Science.gov

Sample records for gnnqqny heptapeptide decamer

  1. The DECam Legacy Survey

    NASA Astrophysics Data System (ADS)

    Blum, Robert D.; Burleigh, Kaylan; Dey, Arjun; Schlegel, David J.; Meisner, Aaron M.; Levi, Michael; Myers, Adam D.; Lang, Dustin; Moustakas, John; Patej, Anna; Valdes, Francisco; Kneib, Jean-Paul; Huanyuan, Shan; Nord, Brian; Olsen, Knut A.; Delubac, Timothée; Saha, Abi; James, David; Walker, Alistair R.; DECaLS Team

    2016-06-01

    The DECam Legacy Survey (DECaLS) is conducting a 3-band imaging survey of the Sloan Digital Sky Survey (SDSS) extragalactic footprint as part of the Legacy Survey, which is associated with the Dark Energy Spectroscopic Instrument (DESI) redshift survey. The Legacy Survey covers 14000 square degrees in the g, r, and z bands and is being executed on the Blanco 4-m, Mayall 4-m, and Bok 2.3-m telescopes. For DECaLS, the Dark Energy Camera (DECam) will image the footprint overlapping SDSS in the region -20 < Dec < +30 deg, to depths of g=24.7, r=23.9, z=23.0 and will eventually cover a total of 7500 square degrees. The survey began in 2014 and will run through Spring 2017. Images and catalogs were introduced in Public Data Release 2 (DR2), which occurred in January 2016. The algorithm "Tractor" applies multi-wavelength forced photometry to DECam and WISE data to produce galaxy (and star) magnitudes (as well as shape and other information) for the catalogs. In total, the optical data in DR2 cover a disjoint footprint in 2078, 2141 and 5322 square degrees in g, r, and z bands, respectively; 1807 square degrees has been observed in all three optical filters. There are approximately 260 million unique sources in DR2 spread over 97,554 0.25 x 0.25 square degree bricks.The Dark Energy Spectroscopic Instrument (DESI) will observe 30+ million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these DECam data, the MOSAIC camera on the Mayall 4-meter, and the 90Prime camera on the Bok telescope.

  2. Characterization of DECam focal plane detectors

    SciTech Connect

    Diehl, H.Thomas; Angstadt, Robert; Campa, Julia; Cease, Herman; Derylo, Greg; Emes, John H.; Estrada, Juan; Kibik, Donna; Flaugher, Brenna L.; Holland, Steve E.; Jonas, Michelle; /Fermilab /Madrid, CIEMAT /LBL, Berkeley /Argonne /Pennsylvania U.

    2008-06-01

    DECam is a 520 Mpix, 3 square-deg FOV imager being built for the Blanco 4m Telescope at CTIO. This facility instrument will be used for the 'Dark Energy Survey' of the southern galactic cap. DECam has chosen 250 ?m thick CCDs, developed at LBNL, with good QE in the near IR for the focal plane. In this work we present the characterization of these detectors done by the DES team, and compare it to the DECam technical requirements. The results demonstrate that the detectors satisfy the needs for instrument.

  3. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association

    SciTech Connect

    Vitagliano, Luigi; Esposito, Luciana; Pedone, Carlo; De Simone, Alfonso

    2008-12-26

    Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel {beta}-sheets. The data show that GNNQQNY preference for parallel or antiparallel {beta}-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.

  4. Centaur size distribution with DECam

    NASA Astrophysics Data System (ADS)

    Fuentes, Cesar; Trilling, David E.; Schlichting, Hilke

    2014-11-01

    We present the results of the 2014 centaur search campaign on the Dark Energy Camera (DECam) in Tololo, Chile. This is the largest debiased Centaur survey to date, measuring for the first time the size distribution of small Centaurs (1-10km) and the first time the sizes of planetesimals from which the entire Solar System formed are directly detected.The theoretical model for the coagulation and collisional evolution of the outer solar system proposed in Schlichting et al. 2013 predicts a steep rise in the size distribution of TNOs smaller than 10km. These objects are below the detection limit of current TNO surveys but feasible for the Centaur population. By constraining the number of Centaurs and this feature in their size distribution we can confirm the collisional evolution of the Solar System and estimate the rate at which material is being transferred from the outer to the inner Solar System. If the shallow power law behavior from the TNO size distribution at ~40km can be extrapolated to 1km, the size of the Jupiter Family of Comets (JFC), there would not be enough small TNOs to supply the JFC population (Volk & Malhotra, 2008), debunking the link between TNOs and JFCs.We also obtain the colors of small Centaurs and TNOs, providing a signature of collisional evolution by measuring if there is in fact a relationship between color and size. If objects smaller than the break in the TNO size distribution are being ground down by collisions then their surfaces should be fresh, and then appear bluer in the optical than larger TNOs that are not experiencing collisions.

  5. The DECam data acquisition and control system

    NASA Astrophysics Data System (ADS)

    Honscheid, K.; Eiting, J.; Elliott, A.; Annis, J.; Bonati, M.; Buckley-Geer, E.; Castander, F.; da Costa, L.; Haney, M.; Hanlon, W.; Karliner, I.; Kuehn, K.; Kuhlmann, S.; Marshall, S.; Meyer, M.; Neilsen, E.; Ogando, R.; Roodman, A.; Schalk, T.; Schumacher, G.; Selen, M.; Serrano, S.; Thaler, J.; Wester, W.

    2010-07-01

    In this paper we describe the data acquisition and control system of the Dark Energy Camera (DECam), which will be the primary instrument used in the Dark Energy Survey (DES). DES is a high precision multibandpath wide area survey of 5000 square degrees of the southern sky. DECam currently under construction at Fermilab will be a 3 square degree mosaic camera mounted at the prime focus of the Blanco 4m telescope at the Cerro-Tololo International Observatory (CTIO). The DECam data acquisition system (SISPI) is implemented as a distributed multi-processor system with a software architecture built on the Client-Server and Publish-Subscribe design patterns. The underlying message passing protocol is based on PYRO, a powerful distributed object technology system written entirely in Python. A distributed shared variable system was added to support exchange of telemetry data and other information between different components of the system. In this paper we discuss the SISPI infrastructure software, the image pipeline, the observer interface and quality monitoring system, and the instrument control system.

