronic acid have been calculated by ab initio Hatree-Fock (HF) and density functional theory methods. The compound has eight conformers depending on the directions of hydrogen atoms bonded to oxygen. The computational results have diagnosed the most stable conformer of the compound as cis-trans (ctt) form. The calculated frequencies and optimized geometry parameters (bond lengths and bond angles) for the most stable conformer are in a good agreement with the corresponding experimental data.

  20. Molecular and electronic structures of cerium and cerium suboxide clusters

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Topolski, Josey E.; Jarrold, Caroline Chick

    2016-10-01

    The anion photoelectron (PE) spectra of Ce2Oy- (y = 1, 2), Ce3Oy- (y = 0-4), Ce4Oy- (y = 0-2), and Ce5Oy- (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation. A qualitative picture of how electronic structure evolves with an oxidation state emerges from comparison between the spectra and the computational results. The electronic structure of the smallest metallic cluster observed in this study, Ce3, is similar to the bulk structure in terms of atomic orbital occupancy (4f 5d2 6s). Initial cerium cluster oxidation involves largely ionic bond formation via Ce 5d and O 2p orbital overlap (i.e., larger O 2p contribution), with Ce—O—Ce bridge bonding favored over Ce=O terminal bond formation. With subsequent oxidation, the Ce 5d-based molecular orbitals are depleted of electrons, with the highest occupied orbitals described as diffuse Ce 6s based molecular orbitals. In the y ≤ (x + 1) range of oxidation states, each Ce center has a singly occupied non-bonding 4f orbital. The PE spectrum of Ce3O4- is unique in that it exhibits a single nearly vertical transition. The highly symmetric structure predicted computationally is the same structure determined from Ce3O4+ IR predissociation spectra [A. M. Burow et al., Phys. Chem. Chem. Phys. 13, 19393 (2011)], indicating that this structure is stable in -1, 0, and +1 charge states. Spectra of clusters with x ≥ 3 exhibit considerable continuum signal above the ground state transition; the intensity of the continuum signal decreases with increasing oxidation. This feature is likely the result of numerous quasi-bound anion states or two

  1. Molecular Simulations of Hydrated Proton Exchange Membranes: the Structure

    NASA Astrophysics Data System (ADS)

    Marchand, Gabriel; Bopp, Philippe A.; Spohr, Eckhard

    2013-02-01

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion® (Dupont) and Hyflon® (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms.

  2. Molecular structure of uranium carbides: isomers of UC3.

    PubMed

    Zalazar, M Fernanda; Rayón, Víctor M; Largo, Antonio

    2013-03-21

    In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104-125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.

  3. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  4. Noninvasive structural, functional, and molecular imaging in drug development.

    PubMed

    Rudin, Markus

    2009-06-01

    Modern drug research is mechanism-based and the development of disease modifying therapies involves the identification of molecular key players in the pathological cascade. Today, noninvasive imaging tools enable the visualization and quantitative assessment of the expression of molecular targets, of their interaction with potential ligands, as well as of the functional consequence of this interaction at a molecular (e.g. activation of signaling cascades), cellular, metabolic, physiological, and morphological level in a temporo-spatially resolved manner. The ability to gather such information from the intact organism with all regulatory processes in place renders imaging highly attractive for the biomedical researcher and for the drug developer in particular. Molecular imaging is potentially capable of providing this information. Today, proof-of-principle has been established that imaging is in fact adding value to the drug discovery and development processes. Numerous studies have used structural and functional imaging readouts to document therapy efficacy, mainly during lead optimization. Similarly, major efforts have been devoted to the development and evaluation of imaging biomarkers that might serve as early readouts for therapy response with the potential of being used in the clinical drug evaluation thereby facilitating translational research. In this contribution, we illustrate the role and potential of imaging in modern drug discovery and development with selected examples. Yet, despite its huge potential the impact of imaging on drug discovery has been modest in the past; potential reasons will be discussed. Nevertheless, noninvasive imaging methods are rapidly evolving and it is beyond doubt that their importance for biomedical research will increase.

  5. Phenol-formaldehyde resins: A quantitative NMR study of molecular structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ottenbourgs, Benjamin Tony

    Phenol-formaldehyde (PF) resins have been the subject of this work. 13C liquid-state and solid-state NMR has been used to investigate the molecular structure of mainly novolak and partially of resole resins. 1H wideline in combination with 13C solid-state NMR relaxometry has been applied to study the curing and the molecular dynamics of phenolic resins. It was the intention to provide an insight in the relationship between resin composition, resin structure and subsequent resin properties (by means of the molecular dynamics). An improved 13C liquid-state NMR quantification technique of novolaks in THF-CDCl3 solutions is demonstrated. Full quantitative 13C liquid-state spectra of phenol-formaldehyde resins with high signal- to-noise ratio were obtained by using chromium acetylacetonate under optimized spectral conditions within a few hours spectrometer time. Attached proton test (APT) spectra enabled proper peak assignments in the region with significant overlap. For several novolaks, prepared under different catalytic conditions, the degree of polymerization, degree of branching, number average molecular weight, isomeric distribution, and the number of unreacted ortho and para phenol ring positions was determined with a reduced margin of error, by analyzing and integrating the 13C spectra. The power of 13C solid-state NMR in the analysis of cured PF resins is shown. Particular importance was ascribed to the question of the quantifiability of the experiments when it was desired to measure the degree of conversion by means of a 13C CP/MAS contact time study. The network structure present, and thus also the mechanical properties, is critically dependent upon the final degree of conversion obtained after curing. The degree of conversion, which depended on the cure conditions (cure temperature, cure pressure and cure time), was limited by vitrification as was demonstrated by DSC experiments. Changes in the spin-lattice relaxation time T 1H were observed, providing

  6. Micro structure processing on plastics by accelerated hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  7. Anti-cancer chalcones: Structural and molecular target perspectives.

    PubMed

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-06-15

    Chalcone or (E)-1,3-diphenyl-2-propene-1-one scaffold remained a fascination among researchers in the 21st century due to its simple chemistry, ease of synthesis and a wide variety of promising biological activities. Several natural and (semi) synthetic chalcones have shown anti-cancer activity due to their inhibitory potential against various targets namely ABCG2/P-gp/BCRP, 5α-reductase, aromatase, 17-β-hydroxysteroid dehydrogenase, HDAC/Situin-1, proteasome, VEGF, VEGFR-2 kinase, MMP-2/9, JAK/STAT signaling pathways, CDC25B, tubulin, cathepsin-K, topoisomerase-II, Wnt, NF-κB, B-Raf and mTOR etc. In this review, a comprehensive study on molecular targets/pathways involved in carcinogenesis, mechanism of actions (MOAs), structure activity relationships (SARs) and patents granted have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-cancer chalcones.

  8. The molecular structure of waxy maize starch nanocrystals.

    PubMed

    Angellier-Coussy, Hélène; Putaux, Jean-Luc; Molina-Boisseau, Sonia; Dufresne, Alain; Bertoft, Eric; Perez, Serge

    2009-08-17

    The insoluble residues obtained by submitting amylopectin-rich native starch granules from waxy maize to a mild acid hydrolysis consist of polydisperse platelet nanocrystals that have retained the allomorphic type of the parent granules. The present investigation is a detailed characterization of their molecular composition. Two major groups of dextrins were found in the nanocrystals and were isolated. Each group was then structurally characterized using beta-amylase and debranching enzymes (isoamylase and pullulanase) in combination with anion-exchange chromatography. The chain lengths of the dextrins in both groups corresponded with the thickness of the crystalline lamellae in the starch granules. Only approximately 62 mol% of the group of smaller dextrins with an average degree of polymerization (DP) 12.2 was linear, whereas the rest consisted of branched dextrins. The group of larger dextrins (DP 31.7) apparently only consisted of branched dextrins, several of which were multiply branched molecules. It was shown that many of the branch linkages were resistant to the action of the debranching enzymes. The distribution of branched molecules in the two populations of dextrins suggested that the nanocrystals possessed a regular and principally homogeneous molecular structure.

  9. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity.

  10. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  11. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    ERIC Educational Resources Information Center

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  12. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    ERIC Educational Resources Information Center

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  13. Electronic and Magnetic Structure of Octahedral Molecular Sieves

    NASA Astrophysics Data System (ADS)

    Morey-Oppenheim, Aimee M.

    The major part of this research consists of magnetic and electronic studies of metal doped cryptomelane-type manganese oxide octahedral molecular sieves (KOMS-2). The second part of this study involves the magnetic characterization of cobalt doped MCM-41 before and after use in the synthesis of single walled carbon nanotubes. Manganese oxides have been used widely as bulk materials in catalysis, chemical sensors, and batteries due to the wide range of possible stable oxidation states. The catalytic function of manganese oxides is further tuned by doping the material with numerous transition metals. It is of particular interest the oxidation states of Mn present after doping. New titrations to determine the oxidation state of Mn were investigated. To further examine the structure of KOMS-2, the magnetic contribution of dopant metals was also examined. The KOMS-2 structure having both diamagnetic and paramagnetic metal ions substitutions was studied. MCM-41 with the incorporation of cobalt into the structure was analyzed for its magnetic properties. The material undergoes significant structural change during the synthesis of single walled carbon nanotubes. It was the focus of this portion of the research to do a complete magnetic profile of both the before and after reaction material.

  14. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

    PubMed

    Tao, Peng; Wu, Xiongwu; Brooks, Bernard R

    2012-10-07

    An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.

  15. The Density and Molecular Column Density Structure of Three Molecular Cloud Cores

    NASA Astrophysics Data System (ADS)

    Mundy, Lee George

    Multi-transition studies using CS, C('34)S, and H(,2)CO are presented for the dense cores in the molecular clouds M17, S140, and NGC 2024. The typical peak density derived for these cores is -10('6) cm('-3), much larger than the average density in molecular clouds, but the gas density is not strongly correlated with the line intensities within the core itself. A map of line intensity appears to be a map of molecular column density whereas the gas density is evident in the ratios of intensities of different lines. Although the data do not have the spatial resolution to directly "see" clumps in the core, statistical equilibrium modeling of the data does provide evidence for an inhomogeneous distribution of the dense gas within the telescope beam. Many aspects of the data can best be explained by a model in which the gas with density > 10('5) cm('-3) is distributed in numerous small (< 1 are minmute) clumps. In the context of this model, the molecular column density structure of the core is caused by a decrease in the number density of clumps with increasing radial distance from the center of the core. The large number of observed transitions in the three molecules also allows us to evaluate the effectiveness of the individual molecules as density probes. We find that the gas densities derived from CS, C('34)S, and H(,2)CO are in reasonable agreement and present guidelines for future use of these molecules as density probes.

  16. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    PubMed Central

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  17. Sensitive detection for coralyne and mercury ions based on homo-A/T DNA by exonuclease signal amplification.

    PubMed

    Huang, Hailiang; Shi, Shuo; Zheng, Xuyue; Yao, Tianming

    2015-09-15

    Based on specific homo-A/T DNA binding properties, a strategy for coralyne and mercury ions detection was realised by exonuclease-aided signal amplification. Coralyne could specifically bind homo-A DNA and protect it from the hydrolysis of exonuclease I. The coralyne-protected DNA was subsequently used as a trigger strand to hydrolyze DNA2 in exonuclease-aided signal amplification process. Thiazole orange was used to quantify the remainder DNA2. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of coralyne in the range of 0.2-100 nM with a limit of detection (LOD) of 0.31 nM, which presented the lowest LOD for coralyne among all reported. With homo-T and Hg(2+) taking the place of homo-A DNA and coralyne, respectively, the system could also be used for Hg(2+) detection. The experiments in real samples also showed good results. This method was label-free, low-cost, easy-operating and highly repeatable for the detection of coralyne and mercury ions. It could also be extended to detect various analytes, such as other metal ions, proteins and small molecules by using appropriate aptamers. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Characterization of human herpesvirus 6A/B U94 as ATPase, helicase, exonuclease and DNA-binding proteins

    PubMed Central

    Trempe, Frédéric; Gravel, Annie; Dubuc, Isabelle; Wallaschek, Nina; Collin, Vanessa; Gilbert-Girard, Shella; Morissette, Guillaume; Kaufer, Benedikt B.; Flamand, Louis

    2015-01-01

    Human herpesvirus-6A (HHV-6A) and HHV-6B integrate their genomes into the telomeres of human chromosomes, however, the mechanisms leading to integration remain unknown. HHV-6A/B encode a protein that has been proposed to be involved in integration termed U94, an ortholog of adeno-associated virus type 2 (AAV-2) Rep68 integrase. In this report, we addressed whether purified recombinant maltose-binding protein (MBP)-U94 fusion proteins of HHV-6A/B possess biological functions compatible with viral integration. We could demonstrate that MBP-U94 efficiently binds both dsDNA and ssDNA containing telomeric repeats using gel shift assay and surface plasmon resonance. MBP-U94 is also able to hydrolyze adenosine triphosphate (ATP) to ADP, providing the energy for further catalytic activities. In addition, U94 displays a 3′ to 5′ exonuclease activity on dsDNA with a preference for 3′-recessed ends. Once the DNA strand reaches 8–10 nt in length, the enzyme dissociates it from the complementary strand. Lastly, MBP-U94 compromises the integrity of a synthetic telomeric D-loop through exonuclease attack at the 3′ end of the invading strand. The preferential DNA binding of MBP-U94 to telomeric sequences, its ability to hydrolyze ATP and its exonuclease/helicase activities suggest that U94 possesses all functions required for HHV-6A/B chromosomal integration. PMID:25999342

  19. Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima

    PubMed Central

    Larrea, Andres A.; Pedroso, Ilene M.; Malhotra, Arun; Myers, Richard S.

    2008-01-01

    Exonuclease VII was first identified in 1974 as a DNA exonuclease that did not require any divalent cations for activity. Indeed, Escherichia coli ExoVII was identified in partially purified extracts in the presence of EDTA. ExoVII is comprised of two subunits (XseA and XseB) that are highly conserved and present in most sequenced prokaryotic genomes, but are not seen in eukaryotes. To better understand this exonuclease family, we have characterized an ExoVII homolog from Thermotoga maritima. Thermotoga maritima XseA/B homologs TM1768 and TM1769 were co-expressed and purified, and show robust nuclease activity at 80°C. This activity is magnesium dependent and is inhibited by phosphate ions, which distinguish it from E. coli ExoVII. Nevertheless, both E. coli and T. maritima ExoVII share a similar putative active site motif with two conserved aspartate residues in the large (XseA/TM1768) subunit. We show that these residues, Asp235 and Asp240, are essential for the nuclease activity of T. maritima ExoVII. We hypothesize that the ExoVII family of nucleases can be sub-divided into two sub-families based on EDTA resistance and that T. maritima ExoVII is the first member of the branch that is characterized by EDTA sensitivity and inhibition by phosphate. PMID:18812402

  20. Label-free fluorescence strategy for sensitive detection of exonuclease activity using SYBR Green I as probe.

    PubMed

    Xu, Min; Li, Baoxin

    2015-01-01

    A label-free and sensitive fluorescence assay for exonuclease activity is developed using commercially available SYBR Green I (SG) dye as signal probe. A proof-of-concept of this assay has been demonstrated by using exonuclease III (Exo III) as a model enzyme. In this assay, double-stranded DNA (dsDNA) can bind SG, resulting in a strong fluorescence signal of SG. Upon the addition of Exo III, dsDNA would be digested, and SG emits very weak fluorescence. Thus, Exo III activity can be facilely measured with a simple fluorescence reader. This method has a linear detection range from 1 U/mL to 200 U/mL with a detection limit of 0.7 U/mL. This label-free approach is selective, simple, convenient and cost-efficient without any complex DNA sequence design or fluorescence dye label. The method not only provides a platform for monitoring activity and inhibition of exonuclease but also shows great potential in biological process researches, drug discovery, and clinic diagnostics.

  1. Effects of transcription elongation rate and Xrn2 exonuclease activity on RNA polymerase II termination suggest widespread kinetic competition

    PubMed Central

    Fong, Nova; Brannan, Kristopher; Erickson, Benjamin; Kim, Hyunmin; Cortazar, Michael; Sheridan, Ryan M.; Nguyen, Tram; Karp, Shai; Bentley, David L.

    2015-01-01

    Summary The torpedo model of transcription termination asserts that the exonuclease Xrn2 attacks the 5′PO4-end exposed by nascent RNA cleavage and chases down the RNA polymerase. We tested this mechanism using a dominant-negative human Xrn2 mutant and found that it delayed termination genome-wide. Xrn2 nuclease inactivation caused strong termination defects downstream of most poly(A) sites and modest delays at some histone and U snRNA genes suggesting that the torpedo mechanism is not limited to poly(A) site-dependent termination. A central untested feature of the torpedo model is that there is kinetic competition between the exonuclease and the pol II elongation complex. Using pol II rate mutants, we found that slow transcription robustly shifts termination upstream, and fast elongation extends the zone of termination further downstream. These results suggest that kinetic competition between elongating pol II and the Xrn2 exonuclease is integral to termination of transcription on most human genes. PMID:26474067

  2. Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition.

    PubMed

    Fong, Nova; Brannan, Kristopher; Erickson, Benjamin; Kim, Hyunmin; Cortazar, Michael A; Sheridan, Ryan M; Nguyen, Tram; Karp, Shai; Bentley, David L

    2015-10-15

    The torpedo model of transcription termination asserts that the exonuclease Xrn2 attacks the 5'PO4-end exposed by nascent RNA cleavage and chases down the RNA polymerase. We tested this mechanism using a dominant-negative human Xrn2 mutant and found that it delayed termination genome-wide. Xrn2 nuclease inactivation caused strong termination defects downstream of most poly(A) sites and modest delays at some histone and U snRNA genes, suggesting that the torpedo mechanism is not limited to poly(A) site-dependent termination. A central untested feature of the torpedo model is that there is kinetic competition between the exonuclease and the pol II elongation complex. Using pol II rate mutants, we found that slow transcription robustly shifts termination upstream, and fast elongation extends the zone of termination further downstream. These results suggest that kinetic competition between elongating pol II and the Xrn2 exonuclease is integral to termination of transcription on most human genes. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases

    PubMed Central

    Hodko, Domagoj; Ward, Taylor; Chanfreau, Guillaume

    2016-01-01

    Rtr1p is a phosphatase that impacts gene expression by modulating the phosphorylation status of the C-terminal domain of the large subunit of RNA polymerase II. Here, we show that Rtr1p is a component of a novel mRNA degradation pathway that promotes its autoregulation through turnover of its own mRNA. We show that the 3′UTR of the RTR1 mRNA contains a cis element that destabilizes this mRNA. RTR1 mRNA turnover is achieved through binding of Rtr1p to the RTR1 mRNP in a manner that is dependent on this cis element. Genetic evidence shows that Rtr1p-mediated decay of the RTR1 mRNA involves the 5′-3′ DExD/H-box RNA helicase Dhh1p and the 3′-5′ exonucleases Rex2p and Rex3p. Rtr1p and Rex3p are found associated with Dhh1p, suggesting a model for recruiting the REX exonucleases to the RTR1 mRNA for degradation. Rtr1p-mediated decay potentially impacts additional transcripts, including the unspliced BMH2 pre-mRNA. We propose that Rtr1p may imprint its RNA targets cotranscriptionally and determine their downstream degradation mechanism by directing these transcripts to a novel turnover pathway that involves Rtr1p, Dhh1p, and the REX family of exonucleases. PMID:26843527

  4. Immobilization of Lambda Exonuclease onto Polymer Micropillar Arrays for the Solid-Phase Digestion of dsDNAs

    PubMed Central

    2015-01-01

    The process of immobilizing enzymes onto solid supports for bioreactions has some compelling advantages compared to their solution-based counterpart including the facile separation of enzyme from products, elimination of enzyme autodigestion, and increased enzyme stability and activity. We report the immobilization of λ-exonuclease onto poly(methylmethacrylate) (PMMA) micropillars populated within a microfluidic device for the on-chip digestion of double-stranded DNA. Enzyme immobilization was successfully accomplished using 3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling to carboxylic acid functionalized PMMA micropillars. Our results suggest that the efficiency for the catalysis of dsDNA digestion using λ-exonuclease, including its processivity and reaction rate, were higher when the enzyme was attached to a solid support compared to the free solution digestion. We obtained a clipping rate of 1.0 × 103 nucleotides s–1 for the digestion of λ-DNA (48.5 kbp) by λ-exonuclease. The kinetic behavior of the solid-phase reactor could be described by a fractal Michaelis–Menten model with a catalytic efficiency nearly 17% better than the homogeneous solution-phase reaction. The results from this work will have important ramifications in new single-molecule DNA sequencing strategies that employ free mononucleotide identification. PMID:24628008

  5. Allosteric ring assembly and chemo-mechanical melting by the interaction between 5′-phosphate and λ exonuclease

    PubMed Central

    Yoo, Jungmin; Lee, Gwangrog

    2015-01-01

    Phosphates along the DNA function as chemical energy frequently used by nucleases to drive their enzymatic reactions. Exonuclease functions as a machine that converts chemical energy of the phosphodiester-chain into mechanical work. However, the roles of phosphates during exonuclease activities are unknown. We employed λ exonuclease as a model system and investigated the roles of phosphates during degradation via single-molecule fluorescence resonance energy transfer (FRET). We found that 5′ phosphates, generated at each cleavage step of the reaction, chemo-mechanically facilitate the subsequent post-cleavage melting of the terminal base pairs. Degradation of DNA with a nick requires backtracking and thermal fraying at the cleavage site for re-initiation via the formation of a catalytically active complex. Unexpectedly, we discovered that a phosphate of a 5′ recessed DNA acts as a hotspot for an allosteric trimeric-ring assembly without passing through the central channel. Our study provides new insight into the versatile roles of phosphates during the processive enzymatic reaction. PMID:26527731

  6. Molecular structural characteristics as determinants of estrogen receptor selectivity.

    PubMed

    Agatonovic-Kustrin, S; Turner, J V; Glass, B D

    2008-09-29

    Recent reports that a wide variety of natural and man-made compounds are capable of competing with natural hormones for estrogen receptors serve as timely examples of the need to advance screening techniques to support human health and ascertain ecological risk. Quantitative structure-activity relationships (QSARs) can potentially serve as screening tools to identify and prioritize untested compounds for further empirical evaluations. Computer-based QSAR molecular models have been used to describe ligand-receptor interactions and to predict chemical structures that possess desired pharmacological characteristics. These have recently included combined and differential relative binding affinities of potential estrogenic compounds at estrogen receptors (ER) alpha and beta. In the present study, artificial neural network (ANN) QSAR models were developed that were able to predict differential relative binding affinities of a series of structurally diverse compounds with estrogenic activity. The models were constructed with a dataset of 93 compounds and tested with an additional dataset of 30 independent compounds. High training correlations (r2=0.83-0.91) were observed while validation results for the external compounds were encouraging (r2=0.62-0.86). The models were used to identify structural features of phytoestrogens that are responsible for selective ligand binding to ERalpha and ERbeta. Numerous structural characteristics are required for complexation with receptors. In particular, size, shape and polarity of ligands, heterocyclic rings, lipophilicity, hydrogen bonding, presence of quaternary carbon atom, presence, position, length and configuration of a bulky side chain, were identified as the most significant structural features responsible for selective binding to ERalpha and ERbeta.

  7. Mathematical analysis of compressive/tensile molecular and nuclear structures

    NASA Astrophysics Data System (ADS)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  8. Molecular Clouds in the North American and Pelican Nebulae: Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg2 area toward the North American and Pelican Nebulae in the J = 1-0 transitions of 12CO, 13CO, and C18O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M ⊙ pc-2 and a mean H2 column density of 5.8, 3.4, and 11.9 × 1021 cm-2 for 12CO, 13CO, and C18O, respectively. We obtain a total mass of 5.4 × 104 M ⊙ (12CO), 2.0 × 104 M ⊙ (13CO), and 6.1 × 103 M ⊙ (C18O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (~10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of 13CO emission range within 2-10 pc2 with mass of (1-5) × 103 M ⊙ and line width of a few km s-1. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the 13CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  9. Physics Based Protein Structure Refinement through Multiple Molecular Dynamics Trajectories and Structure Averaging

    PubMed Central

    Mirjalili, Vahid; Noyes, Keenan; Feig, Michael

    2014-01-01

    We used molecular dynamics (MD) simulations for structure refinement of CASP10 targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations vs. a single long simulation, the success of a quality assessment criterion, the application of scoring vs. averaging, and the impact of a final refinement step are discussed in detail. PMID:23737254

  10. A label-free fluorescent probe based on DNA-templated silver nanoclusters and exonuclease III-assisted recycling amplification detection of nucleic acid.

    PubMed

    Yang, Wen; Tian, Jianniao; Ma, Yefei; Wang, Lijun; Zhao, Yanchun; Zhao, Shulin

    2015-11-05

    A number of specific nucleic acids are closely related with many serious diseases, in the current research, a platform taking advantage of exonuclease III (Exo III) to realize double recycling amplification and label-free fluorescent DNA-templated silver nanoclusters (DNA-AgNCs) for detecting of nucleic acid had been developed. In this method, a molecular beacon (MB) with 3'-protruding termini and a single-stranded cytosine-rich (C-rich) probe were designed that coexist stably with Exo III. Once the target DNA appeared, portion of the MB could hybridize with target DNA and was digested by Exo III, which allowed the release of target DNA and a residual sequence. Subsequently, the residual sequence could trigger the Exo III to digest C-rich probe, and the DNA-AgNCs was not able to be synthesized because of the C-rich probe was destroyed; finally the fluorescent of solution was quenched. This assay enables to monitor human hemochromatosis gene (as a model) with high sensitivity, the detection limit is as low as 120 pM compared with other fluorescence DNA-AgNCs methods, this assay also exhibits superior specificity even against single base mismatch. The strategy is applied to detect human hemochromatosis gene in real human serum samples successfully. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Structured illumination microscopy for vibrational molecular imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Watanabe, Kozue; Palonpon, Almar F.; Smith, Nicholas I.; Chiu, Liang-da; Kasai, Atsushi; Hashimoto, Hitoshi; Kawata, Satoshi; Fujita, Katsumasa

    2016-09-01

    Raman microscopy is a powerful tool for analytical imaging. The wavelength shift of Raman scattering corresponds to molecular vibrational energy. Therefore, we can access rich chemical information, such as distribution, concentration, and chemical environment of sample molecules. Despite these strengths of Raman microscopy, the spatial resolution has been a limiting factor for many practical applications. In this study, we developed a large-area, high-resolution Raman microscope by utilizing structured illumination microscopy (SIM) to overcome the spatial resolution limit. A structured line-illumination (SLI) Raman microscope was constructed. The structured illumination is introduced along the line direction by the interference of two line-shaped beams. In SIM, the spatial frequency mixing between structured illumination and Raman scattering from the sample allows access to the high spatial frequency information beyond the conventional cut-off. As a result, the FWHM of 40-nm fluorescence particle images showed a clear resolution enhancement in the line direction: 366 nm in LI and 199 nm in SLI microscope. Using the developed microscope, we successfully demonstrated high-resolution Raman imaging of various kinds of specimens, such as few-layer graphene, graphite, mouse brain tissue, and polymer nanoparticles. The high resolution Raman images showed the capability to extract original spectral features from the mixed Raman spectra of a multi-component sample because of the enhanced spatial resolution, which is advantageous in observing complex spectral features. The Raman microscopy technique reported here enables us to see the detailed chemical structures of chemical, biological, and medical samples with a spatial resolution smaller than 200 nm.

  12. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    SciTech Connect

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.

    2010-11-01

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  13. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    SciTech Connect

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li

    2011-12-31

    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  14. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  15. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  16. Structural and molecular comparison of bacterial and eukaryotic trigger factors.

    PubMed

    Ries, Fabian; Carius, Yvonne; Rohr, Marina; Gries, Karin; Keller, Sandro; Lancaster, C Roy D; Willmund, Felix

    2017-09-06

    A considerably small fraction of approximately 60-100 proteins of all chloroplast proteins are encoded by the plastid genome. Many of these proteins are major subunits of complexes with central functions within plastids. In comparison with other subcellular compartments and bacteria, many steps of chloroplast protein biogenesis are not well understood. We report here on the first study of chloroplast-localised trigger factor. In bacteria, this molecular chaperone is known to associate with translating ribosomes to facilitate the folding of newly synthesized proteins. Chloroplast trigger factors of the unicellular green algae Chlamydomonas reinhardtii and the vascular land plant Arabidopsis thaliana were characterized by biophysical and structural methods and compared to the Escherichia coli isoform. We show that chloroplast trigger factor is mainly monomeric and displays only moderate stability against thermal unfolding even under mild heat-stress conditions. The global shape and conformation of these proteins were determined in solution by small-angle X-ray scattering and subsequent ab initio modelling. As observed for bacteria, plastidic trigger factors have a dragon-like structure, albeit with slightly altered domain arrangement and flexibility. This structural conservation despite low amino acid sequence homology illustrates a remarkable evolutionary robustness of chaperone conformations across various kingdoms of life.

  17. Cluster and Shell Structures in the Fermionic Molecular Dynamics Approach

    NASA Astrophysics Data System (ADS)

    Neff, Thomas; Feldmeier, Hans

    Nuclei in the p- and sd-shell are studied within the Fermionic Molecular Dynamics (FMD) model that uses Gaussian wave packets as single-particle states. Intrinsic many-body basis states are given by Slater determinants which have to be projected on parity, angular momentum and total linear momentum to restore the symmetries of the Hamiltonian. The flexibility of the Gaussian basis allows to economically describe states with shell structures as well as states featuring clustering or halos. The same effective interaction derived from the realistic Argonne V18 interaction in the Unitary Correlation Operator Method (UCOM) framework is used for all nuclei. We discuss the spectrum of 12C with a special emphasis on the structure of the first excited 0+ state, the famous Hoyle state. In the FMD approach the Hoyle state is found to be dominated by dilute α-cluster configurations. Recent measurements of the charge radii of Neon isotopes show an intriguing behaviour. This can be explained in FMD calculations by a structure change from 17Ne and 18Ne which can be essentially considered as an 15O or 16O core plus two protons in s2 or d2 configurations, respectively. For the heavier isotopes we find that the admixture of 3He and 4He cluster configurations in the ground states leads to much larger charge radii than obtained in a mean-field calculation.

  18. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  19. Hydration structure of salt solutions from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  20. Hydration structure of salt solutions from ab initio molecular dynamics.

    PubMed

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L

    2013-01-07

    The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  1. Molecular and structural insight into plasmodium falciparum RIO2 kinase.

    PubMed

    Chouhan, Devendra K; Sharon, Ashoke; Bal, Chandralata

    2013-02-01

    Among approximately 65 kinases of the malarial genome, RIO2 (right open reading frame) kinase belonging to the atypical class of kinase is unique because along with a kinase domain, it has a highly conserved N-terminal winged helix (wHTH) domain. The wHTH domain resembles the wing like domain found in DNA binding proteins and is situated near to the kinase domain. Ligand binding to this domain may reposition the kinase domain leading to inhibition of enzyme function and could be utilized as a novel allosteric site to design inhibitor. In the present study, we have generated a model of RIO2 kinase from Plasmodium falciparum utilizing multiple modeling, simulation approach. A novel putative DNA-binding site is identified for the first time in PfRIO2 kinase to understand the DNA binding events involving wHTH domain and flexible loop. Induced fit DNA docking followed by minimization, molecular dynamics simulation, energetic scoring and binding mode studies are used to reveal the structural basis of PfRIO2-ATP-DNA complex. Ser105 as a potential site of phosphorylation is revealed through the structural studies of ATP binding in PfRIO2. Overall the present study discloses the structural facets of unknown PfRIO2 complex and opens an avenue toward exploration of novel drug target.

  2. Structure and function of the molecular chaperone Trigger Factor.

    PubMed

    Hoffmann, Anja; Bukau, Bernd; Kramer, Günter

    2010-06-01

    Newly synthesized proteins often require the assistance of molecular chaperones to efficiently fold into functional three-dimensional structures. At first, ribosome-associated chaperones guide the initial folding steps and protect growing polypeptide chains from misfolding and aggregation. After that folding into the native structure may occur spontaneously or require support by additional chaperones which do not bind to the ribosome such as DnaK and GroEL. Here we review the current knowledge on the best-characterized ribosome-associated chaperone at present, the Escherichia coli Trigger Factor. We describe recent progress on structural and dynamic aspects of Trigger Factor's interactions with the ribosome and substrates and discuss how these interactions affect co-translational protein folding. In addition, we discuss the newly proposed ribosome-independent function of Trigger Factor as assembly factor of multi-subunit protein complexes. Finally, we cover the functional cooperation between Trigger Factor, DnaK and GroEL in folding of cytosolic proteins and the interplay between Trigger Factor and other ribosome-associated factors acting in enzymatic processing and translocation of nascent polypeptide chains.

  3. Structural and molecular interrogation of intact biological systems

    PubMed Central

    Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

    2014-01-01

    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

  4. Molecular origin of the vibrational structure of ice Ih

    DOE PAGES

    Moberg, Daniel R.; Straight, Shelby C.; Knight, Christopher; ...

    2017-05-25

    Here, an unambiguous assignment of the vibrational spectra of ice Ih remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice Ih in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations asmore » well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.« less

  5. Unraveling the Structure of Ultracold Mesoscopic Collinear Molecular Ions

    NASA Astrophysics Data System (ADS)

    Schurer, J. M.; Negretti, A.; Schmelcher, P.

    2017-08-01

    We present an in-depth many-body investigation of the so-called mesoscopic molecular ions that can buildup when an ion is immersed into an atomic Bose-Einstein condensate in one dimension. To this end, we employ the multilayer multiconfiguration time-dependent Hartree method for mixtures of ultracold bosonic species for solving the underlying many-body Schrödinger equation. This enables us to unravel the actual structure of such massive charged molecules from a microscopic perspective. Laying out their phase diagram with respect to atom number and interatomic interaction strength, we determine the maximal number of atoms bound to the ion and reveal spatial densities and molecular properties. Interestingly, we observe a strong interaction-induced localization, especially for the ion, that we explain by the generation of a large effective mass, similarly to ions in liquid Helium. Finally, we predict the dynamical response of the ion to small perturbations. Our results provide clear evidence for the importance of quantum correlations, as we demonstrate by benchmarking them with wave function ansatz classes employed in the literature.

  6. Solving structures of protein complexes by molecular replacement with Phaser

    SciTech Connect

    McCoy, Airlie J.

    2007-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases.

  7. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2′-deoxyuridine, low concentration of hydrochloric acid and exonuclease III

    PubMed Central

    Konečný, Petr; Frydrych, Ivo; Koberna, Karel

    2017-01-01

    The approach for the detection of replicational activity in cells using 5-bromo-2′-deoxyuridine, a low concentration of hydrochloric acid and exonuclease III is presented in the study. The described method was optimised with the aim to provide a fast and robust tool for the detection of DNA synthesis with minimal impact on the cellular structures using image and flow cytometry. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Our data showed that the method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing Fluorescent Ubiquitin Cell Cycle Indicator. In the case of the short labelling pulses that disabled the use of 5-ethynyl-2′-deoxyuridine because of the low specific signal, the described method provided a bright signal enabling reliable recognition of replicating cells. The optimized protocol was also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer. PMID:28426799

  8. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2'-deoxyuridine, low concentration of hydrochloric acid and exonuclease III.

    PubMed

    Ligasová, Anna; Konečný, Petr; Frydrych, Ivo; Koberna, Karel

    2017-01-01

    The approach for the detection of replicational activity in cells using 5-bromo-2'-deoxyuridine, a low concentration of hydrochloric acid and exonuclease III is presented in the study. The described method was optimised with the aim to provide a fast and robust tool for the detection of DNA synthesis with minimal impact on the cellular structures using image and flow cytometry. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Our data showed that the method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing Fluorescent Ubiquitin Cell Cycle Indicator. In the case of the short labelling pulses that disabled the use of 5-ethynyl-2'-deoxyuridine because of the low specific signal, the described method provided a bright signal enabling reliable recognition of replicating cells. The optimized protocol was also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer.

  9. Complementation between polymerase- and exonuclease-deficient mitochondrial DNA polymerase mutants in genomically engineered flies

    PubMed Central

    Macao, Bertil; Grönke, Sebastian; Siibak, Triinu; Stewart, James B; Baggio, Francesca; Dols, Jacqueline; Partridge, Linda; Falkenberg, Maria; Wredenberg, Anna; Larsson, Nils-Göran

    2016-01-01

    Replication errors are the main cause of mtDNA mutations and a compelling approach to decrease mutation levels would therefore be to increase the fidelity of the catalytic subunit (POLγA) of the mtDNA polymerase. Here we genomically engineered the tamas locus, encoding fly POLγA, and introduced alleles expressing exonuclease- (exo-) and polymerase-deficient (pol-) POLγA versions. The exo- mutant leads to accumulation of point mutations and linear deletions of mtDNA, whereas pol- mutants cause mtDNA depletion. The mutant tamas alleles are developmentally lethal but can complement each other in trans resulting in viable flies with clonally expanded mtDNA mutations. Reconstitution of human mtDNA replication in vitro confirms that replication is a highly dynamic process where POLγA goes on and off the template to allow complementation during proofreading and elongation. The created fly models are valuable tools to study germ line transmission of mtDNA and the pathophysiology of POLγA mutation disease. PMID:26554610

  10. Exonuclease I manipulating primer-modified gold nanoparticles for colorimetric telomerase activity assay.

    PubMed

    Zhang, Lei; Zhang, Sijin; Pan, Wei; Liang, Qingcheng; Song, Xingyu

    2016-03-15

    Telomerase is a widely accepted cancer biomarker. The conventional method for telomerase activity assay, the telomeric repeat amplification protocol (TRAP), is time-consuming and susceptible to contaminants. Therefore, development of simple and sensitive strategies for telomerase detection is still a challenging subject. Here we develop a highly sensitive method for telomerase detection based on primer-modified gold nanoparticles (GNPs) manipulated by exonuclease I (Exo I). In the absence of telomerase, Exo I digests the substrate nucleic acid on the surface of GNPs, inducing the GNPs' aggregation. In the presence of telomerase, the telomerase elongation products which fold into G-quadruplex are resistant to the digestion of Exo I, and protect the GNPs from aggregation. By using this method, we can detect telomerase activity in 100 HL-60 cancer cells mL(-1) by naked eyes, and the detection limit is 29 HL-60 cells mL(-1). This method is very simple and reliable, without any separation and amplification procedure. We also demonstrate the feasibility of this protocol for screening of telomerase inhibitors as anticancer agents. This method is promising to be applied in early clinical diagnosis and drug discovery. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Ultrasensitive Electrochemical Biosensor for HIV Gene Detection Based on Graphene Stabilized Gold Nanoclusters with Exonuclease Amplification.

    PubMed

    Wang, Yijia; Bai, Xiaoning; Wen, Wei; Zhang, Xiuhua; Wang, Shengfu

    2015-08-26

    Because human immunodeficiency virus (HIV) has been one of the most terrible viruses in recent decades, early diagnosis of the HIV gene is of great importance for all scientists around the world. In our work, we developed a novel electrochemical biosensor based on one-step ultrasonic synthesized graphene stabilized gold nanocluster (GR/AuNC) modified glassy carbon electrode (GCE) with an exonuclease III (Exo III)-assisted target recycling amplification strategy for the detection of HIV DNA. It is the first time that GR/AuNCs have been used as biosensor platform and aptamer with cytosine-rich base set as capture probe to construct the biosensor. With the combination of cytosine-rich capture probe, good conductivity and high surfaces of GR/AuNCs, and Exo III-assisted target recycling amplification, we realized high sensitivity and good selectivity detection of target HIV DNA with a detection limit of 30 aM (S/N = 3). Furthermore, the proposed biosensor has a promising potential application for target detection in human serum analysis.

  12. Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection.

    PubMed

    Xiao, Xue; Tao, Jing; Zhang, Hong Zhi; Huang, Cheng Zhi; Zhen, Shu Jun

    2016-11-15

    Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer.

  13. Structural Determinations and Dynamics on Floppy Molecular Systems

    NASA Astrophysics Data System (ADS)

    Pietraperzia, G.; Becucci, M.; Zoppi, A.; Pasquini, M.; Piani, G.; Castellucci, E.

    2005-05-01

    We discuss on the central role of very high resolution spectroscopy for the study of molecular systems weakly bonded or flexible. It will appear evident how the lack of high resolution results can lead to wrong conclusions. The paper will focalize the attention in particular on two different cases: one involving the hydrogen bonded complex anisole-water, the other involving the very floppy 1,3-benzodioxole (BDO) molecule. In the first case the issue is the determination of the structure of the complex that cannot be correctly inferred from resonance enhanced multi photon ionization (REMPI) data and ab initio calculations. In the second case the non-rigidity of the molecule and the possibility of the interaction of two low frequency modes (ring-puckering and ring-butterfly) have lead to a wrong assignment of the laser induced fluorescence (LIF) vibronic spectrum.

  14. Diffusion and structure in silica liquid: a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Hung, P. K.; Hong, N. V.; Vinh, L. T.

    2007-11-01

    Diffusion and structure in liquid silica under pressure have been investigated by a molecular dynamics model of 999 atoms with the inter-atomic potentials of van Beest, Kramer and van Santen. The simulation reveals that silica liquid is composed of the species SiO4, SiO5 and SiO6 with a fraction dependent on pressure. The density as well as volume of voids can be expressed as a linear function of the fraction of those species. Low-density liquid is mainly constructed of SiO4 and has a large number of O- and Si-voids and a large void tube. This tube contains most O-voids and is spread over the whole system. The anomalous diffusion behavior is observed and discussed.

  15. The molecular structure of naphthalene by electron diffraction

    NASA Astrophysics Data System (ADS)

    Ketkar, S. N.; Fink, M.

    1981-11-01

    The molecular structure of gaseous naphthalene has been studied by electron diffraction at a nozzle tip temperature of about 25°C. The molecule has D 2h symmetry to within experimental error. The results for the distances ( ra), bond angle and r.m.s. amplitude ( l) are r(CH) = 1.092(6) Å, r(C 9C 1) = 1.422(2) Å, r(C 1C 2) = 1.381(2) Å, r(C 2C 3) = 1.417(4) Å, r(C 10C 9) = 1.412(8) Å, ∠C 10C 9C 1 = 119.5(3)°, ∠CCH = 119.9(7)°, l(CH) = 0.076(6) Å, l(CC) = 0.047(2) Å.

  16. Guiding Molecular Motors with Nano-Imprinted Structures

    NASA Astrophysics Data System (ADS)

    Bunk, Richard; Carlberg, Patrick; Månsson, Alf; Nicholls, Ian A.; Omling, Pär; Sundberg, Mark; Tågerud, Sven; Montelius, Lars

    2005-05-01

    This work, for the first time, demonstrates that nano-imprinted samples, with 100 nm wide polymer lines, can act as guides for molecular motors consisting of motor proteins actin and myosin. The motor protein function was characterized using fluorescence microscopy and compared to actomyosin motility on non-structured nitrocellulose surfaces. Our results open for further use of the nano-imprint technique in the production of disposable chips for bio-nanotechnological applications and miniaturized biological test systems. We discuss how the nano-imprinted motor protein assay system may be optimized and also how it compares to previously tested assay systems involving low-resolution UV-lithography and low throughput but high-resolution electron beam lithography.

  17. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  18. Molecular structure and exciton dynamics in organic conjugated polymers

    NASA Astrophysics Data System (ADS)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  19. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution

    SciTech Connect

    Frederick, C.A.; Coll, M.; van der Marel, G.A.; van Boom, J.H.; Wang, A.H.J.

    1988-11-01

    The molecular structure of a small cycle nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-/Angstrom/ resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) /Angstrom/, b = 24.785 (3) /Angstrom/, c = 13.743 (3) /Angstrom/, and ..beta.. = 94.02 (2)/degrees/. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles ..cap alpha..//zeta/ in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associated with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  20. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

    PubMed

    Frederick, C A; Coll, M; van der Marel, G A; van Boom, J H; Wang, A H

    1988-11-01

    The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

  1. Molecular quantum-dot cellular automata--from molecular structure to circuit dynamics

    NASA Astrophysics Data System (ADS)

    Lu, Yuhui; Lent, Craig

    2008-03-01

    Quantum-dot cellular automata (QCA) [1] provides a transistor-less paradigm for molecular electronics. In the QCA approach, binary information is stored in the charge configuration of single cells, and transferred via Coulomb coupling between neighboring cells. Single-molecule QCA cells can be realized by using as quantum dots the localized states of mixed-valence complexes. Several candidate QCA molecules have been synthesized and shown to have the required field-induced switching properties [2]. We report progress towards a hierarchic dynamic theory of QCA circuits. We use ab initio techniques to calculate the relevant molecular electronic structure, and extract parameters for a simpler Hamiltonian to describe switching behavior. We then apply a coherence vector formalism to model interaction with the thermal environment and generate a circuit-dynamic description. [1] C. S. Lent, P. D. Tougaw, W. Porod, and G. H. Bernstein, Nanotechnology, vol. 4, pp. 49, 1993. [2] H. Qi, S. Sharma, Z. Li, G. L. Snider, A. O. Orlov, C. S. Lent, and T. P. Fehlner, J.Am.Chem.Soc., vol. 125, pp. 15250, 2003.

  2. MacMolecular: a program for visualization of molecular structures on the Macintosh.

    PubMed

    Weaver, T D; Islam, S A; Weaver, D L

    1994-09-01

    MacMolecular displays small- to medium-sized biomolecules, with particular emphasis on peptides. It has been developed to run on color Macintosh computers. The display can be stick, ball and stick, depth cued by thickness stick, or several types of space-filling representations. The program takes input from standard PDB files, simple Cartesian coordinate files, and, in addition, from Kinemage files in which atom information has been included. The program allows color changes of various types as well as the normal functions of translation, rotation, and zooming. In addition, animation files may be produced for subsequent display. Bonding of atoms is done by a distance algorithm (standard) or sequentially to properly display C alpha traces and traces of peptides containing simplified representations of amino acids. Stereo viewing is available, and manipulated structures which were drawn from PDB files can be written out to new PDB files. In addition, PICT files of the drawing window can be generated.