  6. Status of the Dark Energy Survey Camera (DECam) project

    NASA Astrophysics Data System (ADS)

    Flaugher, Brenna L.; Abbott, Timothy M. C.; Angstadt, Robert; Annis, Jim; Antonik, Michelle L.; Bailey, Jim; Ballester, Otger; Bernstein, Joseph P.; Bernstein, Rebecca A.; Bonati, Marco; Bremer, Gale; Briones, Jorge; Brooks, David; Buckley-Geer, Elizabeth J.; Campa, Juila; Cardiel-Sas, Laia; Castander, Francisco; Castilla, Javier; Cease, Herman; Chappa, Steve; Chi, Edward C.; da Costa, Luis; DePoy, Darren L.; Derylo, Gregory; de Vincente, Juan; Diehl, H. Thomas; Doel, Peter; Estrada, Juan; Eiting, Jacob; Elliott, Anne E.; Finley, David A.; Flores, Rolando; Frieman, Josh; Gaztanaga, Enrique; Gerdes, David; Gladders, Mike; Guarino, V.; Gutierrez, G.; Grudzinski, Jim; Hanlon, Bill; Hao, Jiangang; Holland, Steve; Honscheid, Klaus; Huffman, Dave; Jackson, Cheryl; Jonas, Michelle; Karliner, Inga; Kau, Daekwang; Kent, Steve; Kozlovsky, Mark; Krempetz, Kurt; Krider, John; Kubik, Donna; Kuehn, Kyler; Kuhlmann, Steve E.; Kuk, Kevin; Lahav, Ofer; Langellier, Nick; Lathrop, Andrew; Lewis, Peter M.; Lin, Huan; Lorenzon, Wolfgang; Martinez, Gustavo; McKay, Timothy; Merritt, Wyatt; Meyer, Mark; Miquel, Ramon; Morgan, Jim; Moore, Peter; Moore, Todd; Neilsen, Eric; Nord, Brian; Ogando, Ricardo; Olson, Jamieson; Patton, Kenneth; Peoples, John; Plazas, Andres; Qian, Tao; Roe, Natalie; Roodman, Aaron; Rossetto, B.; Sanchez, E.; Soares-Santos, Marcelle; Scarpine, Vic; Schalk, Terry; Schindler, Rafe; Schmidt, Ricardo; Schmitt, Richard; Schubnell, Mike; Schultz, Kenneth; Selen, M.; Serrano, Santiago; Shaw, Terri; Simaitis, Vaidas; Slaughter, Jean; Smith, R. Christopher; Spinka, Hal; Stefanik, Andy; Stuermer, Walter; Sypniewski, Adam; Talaga, R.; Tarle, Greg; Thaler, Jon; Tucker, Doug; Walker, Alistair R.; Weaverdyck, Curtis; Wester, William; Woods, Robert J.; Worswick, Sue; Zhao, Allen

    2012-09-01

    The Dark Energy Survey Collaboration has completed construction of the Dark Energy Camera (DECam), a 3 square degree, 570 Megapixel CCD camera which will be mounted on the Blanco 4-meter telescope at CTIO. DECam will be used to perform the 5000 sq. deg. Dark Energy Survey with 30% of the telescope time over a 5 year period. During the remainder of the time, and after the survey, DECam will be available as a community instrument. All components of DECam have been shipped to Chile and post-shipping checkout finished in Jan. 2012. Installation is in progress. A summary of lessons learned and an update of the performance of DECam and the status of the DECam installation and commissioning will be presented.

  7. Status of the Dark Energy Survey Camera (DECam) Project

    SciTech Connect

    Flaugher, Brenna L.; Abbott, Timothy M.C.; Angstadt, Robert; Annis, Jim; Antonik, Michelle, L.; Bailey, Jim; Ballester, Otger.; Bernstein, Joseph P.; Bernstein, Rebbeca; Bonati, Marco; Bremer, Gale; /Fermilab /Cerro-Tololo InterAmerican Obs. /ANL /Texas A-M /Michigan U. /Illinois U., Urbana /Ohio State U. /University Coll. London /LBNL /SLAC /IFAE

    2012-06-29

    The Dark Energy Survey Collaboration has completed construction of the Dark Energy Camera (DECam), a 3 square degree, 570 Megapixel CCD camera which will be mounted on the Blanco 4-meter telescope at CTIO. DECam will be used to perform the 5000 sq. deg. Dark Energy Survey with 30% of the telescope time over a 5 year period. During the remainder of the time, and after the survey, DECam will be available as a community instrument. All components of DECam have been shipped to Chile and post-shipping checkout finished in Jan. 2012. Installation is in progress. A summary of lessons learned and an update of the performance of DECam and the status of the DECam installation and commissioning will be presented.

  8. Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

    PubMed Central

    Nasica-Labouze, Jessica; Mousseau, Normand

    2012-01-01

    The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate. PMID:23209391

  9. Serinocyclins A and B, Cyclic Heptapeptides from Metarhizium anisopliae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two new cyclic heptapeptides, serinocyclins A (1) and B (2), were isolated from conidia of the entomopathogenic fungus Metarhizium anisopliae. Structures were elucidated by a combination of mass spectrometric, NMR, and X-ray diffraction techniques. Serinocyclin A (1) contains three serine units, a...

  10. FORS2 spectroscopic classification of DECam SN candidates

    NASA Astrophysics Data System (ADS)

    Anderson, J.; Bufano, F.; Forster, F.; Hamuy, M.; Gonzalez-Gaitan, S.; Galbany, L.; Kuncarayakti, Hanin; Pignata, G.