  3. Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

    NASA Astrophysics Data System (ADS)

    Ivanova, Bojidarka B.; Spiteller, Michael

    2012-09-01

    A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

  4. Purification and characterization of exonuclease-free Artemis: Implications for DNA-PK – dependent processing of DNA termini in NHEJ catalyzed DSB repair

    PubMed Central

    Pawelczak, Katherine S.; Turchi, John J.

    2010-01-01

    Artemis is a member of the β–CASP family of nucleases in the metallo-β-lactamase superfamily of hydrolases. Artemis has been demonstrated to be involved in V(D)J-recombination and in the NHEJ-catalyzed repair of DNA DSBs. In vitro, both DNA-PK independent 5’ to 3’ exonuclease activity and DNA-PK dependent endonuclease activity have been attributed to Artemis, though mutational analysis of the Artemis active site only disrupts endonuclease activity. This suggests that either the enzyme contains two different active sites, or the exonuclease activity is not intrinsic to the Artemis polypeptide. To distinguish between these possibilities, we sought to determine if it was possible to biochemically separate Artemis endonuclease activity from exonuclease activity. Recombinant [His]6–Artemis was expressed in a Baculovirus insect-cell expression system and isolated using a three-column purification methodology. Exonuclease and endonuclease activity, the ability to be phosphorylated by DNA-PK, and Artemis antibody reactivity was monitored throughout the purification and to characterize final pools of protein preparation. Results demonstrated the co-elution of exonuclease and endonuclease activity on a Ni-Agarose affinity column but separation of the two enzymatic activities upon fractionation on a hydroxyapatite column. An exonuclease free fraction of Artemis was obtained that retained DNA-PK dependent endonuclease activity, was phosphorylated by DNA-PK and reacted with an Artemis specific antibody. These data demonstrate that the exonuclease activity thought to be intrinsic to Artemis can be biochemically separated from the Artemis endonuclease. PMID:20347402

  5. Purification and characterization of exonuclease-free Artemis: Implications for DNA-PK-dependent processing of DNA termini in NHEJ-catalyzed DSB repair.

    PubMed

    Pawelczak, Katherine S; Turchi, John J

    2010-06-04

    Artemis is a member of the beta-CASP family of nucleases in the metallo-beta-lactamase superfamily of hydrolases. Artemis has been demonstrated to be involved in V(D)J-recombination and in the NHEJ-catalyzed repair of DNA DSBs. In vitro, both DNA-PK independent 5'-3' exonuclease activities and DNA-PK dependent endonuclease activity have been attributed to Artemis, though mutational analysis of the Artemis active site only disrupts endonuclease activity. This suggests that either the enzyme contains two different active sites, or the exonuclease activity is not intrinsic to the Artemis polypeptide. To distinguish between these possibilities, we sought to determine if it was possible to biochemically separate Artemis endonuclease activity from exonuclease activity. Recombinant [His](6)-Artemis was expressed in a Baculovirus insect-cell expression system and isolated using a three-column purification methodology. Exonuclease and endonuclease activities, the ability to be phosphorylated by DNA-PK, and Artemis antibody reactivity was monitored throughout the purification and to characterize final pools of protein preparation. Results demonstrated the co-elution of exonuclease and endonuclease activities on a Ni-agarose affinity column but separation of the two enzymatic activities upon fractionation on a hydroxyapatite column. An exonuclease-free fraction of Artemis was obtained that retained DNA-PK dependent endonuclease activity, was phosphorylated by DNA-PK and reacted with an Artemis specific antibody. These data demonstrate that the exonuclease activity thought to be intrinsic to Artemis can be biochemically separated from the Artemis endonuclease. Copyright 2010 Elsevier B.V. All rights reserved.

  6. A label-free signal amplification assay for DNA detection based on exonuclease III and nucleic acid dye SYBR Green I.

    PubMed

    Zheng, Aihua; Luo, Ming; Xiang, Dongshan; Xiang, Xia; Ji, Xinghu; He, Zhike

    2013-09-30

    We have developed a new fluorescence method for specific single-stranded DNA sequences with exonuclease III (Exo III) and nucleic acid dye SYBR Green I. It is demonstrated by a reverse transcription oligonucleotide sequence (target DNA, 27 bases) of RNA fragment of human immunodeficiency virus (HIV) as a model system. In the absence of the target DNA, the hairpin-probe is in the stem-closed structure, the fluorescence of SYBR Green I is very strong. In the presence of the target DNA, the hairpin-probe hybridizes with the target DNA to form double-stranded structure with a blunt 3'-terminus. Thus, in the presence of Exo III, only the 3'-terminus of probe is subjected to digestion. Exo III catalyzes the stepwise removal of mononucleotides from this terminus, releasing the target DNA. The released target DNA then hybridizes with another probe, whence the cycle starts anew. The signal of SYBR Green I decreases greatly. This system provides a detection limit of 160 pM, which is comparable to the existing signal amplification methods that utilized Exo III as a signal amplification nuclease. Due to the unique property of Exo III, this method shows excellent detection selectivity for single-base discrimination. More importantly, superiors to other methods based on Exo III, these probes have the advantages of easier to design, synthesize, purify and thus are much cheaper and more applicable. This new approach could be widely applied to sensitive and selective nucleic acids detection.

  7. Molecular Structure and Mobility in Ultrasonically Treated Unfilled Polybutadiene Rubber

    NASA Astrophysics Data System (ADS)

    von Meerwall, E.; Oh, J.-S.; Wagler, T.; Rinaldi, P.; Isayev, A. I.

    2003-10-01

    Ultrasound can change the molecular structure of rubbery polymers in several ways at once, including network formation (crosslinking) and degradation (devulcanization). We have used wide-line proton and spectroscopic 13C transverse NMR relaxation, and the proton pulsed-gradient spin echo method, to examine sonicated unfilled polybutadiene gum rubber. Results correlate well with ultrasound amplitude. The proton T2 relaxation at 70.5 deg. C exhibits three discrete components, due to entangled sol and network; unentangled (light) sol plus dangling chain ends; and oligomer remnants. The 25 deg. C carbon T2 values show no effects of sonication. The diffusivity spectrum of the light sol displays a wide rate distribution, including a fast component from oligomers. Ultrasound exposure increases all diffusion rates, and substantially lowers the relative contribution of the two fastest proton T2 decay components with only small decreases in relaxation times. Ultrasound treatment results in significant isomerization; the cis/trans ratio decreases sharply for samples subjected to the highest amplitudes. The structural implications of these findings will be discussed.

  8. Molecular structure of tetramethylgermane from gas electron diffraction

    NASA Astrophysics Data System (ADS)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  9. Bonding and structure in dense multi-component molecular mixtures

    DOE PAGES

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; ...

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systemsmore » engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.« less

  10. Bonding and structure in dense multi-component molecular mixtures

    SciTech Connect

    Meyer, Edmund R.; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D.; Collins, Lee A.

    2015-10-30

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. As a result, a basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  11. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  12. Chitosan Molecular Structure as a Function of N-Acetylation

    SciTech Connect

    Franca, Eduardo F.; Freitas, Luiz C.; Lins, Roberto D.

    2011-07-01

    Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with f and w values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3- HO3(n) ... O5(n+ 1) hydrogen bond, which in turn controls particle aggregation.

  13. Structural and electronic properties of Diisopropylammonium bromide molecular ferroelectric crystal

    NASA Astrophysics Data System (ADS)

    Alsaad, A.; Qattan, I. A.; Ahmad, A. A.; Al-Aqtash, N.; Sabirianov, R. F.

    2015-10-01

    We report the results of ab-initio calculations based on Generalized Gradient Approximation (GGA) and hybrid functional (HSE06) of electronic band structure, density of states and partial density of states to get a deep insight into structural and electronic properties of P21 ferroelectric phase of Diisopropylammonium Bromide molecular crystal (DIPAB). We found that the optical band gap of the polar phase of DIPAB is ∼ 5 eV confirming it as a good dielectric. Examination of the density of states and partial density of states reveal that the valence band maximum is mainly composed of bromine 4p orbitals and the conduction band minimum is dominated by carbon 2p, carbon 2s, and nitrogen 2s orbitals. A unique aspect of P21 ferroelectric phase is the permanent dipole within the material. We found that P21 DIPAB has a spontaneous polarization of 22.64 consistent with recent findings which make it good candidate for the creation of ferroelectric tunneling junctions (FTJs) which have the potential to be used as memory devices.

  14. Structural and molecular basis of starch viscosity in hexaploid wheat.

    PubMed

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  15. Nuclear structure and reactions in the fermionic molecular dynamics approach

    NASA Astrophysics Data System (ADS)

    Neff, T.; Feldmeier, H.

    2008-05-01

    The Fermionic Molecular Dynamics (FMD) model uses Gaussian wave packets as single-particle states. Intrinsic many-body basis states are constructed as Slater determinants which have to be projected on parity, angular momentum and total linear momentum to restore the symmetries of the Hamiltonian. The flexibility of the Gaussian basis allows to economically describe states with shell structures as well as states featuring clustering or halos. We use an effective interaction that is derived from the realistic Argonne V18 interaction by means of the Unitary Correlation Operator Method (UCOM). A phenomenological momentum-dependent two-body correction simulates contributions from missing three-body forces and three-body correlations. We discuss 12C with a special emphasis on the structure of the excited 0+ and 2+ states. We analyze the degree of α-clustering and confirm, taking inelastic electron scattering data into account, the conjecture that the Hoyle state has to be understood as a loosely bound system of alpha particles. We will also present first results on the application of FMD for the calculation of scattering phase shifts in 3He — 4He.

  16. Molecular Structures and Interactions in the Yeast Kinetochore

    PubMed Central

    Cho, U.-S.; Corbett, K.D.; Al-Bassam, J.; Bellizzi, J.J.; De Wulf, P.; Espelin, C.W.; Miranda, J.J.; Simons, K.; Wei, R.R.; Sorger, P.K.; Harrison, S.C.

    2011-01-01

    Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes. PMID:21467141

  17. Magnetic Field Structure in Molecular Clouds by Polarization Measurements

    NASA Astrophysics Data System (ADS)

    Chen, W. P.; Su, B. H.; Eswaraiah, C.; Pandey, A. K.; Wang, C. W.; Lai, S. P.; Tamura, M.; Sato, S.

    2015-03-01

    We report on a program to delineate magnetic field structure inside molecular clouds by optical and infrared polarization observations. An ordered magnetic field inside a dense cloud may efficiently align the spinning dust grains to cause a detectable level of optical and near-infrared polarization of otherwise unpolarized background starlight due to dichroic extinction. The near-infrared polarization data were taken by SIRPOL mounted on IRSF in SAAO. Here we present the SIRPOL results in RCW 57, for which the magnetic field is oriented along the cloud filaments, and in Carina Nebula, for which no intrinsic polarization is detected in the turbulent environment. We further describe TRIPOL, a compact and efficient polarimer to acquire polarized images simultaneously at g', r', and i' bands, which is recently developed at Nagoya University for adaption to small-aperture telescopes. We show how optical observations probe the translucent outer parts of a cloud, and when combining with infrared observations probing the dense parts, and with millimeter and submillimeter observations to sutdy the central embedded protostar, if there is one, would yield the magnetic field structure on different length scales in the star-formation process.

  18. Molecular clouds in the North American and Pelican Nebulae: structures

    SciTech Connect

    Zhang, Shaobo; Xu, Ye; Yang, Ji

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  19. Ab initio study of structural and mechanical property of solid molecular hydrogens

    NASA Astrophysics Data System (ADS)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  20. Synchrotron-based and globar-sourced molecular (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery.

    PubMed

    Yang, Ling; Yu, Peiqiang

    2017-01-02

    This paper aimed to review synchrotron-based and globar-sourced molecular infrared (micro)spectroscopy contributions to advances in new hulless barley (with structure alteration) research on molecular structure, molecular nutrition, and nutrient delivery in ruminants. It reviewed recent progress in barley varieties, its utilization for animal and human, inherent structure features and chemical make-up, evaluation and research methodology, breeding progress, rumen degradation, and intestinal digestion. The emphasis of this review was focused on the effect of alteration of carbohydrate traits of newly developed hulless barley on molecular structure changes and nutrient delivery and quantification of the relationship between molecular structure features and changes and truly absorbed nutrient supply to ruminants. This review provides an insight into how inherent structure changes on a molecular basis affect nutrient utilization and availability in ruminants.

  1. A tellurium-based cathepsin B inhibitor: Molecular structure, modelling, molecular docking and biological evaluation

    NASA Astrophysics Data System (ADS)

    Caracelli, Ignez; Vega-Teijido, Mauricio; Zukerman-Schpector, Julio; Cezari, Maria H. S.; Lopes, José G. S.; Juliano, Luiz; Santos, Paulo S.; Comasseto, João V.; Cunha, Rodrigo L. O. R.; Tiekink, Edward R. T.

    2012-04-01

    The crystallographically determined structure of biologically active 4,4-dichloro-1,3-diphenyl-4-telluraoct-2-en-1-one, 3, shows the coordination geometry for Te to be distorted ψ-pentagonal bipyramidal based on a C2OCl3(lone pair) donor set. Notable is the presence of an intramolecular axial Te⋯O(carbonyl) interaction, a design element included to reduce hydrolysis. Raman and molecular modelling studies indicate the persistence of the Te⋯O(carbonyl) interaction in the solution (CHCl3) and gas-phases, respectively. Docking studies of 3' (i.e. original 3 less one chloride) with Cathepsin B reveals a change in the configuration about the vinyl Cdbnd C bond, i.e. to E from Z (crystal structure). This isomerism allows the optimisation of interactions in the complex which features a covalent Tesbnd SGCys29 bond. Crucially, the E configuration observed for 3' allows for the formation of a hypervalent Te⋯O interaction as well as an O⋯Hsbnd O hydrogen bond with the Gly27 and Glu122 residues, respectively. Additional stabilisation is afforded by a combination of interactions spanning the S1, S2, S1' and S2' sub-sites of Cathepsin B. The greater experimental inhibitory activity of 3 compared with analogues is rationalised by the additional interactions formed between 3' and the His110 and His111 residues in the occluding loop, which serve to hinder the entrance to the active site.

  2. Prediction of molecular properties including symmetry from quantum-based molecular structural formulas, VIF.

    PubMed

    Alia, Joseph D; Vlaisavljevich, Bess; Abbot, Matthew; Warneke, Hallie; Mastin, Tyson

    2008-10-09

    Structurally covariant valency interaction formulas, VIF, gain chemical significance by comparison with resonance structures and natural bond orbital, NBO, bonding schemes and at the same time allow for additional prediction such as symmetry of ring systems and destabilization of electron pairs with respect to reference energy of -1/2 Eh. Comparisons are based on three chemical interpretations of Sinanoğlu's theory of structural covariance: (1) sets of structurally covariant quantum structural formulas, VIF, are interpreted as the same quantum operator represented in linearly related basis frames; (2) structurally covariant VIF pictures are interpreted as sets of molecular species with similar energy; and (3) the same VIF picture can be interpreted as different quantum operators, one-electron density or Hamiltonian; for example. According to these three interpretations, bond pair, lone pair, and free radical electrons understood in terms of a localized orbital representation are recognized as having energies above, below, or equal to a predetermined reference, frequently-1/2 Eh. The probable position of electron pairs and radical electrons is predicted. The selectivity of concerted ring closures in allyl anion and cation is described. Symmetries of conjugated ring systems are predicted according to their numbers of pi-electrons and spin-multiplicity. The pi-distortivity of benzene is predicted.The 3c/2e- H-bridging bonds in diborane are derived in a natural way according to the notion that the bridging bonds will have delocalizing interactions between them consistent with results of the NBO method. Key chemical bonding motifs are described using VIF. These include 2c/1e-, 2c/2e-, 2c/3e-, 3c/2e-, 3c/3e-,3c/4e-, 4n antiaromatic, and 4n+2 aromatic bonding systems. Some common organic functional groups are represented as VIF pictures and because these pictures can be interpreted simultaneously as one-electron density and Hamiltonian operators, the valence shell

  3. Light-operated machines based on threaded molecular structures.

    PubMed

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  4. Associations between single-nucleotide polymorphisms of human exonuclease 1 and the risk of hepatocellular carcinoma

    PubMed Central

    Tan, Shengkui; Qin, Ruoyun; Zhu, Xiaonian; Tan, Chao; Song, Jiale; Qin, Linyuan; Liu, Liu; Huang, Xiong; Li, Anhua; Qiu, Xiaoqiang

    2016-01-01

    Human exonuclease 1 (hEXO1) is an important nuclease involved in mismatch repair system that contributes to maintain genomic stability and modulate DNA recombination. This study is aimed to explore the associations between single-nucleotide polymorphisms (SNPs) of hEXO1 and the hereditary susceptibility of hepatocellular carcinoma (HCC). SNPs rs1047840, rs1776148, rs3754093, rs4149867, rs4149963, and rs1776181 of hEXO1 were examined from a hospital-based case-control study including 1,196 cases (HCC patients) and 1,199 controls (non-HCC patients) in Guangxi, China. We found the rs3754093 AG genotype decreased the risk of HCC (OR=0.714, 95% CI: 0.539∼0.946). According to the results of stratification analysis, rs3754093 mutant genotype AG/GG decreased the risk of HCC with some HCC protective factors such as non-smoking, non-alcohol consumption and non-HCC family history, but also decreased the risk of HCC with HBV infection. Moreover, it was correlated to non-tumor metastasis and increased the survival of HCC patients. The results from gene-environment interaction assay indicated all hEXO1 SNPs interacted with smoking, alcohol consumption, HBV infection in pathogenesis of HCC. However, gene-gene interaction assay suggested the interaction between rs3754093 and other 5 SNPs were associated with reducing the HCC risk. These results suggest rs3754093 exhibits a protective activity to decrease the incidence risk of HCC in Guangxi, China. In addition, all SNPs in this study interacted with environment risk factors in pathogenesis of HCC. PMID:27894089

  5. Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria.

    PubMed

    Zhang, Qingfeng; Siegel, T Nicolai; Martins, Rafael M; Wang, Fei; Cao, Jun; Gao, Qi; Cheng, Xiu; Jiang, Lubin; Hon, Chung-Chau; Scheidig-Benatar, Christine; Sakamoto, Hiroshi; Turner, Louise; Jensen, Anja T R; Claes, Aurelie; Guizetti, Julien; Malmquist, Nicholas A; Scherf, Artur

    2014-09-18

    Antigenic variation of the Plasmodium falciparum multicopy var gene family enables parasite evasion of immune destruction by host antibodies. Expression of a particular var subgroup, termed upsA, is linked to the obstruction of blood vessels in the brain and to the pathogenesis of human cerebral malaria. The mechanism determining upsA activation remains unknown. Here we show that an entirely new type of gene silencing mechanism involving an exonuclease-mediated degradation of nascent RNA controls the silencing of genes linked to severe malaria. We identify a novel chromatin-associated exoribonuclease, termed PfRNase II, that controls the silencing of upsA var genes by marking their transcription start site and intron-promoter regions leading to short-lived cryptic RNA. Parasites carrying a deficient PfRNase II gene produce full-length upsA var transcripts and intron-derived antisense long non-coding RNA. The presence of stable upsA var transcripts overcomes monoallelic expression, resulting in the simultaneous expression of both upsA and upsC type PfEMP1 proteins on the surface of individual infected red blood cells. In addition, we observe an inverse relationship between transcript levels of PfRNase II and upsA-type var genes in parasites from severe malaria patients, implying a crucial role of PfRNase II in severe malaria. Our results uncover a previously unknown type of post-transcriptional gene silencing mechanism in malaria parasites with repercussions for other organisms. Additionally, the identification of RNase II as a parasite protein controlling the expression of virulence genes involved in pathogenesis in patients with severe malaria may provide new strategies for reducing malaria mortality.

  6. Association between three exonuclease 1 polymorphisms and cancer risks: a meta-analysis

    PubMed Central

    Chen, Zi-Yu; Zheng, Si-Rong; Zhong, Jie-Hui; Zhuang, Xiao-Duan; Zhou, Jue-Yu

    2016-01-01

    To date, the results of studies exploring the relation between exonuclease 1 (Exo1) polymorphisms and cancer risks have differed. In this study, we performed a meta-analysis to investigate the effect of the three most extensively studied Exo1 polymorphisms (Pro757Leu, Glu589Lys, and Glu670Gly) on cancer susceptibility. The related studies published before August 5, 2015, were collected by searching the PubMed and EMBASE databases. We found 16 publications containing studies that were eligible for our study, including 10 studies for Pro757Leu polymorphism (4,093 cases and 3,834 controls), 12 studies for Glu589Lys polymorphism (6,479 cases and 6,550 controls), and 7 studies for Glu670Gly polymorphism (3,700 cases and 3,496 controls). Pooled odds ratios and 95% confidence intervals were used to assess the strength of the associations, and all the statistical analyses were calculated using the software program STATA version 12.0. Our results revealed that the Pro757Leu polymorphism was significantly associated with a reduced cancer risk, whereas an inverse association was found for the Glu589Lys polymorphism. Furthermore, subgroup analysis of smoking status indicated that the Glu589Lys polymorphism was significantly associated with an increased cancer risk in smokers, but not in nonsmokers. However, no evidence was found for an association between the Glu670Gly polymorphism and cancer risk. In conclusion, this meta-analysis suggests that the Pro757Leu polymorphism may provide protective effects against cancer, while the Glu589Lys polymorphism may be a risk factor for cancer. Moreover, the Glu670Gly polymorphism may have no influence on cancer susceptibility. In the future, large-scaled and well-designed studies are needed to achieve a more precise and comprehensive result. PMID:26966378

  7. Quantitative structure-property relationships for predicting Henry's law constant from molecular structure.

    PubMed

    Dearden, John C; Schüürmann, Gerrit

    2003-08-01

    Various models are available for the prediction of Henry's law constant (H) or the air-water partition coefficient (Kaw), its dimensionless counterpart. Incremental methods are based on structural features such as atom types, bond types, and local structural environments; other regression models employ physicochemical properties, structural descriptors such as connectivity indices, and descriptors reflecting the electronic structure. There are also methods to calculate H from the ratio of vapor pressure (p(v)) and water solubility (S(w)) that in turn can be estimated from molecular structure, and quantum chemical continuum-solvation models to predict H via the solvation-free energy (deltaG(s)). This review is confined to methods that calculate H from molecular structure without experimental information and covers more than 40 methods published in the last 26 years. For a subset of eight incremental methods and four continuum-solvation models, a comparative analysis of their prediction performance is made using a test set of 700 compounds that includes a significant number of more complex and drug-like chemical structures. The results reveal substantial differences in the application range as well as in the prediction capability, a general decrease in prediction performance with decreasing H, and surprisingly large individual prediction errors, which are particularly striking for some quantum chemical schemes. The overall best-performing method appears to be the bond contribution method as implemented in the HENRYWIN software package, yielding a predictive squared correlation coefficient (q2) of 0.87 and a standard error of 1.03 log units for the test set.

  8. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed

    Karle, J M; Karle, I L

    1989-07-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  9. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  10. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  11. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    PubMed Central

    de Steenhuijsen Piters, Wouter A. A.

    2016-01-01

    ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

  12. Pervasive small-scale structure in molecular clouds

    NASA Technical Reports Server (NTRS)

    Martin, B.; Lada, E.

    1986-01-01

    An unbiased CO survey of molecular cloud cores was completed, and the profiles were analyzed within the context of a model for emission from clumpy clouds. It was found that all sources observed contain a significant amount of structure that is not resolved with our 2.3-arcmin beam, and that the parameters which describe the degree of clumping span a remarkably narrow range of the possible values. We studied two separate samples of cloud cores: a large sample of warm cores from the Massachusetts-Stony Brook 12CO survey of the first galactic quadrant, and a sample of cool cores in the Taurus dark clouds chosen primarily on the basis of H2CO emission. We observed all sources in the 1-0 transition of 12CO and 13CO with the 5-m telescope of the Millimeter Wave Observatory. The 12CO/13CO ratios can be explained if there is unresolved structure giving rise to significant variations of opacity across the beam. Our model cloud consists of a large number of identical clumps distributed randomly in the beam. These clumps have velocity widths v small compared to the width of the observed profile, which is determined by the relative motion of the clumps. The entire cloud is isothermal and in local thermodynamic equilibrium. With these assumptions the intensity and linewidth ratios depend on three parameters: the abundance ratio; the peak 13CO opacity through a single clump, tau(0); and the average number of clumps on a line of sight N. Small tau(0) and large N correspond to the microturbulent limit, which is indistinguishable from a uniform gas distribution. In the other extreme, large tau(0) and snall N, at a given velocity at most one clump contributes to the profile on each line of sight. A figure is presented which shows the model parameters which reproduce the measured intensity and linewidth ratios for the sample of warm cores, assuming an abundance ratio of 75.

  13. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  14. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  15. Structural basis for the antifolding activity of a molecular chaperone.

    PubMed

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G

    2016-09-08

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

  16. Molecular structures of fructans from Agave tequilana Weber var. azul.

    PubMed

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  17. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; vonAllmen, Paul

    2007-01-01

    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  18. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    PubMed Central

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-01-01

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1. PMID:23880846

  19. Death associated protein kinases: molecular structure and brain injury.

    PubMed

    Nair, Syam; Hagberg, Henrik; Krishnamurthy, Rajanikant; Thornton, Claire; Mallard, Carina

    2013-07-04

    Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk) family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  20. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks.

  1. Structural basis for the antifolding activity of a molecular chaperone

    PubMed Central

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-01-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase (PhoA) and maltose binding protein (MBP) captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of the non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone. PMID:27501151

  2. Molecular structural characteristics governing biocatalytic oxidation of PAHs with hemoglobin.

    PubMed

    Niu, Junfeng; Yu, Gang

    2004-09-01

    Based on some fundamental quantum chemical descriptors computed by PM3 hamiltonian, two quantitative structure-activity relationship (QSAR) models for biocatalytic oxidation specific activity of unmodified and chemically modified hemoglobin in the oxidation of different polycyclic aromatic hydrocarbons (PAHs) in 15% acetonitrile were developed, respectively, using partial least squares analysis (PLS). The cross-validated Q(cum)(2) values for the two optimal QSAR models are 0.785 and 0.747, respectively, indicating a good predictive ability for biocatalytic oxidation specific activity of PAHs. The main factors affecting specific activity of PAHs are most positive net atomic charges on a hydrogen atom (q(H)(+)), largest negative atomic charge on a carbon atom (q(C)(-)), dipole moment (μ), the energy of the highest occupied molecular orbital (E(HOMO)), and (E(LUMO) - E(HOMO))(2). The biocatalytic oxidation specific activity of PAHs with big q(C)(-) and (E(LUMO) - E(HOMO))(2) values tends to be slow. Increasing q(H)(+), μ, and E(HOMO) values of PAHs leads to increase of specific activity.

  3. Structural basis for the antifolding activity of a molecular chaperone

    NASA Astrophysics Data System (ADS)

    Huang, Chengdong; Rossi, Paolo; Saio, Tomohide; Kalodimos, Charalampos G.

    2016-09-01

    Molecular chaperones act on non-native proteins in the cell to prevent their aggregation, premature folding or misfolding. Different chaperones often exert distinct effects, such as acceleration or delay of folding, on client proteins via mechanisms that are poorly understood. Here we report the solution structure of SecB, a chaperone that exhibits strong antifolding activity, in complex with alkaline phosphatase and maltose-binding protein captured in their unfolded states. SecB uses long hydrophobic grooves that run around its disk-like shape to recognize and bind to multiple hydrophobic segments across the length of non-native proteins. The multivalent binding mode results in proteins wrapping around SecB. This unique complex architecture alters the kinetics of protein binding to SecB and confers strong antifolding activity on the chaperone. The data show how the different architectures of chaperones result in distinct binding modes with non-native proteins that ultimately define the activity of the chaperone.

  4. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  5. Accessory proteins assist exonuclease-deficient bacteriophage T4 DNA polymerase in replicating past an abasic site

    PubMed Central

    Blanca, Giuseppina; Delagoutte, Emmanuelle; Tanguy le gac, Nicolas; Johnson, Neil P.; Baldacci, Giuseppe; Villani, Giuseppe

    2006-01-01

    Replicative DNA polymerases, such as T4 polymerase, possess both elongation and 3′–5′ exonuclease proofreading catalytic activities. They arrest at the base preceding DNA damage on the coding DNA strand and specialized DNA polymerases have evolved to replicate across the lesion by a process known as TLS (translesion DNA synthesis). TLS is considered to take place in two steps that often require different enzymes, insertion of a nucleotide opposite the damaged template base followed by extension from the inserted nucleotide. We and others have observed that inactivation of the 3′–5′ exonuclease function of T4 polymerase enables TLS across a single site-specific abasic [AP (apurinic/apyrimidinic)] lesion. In the present study we report a role for auxiliary replicative factors in this reaction. When replication is performed with a large excess of DNA template over DNA polymerase in the absence of auxiliary factors, the exo− polymerase (T4 DNA polymerase deficient in the 3′–5′ exonuclease activity) inserts one nucleotide opposite the AP site but does not extend past the lesion. Addition of the clamp processivity factor and the clamp loader complex restores primer extension across an AP lesion on a circular AP-containing DNA substrate by the exo− polymerase, but has no effect on the wild-type enzyme. Hence T4 DNA polymerase exhibits a variety of responses to DNA damage. It can behave as a replicative polymerase or (in the absence of proofreading activity) as a specialized DNA polymerase and carry out TLS. As a specialized polymerase it can function either as an inserter or (with the help of accessory proteins) as an extender. The capacity to separate these distinct functions in a single DNA polymerase provides insight into the biochemical requirements for translesion DNA synthesis. PMID:17064253

  6. Mutant poisoning demonstrates a nonsequential mechanism for digestion of double-stranded DNA by λ exonuclease trimers.

    PubMed

    Pan, Xinlei; Yan, Jing; Patel, Aalapi; Wysocki, Vicki H; Bell, Charles E

    2015-01-27

    λ Exonuclease (λexo) is a highly processive 5'-3' exonuclease that binds double-stranded DNA (dsDNA) ends and digests the 5'-strand into mononucleotides. The enzyme forms a toroidal homotrimer with a central tapered channel for tracking along the DNA. During catalysis, dsDNA enters the open end of the channel, and the 5'-strand is digested at one of the three active sites. It is currently not known if λexo uses a sequential mechanism, in which the DNA moves from one active site to the next around the trimer for each round of catalysis or a nonsequential mechanism, in which the DNA locks onto a single active site for multiple rounds. To understand how λexo uses its three active sites, we used a mutant poisoning approach, in which a 6xHis-tagged K131A inactive mutant of λexo was mixed with untagged wild type (WT) to form hybrid trimers. Nickel-spin pull-down analysis confirmed complete subunit exchange after 1 h at 37 °C. Exonuclease assays revealed an approximately linear decrease in activity with increasing fraction of mutant, as expected for a nonsequential mechanism. By fitting the observed rates of digestion to a simple mathematical model, the individual rates of the two hybrid species of trimer were determined. This analysis showed that trimers containing only one or two WT subunits contribute significantly to the observed activity, in further agreement with a nonsequential mechanism. Finally, purification of hybrid trimer mixtures by Ni-spin chromatography, to remove the contribution from fully WT trimers, also resulted in significant levels of activity, again consistent with a nonsequential mechanism.

  7. Poly(ADP-ribose) polymerase 1 regulates both the exonuclease and helicase activities of the Werner syndrome protein.

    PubMed

    von Kobbe, Cayetano; Harrigan, Jeanine A; Schreiber, Valérie; Stiegler, Patrick; Piotrowski, Jason; Dawut, Lale; Bohr, Vilhelm A

    2004-01-01

    Werner syndrome (WS) is a genetic premature aging disorder in which patients appear much older than their chronological age. The gene mutated in WS encodes a nuclear protein (WRN) which possesses 3'-5' exonuclease and ATPase-dependent 3'-5' helicase activities. The genomic instability associated with WS cells and the biochemical characteristics of WRN suggest that WRN plays a role in DNA metabolic pathways such as transcription, replication, recombination and repair. Recently we have identified poly(ADP-ribose) polymerase-1 (PARP-1) as a new WRN interacting protein. In this paper, we further mapped the interacting domains. We found that PARP-1 bound to the N-terminus of WRN and to the C-terminus containing the RecQ-conserved (RQC) domain. WRN bound to the N-terminus of PARP-1 containing DNA binding and BRCA1 C-terminal (BRCT) domains. We show that unmodified PARP-1 inhibited both WRN exonuclease and helicase activities, and to our knowledge is the only known WRN protein partner that inactivates both of the WRN's catalytic activities suggesting a biologically significant regulation. Moreover, this dual inhibition seems to be specific for PARP-1, as PARP-2 did not affect WRN helicase activity and only slightly inhibited WRN exonuclease activity. The differential effect of PARP-1 and PARP-2 on WRN catalytic activity was not due to differences in affinity for WRN or the DNA substrate. Finally, we demonstrate that the inhibition of WRN by PARP-1 was influenced by the poly(ADP-ribosyl)ation state of PARP-1. The biological relevance of the specific modulation of WRN catalytic activities by PARP-1 are discussed in the context of pathways in which these proteins may function together, namely in the repair of DNA strand breaks.

  8. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

    PubMed

    Walsh, Tiffany R

    2017-07-18

    An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

  9. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  10. How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

    NASA Technical Reports Server (NTRS)

    Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

    2000-01-01

    density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

  11. Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae

    PubMed Central

    2011-01-01

    Background SXT is an integrating conjugative element (ICE) originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively. Results SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo. Conclusions The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V. cholerae cells, through

  12. Functional characterization of an alkaline exonuclease and single strand annealing protein from the SXT genetic element of Vibrio cholerae.

    PubMed

    Chen, Wen-yang; Ho, John Ws; Huang, Jian-dong; Watt, Rory M

    2011-04-18

    SXT is an integrating conjugative element (ICE) originally isolated from Vibrio cholerae, the bacterial pathogen that causes cholera. It houses multiple antibiotic and heavy metal resistance genes on its ca. 100 kb circular double stranded DNA (dsDNA) genome, and functions as an effective vehicle for the horizontal transfer of resistance genes within susceptible bacterial populations. Here, we characterize the activities of an alkaline exonuclease (S066, SXT-Exo) and single strand annealing protein (S065, SXT-Bet) encoded on the SXT genetic element, which share significant sequence homology with Exo and Bet from bacteriophage lambda, respectively. SXT-Exo has the ability to degrade both linear dsDNA and single stranded DNA (ssDNA) molecules, but has no detectable endonuclease or nicking activities. Adopting a stable trimeric arrangement in solution, the exonuclease activities of SXT-Exo are optimal at pH 8.2 and essentially require Mn2+ or Mg2+ ions. Similar to lambda-Exo, SXT-Exo hydrolyzes dsDNA with 5'- to 3'-polarity in a highly processive manner, and digests DNA substrates with 5'-phosphorylated termini significantly more effectively than those lacking 5'-phosphate groups. Notably, the dsDNA exonuclease activities of both SXT-Exo and lambda-Exo are stimulated by the addition of lambda-Bet, SXT-Bet or a single strand DNA binding protein encoded on the SXT genetic element (S064, SXT-Ssb). When co-expressed in E. coli cells, SXT-Bet and SXT-Exo mediate homologous recombination between a PCR-generated dsDNA fragment and the chromosome, analogous to RecET and lambda-Bet/Exo. The activities of the SXT-Exo protein are consistent with it having the ability to resect the ends of linearized dsDNA molecules, forming partially ssDNA substrates for the partnering SXT-Bet single strand annealing protein. As such, SXT-Exo and SXT-Bet may function together to repair or process SXT genetic elements within infected V. cholerae cells, through facilitating homologous DNA

  13. Spontaneous induction of colicin E1 in Escherichia coli strains deficient in both exonucleases I and V.

    PubMed Central

    Bassett, C L; Kushner, S R

    1985-01-01

    Colicin E1 synthesis is spontaneously induced in pRSF2124-carrying strains of Escherichia coli deficient in exonucleases I (sbcB) and V (recB recC). In contrast, the specific activity of beta-lactamase, which is also encoded by pRSF2124, is not affected by the absence of these enzymes. These results suggest that colicin E1 induction is specific and does not result either from a significant change in overall plasmid transcription or copy number. Furthermore, the level of spontaneous induction was similar to that obtained with mitomycin C. PMID:3934144

  14. Cloning of thermostable DNA polymerases from hyperthermophilic marine Archaea with emphasis on Thermococcus sp. 9 degrees N-7 and mutations affecting 3'-5' exonuclease activity.

    PubMed Central

    Southworth, M W; Kong, H; Kucera, R B; Ware, J; Jannasch, H W; Perler, F B

    1996-01-01

    Five extremely thermophilic Archaea from hydrothermal vents were isolated, and their DNA polymerases were cloned and expressed in Escherichia coli. Protein splicing elements (inteins) are present in many archaeal DNA polymerases, but only the DNA polymerase from strain GB-C contained an intein. Of the five cloned DNA polymerases, the Thermococcus sp. 9 degrees N-7 DNA polymerase was chosen for biochemical characterization. Thermococcus sp. 9 degrees N-7 DNA polymerase exhibited temperature-sensitive strand displacement activity and apparent Km values for DNA and dNTP similar to those of Thermococcus litoralis DNA polymerase. Six substitutions in the 3'-5' exonuclease motif I were constructed in an attempt to reduce the 3'-5' exonuclease activity of Thermococcus sp. 9 degrees N-7 DNA polymerase. Five mutants resulted in no detectable 3'-5' exonuclease activity, while one mutant (Glul43Asp) had <1% of wild-type activity. Images Fig. 2 Fig. 3 PMID:8643567

  15. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  16. A Structural and Molecular Approach for the Study Biomarkers

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie; Vali, Hojatollah; Sears, S. Kelly; Roh, Yul

    2001-01-01

    Investigation of the nucleation and growth of crystals in both abiotic and biotic systems is critical to seemingly diverse disciplines of geology, biology, environmental science, and astrobiology. While there are abundant studies devoted to the determination of the structure and composition of inorganic crystals, as well as to the development of thermodynamic and kinetic models, it is only recently that research efforts have been directed towards understanding mineralization in biological systems (i.e., biomineralization). Biomineralization refers to the processes by which living organisms form inorganic solids. Studies of the processes of biomineralization under low temperature aqueous conditions have focused primarily on magnetite forming bacteria and shell forming marine organisms. Many of the biological building materials consist of inorganic minerals (calcium carbonate, calcium phosphate, silica or iron oxide) intricately combined with organic polymers (like proteins). More recently, efforts have been undertaken to explore the nature of biological activities in ancient rocks. In the absence of well-preserved microorganisms or genetic material required for the polmerase chain reaction (PCR) method in molecular phylogenetic studies, using biominerals as biomarkers offers an alternative approach for the recognition of biogenic activity in both terrestrial and extraterrestrial environments. The primary driving force in biomineralization is the interaction between organic and inorganic phases. Thus, the investigation of the ultrastructure and the nature of reactions at the molecular level occurring at the interface between inorganic and organic phases is essential to understanding the processes leading to the nucleation and growth of crystals. It is recognized that crystal surfaces can serve as the substrate for the organization of organic molecules that lead to the formation of polymers and other complex organic molecules, and in discussions of the origins of life

  17. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  18. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  19. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    ERIC Educational Resources Information Center

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  20. Probing the molecular structure of interfacial films and crystals

    NASA Astrophysics Data System (ADS)

    Wang, Anfeng

    The properties of outside surfaces were found to play an important role in the nucleation and crystallization processes. Thus controlling the surface properties would provide an effective means for crystal engineering. Hydrophobic surface is prepared by self-assembled monolayer (SAM) formation of octadecyltrichlorosilane (OTS) on silicon surface, with the hydrophobicity adjusted by the monolayer coverage. Silicon wafer treated by RCA method is hydrophilic, so are SAMs formed by two amine-terminated organosilanes on silicon. However these three hydrophilic surfaces are unstable, due to contamination of the amine-terminated SAMs and hydrolysis of RCA treated silicon. Polymethine dyes, BDH+Cl- and BDH +ClO4-, are synthesized and characterized by UV spectra and crystal morphology. They have identical UV spectrum in dilute solutions due to the same chromophore, and J-aggregation happens at much higher concentrations. IR spectra are analyzed to monitor the crystallization process of BDH+Cl- OTS SAM surface and the crystallization process of BDH+Cl- on substrates with varying hydrophobicity was monitored by optical microscopy and compared. Due to the extreme flexibility of polysiloxane, silicone surfactants can arrange themselves at the interfaces quickly to adopt configurations with minimum free energy. Polysiloxane is hydrophobic but not oleophilic, which makes them effective emulsifiers and stabilizers in aqueous and nonaqueous media. The interaction between an AFM Si3N4 tip and a hydrophobic surface in silicone polyether (SPE) solution in the presence of ethanol was investigated by Atomic Force Microscopy (AFM) force measurement. ABA triblock type and comb-type SPE surfactants, adsorbed at the liquid-solid interface, provide steric barriers, even with significant addition of ethanol. On the contrary, conventional low-molecular weight and polymeric alkyl surfactants display no steric barrier even in the presence of moderate amount of ethanol. This unique property makes

  1. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    PubMed

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M.; Prates, Luciana L.; Yu, Peiqiang

    2017-08-01

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions.

  3. Insight into mechanisms of 3′-5′ exonuclease activity and removal of bulky 8,5′-cyclopurine adducts by apurinic/apyrimidinic endonucleases

    PubMed Central

    Mazouzi, Abdelghani; Vigouroux, Armelle; Aikeshev, Bulat; Brooks, Philip J.; Saparbaev, Murat K.; Morera, Solange; Ishchenko, Alexander A.

    2013-01-01

    8,5′-cyclo-2'-deoxyadenosine (cdA) and 8,5′-cyclo-2'-deoxyguanosine generated in DNA by both endogenous oxidative stress and ionizing radiation are helix-distorting lesions and strong blocks for DNA replication and transcription. In duplex DNA, these lesions are repaired in the nucleotide excision repair (NER) pathway. However, lesions at DNA strand breaks are most likely poor substrates for NER. Here we report that the apurinic/apyrimidinic (AP) endonucleases—Escherichia coli Xth and human APE1—can remove 5′S cdA (S-cdA) at 3′ termini of duplex DNA. In contrast, E. coli Nfo and yeast Apn1 are unable to carry out this reaction. None of these enzymes can remove S-cdA adduct located at 1 or more nt away from the 3′ end. To understand the structural basis of 3′ repair activity, we determined a high-resolution crystal structure of E. coli Nfo-H69A mutant bound to a duplex DNA containing an α-anomeric 2′-deoxyadenosine:T base pair. Surprisingly, the structure reveals a bound nucleotide incision repair (NIR) product with an abortive 3′-terminal dC close to the scissile position in the enzyme active site, providing insight into the mechanism for Nfo-catalyzed 3′→5′ exonuclease function and its inhibition by 3′-terminal S-cdA residue. This structure was used as a template to model 3′-terminal residues in the APE1 active site and to explain biochemical data on APE1-catalyzed 3′ repair activities. We propose that Xth and APE1 may act as a complementary repair pathway to NER to remove S-cdA adducts from 3′ DNA termini in E. coli and human cells, respectively. PMID:23898172

  4. 3'-5' exonuclease of Klenow fragment: role of amino acid residues within the single-stranded DNA binding region in exonucleolysis and duplex DNA melting.

    PubMed

    Lam, Wai-Chung; Thompson, Elizabeth H Z; Potapova, Olga; Sun, Xiaojun Chen; Joyce, Catherine M; Millar, David P

    2002-03-26

    The mechanism of the 3'-5' exonuclease activity of the Klenow fragment of DNA polymerase I has been investigated with a combination of biochemical and spectroscopic techniques. Site-directed mutagenesis was used to make alanine substitutions of side chains that interact with the DNA substrate on the 5' side of the scissile phosphodiester bond. Kinetic parameters for 3'-5' exonuclease cleavage of single- and double-stranded DNA substrates were determined for each mutant protein in order to probe the role of the selected side chains in the exonuclease reaction. The results indicate that side chains that interact with the penultimate nucleotide (Q419, N420, and Y423) are important for anchoring the DNA substrate at the active site or ensuring proper geometry of the scissile phosphate. In contrast, side chains that interact with the third nucleotide from the DNA terminus (K422 and R455) do not participate directly in exonuclease cleavage of single-stranded DNA. Alanine substitutions of Q419, Y423, and R455 have markedly different effects on the cleavage of single- and double-stranded DNA, causing a much greater loss of activity in the case of a duplex substrate. Time-resolved fluorescence anisotropy decay measurements with a dansyl-labeled primer/template indicate that the Q419A, Y423A, and R455A mutations disrupted the ability of the Klenow fragment to melt duplex DNA and bind the frayed terminus at the exonuclease site. In contrast, the N420A mutation stabilized binding of a duplex terminus to the exonuclease site, suggesting that the N420 side chain facilitates the 3'-5' exonuclease reaction by introducing strain into the bound DNA substrate. Together, these results demonstrate that protein side chains that interact with the second or third nucleotides from the terminus can participate in both the chemical step of the exonuclease reaction, by anchoring the substrate in the active site or by ensuring proper geometry of the scissile phosphate, and in the prechemical

  5. Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development.

    PubMed

    Chen, Zhen; Wilmanns, Matthias; Zeng, An-Ping

    2010-10-01

    The future of industrial biotechnology requires efficient development of highly productive and robust strains of microorganisms. Present praxis of strain development cannot adequately fulfill this requirement, primarily owing to the inability to control reactions precisely at a molecular level, or to predict reliably the behavior of cells upon perturbation. Recent developments in two areas of biology are changing the situation rapidly: structural biology has revealed details about enzymes and associated bioreactions at an atomic level; and synthetic biology has provided tools to design and assemble precisely controllable modules for re-programming cellular metabolic circuitry. However, because of different emphases, to date, these two areas have developed separately. A linkage between them is desirable to harness their concerted potential. We therefore propose structural synthetic biotechnology as a new field in biotechnology, specifically for application to the development of industrial microbial strains. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

    PubMed Central

    Shinbrot, Eve; Henninger, Erin E.; Weinhold, Nils; Covington, Kyle R.; Göksenin, A. Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M.; Gibbs, Richard A.; Sander, Chris; Pursell, Zachary F.