    2014-03-01

    We report the spectroscopic classification of 3 SNe discovered by the DECam high cadence transient search (see ATELs #5956, #5949), using FORS2 on the UT1 telescope at Cerro Paranal (through DDT proposal 292.D-042). ...

  11. Identification and characterization of heptapeptide modulators of the glycine receptor.

    PubMed

    Cornelison, Garrett L; Pflanz, Natasha C; Tipps, Megan E; Mihic, S John

    2016-06-01

    The glycine receptor is a member of the Cys-loop receptor superfamily of ligand-gated ion channels and is implicated as a possible therapeutic target for the treatment of diseases such as alcoholism and inflammatory pain. In humans, four glycine receptor subtypes (α1, α2, α3, and β) co-assemble to form pentameric channel proteins as either α homomers or αβ heteromers. To date, few agents have been identified that can selectively modulate the glycine receptor, especially those possessing subtype specificity. We used a cell-based method of phage display panning, coupled with two-electrode voltage-clamp electrophysiology in Xenopus laevis oocytes, to identify novel heptapeptide modulators of the α1β glycine receptor. This involved a panning procedure in which the phage library initially underwent subtractive panning against Human Embryonic Kidney (HEK) 293 cells expressing alternative glycine receptor subtypes before panning the remaining library over HEK 293 cells expressing the target, the α1β glycine receptor. Peptides were identified that act with selectivity on α1β and α3β, compared to α2β, glycine receptors. In addition, peptide activity at the glycine receptor decreased when zinc was chelated by tricine, similar to previous observations of a decrease in ethanol's enhancing actions at the receptor in the absence of zinc. Comparisons of the amino acid sequences of heptapeptides capable of potentiating glycine receptor function revealed several consensus sequences that may be predictive of a peptide's enhancing ability. PMID:27038522

  12. Dynamic nuclear polarization-enhanced solid-state NMR spectroscopy of GNNQQNY nanocrystals and amyloid fibrils

    PubMed Central

    Debelouchina, Galia T.; Bayro, Marvin J.; van der Wel, Patrick C. A.; Caporini, Marc A.; Barnes, Alexander B.; Rosay, Melanie; Maas, Werner E.; Griffin, Robert G.

    2015-01-01

    Dynamic nuclear polarization (DNP) utilizes the inherently larger polarization of electrons to enhance the sensitivity of conventional solid-state NMR experiments at low temperature. Recent advances in instrumentation development and sample preparation have transformed this field and have opened up new opportunities for its application to biological systems. Here, we present DNP-enhanced 13C–13C and 15N–13C correlation experiments on GNNQQNY nanocrystals and amyloid fibrils acquired at 9.4 T and 100 K and demonstrate that DNP can be used to obtain assignments and site-specific structural information very efficiently. We investigate the influence of temperature on the resolution, molecular conformation, structural integrity and dynamics in these two systems. In addition, we assess the low-temperature performance of two commonly used solid-state NMR experiments, proton-driven spin diffusion (PDSD) and transferred echo double resonance (TEDOR), and discuss their potential as tools for measurement of structurally relevant distances at low temperature in combination with DNP. PMID:20454733

  13. Identifying Electromagnetic Counterparts to Gravitational Wave Triggers With DECam

    NASA Astrophysics Data System (ADS)

    Cowperthwaite, Philip

    2016-03-01

    Identifying the electromagnetic counterpart to a gravitational wave (GW) event is one of the great observational challenges in modern astronomy. We report on our work to overcome this challenge by investigating the theoretical and practical issues associated with optical follow-up of a GW event. This includes a systematic study of the potential contaminant population and their impact on counterpart detectability in simulated observations. Additionally, we utilize data taken with the Dark Energy Camera (DECam) on the Blanco 4-m telescope at CTIO. These data serve as a mock follow-up to a GW event and assist in the characterization of contamination not captured in simulations. P.S.C. is grateful for support provided by the NSF through the Graduate Research Fellowship Program, Grant DGE1144152.

  14. The Dark Energy Spectroscopic Instrument (DESI): The NOAO DECam Legacy Imaging Survey and DESI Target Selection

    NASA Astrophysics Data System (ADS)

    Schlegel, David J.; Blum, Robert D.; Castander, Francisco Javier; Dey, Arjun; Finkbeiner, Douglas P.; Foucaud, Sebastien; Honscheid, Klaus; James, David; Lang, Dustin; Levi, Michael; Moustakas, John; Myers, Adam D.; Newman, Jeffrey; Nord, Brian; Nugent, Peter E.; Patej, Anna; Reil, Kevin; Rudnick, Gregory; Rykoff, Eli S.; Ford Schlafly, Eddie; Stark, Casey; Valdes, Francisco; Walker, Alistair R.; Weaver, Benjamin; DECam Legacy Survey Collaboration

    2015-01-01

    The DECam Legacy Survey will conduct a 3-band imaging survey of the Sloan Digital Sky Survey (SDSS) extragalactic footprint. The Dark Energy Camera (DECam) will be used to image the 6700 square degree footprint overlapping SDSS in the region -20 < Dec < +30 deg, to depths of g=24.7, r=23.9, z=23.0. The survey will be conducted from Fall 2014 through Spring 2017, with periodic data releases beginning in March 2015. These releases will include catalogs constructed with the Tractor-based multi-wavelength forced photometry applied to the DECam and WISE satellite data.The Dark Energy Spectroscopic Instrument (DESI) will observe 24 million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these DECam data, the MOSAIC camera on the Mayall 4-meter, and the 90Prime camera on the Bok Telescope.

  15. Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors.

    PubMed

    Zhao, Jian-Hua; Liu, Hsuan-Liang; Elumalai, Pavadai; Chen, Wei-Hsi; Men, Lee-Chung; Liu, Kung-Tien

    2013-01-01

    Understanding the nature of the recognition between amyloid protofibrils and dye molecules at the molecular level is essential to improving instructive guides for designing novel molecular probes or new inhibitors. However, the atomic details of the binding between dyes and amyloid fibrils are still not fully understood. In this study, molecular docking, consensus scoring, molecular dynamics (MD), and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analyses were integrated to investigate the binding between Congo red (CR) and the GNNQQNY protofibril from yeast prion protein Sup35 and to further evaluate their binding stabilities and affinities. Our results reveal that there are four CR binding sites located on GNNQQNY protofibril surface. These four CR binding sites adopt dual binding modes by which CR binding with its long axis parallel and perpendicular to the long axis of the protofibril. In addition, CR was also found to bind to the edge of the protofibril via hydrophobic/aromatic and hydrogen-bonding interactions, which is inferred as the possible inhibition mechanism to prevent the elongation of the protofibril from the addition of incoming peptides. Virtual screening from National Cancer Institute (NCI) database obtained three hit compounds with higher binding affinity than CR to the edge of the protofibril due to the fact that the central parts of these compounds are able to form additional hydrogen bonds with the protofibril. The results of the study could be useful for the development of new molecular probes or inhibitors for clinical applications. PMID:22836831

  16. Photometric Calibration of DECam Images of the Sextans Dwarf Spheroidal Galaxy

    NASA Astrophysics Data System (ADS)

    Howard, Brittany; Vivas, Kathy

    2016-01-01

    As part of an ongoing study on the variable star population of the Sextans Dwarf Spheroidal Galaxy, we present here details on the photometric calibration of the data, which were obtained with the Dark Energy Camera (DECam) at the Blanco 4mTelescope at the Cerro Tololo Interamerican Observatory. Since DECam is a relatively new instrument, we tested different calibration strategies including calibrating each chip individually and all together. Our results indicate that the color terms and zero points are constant across the camera, at least in the g, r and i bands. We present preliminary results on the location of variable stars in the Sextans dwarf galaxy.

  17. Heptapeptide ligands against receptor-binding sites of influenza hemagglutinin toward anti-influenza therapy.

    PubMed

    Matsubara, Teruhiko; Onishi, Ai; Yamaguchi, Daisuke; Sato, Toshinori

    2016-03-01

    The initial attachment of influenza virus to cells is the binding of hemagglutinin (HA) to the sialyloligosaccharide receptor; therefore, the small molecules that inhibit the sugar-protein interaction are promising as HA inhibitors to prevent the infection. We herein demonstrate that sialic acid-mimic heptapeptides are identified through a selection from a primary library against influenza virus HA. In order to obtain lead peptides, an affinity selection from a phage-displayed random heptapeptide library was performed with the HAs of the H1 and H3 strains, and two kinds of the HA-binding peptides were identified. The binding of the peptides to HAs was inhibited in the presence of sialic acid, and plaque assays indicated that the corresponding N-stearoyl peptide strongly inhibited infections by the A/Aichi/2/68 (H3N2) strain of the virus. Alanine scanning of the peptides indicated that arginine and proline were responsible for binding. The affinities of several mutant peptides with single-amino-acid substitutions against H3 HA were determined, and corresponding docking studies were performed. A Spearman analysis revealed a correlation between the affinity of the peptides and the docking study. These results provide a practicable method to design of peptide-based HA inhibitors that are promising as anti-influenza drugs. PMID:26833245

  18. A single mutation in the hepta-peptide active site of Aspergillus niger PhyA phytase leads to myriad of biochemical changes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The active site motif of proteins belonging to ‘Histidine Acid Phosphatase’ (HAP) contains a hepta-peptide region, RHGXRXP. A close comparison among fungal and yeast HAPs has revealed the fourth residue of the hepta-peptide to be E instead of A, which is the case with A. niger phyA phytase. However,...

  19. The Search for Light Echoes of Historic SNe in the Southern Hemisphere with DECam

    NASA Astrophysics Data System (ADS)

    Rest, Armin; Bianco, Federica; Chornock, Ryan; Clocchiatti, Alejandro; Foley, Ryan J.; James, David; Matheson, Thomas; Narayan, Gautham; Olsen, Knut A.; Points, Sean; Prieto, Jose Luis; Smith, R. Chris; Smith, Nathan; Suntzeff, Nicholas B.; Welch, Douglas L.; Zenteno, Alfredo

    2015-01-01

    In recent years, light echoes of ancient SNe have been discovered with the Mosaic II cameras at the CTIO Blanco and KPNO Mayall telescopes. We have found light echoes in the LMC (Rest et al. 2005, 2008a) and near the historical Galactic events Cas A, Tycho, and Eta Car (Rest et al. 2008b, 2011a, 2012). However, searches for light echoes near the Kepler SN and SN 1006 have not yet been successful. We have started a search for light echoes in the southern hemisphere using DECam at the CTIO Blanco telescope. DECam is an excellent light echo detection system with its larger field of view and much faster read time compared to Mosaic II. This increases the efficiency of the search by more than a factor of 10, allowing us to cover significantly larger areas of the sky. We report on strategy, progress, current coverage, and first results of our project.

  20. Hydrogen Bond Network Isomers of the Water Nonamer and Decamer Observed by Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Zaleski, Daniel P.; Seifert, Nathan A.; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2013-06-01

    After our previous study of the rotational spectrum of water clusters in the 6-18 GHz region, in order to study clusters of larger size (>8 water molecules), a chirped-pulse Fourier transform microwave spectrometer in the 2-8 GHz frequency range has been used to obtain the broadband rotational spectra of five water nonamer isomers and four water decamer isomers in a pulsed molecular beam. The oxygen atom framework geometries for three nonamers and two decamers have also been unambiguously identified from isotopic labeling measurements using an H_{2}^{18}O enriched sample. Three of the four observed water decamer show tunneling effect associated with the internal dynamics of hydrogen-bond network in a similar fashion as the prism water hexamer. These tunneling paths are quenched upon a single incorporation of a H_{2}^{18}O molecule in the cluster. Due the large amount of closely-spaced rotational transitions in the H_{2}^{18}O spectrum, automated fitting tools were employed to extract the corresponding rotational spectra, which will be also briefly described. C. Perez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, and B. H. Pate, Science 336, 897 (2012).