    2014-01-01

    Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication. PMID:25228659

  7. Mediator-free triple-enzyme cascade electrocatalytic aptasensor with exonuclease-assisted target recycling and hybridization chain reaction amplification.

    PubMed

    Peng, Kanfu; Zhao, Hongwen; Yuan, Yali; Yuan, Ruo; Wu, Xiongfei

    2014-05-15

    The amplified sensitive detection of protein is essential to biomedical research as well as clinical diagnosis. Here, we developed an ultrasensitive mediator-free triple-enzyme cascade electrocatalytic aptasensor for thrombin detection on the basis of exonuclease-assisted target recycling and hybridization chain reaction (HCR) amplification strategy. The double strands constructed by the hybridization of thrombin binding aptamer (S1) with its complementary strand (S2) were firstly assembled on the electrode. Upon addition of target to the system, the S1 recognized thrombin and left off electrode to make space for assembly of hybrid-primer probe (H0). Then, the H0 triggered the HCR to form the multi-functional hemin/G-quadruplex DNAzyme nanowires. In the mediator-free triple-enzyme cascade electrocatalytic amplification system, the hemin/G-quadruplex DNAzyme nanowires here simultaneously played three roles: the redox probe, NADH oxidase and HRP-mimicking DNAzyme, respectively, which effectively avoided the fussy redox probe and enzyme labeling process, serving a useful alternative or supplement to conventional assays that typically suffer from complexity and poor sensitivity. Additionally, in order to improve the assembly amount of hemin/G-quadruplex DNAzyme nanowire, the exonuclease-assisted target recycling amplification was used for the continuous removal of S1. As a result, the proposed method can detect thrombin specifically with a detection limit as low as 20 fM. © 2013 Published by Elsevier B.V.

  8. Electrochemical DNA sensor for specific detection of picomolar Hg(II) based on exonuclease III-assisted recycling signal amplification.

    PubMed

    Gan, Xiaorong; Zhao, Huimin; Chen, Shuo; Quan, Xie

    2015-03-21

    An ultrasensitive methodology was successfully developed for the quantitative detection of picomolar Hg(2+) based on the combination of thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry and exonuclease III-aided recycling signal amplification. Single-strand probe DNA was immobilized on an Au electrode via an Au-S bond. In the presence of Hg(2+), the probe DNA hybridized with the target DNA containing four thymine-thymine (T-T) mismatches via the Hg(2+)-mediated coordination of T-Hg(2+)-T base pairs. Then the probe DNA in the DNA duplex was specifically recognized and selectively digested by exonuclease III; in contrast the target DNA was safely dissociated from the DNA duplexes to subsequently hybridize with a new signal probe, leading to target recycling and signal amplification. As a result, the peak current caused by the electrostatic interactions of [Ru(NH3)6](3+) cations with the backbone of the probe DNA decreased by different degrees, corresponding to the Hg(2+) concentrations. Under the optimum conditions, the proposed electrochemical DNA biosensor showed a robust detection limit as low as 1 pM (S/N = 3), with a wide linear range from 0.01 to 500 nM and good selectivity. In addition, the proposed method was successfully applied to assay Hg(2+) in real environmental samples.

  9. Application of exonuclease III-aided target recycling in flow cytometry: DNA detection sensitivity enhanced by orders of magnitude.

    PubMed

    Lu, Jie; Paulsen, Ian T; Jin, Dayong

    2013-09-03

    DNA-functionalized microspheres in conjugation with flow cytometry detection are widely used for high-throughput nucleic acid assays. Although such assays are rapid and capable of simultaneous analysis of multiple nucleic acid analytes in a single test, the intrinsic limitation in sensitivity remains challenging. Here we report a simple, highly sensitive, and reproducible method based on Exonuclease III-aided target recycling technique applied for DNA quantification in flow cytometry. By loading a high density of Cy5-labeled probe DNA on microspheres (15 μm), we achieved hitherto unreported DNA detection limit of 3.2 pM in flow cytometry bead assay, enhancing the sensitivity by a factor of over 56.8 compared to the conventional direct hybridization bead assay. Furthermore, we evaluated multiplexing capability by simultaneous detections of two target DNAs with FAM and Cy5 reporter conjugated probes. Therefore, the novel Exonuclease III-amplified flow cytometry bead assay has great potential for the rapid, sensitive, and accurate detection and quantification of nucleic acids in clinical diagnosis and biomedical research.

  10. The exonuclease and host shutoff functions of the SOX protein of Kaposi's sarcoma-associated herpesvirus are genetically separable.

    PubMed

    Glaunsinger, Britt; Chavez, Leonard; Ganem, Don

    2005-06-01

    The Kaposi's sarcoma-associated herpesvirus (KSHV) SOX protein, encoded by ORF37, promotes shutoff of host cell gene expression during lytic viral replication by dramatically impairing mRNA accumulation. SOX is the KSHV homolog of the alkaline exonuclease of other herpesviruses, which has been shown to function as a DNase involved in processing and packaging the viral genome. Although the exonuclease activity of these proteins is widely conserved across all herpesviruses, the host shutoff activity observed for KSHV SOX is not. We show here that SOX expression sharply reduces the half-life of target mRNAs. Extensive mutational analysis reveals that the DNase and host shutoff activities of SOX are genetically separable. Lesions affecting the DNase activity cluster in conserved regions of the protein, but residues critical for mRNA degradation are not conserved across the viral family. Additionally, we present evidence suggesting that the two different functions of SOX occur within distinct cellular compartments-DNase activity in the nucleus and host shutoff activity in the cytoplasm.

  11. Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease

    PubMed Central

    Nicholls, Thomas J.; Zsurka, Gábor; Peeva, Viktoriya; Schöler, Susanne; Szczesny, Roman J.; Cysewski, Dominik; Reyes, Aurelio; Kornblum, Cornelia; Sciacco, Monica; Moggio, Maurizio; Dziembowski, Andrzej; Kunz, Wolfram S.; Minczuk, Michal

    2014-01-01

    MGME1, also known as Ddk1 or C20orf72, is a mitochondrial exonuclease found to be involved in the processing of mitochondrial DNA (mtDNA) during replication. Here, we present detailed insights on the role of MGME1 in mtDNA maintenance. Upon loss of MGME1, elongated 7S DNA species accumulate owing to incomplete processing of 5′ ends. Moreover, an 11-kb linear mtDNA fragment spanning the entire major arc of the mitochondrial genome is generated. In contrast to control cells, where linear mtDNA molecules are detectable only after nuclease S1 treatment, the 11-kb fragment persists in MGME1-deficient cells. In parallel, we observed characteristic mtDNA duplications in the absence of MGME1. The fact that the breakpoints of these mtDNA rearrangements do not correspond to either classical deletions or the ends of the linear 11-kb fragment points to a role of MGME1 in processing mtDNA ends, possibly enabling their repair by homologous recombination. In agreement with its functional involvement in mtDNA maintenance, we show that MGME1 interacts with the mitochondrial replicase PolgA, suggesting that it is a constituent of the mitochondrial replisome, to which it provides an additional exonuclease activity. Thus, our results support the viewpoint that MGME1-mediated mtDNA processing is essential for faithful mitochondrial genome replication and might be required for intramolecular recombination of mtDNA. PMID:24986917

  12. Coordinated Ribosomal ITS2 RNA Processing by the Las1 Complex Integrating Endonuclease, Polynucleotide Kinase, and Exonuclease Activities.

    PubMed

    Gasse, Lisa; Flemming, Dirk; Hurt, Ed

    2015-12-03

    The rapidly evolving internal transcribed spacer 2 (ITS2) in the pre-ribosomal RNA is one of the most commonly applied phylogenetic markers at species and genus level. Yet, during ribosome biogenesis ITS2 is removed in all eukaryotes by a common, but still unknown, mechanism. Here we describe the existence of an RNA processome, assembled from four conserved subunits, Las1-Grc3-Rat1-Rai1, that carries all the necessary RNA processing enzymes to mediate coordinated ITS2 rRNA removal. Las1 is the long-sought-after endonuclease cleaving 27SB pre-rRNA at site C2 to yield a 5'-OH end at the 26S pre-rRNA and 2',3' cyclic phosphate at the 3' end of 7S pre-rRNA. Subsequently, polynucleotide kinase Grc3 catalyzes ATP-dependent 5'-OH phosphorylation of 26S pre-rRNA, which in turn enables Rat1-Rai1 exonuclease to generate 25S' pre-rRNA. ITS2 processing is reminiscent of tRNA splicing, but instead of subsequent tRNA ligation, the Las1 complex carries along an exonuclease tool to degrade the ITS2 rRNA. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. ATM-dependent phosphorylation of MRE11 controls extent of resection during homology directed repair by signalling through Exonuclease 1.

    PubMed

    Kijas, Amanda W; Lim, Yi Chieh; Bolderson, Emma; Cerosaletti, Karen; Gatei, Magtouf; Jakob, Burkhard; Tobias, Frank; Taucher-Scholz, Gisela; Gueven, Nuri; Oakley, Greg; Concannon, Patrick; Wolvetang, Ernst; Khanna, Kum Kum; Wiesmüller, Lisa; Lavin, Martin F

    2015-09-30

    The MRE11/RAD50/NBS1 (MRN) complex plays a central role as a sensor of DNA double strand breaks (DSB) and is responsible for the efficient activation of ataxia-telangiectasia mutated (ATM) kinase. Once activated ATM in turn phosphorylates RAD50 and NBS1, important for cell cycle control, DNA repair and cell survival. We report here that MRE11 is also phosphorylated by ATM at S676 and S678 in response to agents that induce DNA DSB, is dependent on the presence of NBS1, and does not affect the association of members of the complex or ATM activation. A phosphosite mutant (MRE11S676AS678A) cell line showed decreased cell survival and increased chromosomal aberrations after radiation exposure indicating a defect in DNA repair. Use of GFP-based DNA repair reporter substrates in MRE11S676AS678A cells revealed a defect in homology directed repair (HDR) but single strand annealing was not affected. More detailed investigation revealed that MRE11S676AS678A cells resected DNA ends to a greater extent at sites undergoing HDR. Furthermore, while ATM-dependent phosphorylation of Kap1 and SMC1 was normal in MRE11S676AS678A cells, there was no phosphorylation of Exonuclease 1 consistent with the defect in HDR. These results describe a novel role for ATM-dependent phosphorylation of MRE11 in limiting the extent of resection mediated through Exonuclease 1.

  14. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication.

    PubMed

    Shinbrot, Eve; Henninger, Erin E; Weinhold, Nils; Covington, Kyle R; Göksenin, A Yasemin; Schultz, Nikolaus; Chao, Hsu; Doddapaneni, HarshaVardhan; Muzny, Donna M; Gibbs, Richard A; Sander, Chris; Pursell, Zachary F; Wheeler, David A

    2014-11-01

    Tumors with somatic mutations in the proofreading exonuclease domain of DNA polymerase epsilon (POLE-exo*) exhibit a novel mutator phenotype, with markedly elevated TCT→TAT and TCG→TTG mutations and overall mutation frequencies often exceeding 100 mutations/Mb. Here, we identify POLE-exo* tumors in numerous cancers and classify them into two groups, A and B, according to their mutational properties. Group A mutants are found only in POLE, whereas Group B mutants are found in POLE and POLD1 and appear to be nonfunctional. In Group A, cell-free polymerase assays confirm that mutations in the exonuclease domain result in high mutation frequencies with a preference for C→A mutation. We describe the patterns of amino acid substitutions caused by POLE-exo* and compare them to other tumor types. The nucleotide preference of POLE-exo* leads to increased frequencies of recurrent nonsense mutations in key tumor suppressors such as TP53, ATM, and PIK3R1. We further demonstrate that strand-specific mutation patterns arise from some of these POLE-exo* mutants during genome duplication. This is the first direct proof of leading strand-specific replication by human POLE, which has only been demonstrated in yeast so far. Taken together, the extremely high mutation frequency and strand specificity of mutations provide a unique identifier of eukaryotic origins of replication.

  15. Advanced synchrotron-based and globar-sourced molecular (micro) spectroscopy contributions to advances in food and feed research on molecular structure, mycotoxin determination, and molecular nutrition.

    PubMed

    Shi, Haitao; Yu, Peiqiang

    2017-04-17

    Mycotoxin contamination has been a worldwide problem for food and feeds production for a long time. There is an obviously increased focus of the food and feed industry toward the reduction of mycotoxin concentration in both the raw materials and finished products. Therefore, both effective qualitative and quantitative techniques for the determination of mycotoxins are required to minimize their harmful effects. Conventional wet chemical methods usually are time-consuming, expensive, and rely on complex extraction and cleanup pretreatments. Synchrotron-based and globar-based molecular spectroscopy have shown great potential to be developed as rapid and nondestructive tools for the determination of molecular structure, molecular nutrition and mycotoxins in feed and food. This article reviews the common types of mycotoxins in feed and food, their toxicity, as well as the conventional detection methods. The principle of advanced molecular spectroscopy techniques and their application prospects for mycotoxin detection are discussed. Recent progress in food and feed research with molecular spectroscopy techniques is highlighted. This review provides a potential and insight into how to determine the structure and mycotoxins of feed and food on a molecular basis with advanced Synchrotron-based and globar-based molecular (micro) spectroscopy.

  16. Chemical biology at the crossroads of molecular structure and mechanism.

    PubMed

    Doudna, Jennifer A

    2005-11-01

    Chemical insight into biological function is the holy grail of structural biology. Small molecules are central players as building blocks, effectors and probes of macromolecular structure and function.

  17. Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Reilly, Anthony M.; Habershon, Scott; Morrison, Carole A.; Rankin, David W. H.

    2010-03-01

    Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

  18. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  19. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    PubMed

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  20. Effect of valence of lanthanide ion and molecular symmetry in polyoxotungstoborate on the molecular structure and spectrochemical properties

    NASA Astrophysics Data System (ADS)

    Iijima, Jun; Naruke, Haruo

    2017-01-01

    The compound K9(NH4)H[CeIV(α-BW11O39)(W5O18)]·16H2O (1) was successfully isolated and structurally characterized. The structural investigation revealed that 1 displayed a less molecular distortion, whereas Ln3+-analogs exhibited a large molecular distortion. IR spectroscopy demonstrated that the spectral patterns of 1 and Ce3+-analog were depending on each valence of Ce (IV/III). 11B-NMR spectroscopy showed that a decrease in site symmetry of B atom in the polyoxotungstoborate was related with an increase in a half width of NMR peak. There is a difference in molecular distortion between 1 and Ce3+-analog, but they have similar large half widths because of the same site symmetry of B atom. The 4f electron in Ce atom exhibited less effect on the chemical shift.

  1. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  2. Effect of Processing on the Molecular Structure, Rheology, Crystallization, Morphology and Physical Properties of Polyethylenes

    NASA Astrophysics Data System (ADS)

    Prasad, A.

    1997-03-01

    To develop an understanding of the physical properties of polyolefins, the basic thermodynamic, rheological and molecular structural features that characterize the melt and the crystalline state must be understood. The molecular structure; which includes molecular weight (MW), molecular weight distribution (MWD), short and long chain branching and the state of entanglement; strongly influence the processing and the physical properties of polyethylenes. In this presnetation we will focus on the role of long chain branching (LCB) and state of entanglement on the processing and properties of the linear polyethylenes (HDPE), high pressure branched polyethylenes (LDPE) and alpha-olefin copolymers (LLDPE).

  3. Molecular structure of amino alcohols on aluminum surface

    NASA Astrophysics Data System (ADS)

    Masoud, M. S.; Awad, M. K.; Ali, Alaa E.; El-Tahawy, M. M. T.

    2014-04-01

    Quantum chemical calculations were applied on monoethanolamine (MEA), diethanolamine (DEA) and triethanolamine (TEA) as corrosion inhibitors for aluminum exterior using ab initio Møller-Plesset (MP2) and Density Function Theory (DFT-B3LYP) at 6-311++G(d,p) ground set. Quantum chemical parameters such as the maximum employed molecular orbital energy (EHOMO), the minimum unemployed molecular orbital energy (ELUMO), energy disparity (ΔE), dipole moment (μ), sum of the total negative charge (TNC), molecular volume (MV), electronegativity (χ), chemical potential (Pi), global hardness (η), softness (σ) and the fraction of electrons transferred (ΔN), were calculated. Further calculations were done to explore the effects of inhibitors and solvent. Furthermore, the inhibitors’ interactions with the metal exterior were studied by applying COMPASS method. R2 values showed good correlations between the corrosion inhibitors’ effectiveness and several quantum parameters.

  4. Molecular analysis of neocortical layer structure in the ferret

    PubMed Central

    Rowell, Joanna J.; Mallik, Atul K.; Dugas-Ford, Jennifer; Ragsdale, Clifton W.

    2010-01-01

    Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals is, however, unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for fifteen layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: (1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; (2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layer 5 and 6 into 5a, 5b, 6a and 6b are also conserved between rodents and carnivores. (3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; (4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals. PMID:20575059

  5. Label-free fluorescence dual-amplified detection of adenosine based on exonuclease III-assisted DNA cycling and hybridization chain reaction.

    PubMed

    Sun, Jiewei; Jiang, Wei; Zhu, Jing; Li, Wei; Wang, Lei

    2015-08-15

    In this work, we constructed a label-free and dual-amplified fluorescence aptasensor for sensitive analysis of adenosine based on exonuclease III (Exo III)-assisted DNA cycling and hybridization chain reaction (HCR). Firstly, we fabricated a trifunctional probe that consisting of the catalytic strand, the aptamer sequence and a streptavidin-magnetic nanobead (streptavidin-MNB). The streptavidin-MNB played a role of enrichment and separation to achieve a low background. The aptamer sequence was employed as a recognition element to bind the target adenosine, leading to the releasing of the catalytic stand. Then, the catalytic strand induced the Exo III-assisted DNA cycling reaction and produced a large amount of DNA fragments, which got a primary amplification. Subsequently, the DNA fragments acted as trigger strands to initiate HCR, forming nicked double helices with multiple G-quadruplex structures, which achieved a secondary amplification. Finally, the G-quadruplex structures bonded with the N-nethyl mesopor-phyrin IX (NMM) and yielded an enhanced fluorescence signal, realizing the label-free detection. In the proposed strategy, a small amount of adenosine can be converted to a large amount of DNA triggers, leading to a significant amplification for the target. This method exhibited a high sensitivity toward adenosine with a detection limit of 4.2×10(-7) mol L(-1), which was about 10 times lower than that of the reported label-free strategies. Moreover, this assay can significantly distinguish the content of adenosine in urine samples of cancer patients and normal human, indicating that our method will offer a new strategy for reliable quantification of adenosine in medical research and early clinical diagnosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Molecular and crystal structures of noble gas compounds

    NASA Astrophysics Data System (ADS)

    Nabiev, Sh Sh; Sokolov (deceased, V. B.; Chaivanov, B. B.

    2014-12-01

    Data on the structures of xenon and krypton compounds in various physical states are analyzed and generalized. The structures of simple, coordination, polymeric and clathrate-like compounds of these elements with various types of bonds are considered. Characteristic features of their vibrational spectra are discussed in relation to structural transformations caused by cation-anion interactions, structurally non-rigid intramolecular rearrangements and other factors. The bibliography includes 332 references.

  7. Attosecond time-resolved imaging of molecular structure by photoelectron holography.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2012-06-29

    Dynamic imaging of the molecular structure of H(2)(+) is investigated by attosecond photoelectron holography. The interference between direct (reference) and backward rescattered (signal) photoelectrons in attosecond photoelectron holography reveals the birth time of both channels and the spatial information of molecular structure. This is confirmed by simulations with a semiclassical model and numerical solutions of the corresponding time-dependent Schrödinger equation, suggesting an attosecond time-resolved way of imaging molecular structure obtained from laser induced rescattering of ionized electrons. It is shown that both short and long rescattered electron trajectories can be imaged from the momentum distribution.

  8. Molecular structure of the number 21 chromosome and Down syndrome

    SciTech Connect

    Smith, G.F.

    1985-01-01

    This book contains 19 papers. Some of the titles are: The Biology of Down Syndrome, Human Chromosome Analysis, Expression of Genes on Human Chromosome 21, Comparative Gene Mapping of Human Chromosome 21 and Mouse Chromosome 16, and Relating Molecular Specificity to Normal and Abnormal Brain Development.

  9. Supersonic turbulence and structure of interstellar molecular clouds.

    PubMed

    Boldyrev, Stanislav; Nordlund, Ake; Padoan, Paolo

    2002-07-15

    The interstellar medium provides a unique laboratory for highly supersonic, driven hydrodynamic turbulence. We propose a theory of such turbulence, test it by numerical simulations, and use the results to explain observational scaling properties of interstellar molecular clouds, the regions where stars are born.

  10. Study on molecular structural characteristics of tea polysaccharide.

    PubMed

    Guo, Li; Du, Xianfeng; Lan, Jing; Liang, Qin

    2010-08-01

    Tea polysaccharide (TPS) is attracting more attention gradually due to its particular biological properties. However, molecular characteristics of TPS are unclear since appropriate method is still absent. So, study on the molecular characteristics of TPS was carried out by high-performance size-exclusion chromatography (HPSEC), multi-angle laser light scattering (MALLS) and viscosimetry. The results showed that the molar masses of TPS ranged from 2.287 x 10(5) to 2.762 x 10(5)gmol(-1), the RMS radii distributed from 132.1 to 145.9 nm, and M(w)/M(n) is 1.028. The Mark-Houwink equation was established as [eta]=0.5423 M(w)(0.5379), and the intrinsic viscosity and molecular chain parameters were as follows: [eta]=1.007 dL g(-1), k(H)=0.845, k(K)=0.387, alpha=0.5379, K=0.5423. In addition, based on the slope of the RMS radius versus molar mass conformational plot being 0.24+/-0.00, we suggest that the molecular morphology of TPS is a homogeneous and spherical polymer with branch in solution.

  11. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    NASA Astrophysics Data System (ADS)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  12. Ultrasensitive Label-Free Resonance Rayleigh Scattering Aptasensor for Hg(2+) Using Hg(2+)-Triggered Exonuclease III-Assisted Target Recycling and Growth of G-Wires for Signal Amplification.