  1. Structures of the Lowest Energy Nonamer and Decamer Water Clusters from Chirped-Pulse Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2013-06-01

    In the breakthrough paper reporting observation and analysis of pure rotational spectra of the hexamer, heptamer and nonamer water clusters only one nonamer species was identified. The advances in this experiment, as described in the previous talk, allowed identification, among others, of five different nonamer, (H_2O)_9, conformers and of four different decamer, (H_2O)_{10}, conformers. Analysis of ^{18}O enriched spectra resulted in determination of oxygen framework geometries for three of the water nonamers and two of the water decamers. Determination of experimental geometries proved considerably more challenging than for the lighter clusters since isotopic changes to moments of inertia are proportionally smaller, and there are multiple instances of near-zero principal coordinates. There are also more indications of the effect of internal motions. These problems have been overcome by careful application of r_s and least-squares r_m techniques in concert with ab initio calculations so that it was possible to match the experimental and theoretical geometries unambiguously. The precise oxygen framework geometries obtained from chirped-pulse spectroscopy for water clusters ranging in size from the hexamer to the decamer allow, for the first time, to identify some common features of the underlying hydrogen bonding from direct experimental evidence. C. Perez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, and B. H. Pate, Science {336}, 897 (2012).

  2. Stabilized Heptapeptide A7R for Enhanced Multifunctional Liposome-Based Tumor-Targeted Drug Delivery.

    PubMed

    Ying, Man; Shen, Qing; Liu, Yu; Yan, Zhiqiang; Wei, Xiaoli; Zhan, Changyou; Gao, Jie; Xie, Cao; Yao, Bingxin; Lu, Weiyue

    2016-06-01

    (L)A7R (ATWLPPR) is a heptapeptide with high binding affinity in vitro to vascular endothelial growth factor receptor 2 (VEGFR2) and neuropilin-1 (NRP-1) overexpressed on glioma, glioma vasculogenic mimicry and neovasculature. However, its tumor targeting efficacy is significantly reduced in vivo due to proteolysis in blood circulation. To improve the in vivo stability and targeting efficacy, the retro inverso isomer of (L)A7R ((D)A7R) was developed for glioma-targeted drug delivery. (D)A7R was expected to have a similar binding affinity to its receptors in vitro (VEGFR2 and NRP-1), which was experimentally confirmed. In vivo, (D)A7R-modified liposomes achieved improved glioma-targeted efficiency than did (L)A7R-modified liposomes. After loading a chemotherapeutic agent (doxorubicin), (D)A7R-modified liposomes significantly inhibited subcutaneous model tumor in comparison to free doxorubicin, plain liposomes and (L)A7R-modified liposomes. In summary, the present study presented the potential of a proteolytically stable d-peptide ligand for in vivo tumor-targeted drug delivery. PMID:27195531

  3. The DECam NEO Survey: A sensitive, wide-field search for near-Earth asteroids

    NASA Astrophysics Data System (ADS)

    Allen, Lori; Trilling, David; Valdes, Frank; Fuentes, Cesar; James, David; Herrera, David; Rajagopal, Jayadev; Burt, Brian; Axelrod, Tim

    2014-11-01

    We report preliminary results from a survey for near-Earth asteroids with the Dark Energy Camera. DECam is a facility-class 520 Megapixel wide-field imager on the 4m Blanco telescope at Cerro Tololo Inter-american Observatory. It has a 3.2 square degree field of view, and a focal plane consisting of 62 2Kx4K red-optimized CCDs. In spite of its large number of pixels, DECam reads out in less than 30 seconds, making it possible to cover a large area of sky efficiently. Compared to the largest aperture of the currently most productive NEO searches, the Blanco has an aperture that is several times larger and a comparable field of view. Our goal is to measure the size distribution of NEOs well below 140m, and we have been allocated 30 nights through the NOAO Survey program to achieve it. Here we report on results from the first 10 nights of our survey.

  4. Hydrogen bond cooperativity and the three-dimensional structures of water nonamers and decamers.

    PubMed

    Pérez, Cristóbal; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

    2014-12-22

    Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor OO distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three-body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical OO distances are in good agreement. The cooperativity effects revealed by the hydrogen bond OO distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules. PMID:25348841

  5. A Glimpse of Optically Variable Galactic Bulge X-ray Sources: A Comparison of Mosaic-II and DECam Photometry

    NASA Astrophysics Data System (ADS)

    Johnson, Christopher Bradley; Hynes, Robert I.; Jonker, Peter; Torres, Manuel; Britt, Chris; Steeghs, Danny; Maccarone, Tom; Nelemans, Gijs; Greiss, Sandra; Baldwin, Austin

    2014-06-01

    We present optical photometry and spectroscopy of selected sources from the Galactic Bulge Survey (GBS) using the new DECam imager and the previous Mosaic-II imager on the 4m Blanco telescope at Cerro-Tololo Inter-American Observatory (CTIO). The goal of the GBS is to detect quiescent Low-Mass X-Ray Binaries (LMXB) and identify eclipsing systems for follow-up mass determination to test binary population models and to better determine black hole and neutron star mass distributions. We compare the light curves of spectroscopically intriguing sources with both instruments and show that the DECam observations demonstrate large improvements in sensitivity to short-period binary systems. Because of DECam's field of view of 2.2 degrees, our survey area can be covered in 4 pointings as opposed to 64 with Mosaic-II. This increased our sampling rate from 2-5 times to 28-56 times per target per night, which includes dithering. We find that combining 2x1 secs and 2x90 secs exposures over a two day observing run, we can detect targets between 12th and 23rd magnitude. Overall, we are finding that DECam is a superb instrument for detecting variability of sources in wide-field optical surveys. This work was supported by the National Science Foundation under Grant No. AST-0908789 and by NASA through Chandra Award Number AR3-14002X issued by the Chandra X-ray Observatory Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of the National Aeronautics Space Administration under contract NAS8-03060.