    PubMed

    Ren, Wang; Zhang, Ying; Chen, Hong Guo; Gao, Zhong Feng; Li, Nian Bing; Luo, Hong Qun

    2016-01-19

    A novel signal-on and label-free resonance Rayleigh scattering (RRS) aptasensor was constructed for detection of Hg(2+) based on Hg(2+)-triggered Exonuclease III-assisted target recycling and growth of G-quadruplex nanowires (G-wires) for signal amplification. The hairpin DNA (H-DNA) was wisely designed with thymine-rich recognition termini and a G-quadruplex sequence in the loop and employed as a signal probe for specially recognizing trace Hg(2+) by a stable T-Hg(2+)-T structure, which automatically triggered Exonuclease III (Exo-III) digestion to recycle Hg(2+) and liberate the G-quadruplex sequence. The free G-quadruplex sequences were self-assembled into guanine nanowire (G-wire) superstructure in the presence of Mg(2+) and demonstrated by gel electrophoresis. The RRS intensity was dramatically amplified by the resultant G-wires, and the maximum RRS signal at 370 nm was linear with the logarithm of Hg(2+) concentration in the range of 50.0 pM to 500.0 nM (R = 0.9957). Selectivity experiments revealed that the as-prepared RRS sensor was specific for Hg(2+), even coexisting with high concentrations of other metal ions. This optical aptasensor was successfully applied to identify Hg(2+) in laboratory tap water and river water samples. With excellent sensitivity and selectivity, the proposed RRS aptasensor was potentially suitable for not only routine detection of Hg(2+) in environmental monitoring but also various target detection just by changing the recognition sequence of the H-DNA probe.

  13. The Atom in a Molecule: Implications for Molecular Structure and Properties

    DTIC Science & Technology

    2016-05-23

    For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  14. Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation

    NASA Astrophysics Data System (ADS)

    Stein, Evan G.; Rice, Luke M.; Brünger, Axel T.

    1997-01-01

    Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances andJ-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix distance geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T, a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.

  15. [Cajal bodies and histone locus bodies: molecular structure and function].

    PubMed

    Khodiuchenko, T A; Krasikova, A V

    2014-01-01

    The review provides modern classification of evolutionarily conserved coilin-containing nuclear bodies of somatic and germ cells that is based on the characteristic features of their molecular composition and the nature of their functions. The main differences between Cajal bodies and histone locus bodies, which are involved in the biogenesis of small nuclear spliceosomal and nucleolar RNAs and in the 3'-end processing of histone precursor messenger RNA, respectively, are considered. It is shown that a significant contribution to the investigation of the diversity of coilin-containing bodies was made by the studies on the architecture of the RNA processing machinery in oocyte nuclei in a number of model organisms. The characteristics features of the molecular composition of coilin-containing bodies in the nuclei of growing oocytes (the so-called germinal vesicles) of vertebrates, including amphibians and birds, are described.

  16. Molecular Structures and Functional Relationships in Clostridial Neurotoxins

    SciTech Connect

    Swaminathan S.

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  17. Molecular structures and functional relationships in clostridial neurotoxins.

    PubMed

    Swaminathan, Subramanyam

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here.

  18. [Structural and molecular origin of information recording/reading].

    PubMed

    Kuzurman, P A; Arkhipova, G V

    2002-01-01

    On the basis of experimental data on the thermoinduced state of water dispersions of natural and synthetic phospholipids in the presence of nootropic agents, a new phenomenological molecular mechanism of information recording/reading was proposed. The mechanism is based on the polymorphism of membrane lipids. A new approach, to the problem of memory was suggested, which considers memory as an information data bank and separates this concept from the concept of the mechanisms of information recording/reading.

  19. Probing the structural and molecular diversity of tumor vasculature.

    PubMed

    Pasqualini, Renata; Arap, Wadih; McDonald, Donald M

    2002-12-01

    The molecular diversity of the vasculature provides a rational basis for developing targeted diagnostics and therapeutics for cancer. Targeted imaging agents would offer better localization of primary tumors and metastases, and targeted therapies would improve efficacy and reduce side effects. The development of targeted pharmaceuticals requires the identification of specific ligand-receptor pairs, and knowledge of their cellular distribution and accessibility. Using in vivo phage display, a technique by which we can identify organ-specific and disease-specific proteins expressed on the endothelial surface, it is now possible to decipher the molecular signature of blood vessels in normal and diseased tissues. These studies have already led to the identification of peptides that target the normal vasculature of the brain, kidney, pancreas, lung and skin, as well as the abnormal vasculature of tumors, arthritis and atherosclerosis. Membrane dipeptidase in the lungs, interleukin-11 receptor in the prostate, and aminopeptidase N in tumors are examples of molecular targets on blood vessels. Corresponding confocal-microscopic imaging and ultrastructural studies are providing a more complete understanding of the cellular abnormalities of tumor blood vessels, and the distribution and accessibility of potential targets. The combined approach offers a strategy for creating a ligand-receptor map of the human vasculature, and forms a foundation for the development and application of targeted therapies in cancer and other diseases.

  20. Molecular Structure and Transport Dynamics in Perfluoro Sulfonyl Imide Membranes

    SciTech Connect

    Idupulapati, Nagesh B.; Devanathan, Ramaswami; Dupuis, Michel

    2011-05-25

    We report a detailed and comprehensive analysis of the nanostructure, transport dynamics of water and hydronium and water percolation in hydrated perfluoro sulfonyl imides (PFSI), a polymer considered for proton transport in PEM fuel cells, using classical molecular dynamics simulations. The dynamical changes are related to the changes in the membrane nanostructure. Water network percolation threshold, the level at which a consistent spanning water network starts to develop in the membrane, lies between hydration level (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to Nafion reported in our earlier ab initio study, translates into more free hydronium ions at low hydration levels. Nevertheless, the calculated diffusion coefficients of the H3O+ ions and H2O molecules as a function the hydration level were observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with the experimental observations. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  1. Quantitative structure-activity relationship correlation between molecular structure and the Rayleigh enantiomeric enrichment factor.

    PubMed

    Jammer, S; Rizkov, D; Gelman, F; Lev, O

    2015-08-01

    It was recently demonstrated that under environmentally relevant conditions the Rayleigh equation is valid to describe the enantiomeric enrichment - conversion relationship, yielding a proportional constant called the enantiomeric enrichment factor, εER. In the present study we demonstrate a quantitative structure-activity relationship model (QSAR) that describes well the dependence of εER on molecular structure. The enantiomeric enrichment factor can be predicted by the linear Hansch model, which correlates biological activity with physicochemical properties. Enantioselective hydrolysis of sixteen derivatives of 2-(phenoxy)propionate (PPMs) have been analyzed during enzymatic degradation by lipases from Pseudomonas fluorescens (PFL), Pseudomonas cepacia (PCL), and Candida rugosa (CRL). In all cases the QSAR relationships were significant with R(2) values of 0.90-0.93, and showed high predictive abilities with internal and external validations providing QLOO(2) values of 0.85-0.87 and QExt(2) values of 0.8-0.91. Moreover, it is demonstrated that this model enables differentiation between enzymes with different binding site shapes. The enantioselectivity of PFL and PCL was dictated by electronic properties, whereas the enantioselectivity of CRL was determined by lipophilicity and steric factors. The predictive ability of the QSAR model demonstrated in the present study may serve as a helpful tool in environmental studies, assisting in source tracking of unstudied chiral compounds belonging to a well-studied homologous series.

  2. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge.

    PubMed

    de la Llave, Ezequiel; Herrera, Santiago E; Adam, Catherine; Méndez De Leo, Lucila P; Calvo, Ernesto J; Williams, Federico J

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  3. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    SciTech Connect

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  4. Molecular dynamics of transient oil flows in nanopores. II. Density profiles and molecular structure for decane in carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Supple, S.; Quirke, N.

    2005-03-01

    We report molecular dynamics simulations of nanotubes imbibing decane at an oil/vapor interface at 300K. We find that the smallest (7,7) nanotubes imbibe extremely rapidly (⩽800m/s), with the imbibition speed slowing as the tube's radius increases. The density profiles of the imbibing fluid in the pores are analyzed as a function of time. We find that the imbibing liquid is well described by the advection-diffusion equation and present expressions for the density profiles (in x and t) of the imbibing fluid as a function of the adsorption energy and surface friction of the pore. In addition we have analyzed the molecular structure of the imbibed fluid in nanotubes and describe how molecular conformations change with nanotube radius and position in the pore. We are therefore able to provide a complete description of the imbibition of a wetting fluid, decane, for a wide range of nanopores.

  5. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations.

    PubMed

    Fang, Jiansong; Pang, Xiaocong; Wu, Ping; Yan, Rong; Gao, Li; Li, Chao; Lian, Wenwen; Wang, Qi; Liu, Ai-lin; Du, Guan-hua

    2016-05-01

    A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.

  6. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  7. Ultra-low-molecular-weight heparins: precise structural features impacting specific anticoagulant activities.

    PubMed

    Lima, Marcelo A; Viskov, Christian; Herman, Frederic; Gray, Angel L; de Farias, Eduardo H C; Cavalheiro, Renan P; Sassaki, Guilherme L; Hoppensteadt, Debra; Fareed, Jawed; Nader, Helena B

    2013-03-01

    Ultra-low-molecular-weight heparins (ULMWHs) with better efficacy and safety ratios are under development; however, there are few structural data available. The main structural features and molecular weight of ULMWHs were studied and compared to enoxaparin. Their monosaccharide composition and average molecular weights were determined and preparations studied by nuclear magnetic resonance spectroscopy, scanning ultraviolet spectroscopy, circular dichroism and gel permeation chromatography. In general, ULMWHs presented higher 3-O-sulphated glucosamine and unsaturated uronic acid residues, the latter being comparable with their higher degree of depolymerisation. The analysis showed that ULMWHs are structurally related to LMWHs; however, their monosaccharide/oligosaccharide compositions and average molecular weights differed considerably explaining their different anticoagulant activities. The results relate structural features to activity, assisting the development of new and improved therapeutic agents, based on depolymerised heparin, for the prophylaxis and treatment of thrombotic disorders.

  8. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  9. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

    PubMed

    Cramer, Patrick

    2017-08-18

    Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. ONTOGENETIC ALTERATIONS IN MOLECULAR AND STRUCTURAL CORRELATES OF DENDRITIC GROWTH FOLLOWING DEVELOPMENTAL EXPOSURE TO POLYCHLORINATED BIPHENYLS.

    EPA Science Inventory

    This is the first report showing both molecular and structural changes in brain following developmental exposure to a neurotoxicant. It is known that perinatal exposure to a neurotoxicant, polychlorinated biphenyls (PCBs), is associated with decreased IQ scores, impaired learnin...

  11. ONTOGENETIC ALTERATIONS IN MOLECULAR AND STRUCTURAL CORRELATES OF DENDRITIC GROWTH FOLLOWING DEVELOPMENTAL EXPOSURE TO POLYCHLORINATED BIPHENYLS.

    EPA Science Inventory

    This is the first report showing both molecular and structural changes in brain following developmental exposure to a neurotoxicant. It is known that perinatal exposure to a neurotoxicant, polychlorinated biphenyls (PCBs), is associated with decreased IQ scores, impaired learnin...

  12. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  13. Exonuclease I-aided homogeneous electrochemical strategy for organophosphorus pesticide detection based on enzyme inhibition integrated with a DNA conformational switch.

    PubMed

    Wang, Xiuzhong; Dong, Shanshan; Hou, Ting; Liu, Lei; Liu, Xiaojuan; Li, Feng

    2016-03-07

    A novel enzyme inhibition-based homogeneous electrochemical biosensing strategy was designed for an organophosphorus pesticide assay based on exploiting the resistance of a mercury ion-mediated helper probe (HP) toward nuclease-catalyzed digestion and the remarkable diffusivity difference between HPs and the mononucleotides toward a negatively charged indium tin oxide (ITO) electrode. In particular, the mercury ion-mediated T-Hg(2+)-T base pairs facilitate the HP labeled with methylene blue (MB) to fold into a hairpin structure, preventing its digestion by exonuclease I, and thus resulting in a low electrochemical response because of the large electrostatic repulsion between the negatively charged ITO electrode and the HPs. The competitive binding by a thiol group (-SH), produced in the hydrolysis reaction of acetylthiocholine (ACh) chloride with acetylcholinesterase (AChE), removes mercury ions from the base pairs, causing a nuclease-catalyzed digestion, and the subsequent electrochemical response increase due to the weak electrostatic repulsion between the product-mononucleotides and the ITO electrode. Mercury ion-mediated HPs were first designed for pesticide detection and diazinon was chosen as the model target. Under the optimal experimental conditions, the approach exhibited high sensitivity for diazinon detection with a detection limit of 0.25 μg L(-1). The satisfactory results in the determination of diazinon in real samples demonstrate that the method possesses great potential for detecting organophosphorus pesticides. This new approach is expected to promote the exploitation of mercury-mediated base pair-based homogenous electrochemical biosensors in biochemical studies and in the food safety field.

  14. A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease

    PubMed Central

    Granneman, Sander; Petfalski, Elisabeth; Tollervey, David

    2011-01-01

    The 5′-exonuclease Rat1 degrades pre-rRNA spacer fragments and processes the 5′-ends of the 5.8S and 25S rRNAs. UV crosslinking revealed multiple Rat1-binding sites across the pre-rRNA, consistent with its known functions. The major 5.8S 5′-end is generated by Rat1 digestion of the internal transcribed spacer 1 (ITS1) spacer from cleavage site A3. Processing from A3 requires the ‘A3-cluster' proteins, including Cic1, Erb1, Nop7, Nop12 and Nop15, which show interdependent pre-rRNA binding. Surprisingly, A3-cluster factors were not crosslinked close to site A3, but bound sites around the 5.8S 3′- and 25S 5′-regions, which are base paired in mature ribosomes, and in the ITS2 spacer that separates these rRNAs. In contrast, Nop4, a protein required for endonucleolytic cleavage in ITS1, binds the pre-rRNA near the 5′-end of 5.8S. ITS2 was reported to undergo structural remodelling. In vivo chemical probing indicates that A3-cluster binding is required for this reorganization, potentially regulating the timing of processing. We predict that Nop4 and the A3 cluster establish long-range interactions between the 5.8S and 25S rRNAs, which are subsequently maintained by ribosomal protein binding. PMID:21811236

  15. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

    PubMed Central

    Foulk, Michael S.; Urban, John M.; Casella, Cinzia; Gerbi, Susan A.

    2015-01-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand–independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo–controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq. PMID:25695952

  16. A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification

    PubMed Central

    Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

    2016-01-01

    Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of “G-quadruplex” in lantern-like structures. Finally, the continuously enriched “G-quadruplex lanterns” were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10−17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring. PMID:28335318

  17. A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification.

    PubMed

    Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

    2016-10-21

    Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of "G-quadruplex" in lantern-like structures. Finally, the continuously enriched "G-quadruplex lanterns" were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10(-17) M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring.

  18. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

    PubMed Central

    Manara, Richard M. A.; Tomasio, Susana; Khalid, Syma

    2015-01-01

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  19. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.

    PubMed

    Manara, Richard M A; Tomasio, Susana; Khalid, Syma

    2015-01-27

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is "exonuclease sequencing", in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  20. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    PubMed

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  1. Template length, sequence context, and 3 prime -5 prime exonuclease activity modulate replicative bypass of thymine glycol lesions in vitro

    SciTech Connect

    Clark, J.M.; Beardsley G.P. )

    1989-01-24

    cis-Thymine glycol, a product of ionizing radiation damage to DNA, has been introduced quantitatively at a single site into oligonucleotide templates. The ability of DNA polymerases to replicate templates containing thymine glycol was studied by a primer extension assay, and three factors that influence replicative bypass of this lesion in vitro have been identified. These factors include template length, sequence context, and 3{prime}-5{prime} exonuclease activity. Synthesis by the large fragment of DNA polymerase I (Klenow fragment) terminates quantitatively opposite thymine glycol when the template strand extends only two nucleotides beyond the lesion. Significant bypass is observed when the length of the template beyond the lesion is increased to six nucleotides. On the longer templates, the frequency of bypass of the Klenow fragment depends upon the identity of the base immediately 5{prime} to thymine glycol. The extent of bypass is greatest with cytosine and least with adenine at this position. Bypass of thymine glycol lesions by DNA polymerase {alpha}{sub 2} from HeLa cells shows a qualitatively similar dependence upon local sequence context. In contrast, synthesis by T4 DNA polymerase is quantitatively blocked opposite the lesion regardless of template length or DNA sequence context. Synthesis by a mutant Klenow fragment that is deficient in 3{prime}-5{prime} exonuclease activity, or by AMV reverse transcriptase, results in a significant increase in the frequency of bypass. Thus, increased nucleotide turnover at, or beyond, the site of the lesion is likely to contribute significantly to the arrest of synthesis provoked by cis-thymine glycol in vitro.

  2. Molecular structure of the coalescence of liquid interfaces

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1992-01-01

    When two bodies of liquid merge, their interfaces must also rupture and rearrange into one. Virtually no information is available concerning the small-scale dynamics of this process. Molecular dynamics simulations of coalescence in systems of about 10,000 Lennard-Jones particles have been performed, arranged so as to mimic laboratory experiments on dense liquids. The coalescence event begins when molecules near the boundary of one liquid body thermally fluctuate into the range of attraction of the other, forming a string of mutually attracting molecules. These molecules gradually thicken into a tendril, which continues to thicken as the bodies smoothly combine in a zipper-like merger.

  3. Molecular structure of the coalescence of liquid interfaces

    NASA Technical Reports Server (NTRS)

    Koplik, Joel; Banavar, Jayanth R.

    1992-01-01

    When two bodies of liquid merge, their interfaces must also rupture and rearrange into one. Virtually no information is available concerning the small-scale dynamics of this process. Molecular dynamics simulations of coalescence in systems of about 10,000 Lennard-Jones particles have been performed, arranged so as to mimic laboratory experiments on dense liquids. The coalescence event begins when molecules near the boundary of one liquid body thermally fluctuate into the range of attraction of the other, forming a string of mutually attracting molecules. These molecules gradually thicken into a tendril, which continues to thicken as the bodies smoothly combine in a zipper-like merger.

  4. Protein structure in context: The molecular landscape of angiogenesis

    PubMed Central

    Span, Elise A.; Goodsell, David S.; Ramchandran, Ramani; Franzen, Margaret; Herman, Timothy; Sem, Daniel S.

    2014-01-01

    A team of students, educators, and researchers has developed new materials to teach cell signaling within its cellular context. Two non-traditional modalities are employed: physical models, to explore the atomic details of several of the proteins in the angiogenesis signaling cascade, and illustrations of the proteins in their cellular environment, to give an intuitive understanding of the cellular context of the pathway. The experiences of the team underscore the utility of these types of materials as an effective mode for fostering students’ understanding of the molecular world, and the scientific method used to define it. PMID:23868376

  5. VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

    PubMed

    Weber, Julia; Achenbach, Janosch; Moser, Daniel; Proschak, Ewgenij

    2013-06-27

    Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.

  6. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    PubMed

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-07

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches.

  7. Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.

    PubMed

    Parker, David; Bryant, Zev; Delp, Scott L

    2009-09-01

    Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org.

  8. Diverse functional manifestations of intrinsic structural disorder in molecular chaperones.

    PubMed

    Kovacs, Denes; Tompa, Peter

    2012-10-01

    IDPs (intrinsically disordered proteins) represent a unique class of proteins which show diverse molecular mechanisms in key biological functions. The aim of the present mini-review is to summarize IDP chaperones that have increasingly been studied in the last few years, by focusing on the role of intrinsic disorder in their molecular mechanism. Disordered regions in both globular and disordered chaperones are often involved directly in chaperone action, either by modulating activity or through direct involvement in substrate identification and binding. They might also be responsible for the subcellular localization of the protein. In outlining the state of the art, we survey known IDP chaperones discussing the following points: (i) globular chaperones that have an experimentally proven functional disordered region(s), (ii) chaperones that are completely disordered along their entire length, and (iii) the possible mechanisms of action of disordered chaperones. Through all of these details, we chart out how far the field has progressed, only to emphasize the long road ahead before the chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.

  9. Exponential repulsion improves structural predictability of molecular docking.

    PubMed

    Bazgier, Václav; Berka, Karel; Otyepka, Michal; Banáš, Pavel

    2016-10-30

    Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Structural analysis of the yeast exosome Rrp6p–Rrp47p complex by small-angle X-ray scattering

    SciTech Connect

    Dedic, Emil; Seweryn, Paulina; Jonstrup, Anette Thyssen; Flygaard, Rasmus Koch; Fedosova, Natalya U.; Hoffmann, Søren Vrønning; Boesen, Thomas; Brodersen, Ditlev Egeskov

    2014-07-18

    Highlights: • We show that S. cerevisiae Rrp6p and Rrp47p stabilise each other in vitro. • We determine molecular envelopes of the Rrp6p–Rrp47p complex by SAXS. • Rrp47p binds at the top of the Rrp6p exonuclease domain. • Rrp47p modulates the activity of Rrp6p on a variety of RNA substrates. • Rrp47p does not affect RNA affinity by Rrp6p. - Abstract: The RNase D-type 3′–5′ exonuclease Rrp6p from Saccharomyces cerevisiae is a nuclear-specific cofactor of the RNA exosome and associates in vivo with Rrp47p (Lrp1p). Here, we show using biochemistry and small-angle X-ray scattering (SAXS) that Rrp6p and Rrp47p associate into a stable, heterodimeric complex with an elongated shape consistent with binding of Rrp47p to the nuclease domain and opposite of the HRDC domain of Rrp6p. Rrp47p reduces the exonucleolytic activity of Rrp6p on both single-stranded and structured RNA substrates without significantly altering the affinity towards RNA or the ability of Rrp6p to degrade RNA secondary structure.

  11. Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

    PubMed

    Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

    2014-05-01

    The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Accessing gap-junction channel structure-function relationships through molecular modeling and simulations.

    PubMed

    Villanelo, F; Escalona, Y; Pareja-Barrueto, C; Garate, J A; Skerrett, I M; Perez-Acle, T

    2017-01-17

    Gap junction channels (GJCs) are massive protein channels connecting the cytoplasm of adjacent cells. These channels allow intercellular transfer of molecules up to ~1 kDa, including water, ions and other metabolites. Unveiling structure-function relationships coded into the molecular architecture of these channels is necessary to gain insight on their vast biological function including electrical synapse, inflammation, development and tissular homeostasis. From early works, computational methods have been critical to analyze and interpret experimental observations. Upon the availability of crystallographic structures, molecular modeling and simulations have become a valuable tool to assess structure-function relationships in GJCs. Modeling different connexin isoforms, simulating the transport process, and exploring molecular variants, have provided new hypotheses and out-of-the-box approaches to the study of these important channels. Here, we review foundational structural studies and recent developments on GJCs using molecular modeling and simulation techniques, highlighting the methods and the cross-talk with experimental evidence. By comparing results obtained by molecular modeling and simulations techniques with structural and functional information obtained from both recent literature and structural databases, we provide a critical assesment of structure-function relationships that can be obtained from the junction between theoretical and experimental evidence.