  6. Characterization and correction of charge-induced pixel shifts in DECam

    DOE PAGESBeta

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; Rowe, B.; Vikram, V.; Plazas, A. A.; Seitz, S.

    2015-05-28

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the Poissonian noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field Poissonian noise correlations. The latter fall off approximately as a power-law r-2.5 with pixel separation r, are isotropic except for an asymmetry in the directmore » neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.« less

  7. Adsorption of peptide nucleic acid and DNA decamers at electrically charged surfaces.

    PubMed Central

    Fojta, M; Vetterl, V; Tomschik, M; Jelen, F; Nielsen, P; Wang, J; Palecek, E

    1997-01-01

    Adsorption behavior of peptide nucleic acid (PNA) and DNA decamers (GTAGATCACT and the complementary sequence) on a mercury surface was studied by means of AC impedance measurements at a hanging mercury drop electrode. The nucleic acid was first attached to the electrode by adsorption from a 5-microliter drop of PNA (or DNA) solution, and the electrode with the adsorbed nucleic acid layer was then washed and immersed in the blank background electrolyte where the differential capacity C of the electrode double layer was measured as a function of the applied potential E. It was found that the adsorption behavior of the PNA with an electrically neutral backbone differs greatly from that of the DNA (with a negatively charged backbone), whereas the DNA-PNA hybrid shows intermediate behavior. At higher surface coverage PNA molecules associate at the surface, and the minimum value of C is shifted to negative potentials because of intermolecular interactions of PNA at the surface. Prolonged exposure of PNA to highly negative potentials does not result in PNA desorption, whereas almost all of the DNA is removed from the surface at these potentials. Adsorption of PNA decreases with increasing NaCl concentration in the range from 0 to 50 mM NaCl, in contrast to DNA, the adsorption of which increases under the same conditions. PMID:9129832

  8. Characterization and correction of charge-induced pixel shifts in DECam

    SciTech Connect

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; Rowe, B.; Vikram, V.; Plazas, A. A.; Seitz, S.

    2015-05-01

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the {Poissonian} noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field {Poissonian} noise correlations. The latter fall off approximately as a power-law r(-)(2.5) with pixel separation r, are isotropic except for an asymmetry in the direct neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.

  9. Characterization and correction of charge-induced pixel shifts in DECam

    SciTech Connect

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; Rowe, B.; Vikram, V.; Plazas, A. A.; Seitz, S.

    2015-05-28

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the Poissonian noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field Poissonian noise correlations. The latter fall off approximately as a power-law r-2.5 with pixel separation r, are isotropic except for an asymmetry in the direct neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.

  10. Presence of UDP-N-acetylmuramyl-hexapeptides and -heptapeptides in enterococci and staphylococci after treatment with ramoplanin, tunicamycin, or vancomycin.

    PubMed Central

    Billot-Klein, D; Shlaes, D; Bryant, D; Bell, D; Legrand, R; Gutmann, L; van Heijenoort, J

    1997-01-01

    Analyses of the peptidoglycan nucleotide precursor contents of enterococci and staphylococci treated with ramoplanin, tunicamycin, or vancomycin were carried out by high-pressure liquid chromatography coupled with mass spectrometry (MS). In all cases, a sharp increase in the UDP-N-actetylmuramoyl-pentapeptide or -pentadepsipeptide pool was observed. Concomitantly, new peptidoglycan nucleotide peptides of higher molecular masses with hexa- or heptapeptide moieties were identified: UDP-MurNAc-pentapeptide-Asp or pentadepsipeptide-Asp in enterococci and UDP-MurNAc-pentapeptide-Gly or -Ala and UDP-MurNAc-pentapeptide-Gly-Gly or -Ala-Gly in staphylococci. These new compounds are derivatives of normal UDP-MurNAc-pentapeptide or -pentadepsipeptide precursors with the extra amino acid(s) linked to the lysine epsilon-amino group as established by various analytical procedures (MS, MS-MS fragmentation, chemical analysis, and digestion with R39 D,D carboxypeptidase). Except for tunicamycin-treated cells, it was not possible to ascertain whether these unusual nucleotides were formed by direct addition of the amino acids to UDP-MurNAc-pentapeptide (or -pentadepsipeptide) or whether they arose by reverse reactions from lipid I intermediates to which the amino acids had been added. PMID:9244253

  11. Intragenic and Extragenic Suppressors of Mutations in the Heptapeptide Repeat Domain of Saccharomyces Cerevisiae RNA Polymerase II

    PubMed Central

    Nonet, M. L.; Young, R. A.

    1989-01-01

    The largest subunit of RNA polymerase II contains a repeated heptapeptide sequence at its carboxy terminus. Yeast mutants with certain partial deletions of the carboxy-terminal repeat (CTR) domain are temperature-sensitive, cold-sensitive and are inositol auxotrophs. Intragenic and extragenic suppressors of the cold-sensitive phenotype of CTR domain deletion mutants were isolated and studied to investigate the function of this domain. Two types of intragenic suppressing mutations suppress the temperature-sensitivity, cold-sensitivity and inositol auxotrophy of CTR domain deletion mutants. Most intragenic mutations enlarge the repeat domain by duplicating various portions of the repeat coding sequence. Other intragenic suppressing mutations are point mutations in a conserved segment of the large subunit. An extragenic suppressing mutation (SRB2-1) was isolated that strongly suppresses the conditional and auxotrophic phenotypes of CTR domain mutations. The SRB2 gene was isolated and mapped, and an SRB2 partial deletion mutation (srb2Δ10) was constructed. The srb2Δ10 mutants are temperature-sensitive, cold-sensitive and are inositol auxotrophs. These phenotypes are characteristic of mutations in genes encoding components of the transcription apparatus. We propose that the SRB2 gene encodes a factor that is involved in RNA synthesis and may interact with the CTR domain of the large subunit of RNA polymerase II. PMID:2693207

  12. Spatial structure of heptapeptide Glu-Ile-Leu-Asn-His-Met-Lys, a fragment of the HIV enhancer prostatic acid phosphatase, in aqueous and SDS micelle solutions

    NASA Astrophysics Data System (ADS)

    Bloсhin, Dmitri S.; Aganova, Oksana V.; Yulmetov, Aidar R.; Filippov, Andrei V.; Gizatullin, Bulat I.; Afonin, Sergii; Antzutkin, Oleg N.; Klochkov, Vladimir V.

    2013-02-01

    Prostatic acid phosphatase (PAP) is a protein abundantly present in human seminal fluid. PAP plays important role in fertilization. Its 39-amino-acid fragment, PAP(248-286), is effective in enhancing infectivity of HIV virus. In this work, we determined the spatial structure in aqueous solution of a heptapeptide within the PAP fragment, containing amino acid residues 266-272 (Glu-Ile-Leu-Asn-His-Met-Lys). We also report the structure of the complex formed by this heptapeptide with sodium dodecyl sulfate micelles, a model of a biological membrane, as determined by 1H NMR spectroscopy and 2D NMR (TOCSY, HSQC-HECADE, NOESY) spectroscopy. Complex formation was confirmed by chemical shift alterations in the 1H NMR spectra of the heptapeptide, as well as by the signs and values of NOE effects. We also present a comparison of the spatial structure of Glu-Ile-Leu-Asn-His-Met-Lys in water and in complex with sodium dodecyl sulfate.

  13. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

    PubMed

    Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

    2016-10-15

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27535711

  14. Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA.

    PubMed

    Ramakrishnan, Boopathy; Sekharudu, Chandra; Pan, Baocheng; Sundaralingam, Muttaiya

    2003-01-01

    The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25 A resolution. The decamer crystallized in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 44.3, c = 24.8 A and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to R(work) and R(free) values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles alpha and gamma instead of the usual gauche(-)/gauche(+) conformations, yielding G*(G.C) base triplets. The highly hydrated [Co(NH(3))(6)](3+) ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex. PMID:12499541

  15. How pH Modulates the Dimer-Decamer Interconversion of 2-Cys Peroxiredoxins from the Prx1 Subfamily*

    PubMed Central

    Morais, Mariana A. B.; Giuseppe, Priscila O.; Souza, Tatiana A. C. B.; Alegria, Thiago G. P.; Oliveira, Marcos A.; Netto, Luis E. S.; Murakami, Mario T.

    2015-01-01

    2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His113) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp76 from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress. PMID:25666622

  16. How pH modulates the dimer-decamer interconversion of 2-Cys peroxiredoxins from the Prx1 subfamily.

    PubMed

    Morais, Mariana A B; Giuseppe, Priscila O; Souza, Tatiana A C B; Alegria, Thiago G P; Oliveira, Marcos A; Netto, Luis E S; Murakami, Mario T

    2015-03-27

    2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress. PMID:25666622

  17. Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand.

    PubMed

    Dou, Shuo-Fen; Liu, Hong; Cao, Tong-Mei; Wen, Qing-Li; Li, Jie; Shao, Qing-Chun

    2016-04-01

    The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively. PMID:26972470

  18. A Fluorescence-Labeled Heptapeptide, (FITC)KP6, as an Efficient Probe for the Specific Detection of Oxidized and Minimally Modified Low-Density Lipoprotein.

    PubMed

    Sato, Akira; Ueda, Chiemi; Kimura, Ryu; Kobayashi, Chisato; Yamazaki, Yoji; Ebina, Keiichi

    2016-05-01

    Two oxidized forms of low-density lipoprotein (LDL), oxidized LDL (ox-LDL) and minimally modified LDL (MM-LDL), are believed to play a major role in the pathogenesis of atherosclerosis. Recently, we reported that a heptapeptide (Lys-Trp-Tyr-Lys-Asp-Gly-Asp, KP6) coupled through the ε-amino group of N-terminus Lys to fluorescein isothiocyanate, (FITC)KP6, bound to ox-LDL but not to LDL. In the present study, we investigated whether (FITC)KP6 could be used as a fluorescent probe for the specific detection of MM-LDL and ox-LDL. Results from polyacrylamide gel electrophoresis and surface plasmon resonance proved that (FITC)KP6 could efficiently bind to MM-LDL as well as ox-LDL in a dose-dependent manner and with high affinity (K D = 3.16 and 3.54 ng/mL protein for MM-LDL and ox-LDL, respectively). (FITC) KP6 bound to lysophosphatidylcholine and oxidized phosphatidylcholine, both present abundantly in ox-LDL and MM-LDL, respectively. In vitro, (FITC)KP6 was detected on the surface and/or in the cytosol of human THP-1-derived macrophages incubated with ox-LDL and MM-LDL, but not LDL. These results suggest that (FITC)KP6 could be an efficient fluorescent probe for the specific detection of ox-LDL and MM-LDL and can therefore contribute to the identification, diagnosis, prevention, and treatment of atherosclerosis. PMID:27063871

  19. Heat Shock Protein 27-Targeted Heptapeptide of the PKC{Delta} Catalytic V5 Region Sensitizes Tumors With Radio- and Chemoresistance

    SciTech Connect

    Lee, Hae-June; Kim, Eun-Ho; Seo, Woo Duck; Choi, Tae Hyun; Cheon, Gi-Jeong; Lee, Yoon-Jin; Lee, Yun-Sil