  13. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    SciTech Connect

    Marcia, Marco Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  14. The Molecular Structure of the Liquid Ordered Phase

    NASA Astrophysics Data System (ADS)

    Lyman, Edward

    2014-03-01

    Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld) , are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

  15. Molecular structure, functionality and applications of oxidized starches: A review.

    PubMed

    Vanier, Nathan Levien; El Halal, Shanise Lisie Mello; Dias, Alvaro Renato Guerra; da Rosa Zavareze, Elessandra

    2017-04-15

    During oxidation, the hydroxyl groups of starch molecules are first oxidized to carbonyl groups, then to carboxyl groups. The contents of the carbonyl and carboxyl groups in a starch molecule therefore indicate the extent of starch oxidation. The mechanisms of starch oxidation with different oxidizing agents, including sodium hypochlorite, hydrogen peroxide, ozone and sodium periodate, are described in this review. The effects of these oxidizing agents on the molecular, physicochemical, thermal, pasting and morphological properties of starch are described as well. In addition, the main industrial applications of oxidized starches are presented. The present review is important for understanding the effects of oxidation on starch properties, and this information may facilitate the development of novel oxidized starches for both food and non-food applications.

  16. The Structural, Functional, and Molecular Organization of the Brainstem

    PubMed Central

    Nieuwenhuys, Rudolf

    2011-01-01

    According to His (1891, 1893) the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature) and the ventral basal plate (motor in nature). Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this “four-functional-zones” concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1) the magnocellular vestibular nucleus situated in the viscerosensory zone; (2) the basal plate containing a number of evidently non-motor centers (superior and inferior olives). Nevertheless the “functional zonal model” has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioral profiles, as “local hypertrophies” of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units. PMID:21738499

  17. Microwave spectrum, molecular structure, and quadrupole coupling of vinyl chloroformate

    NASA Astrophysics Data System (ADS)

    Bimler, Jonathan; Broadbent, Stacy; Utzat, Karissa A.; Bohn, Robert K.; Restrepo, Albeiro; Harvey Michels, H.; True, Nancy S.

    2012-09-01

    Vinyl chloroformate is confirmed to have the planar structure reported in an earlier study [1]. Our study uses much higher resolution microwave rotational spectra and ab initio calculations have been extended to a higher level. Naturally abundant isotopologs with single substitution of 37Cl, 13C, and 18O isotopes have also been measured and a substitution structure obtained. The quadrupole coupling constants of the 35Cl and 37Cl isotopologs have been determined. The potential energy profiles of internal rotation about the Odbnd Csbnd Osbnd C and Csbnd Osbnd Cdbnd C dihedral angles have been calculated.

  18. Molecular cloning of the 8000-base thyroglobulin structural gene.

    PubMed

    Christophe, D; Mercken, L; Brocas, H; Pohl, V; Vassart, G

    1982-03-01

    Bovine thyroglobulin mRNA was reverse-transcribed into full-length double-stranded cDNA. The existence of three HindIII restriction endonuclease sites in the 8000-base thyroglobulin structural gene had allowed the easy cloning of the two internal HindIII fragments [Christophe et al. (1980) Eur. J. Biochem. 111, 419-423]. In the present study, the central portion of the structural gene was cloned in Escherichia coli as two individual recombinant plasmids containing 2000-base-pair and 4700-base-pair segments located respectively 5' and 3' relative to the unique BamHI site of the cDNA. BamHI linkers were added to the double-stranded cDNA and, following restriction with HindIII, selective cloning of the 5' (2600-base-pair) and 3' (1000-base-pair) terminal HindIII fragments was achieved by inserting them between the HindIII and BamHI sites of the plasmid pBR322. Partial sequencing of the 1000-base-pair 3'-terminal fragment demonstrated the presence of an A-A-U-A-A-A sequence in the mRNA 14 bases upstream from a poly(A) tract corresponding to the 3' end of the mRNA. Together, the four clones represent about 99% of the thyroglobulin structural gene and provide the starting material for the determination of thyroglobulin primary structure.

  19. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

  20. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    NASA Astrophysics Data System (ADS)

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-03-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  1. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant.

    PubMed

    Li, Hongyan; Fitzgerald, Melissa A; Prakash, Sangeeta; Nicholson, Timothy M; Gilbert, Robert G

    2017-03-06

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch.

  2. The molecular structural features controlling stickiness in cooked rice, a major palatability determinant

    PubMed Central

    Li, Hongyan; Fitzgerald, Melissa A.; Prakash, Sangeeta; Nicholson, Timothy M.; Gilbert, Robert G.

    2017-01-01

    The stickiness of cooked rice is important for eating quality and consumer acceptance. The first molecular understanding of stickiness is obtained from leaching and molecular structural characteristics during cooking. Starch is a highly branched glucose polymer. We find (i) the molecular size of leached amylopectin is 30 times smaller than that of native amylopectin while (ii) that of leached amylose is 5 times smaller than that of native amylose, (iii) the chain-length distribution (CLD: the number of monomer units in a chain on the branched polymer) of leached amylopectin is similar to native amylopectin while (iv) the CLD of leached amylose is much narrower than that of the native amylose, and (v) mainly amylopectin, not amylose, leaches out of the granule and rice kernel during cooking. Stickiness is found to increase with decreasing amylose content in the whole grain, and, in the leachate, with increasing total amount of amylopectin, the proportion of short amylopectin chains, and amylopectin molecular size. Molecular adhesion mechanisms are put forward to explain this result. This molecular structural mechanism provides a new tool for rice breeders to select cultivars with desirable palatability by quantifying the components and molecular structure of leached starch. PMID:28262830

  3. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    properties of the IV curves of single molecule nano-junctions. Specifically, these systems consist of a zinc-porphyrin molecule coupled between two gold electrodes, i.e., a nano-gap. The first observation we want to explain is the asymmetric nature of the experimental IV curve for this porphyrin system, where the IV curve is skewed heavily to the negative bias region. Using a plane-wave DFT calculation, we present the density of states of the porphyrin molecule (both in the presence and absence of the electrodes) and indeed see highly delocalized states (as confirmed by site-projection of the DOS) only in the negative bias region, meaning that the channels with high transmission probability reside there, in agreement with experimental observation. The next problem studied pertains to observed switching in an experimentally-measured IV curve, this time of a longer zinc porphyrin molecule, still within a gold nano-gap. The switching behavior is observed only at 300K, not at 4.2K. The temperature-dependance of this problem renders our previous toolset of DFT calculations void; DFT is a ground-state theory. Instead, we employ a density functional-based tight-binding (DFTB) approach in a molecular dynamics simulation. Basically, the structural configuration evaluated at each time step is based on a tight-binding electronic structure calculation, instead of a typical MD force field. Trajectories are presented at varying temperatures and electric field strengths. Indeed, we observe a conformation of the porphyrin molecule between two configurations of the dihedral angle of the central nitrogen ring, ±15. {o} at 300K, but not 4.2K. These confirmations are equally likely, i.e., the structure assumes these configurations an equal number of teams, meaning the average structure has an angle of 0. {o}. After computing the DOS of all three aforementioned configurations (0. {text{o}} and ±15. {text{o}}), we indeed see a difference between the DOS curves at ±15. {text{o}} (which are

  4. Photoexcited State Molecular Structures in Solution Studied by Pump-Probe XAFS

    NASA Astrophysics Data System (ADS)

    Chen, Lin

    2002-03-01

    The photoexcitation causes displacement of electron densities within or among molecules, which consequently leads to nuclear movements. Such nuclear displacements often occur in transient states with short lifetimes. Knowing transient molecular structures during photochemical reactions is important for understanding fundamental aspects of solar energy conversion and storage. Fast x-ray techniques provide direct probes for these transient structures. Using x-ray pulses from the Advanced Photon Source at Argonne, a laser pulse pump, x-ray pulse probe XAFS technique has been developed to capture transient molecular structures in disordered media with nanosecond time resolution. We have carried out several pump-probe XAFS measurements on 1)identifying a transient molecular structure of the photodissociation product of nickel-tetraphenylporphyrin with piperidine axial ligands (NiTPP-L2); 2)determination of the MLCT state structure of Bis(2,9-dimethyl-1,10-phenanthroline) Copper(I) [Cu(I)(dmp)2]+, and 3) triplet state molecular structures of metalloporphyrins. These studies not only prove the feasibility of the technique, but also gain structural information that otherwise will not be available. Future studies include probing transient structures in electron donor-acceptor complexes and optical polarization selected XAFS (OPS-XAFS) using the same technique with a 100-ps time resolution. This work is supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, U. S. Department of Energy, under contract W-31-109-Eng-38.

  5. The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

    ERIC Educational Resources Information Center

    Mannschreck, Albrecht; von Angerer, Erwin

    2011-01-01

    A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

  6. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    ERIC Educational Resources Information Center

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  7. Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

    ERIC Educational Resources Information Center

    Rižner, Tea Lanišnik

    2014-01-01

    This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

  8. The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

    ERIC Educational Resources Information Center

    Mannschreck, Albrecht; von Angerer, Erwin

    2011-01-01

    A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

  9. Elucidation of Drug Metabolite Structural Isomers Using Molecular Modeling Coupled with Ion Mobility Mass Spectrometry.

    PubMed

    Reading, Eamonn; Munoz-Muriedas, Jordi; Roberts, Andrew D; Dear, Gordon J; Robinson, Carol V; Beaumont, Claire

    2016-02-16

    Ion mobility-mass spectrometry (IM-MS) in combination with molecular modeling offers the potential for small molecule structural isomer identification by measurement of their gas phase collision cross sections (CCSs). Successful application of this approach to drug metabolite identification would facilitate resource reduction, including animal usage, and may benefit other areas of pharmaceutical structural characterization including impurity profiling and degradation chemistry. However, the conformational behavior of drug molecules and their metabolites in the gas phase is poorly understood. Here the gas phase conformational space of drug and drug-like molecules has been investigated as well as the influence of protonation and adduct formation on the conformations of drug metabolite structural isomers. The use of CCSs, measured from IM-MS and molecular modeling information, for the structural identification of drug metabolites has also been critically assessed. Detection of structural isomers of drug metabolites using IM-MS is demonstrated and, in addition, a molecular modeling approach has been developed offering rapid conformational searching and energy assessment of candidate structures which agree with experimental CCSs. Here it is illustrated that isomers must possess markedly dissimilar CCS values for structural differentiation, the existence and extent of CCS differences being ionization state and molecule dependent. The results present that IM-MS and molecular modeling can inform on the identity of drug metabolites and highlight the limitations of this approach in differentiating structural isomers.

  10. Relationships between molecular structure and chromosomal aberrations in virto human lymphocytes induced by substituted nitrobenzenes

    SciTech Connect

    Huang, Q.G.; Kong, L.R.; Liu, Y.B.; Wang, L.S.

    1996-12-31

    Most nitrated aromatics are genotoxic, some structure-activity relationship (SAR) studies have been done about their mutagenicity, but most studies are concerned with the nitrated polycyclic aromatic hydrocarbons. This report studied the substituted nitrobenzenes and the relationship between molecular structure and genotoxicity of these compounds. 8 refs., 1 tab.

  11. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  12. Guided folding takes a start from the molecular imprinting of structured epitopes.

    PubMed

    Cenci, L; Guella, G; Andreetto, E; Ambrosi, E; Anesi, A; Bossi, A M

    2016-08-25

    A biomimetic route towards assisted folding was explored. Molecularly imprinted polymeric nanoparticles (MIP NPs), i.e. biomimetics with entailed molecular recognition properties made by a template assisted synthesis, were prepared to target a structured epitope: the cystine containing peptide CC9ox, which corresponds to the apical portion of the β-hairpin hormone Hepcidin-25. The structural selection was achieved by the MIP NPs; moreover, the MIP NPs demonstrated favouring the folding of the linear random peptide (CC9red) into the structured one (CC9ox), anticipating the future role of the MIP NPs as in situ nanomachines to counteract folding defects.

  13. The observation of correlated velocity structures in a translucent molecular cloud and implications for turbulence

    NASA Technical Reports Server (NTRS)

    Magnani, L.; Larosa, T. N.; Shore, S. N.

    1993-01-01

    We present a formaldehyde map of the translucent high-latitude molecular cloud MBM 16. The molecular gas traced by the H2CO is located in spatially distinct large structures that exhibit velocity coherence on a scale of 0.5 pc. These structures are not pressure-confined and are probably not self-gravitating. They may be transient structures. If so, we suggest that they are produced by shear flows whose scale length is of order the size of the cloud.

  14. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    PubMed

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone.

  15. Structured water and water-polymer interactions in hydrogels of molecularly imprinted polymers.

    PubMed

    Zhao, Zhi-Jian; Wang, Qi; Zhang, Li; Wu, Tao

    2008-06-26

    Recently, molecular imprinting technology has fleetly developed for applications in different fields. It shows great potential in sensor design, drug delivery, chromatography separation, catalysis, chiral synthesis, and especially in the molecular recognition field. In this work, a cubic model of a hydrogel network was developed and an infinite hydrogel backbone network was constructed for molecular dynamics simulation. The water structure and water-polymer interaction was investigated from the radial distribution function and the viewpoint of the hydrogen-bonding system. It is found that the hydrogen bonds between polymer and water strongly depress the diffusion of water molecules and enhance the structure of water in the system. The greater the network mesh size of the polymer, the weaker the structure of the water. The decreasing of the density of hydrogen bonds between polymer and water is the major factor that leads to the weakening of water structure.

  16. Molecular structures of porphyrin-quinone models for electron transfer

    SciTech Connect

    Fajer, J.; Barkigia, K.M.; Melamed, D.; Sweet, R.M.; Kurreck, H.; Gersdorff, J. von; Plato, M.; Rohland, H.C.; Elger, G.; Moebius, K.

    1996-08-15

    Synthetic porphyrin-quinone complexes are commonly used to mimic electron transport in photosynthetic reaction centers and to probe the effects of energetics, distances, and relative orientations on rates of electron transfer between donor-acceptor couples. The structures of two such models have been determined by X-ray diffraction. The redox pairs consist of a zinc porphyrin covalently linked to benzoquinone in cis and trans configurations via a cyclohexanediyl bridge. The crystallographic studies were undertaken to provide a structural foundation for the extensive body of experimental and theoretical results that exists for these compounds in both the ground and photoinduced charge-separated states. The results validate conclusions reached from theoretical calculations, EPR and two-dimensional NMR results for these states. 15 refs., 6 figs., 2 tabs.

  17. Synthesis and Molecular Structure of (99) Tc Corroles.

    PubMed

    Einrem, Rune F; Braband, Henrik; Fox, Thomas; Vazquez-Lima, Hugo; Alberto, Roger; Ghosh, Abhik

    2016-12-23

    The first (99) Tc corroles have been synthesized and fully characterized. A single-crystal X-ray structure of a (99) TcO triarylcorrole revealed nearly identical geometry parameters as the corresponding ReO structure. A significant spectral shift between the Soret maxima of TcO (410-413 nm) and ReO (438-441 nm) corroles was observed and, based on two-component spin-orbit ZORA TDDFT calculations, ascribed to relativistic effects in the Re case. The syntheses reported herein potentially pave the way toward (99m) Tc-porphyrinoid-based radiopharmaceuticals. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Structure of molecular liquids: hard rod-disk mixtures.

    PubMed

    Cheung, David L; Anton, Lucian; Allen, Michael P; Masters, Andrew J

    2008-01-01

    The structure of hard rod-disk mixtures is studied using Monte Carlo simulations and integral equation theory, for a range of densities in the isotropic phase. By extension of methods used in single component fluids, the pair correlation functions of the molecules are calculated and comparisons between simulation and integral equation theory, using a number of different closure relations, are made. Comparison is also made for thermodynamic data and phase behavior.

  19. Electron spectra and structure of atomic and molecular clusters

    SciTech Connect

    Dehmer, Patricia M.

    1980-01-01

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

  20. Laboratory spectra of C60 and related molecular structures

    NASA Technical Reports Server (NTRS)

    Janca, J.; Solc, M.; Vetesnik, M.

    1994-01-01

    The electronic spectra of fullerene structures in high frequency discharge are studied in the plasma chemistry laboratory of the Faculty of Science of Masaryk University in Brno. The ultraviolet and visual spectra are investigated in order to be compared with the diffuse interstellar bands and interpreted within the theory of quantum mechanics. The preliminary results of the study are presented here in the form of a poster.

  1. Quantitative structure-hydrophobicity relationships of molecular fragments and beyond.

    PubMed

    Zou, Jian-Wei; Huang, Meilan; Huang, Jian-Xiang; Hu, Gui-Xiang; Jiang, Yong-Jun

    2016-03-01

    Quantitative structure-property relationship (QSPR) models were firstly established for the hydrophobic substituent constant (πX) using the theoretical descriptors derived solely from electrostatic potentials (EPSs) at the substituent atoms. The descriptors introduced are found to be related to hydrogen-bond basicity, hydrogen-bond acidity, cavity, or dipolarity/polarizability terms in linear solvation energy relationship, which endows the models good interpretability. The predictive capabilities of the models constructed were also verified by rigorous Monte Carlo cross-validation. Then, eight groups of meta- or para-disubstituted benzenes and one group of substituted pyridines were investigated. QSPR models for individual systems were achieved with the ESP-derived descriptors. Additionally, two QSPR models were also established for Rekker's fragment constants (foct), which is a secondary-treatment quantity and reflects average contribution of the fragment to logP. It has been demonstrated that the descriptors derived from ESPs at the fragments, can be well used to quantitatively express the relationship between fragment structures and their hydrophobic properties, regardless of the attached parent structure or the valence state. Finally, the relations of Hammett σ constant and ESP quantities were explored. It implies that σ and π, which are essential in classic QSAR and represent different type of contributions to biological activities, are also complementary in interaction site.

  2. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations

    PubMed Central

    Pérez, Jesús M.; Soriguer, Ramón C.; Granados, José E.

    2017-01-01

    Background Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. Methodology/Principal Findings We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Conclusions Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies. PMID:28135293

  3. Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes.

    PubMed

    Idupulapati, Nagesh; Devanathan, Ram; Dupuis, Michel

    2011-06-15

    We report a detailed and comprehensive analysis from classical molecular dynamics simulations of the nanostructure of a model of hydrated perfluoro sulfonyl imide (PFSI) membrane, a polymeric system of interest as a proton conductor in polymer electrolyte membrane fuel cells. We also report on the transport dynamics of water and hydronium ions, and water network percolation in this system. We find that the water network percolation threshold for PFSI, i.e. the threshold at which a consistent spanning water network starts to develop in the membrane, is found to occur between hydration levels (λ) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to the sulfonic acid group in Nafion, as computationally characterized in our earlier ab initio study (Idupulapati et al 2010 J. Phys. Chem. A 114 6904-12), results in a larger fraction of 'free' hydronium ions at low hydration levels in PFSI compared to Nafion. However, the calculated diffusion coefficients of the H(3)O(+) ions and H(2)O molecules as a function the hydration level are observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with experimental data.

  4. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations.

    PubMed

    Angelone-Alasaad, Samer; Biebach, Iris; Pérez, Jesús M; Soriguer, Ramón C; Granados, José E

    2017-01-01

    Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.

  5. Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

    NASA Astrophysics Data System (ADS)

    Gutiérrez, R.; Caetano, R.; Woiczikowski, P. B.; Kubar, T.; Elstner, M.; Cuniberti, G.

    2010-02-01

    Charge transport through a short DNA oligomer (Dickerson dodecamer (DD)) in the presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics (MD) simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations, arising either from the solvent fluctuations or from base-pair vibrational modes, can be taken into account in a straightforward way through the time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the on-site energies along the DNA wire.

  6. Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

    SciTech Connect

    Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

    1992-05-10

    The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure of MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.

  7. Semifluorinated Alkanes at the Air-Water Interface: Tailoring Structure and Rheology at the Molecular Scale.

    PubMed

    Theodoratou, Antigoni; Jonas, Ulrich; Loppinet, Benoit; Geue, Thomas; Stangenberg, Rene; Keller, Rabea; Li, Dan; Berger, Rüdiger; Vermant, Jan; Vlassopoulos, Dimitris

    2016-04-05

    Semifluorinated alkanes form monolayers with interesting properties at the air-water interface due to their pronounced amphi-solvophobic nature and the stiffness of the fluorocarbons. In the present work, using a combination of structural and dynamic probes, we investigated how small molecular changes can be used to control the properties of such an interface, in particular its organization, rheology, and reversibility during compression-expansion cycles. Starting from a reference system perfluor(dodecyl)dodecane, we first retained the linear structure but changed the linkage groups between the alkyl chains and the fluorocarbons, by introducing either a phenyl group or two oxygens. Next, the molecular structure was changed from linear to branched, with four side chains (two fluorocarbons and two hydrocarbons) connected to extended aromatic cores. Neutron reflectivity at the air-water interface and scanning force microscopy on deposited films show how the changes in the molecular structure affect molecular arrangement relative to the interface. Rheological and compression-expansion measurements demonstrate the significant consequences of these changes in molecular structure and interactions on the interfacial properties. Remarkably, even with these simple molecules, a wide range of surface rheological behaviors can be engineered, from viscous over viscoelastic to brittle solids, for very similar values of the surface pressure.

  8. FlaME: Flash Molecular Editor - a 2D structure input tool for the web.

    PubMed

    Dallakian, Pavel; Haider, Norbert

    2011-02-01

    So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions.

  9. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    SciTech Connect

    Yu,P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  10. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    PubMed Central

    2011-01-01

    Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions. PMID:21284863

  11. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  12. Crystal and molecular structure of barley alpha-amylase.

    PubMed

    Kadziola, A; Abe, J; Svensson, B; Haser, R

    1994-05-27

    The three-dimensional structure of barley malt alpha-amylase (isoform AMY2-2) was determined by multiple isomorphous replacement using three heavy-atom derivatives and solvent flattening. The model was refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinement to an R-factor of 0.153 based on 18,303 independent reflections with F(o) > sigma(F(o)) between 10 and 2.8 A resolution, with root-mean-square deviations of 0.016 A and 3.3 degrees from ideal bond lengths and bond angles, respectively. The final model consists of 403 amino acid residues, three calcium ions and 153 water molecules. The polypeptide chain folds into three domains: a central domain forming a (beta alpha)8-barrel of 286 residues, with a protruding irregular structured loop domain of 64 residues (domain B) connecting strand beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of 53 residues forming a five stranded anti-parallel beta-sheet. Unlike the previously known alpha-amylase structures, AMY2-2 contains three Ca2+ binding sites co-ordinated by seven or eight oxygen atoms from carboxylate groups, main-chain carbonyl atoms and water molecules, all calcium ions being bound to domain B and therefore essential for the structural integrity of that domain. Two of the Ca2+ sites are located only 7.0 A apart with one Asp residue serving as ligand for both. One Ca2+ site located at about 20 A from the other two was found to be exchangeable with Eu3+. By homology with other alpha-amylases, some important active site residues are identified as Asp179, Glu204 and Asp289, and are situated at the C-terminal end of the central beta-barrel. A starch granule binding site, previously identified as Trp276 and Trp277, is situated on alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the enzyme. This binding site region is associated with a considerable disruption of the (beta alpha)8-barrel 8-fold symmetry.

  13. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    NASA Technical Reports Server (NTRS)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  14. Charge-distribution effect of imaging molecular structure by high-order above-threshold ionization

    SciTech Connect

    Wang Bingbing; Fu Panming; Guo Yingchun; Zhang Bin; Zhao Zengxiu; Yan Zongchao

    2010-10-15

    Using a triatomic molecular model, we show that the interference pattern in the high-order above-threshold ionization (HATI) spectrum depends dramatically on the charge distribution of the molecular ion. Therefore the charge distribution can be considered a crucial factor for imaging a molecular geometric structure. Based on this study, a general destructive interference formula for each above-threshold ionization channel is obtained for a polyatomic molecule concerning the positions and charge values of each nuclei. Comparisons are made for the HATI spectra of CO{sub 2}, O{sub 2}, NO{sub 2}, and N{sub 2}. These results may shed light on imaging complex molecular structure by the HATI spectrum.

  15. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    NASA Technical Reports Server (NTRS)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  16. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Zhengqing

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2x1)CO/Ni(110) and the p(2x2)K/Ni(111) adsorption. For the dense p2mg(2x1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16±2° from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94±0.02Å. The first- to second-layer spacing of Ni is 1.27±0.04Å, up from 1.10Å for the clean Ni(110) surface, but close to the 1.25Å Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20Å and 15--23°) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16Å and 19°. This yields an O-O distance of 2.95Å for the two nearest CO molecules, (van der Waals` radius ~ 1.5 Å for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2x2)K/Ni(111) overlayer, ARPEFS {chi}(k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  17. Structural studies of molecular and metallic overlayers using angle- resolved photoemission extended fine structure

    SciTech Connect

    Huang, Z.

    1992-10-01

    Angle-resolved photoemission extended fine structure (ARPEFS) was used to study molecular and metallic overlayers on metal surfaces through analysis of p2mg(2[times]1)CO/Ni(110) and the p(2[times]2)K/Ni(111) adsorption. For the dense p2mg(2[times]1)CO/Ni(110) surface layer, photoemission intensities from C 1s level were measured in three directions at photoelectron kinetic energies 60-400 eV. Using multiple-scattering spherical-wave (MSSW) modeling, it was found that CO molecules are adsorbed on short-bridge sites, with adjacent CO along the [110] direction displaced alternatively in opposite directions towards the [001] azimuths to form a zigzag chain geometry. The tilt angle is 16[plus minus]2[degree] from the surface normal for the direction linking the C atom and the center of the Ni bridge. The carbon C-Ni interatomic distance was determined to be 1.94[plus minus]0.02[Angstrom]. The first- to second-layer spacing of Ni is 1.27[plus minus]0.04[Angstrom], up from 1.10[Angstrom] for the clean Ni(110) surface, but close to the 1.25[Angstrom] Ni interlayer spacing in the bulk. The C-O bond length and tilt angle were varied within small ranges (1.10--1.20[Angstrom] and 15--23[degrees]) in our MSSW simulations. Best agreement between experiment and simulations was achieved at 1.16[Angstrom] and 19[degrees]. This yields an O-O distance of 2.95[Angstrom] for the two nearest CO molecules, (van der Waals' radius [approximately] 1.5 [Angstrom] for oxygen). Two different partial-wave phase-shifts were used in MSSW, and structural results from both are in very good agreement. For the p(2[times]2)K/Ni(111) overlayer, ARPEFS [chi](k) curves from K 1s level measured along [111] and [771] at 130K showed that the K atoms are preferentially adsorbed on the atop sites, in agreement with a LEED study of the same system.

  18. Molecular determinants of staphylococcal biofilm dispersal and structuring

    PubMed Central

    Le, Katherine Y.; Dastgheyb, Sana; Ho, Trung V.; Otto, Michael

    2014-01-01

    Staphylococci are frequently implicated in human infections, and continue to pose a therapeutic dilemma due to their ability to form deeply seated microbial communities, known as biofilms, on the surfaces of implanted medical devices and host tissues. Biofilm development has been proposed to occur in three stages: (1) attachment, (2) proliferation/structuring, and (3) detachment/dispersal. Although research within the last several decades has implicated multiple molecules in the roles as effectors of staphylococcal biofilm proliferation/structuring and detachment/dispersal, to date, only phenol soluble modulins (PSMs) have been consistently demonstrated to serve in this role under both in vitro and in vivo settings. PSMs are regulated directly through a density-dependent manner by the accessory gene regulator (Agr) system. They disrupt the non-covalent forces holding the biofilm extracellular matrix together, which is necessary for the formation of channels, a process essential for the delivery of nutrients to deeper biofilm layers, and for dispersal/dissemination of clusters of biofilm to distal organs in acute infection. Given their relevance in both acute and chronic biofilm-associated infections, the Agr system and the psm genes hold promise as potential therapeutic targets. PMID:25505739

  19. Molecular and crystal structure of anhydrous zirconium perchlorate

    SciTech Connect

    Genkina, E.A.; Babaeva, V.P.; Rosolovskii, V.Ya.

    1985-08-01

    An x-ray diffraction investigation (diffractometer, Mo K..cap alpha.., graphite monochromator, omega scan technique, Theta less than or equal to 30/sup 0/, 1060 reflections, least-squares method in the anisotropic approximation to R = 0.058) of anhydrous zirconium perchlorate has been carried out. The crystals of Zr(Cl0/sub 4/)/sub 4/ are monoclinic: ..cap alpha.. = 12.899(3), b = 13.188(7), c = 7.937(3) A, ..gamma.. = 107.91/sup 0/, Z = 4, space group Bb. The structure has an island character and is built up from isolated Zr(ClO/sub 4/)/sub 4/ molecules. The Zr atom is surrounded by eight O atoms in four bidentate perchlorato groups. The Zr-O distances lie in the range from 2.13 to 2.23 A, averaging 2.19 A. The eight-vertex polyhedron around Zr is the mmmm steroisomer of a dodecahedron. The centers of the perchlorato groups are located at the vertices of flattened tetrahedron. The ClO/sub 4/ groups have a distorted tetrahedral structure, and the mean length of the Cl-O/sub b/ bonds (1.50 A) is 0.11 A greater than the mean length of the Cl-O/sub t/ bonds, pointing out the essentially covalent character of the bonds of the perchlorato groups with the central Zr atom.

  20. DNA damage tolerance by recombination: Molecular pathways and DNA structures.

    PubMed

    Branzei, Dana; Szakal, Barnabas

    2016-08-01

    Replication perturbations activate DNA damage tolerance (DDT) pathways, which are crucial to promote replication completion and to prevent fork breakage, a leading cause of genome instability. One mode of DDT uses translesion synthesis polymerases, which however can also introduce mutations. The other DDT mode involves recombination-mediated mechanisms, which are generally accurate. DDT occurs prevalently postreplicatively, but in certain situations homologous recombination is needed to restart forks. Fork reversal can function to stabilize stalled forks, but may also promote error-prone outcome when used for fork restart. Recent years have witnessed important advances in our understanding of the mechanisms and DNA structures that mediate recombination-mediated damage-bypass and highlighted principles that regulate DDT pathway choice locally and temporally. In this review we summarize the current knowledge and paradoxes on recombination-mediated DDT pathways and their workings, discuss how the intermediate DNA structures may influence genome integrity, and outline key open questions for future research. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

  1. NMR studies of molecular structure in fruit cuticle polyesters.

    PubMed

    Fang, X; Qiu, F; Yan, B; Wang, H; Mort, A J; Stark, R E

    2001-07-01

    The cuticle of higher plants functions primarily as a protective barrier for the leaves and fruits, controlling microbial attack as well as the diffusion of water and chemicals from the outside environment. Its major chemical constituents are waxes (for waterproofing) and cutin (a structural support polymer). However, the insolubility of cutin has hampered investigations of its covalent structure and domain architecture, which are viewed as essential for the design of crop protection strategies and the development of improved synthetic waterproofing materials. Recently developed strategies designed to meet these investigative challenges include partial depolymerization using enzymatic or chemical reagents and spectroscopic examination of the intact polyesters in a solvent-swelled form. The soluble oligomers from degradative treatments of lime fruit cutin are composed primarily of the expected 10,16-dihydroxyhexadecanoic and 16-hydroxy-10-oxo-hexadecanoic acids; low-temperature HF treatments also reveal sugar units that are covalently attached to the hydroxyfatty acids. Parallel investigations of solvent-swollen cutin using 2D NMR spectroscopy assisted by magic-angle spinning yield well-resolved spectra that permit detailed comparisons to be made among chemical moieties present in the intact biopolymer, the soluble degradation products, and the unreacted solid residue.

  2. DFT study of the effect of substitution on the molecular structure of copper phthalocyanine

    NASA Astrophysics Data System (ADS)

    Kaur, Prabhjot; Sachdeva, Ritika; Singh, Sukhwinder; Saini, G. S. S.

    2016-05-01

    To study the effect of sulfonic acid group as substituent on the molecular structure of an organic compound copper Phthalocyanine, the optimized geometry, mulliken charges, energies and dipole momemts of copper phthalocyanine and copper phthalocyaninetetrasulfonic acid tetra sodium salt have been investigated using density functional theory. Also to predict the change in reactive sites after substitution, molecular electrostatic potential maps for both the molecules have been calculated.

  3. The Molecular and Morphologic Structures That Make Saltatory Conduction Possible in Peripheral Nerve.

    PubMed

    Carroll, Steven L

    2017-03-14

    Saltatory conduction is the process by which action potentials are rapidly and efficiently propagated along myelinated axons. In the peripheral nervous system, saltatory conduction is made possible by a series of morphologically and molecularly distinct subdomains in both axons and their associated myelinating Schwann cells. This review briefly summarizes current knowledge on the molecular structure and physiology of the node of Ranvier and adjacent regions of the axoglial unit in peripheral nerve.

  4. The liquid structure of tetrachloroethene: Molecular dynamics simulations and reverse Monte Carlo modeling with interatomic potentials

    NASA Astrophysics Data System (ADS)

    Gereben, Orsolya; Pusztai, László

    2013-10-01

    The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ˜11 Å and a very small third one at ˜16 Å can be found as well, without preference for any axis or plane orientation.

  5. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders.

    PubMed

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-07

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  6. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    NASA Astrophysics Data System (ADS)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  7. A "turn-on" and label-free fluorescent assay for the rapid detection of exonuclease III activity based on Tb(3+)-induced G-quadruplex conjugates.

    PubMed

    Yang, WeiJuan; Ruan, YaJuan; Wu, WeiHua; Chen, PingPing; Xu, LiangJun; Fu, FengFu

    2014-07-01

    A "turn-on" and label-free fluorescent assay for the specific, rapid, and sensitive detection of 3' → 5' exonuclease III activity is reported in this study. The assay is based on the Tb(3+)-promoted G-quadruplex, which lead to the enhancement of Tb(3+) fluorescence due to the energy transfer from guanines. The proposed assay is highly simple, rapid, and cost-effective, and does not require sophisticated experimental techniques such as gel-based equipment or radioactive labels. It can be used for the rapid detection of exonuclease III activity with a detection limit of 0.8 U and a RSD (n = 6) <5 %. Notably, no dye was covalently conjugated to the DNA strands, which offers the advantages of low-cost and being interference-free.

  8. Atomic spectral methods for molecular electronic structure calculations.

    PubMed

    Langhoff, P W; Boatz, J A; Hinde, R J; Sheehy, J A

    2004-11-15

    Theoretical methods are reported for ab initio calculations of the adiabatic (Born-Oppenheimer) electronic wave functions and potential energy surfaces of molecules and other atomic aggregates. An outer product of complete sets of atomic eigenstates familiar from perturbation-theoretical treatments of long-range interactions is employed as a representational basis without prior enforcement of aggregate wave function antisymmetry. The nature and attributes of this atomic spectral-product basis are indicated, completeness proofs for representation of antisymmetric states provided, convergence of Schrodinger eigenstates in the basis established, and strategies for computational implemention of the theory described. A diabaticlike Hamiltonian matrix representative is obtained, which is additive in atomic-energy and pairwise-atomic interaction-energy matrices, providing a basis for molecular calculations in terms of the (Coulombic) interactions of the atomic constituents. The spectral-product basis is shown to contain the totally antisymmetric irreducible representation of the symmetric group of aggregate electron coordinate permutations once and only once, but to also span other (non-Pauli) symmetric group representations known to contain unphysical discrete states and associated continua in which the physically significant Schrodinger eigenstates are generally embedded. These unphysical representations are avoided by isolating the physical block of the Hamiltonian matrix with a unitary transformation obtained from the metric matrix of the explicitly antisymmetrized spectral-product basis. A formal proof of convergence is given in the limit of spectral closure to wave functions and energy surfaces obtained employing conventional prior antisymmetrization, but determined without repeated calculations of Hamiltonian matrix elements as integrals over explicitly antisymmetric aggregate basis states. Computational implementations of the theory employ efficient recursive

  9. Exploring Molecular and Mechanical Gradients in Structural Bioscaffolds†

    PubMed Central

    Waite, J. Herbert; Lichtenegger, Helga C.; Stucky, Galen D.; Hansma, Paul

    2007-01-01

    Most organisms consist of a functionally adaptive assemblage of hard and soft tissues. Despite the obvious advantages of reinforcing soft protoplasm with a hard scaffold, such composites can lead to tremendous mechanical stresses where the two meet. Although little is known about how nature relieves these stresses, it is generally agreed that fundamental insights about molecular adaptation at hard/soft interfaces could profoundly influence how we think about biomaterials. Based on two noncellular tissues, mussel byssus and polychaete jaws, recent studies suggest that one natural strategy to minimize interfacial stresses between adjoining stiff and soft tissue appears to be the creation of a “fuzzy” boundary, which avoids abrupt changes in mechanical properties. Instead there is a gradual mechanical change that accompanies the transcendence from stiff to soft and vice versa. In byssal threads, the biochemical medium for achieving such a gradual mechanical change involves the elegant use of collagen-based self-assembling block copolymers. There are three distinct diblock copolymer types in which one block is always collagenous, whereas the other can be either elastin-like (soft), amorphous polyglycine (intermediate), or silk-like (stiff). Gradients of these are made by an incrementally titrated expression of the three proteins in secretory cells the titration phenotype of which is linked to their location. Thus, reflecting exactly the composition of each thread, the distal cells secrete primarily the silk– and polyglycine–collagen diblocks, whereas the proximal cells secrete the elastin– and polyglycine–collagen diblocks. Those cells in between exhibit gradations of collagens with silk or elastin blocks. Spontaneous self-assembly appears to be by pH triggered metal binding by histidine (HIS)-rich sequences at both the amino and carboxy termini of the diblocks. In the polychaete jaws, HIS-rich sequences are expanded into a major block domain. Histidine

  10. Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations

    PubMed Central

    Flechsig, Holger; Mikhailov, Alexander S.

    2010-01-01

    Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated. PMID:21081697

  11. Structural and dipolar fluctuations in liquid water: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Masia, Marco; Guardia, Elvira

    2016-03-01

    A Car-Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

  12. Current and emerging opportunities for molecular simulations in structure-based drug design

    PubMed Central

    Michel, Julien

    2014-01-01

    An overview of the current capabilities and limitations of molecular simulation of biomolecular complexes in the context of computer-aided drug design is provided. Steady improvements in computer hardware coupled with more refined representations of energetics are leading to a new appreciation of the driving forces of molecular recognition. Molecular simulations are poised to more frequently guide the interpretation of biophysical measurements of biomolecular complexes. Ligand design strategies emerge from detailed analyses of computed structural ensembles. The feasibility of routine applications to ligand optimization problems hinges upon successful extensive large scale validation studies and the development of protocols to intelligently automate computations. PMID:24469595

  13. Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics.

    PubMed

    Vlachakis, Dimitrios; Pavlopoulou, Athanasia; Kazazi, Dorothea; Kossida, Sophia

    2013-10-10

    Microalgae are unicellular microorganisms indispensible for environmental stability and life on earth, because they produce approximately half of the atmospheric oxygen, with simultaneously feeding on the harmful greenhouse gas carbon dioxide. Using gene fusion analysis, a series of five fusion/fission events was identified, that provided the basis for critical insights to their evolutionary history. Moreover, the three-dimensional structures of both the fused and the component proteins were predicted, allowing us to envisage putative protein-protein interactions that are invaluable for the efficient usage, handling and exploitation of microalgae. Collectively, our proposed approach on the five fusion/fission alga protein events contributes towards the expansion of the microalgae knowledgebase, bridging protein evolution of the ancient microalgal species and the rapidly evolving, modern, bioinformatics field. © 2013 Elsevier B.V. All rights reserved.

  14. Crystal and molecular structure of sodium paratungstate 26 hydrate

    SciTech Connect

    Cruywagen, J.J.; Nassibemi, L.R.; Niven, M.L.; Vander Merwe, I.F.

    1986-08-01

    On standing, an acid solution of tungstate yields single crystals of the paratungstate salt Na/sub 10/(H/sub 2/W/sub 12/O/sub 42/ /SUB sd/ /SUP ./ 26H/sub 2/O. The space group is P1, (No. 2), a 11.811(2), b = 12.486(2), c = 12.206(2) A, ..cap alpha.. = 82.29(1), ..beta.. = 115.12(1), ..gamma.. = 113.76(1) /sup 0/, V = 1485.6 A/sup 3/, Z = 1. The structure was solved by direct methods and refined to R = 0.0397, R /SUB w/ = 0.0403 (w = (sigma/sup 2/F)/sup -1/). The 12 WO/sub 6/ octahedra (shared edges and vertices) are distorted from regular geometry; one of the sodium ions exhibits disorder and there is extensive hydrogen bonding between the water molecules and the oxygens of the paratungstate anion.

  15. Molecular tools for investigating ANME community structure and function

    SciTech Connect

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  16. Molecular Structure and Reactivity in the Pyrolysis of Aldehydes

    NASA Astrophysics Data System (ADS)

    Sias, Eric; Cole, Sarah; Sowards, John; Warner, Brian; Wright, Emily; McCunn, Laura R.

    2016-06-01

    The effect of alkyl chain structure on pyrolysis mechanisms has been investigated in a series of aldehydes. Isovaleraldehyde, CH_3CH(CH_3)CH_2CHO, and pivaldehyde, (CH_3)_3CCHO, were subject to thermal decomposition in a resistively heated SiC tubular reactor at 800-1200 °C. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Carbon monoxide and isobutene were major products from each of the aldehydes, which is consistent with what is known from previous studies of unbranched alkyl-chain aldehydes. Other products observed include vinyl alcohol, propene, acetylene, and ethylene, revealing complexities to be considered in the pyrolysis of large, branched-chain aldehydes.

  17. Two-dimensional topological insulator molecular networks: dependence on structure, symmetry, and composition

    NASA Astrophysics Data System (ADS)

    Tan, Liang Z.; Louie, Steven G.

    2014-03-01

    2D molecular networks can be fabricated from a wide variety of molecular building blocks, arranged in many different configurations. Interactions between neighboring molecular building blocks result in the formation of new 2D materials. Examples of 2D organic topological insulators, that contain molecular building blocks and heavy elements arranged in a hexagonal lattice, have been recently proposed by Feng Liu and coworkers (Nano Lett., 13, 2842 (2013)). In this work, we present a systematic study of the design space of 2D molecular network topological insulators, elucidating the role of structure, symmetry, and composition of the networks. We show that the magnitude and presence of spin-orbit gaps in the electronic band structure is strongly dependent on the symmetry properties and arrangement of the individual components of the molecular lattice. We present general rules to maximize the magnitude of spin-orbit gaps and perform ab-initio calculations on promising structures derived from these guidelines. This work was supported by National Science Foundation Grant No. DMR10-1006184, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the NSF through XSEDE resources at NICS.

  18. Molecular and structural analysis of genetic variations in congenital cataract

    PubMed Central

    Kumar, Manoj; Agarwal, Tushar; Kaur, Punit; Kumar, Manoj; Khokhar,, Sudarshan

    2013-01-01

    Objective To determine the relative contributions of mutations in congenital cataract cases in an Indian population by systematic screening of genes associated with cataract. Methods We enrolled 100 congenital cataract cases presenting at the Dr. R. P. Centre for Ophthalmic Sciences, a tertiary research and referral hospital (AIIMS, New Delhi, India). Crystallin, alpha A (CRYAA), CRYAB, CRYGs, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, beaded filament structural protein 1 (BFSP1), gap function protein, alpha 3 (GJA3), GJA8, and heat shock transcription factor 4 gene genes were amplified. Protein structure differences analysis was performed using Discovery Studio (DS) 2.0. Results The mean age of the patients was 17.45±16.51 months, and the age of onset was 1.618±0.7181 months. Sequencing analysis of 14 genes identified 18 nucleotide variations. Fourteen variations were found in the crystallin genes, one in Cx-46 (GJA3), and three in BFSP1. Conclusions Congenital cataract shows marked clinical and genetic heterogeneity. Five nucleotide variations (CRYBA4:p.Y67N, CRYBB1:p.D85N, CRYBB1:p.E75K, CRYBB1:p.E155K, and GJA3:p.M1V) were predicted to be pathogenic. Variants in other genes might also be involved in maintaining lens development, growth, and transparency. The study confirms that the crystallin beta cluster on chromosome 22, Cx-46, and BFSP1 plays a major role in maintaining lens transparency. This study also expands the mutation spectrum of the genes associated with congenital cataract. PMID:24319337

  19. The RecJ2 Protein in the Thermophilic Archaeon Thermoplasma acidophilum Is a 3' 5' Exonuclease and Associates with a DNA Replication Complex.

    PubMed

    Ogino, Hiromi; Ishino, Sonoko; Kohda, Daisuke; Ishino, Yoshizumi

    2017-03-16

    RecJ/cell division cycle 45 (Cdc45) proteins are widely conserved in the three domains of life, i.e., in Bacteria, Eukarya and Archaea. Bacterial RecJ is a 5' 3' exonuclease and functions in DNA repair pathways, while using its 5' 3' exonuclease activity. Eukaryotic Cdc45 has no identified enzymatic activity, but participates in the CMG complex so named because it is composed of Cdc45, minichromosome maintenance protein complex (MCM) proteins 2-7, and GINS complex proteins (Sld5, Psf11 to 3). Eukaryotic Cdc45 and bacterial/archaeal RecJ share similar amino acid sequences and are considered functional counterparts. In Archaea, a RecJ homolog in Thermococcus kodakarensis was shown to associate with GINS and accelerate its nuclease activity and was therefore designated GAN (GINS-associated nuclease); however, to date, no archaeal RecJ MCM GINS complex has been isolated. The thermophilic archaeon Thermoplasma acidophilum has two RecJ like proteins, designated TaRecJ1 and TaRecJ2. TaRecJ1 exhibited DNA-specific 5' 3'exonuclease activity, while TaRecJ2 had 3' 5' exonuclease activity and preferred RNA over DNA. TaRecJ2, but not TaRecJ1, formed a stable complex with TaGINS in a 2:1 molar ratio. Furthermore, the TaRecJ2-TaGINS complex stimulated activity of TaMCM helicase in vitro, and the TaRecJ2-TaMCM-TaGINS complex was also observed in vivo. However, TaRecJ2 did not interact with TaMCM directly and was not required for the helicase activation in vitro. These findings suggest that the function of archaeal RecJ in DNA replication evolved divergently from Cdc45 despite conservation of the CMG-like complex formation between Archaea and Eukarya.

  20. Searching molecular structure databases with tandem mass spectra using CSI:FingerID

    PubMed Central

    Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

    2015-01-01

    Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543