    2011-05-01

    Purpose: Previous data suggest that the PKC{delta} catalytic V5 (PKC{delta}-V5) heptapeptide (HEPT) (FEQFLDI) binds HSP27 and blocks HSP27-mediated radio- or chemoresistance. Here we investigated further the in vivo function of the PKC{delta}-V5 HEPT. Methods and Materials: Labeling of HEPT with Cy5.5 or fluorescein isothiocyanate was performed to evaluate in vitro or in vivo distribution of HEPT. A clonogenic survival assay, flow cytometry, and Western blotting of cleaved caspase-3 were performed to determine in vitro sensitization effects of HEPT plus ionizing radiation (IR) versus IR alone or those of HEPT plus cisplatin(Cis) versus Cis alone. A nude mouse xenografting system was also applied to detect in vivo sensitizing effects of HEPT. Results: HEPT efficiently bound to HSP27 and showed sensitization after combined treatment with IR versus treatment with Cis alone in NCI-H1299 lung carcinoma cells, with higher HSP27 expression, which was similar to that of combined treatment with IR or with Cis alone in NCI-H460 lung carcinoma cells with lower HSP27 expression. In vivo image analysis using Cy5.5-labeled HEPT showed that HEPT was retained in HSP27-overexpressing cancer cells after xenografting to nude mice. Combined treatment of HEPT with IR versus that with Cis alone in xenografted mice showed that HEPT increased radio- or chemosensitization in NCI-H1299 cells compared to that in mice xenografted with NCI-H460 cells. Conclusions: The novel PKC{delta}-V5 HEPT may help overcome HSP27-mediated radio- or chemoresistance.

  20. MicroRNA Profiling of the Effect of the Heptapeptide Angiotensin-(1-7) in A549 Lung Tumor Cells Reveals a Role for miRNA149-3p in Cellular Migration Processes.

    PubMed

    Silva, Brenda de Oliveira da; Lima, Kelvin Furtado; Gonçalves, Letícia Rocha; Silveira, Marina Bonfogo da; Moraes, Karen C M

    2016-01-01

    Lung cancer is one of the most frequent types of cancer in humans and a leading cause of death worldwide. The high mortality rates are correlated with late diagnosis, which leads to high rates of metastasis found in patients. Thus, despite all the improvement in therapeutic approaches, the development of new drugs that control cancer cell migration and metastasis are required. The heptapeptide angiotensin-(1-7) [ang-(1-7)] has demonstrated the ability to control the growth rates of human lung cancer cells in vitro and in vivo, and the elucidation of central elements that control the fine-tuning of cancer cells migration in the presence of the ang-(1-7), will support the development of new therapeutic approaches. Ang-(1-7) is a peptide hormone of the renin-angiotensin system (RAS) and this study investigates the modulatory effect of the heptapeptide on the expression pattern of microRNAs (miRNAs) in lung tumor cells, to elucidate mechanistic concerns about the effect of the peptide in the control of tumor migratory processes. Our primary aim was to compare the miRNA profiling between treated and untreated-heptapeptide cells to characterize the relevant molecule that modulates cellular migration rates. The analyses selected twenty one miRNAs, which are differentially expressed between the groups; however, statistical analyses indicated miRNA-149-3p as a relevant molecule. Once functional analyses were performed, we demonstrated that miRNA-149-3p plays a role in the cellular migration processes. This information could be useful for future investigations on drug development. PMID:27598578

  1. Nuclear magnetic resonance spectroscopic and computer-stimulated structural analyses of a heptapeptide sequence found around the N-glycosylation site of a proline-rich glycoprotein from human parotid saliva.

    PubMed Central

    Loomis, R E; Bhandary, K K; Tseng, C C; Bergey, E J; Levine, M J

    1987-01-01

    The proline-rich glycoprotein from human parotid saliva has a common heptapeptide sequence around four of six N-glycosylation sites (Maeda, N., H. S. Kim, E. A. Azen, and O. J. Smithies, 1985, J. Biol. Chem., 20:11123-11130). A synthetic model of the heptamer protein sequence, NH2-Q(1)-G(2)-G(3)-N(4)-Q(5)-S(6)-Q(7)-CONH2, was examined by nuclear magnetic resonance (NMR) spectroscopy and the ECEPP/2-VAO4A (Empirical Conformation Energy Program for Peptides) energy minimization computer algorithm (Scheraga, H. A., 1982, Quantum Chemistry Program Exchange, 454; Powell, M. J. D., 1964, Quantum Chemistry Program Exchange, 60). The NMR spectrum was almost completely assigned in dimethylsulfoxide-d6 (DMSO), and the amide chemical shift temperature dependence, phi dihedral angles, and chi 1 rotamer populations elucidated. These data indicated that a significant population of the heptamer could exist as a type I beta-turn [4----1 between Q(5) and G(2)] and/or a type II' beta-turn [4----1 between (Q)5 and G(2) and/or a gamma-turn [3----1 between Q(5) and G(3)] with the amino acid chi 1 torsion angles weighted toward the gauche- conformation. Starting from these three possible conformations, the ECEPP/2-VAO4A rigid geometry energy minimization program was used to find the localized predominant in vacuo structures of this heptapeptide sequence. The type II' beta-turn conformation best fits the data based on internuclear hydrogen-bonding distances, minimum potential energy considerations, and the NMR parameters. Images FIGURE 7 FIGURE 8 FIGURE 9 PMID:3828456

  2. Molecular structures of two crystalline forms of the cyclic heptapeptide antibiotic ternatin, cyclo[-beta-OH-D-Leu-D-Ile-(NMe)Ala-(NMe)Leu-Leu-(NMe)Ala-D-(NMe)Ala-].

    PubMed

    Miller, R; Galitsky, N M; Duax, W L; Langs, D A; Pletnev, V Z; Ivanov, V T

    1993-12-01

    The crystal structures of two solvated forms of ternatin, cyclo[-beta-OH-D-Leu-D-Ile-(NMe)Ala-(NMe)Leu-Leu-(NMe)Ala-D-(NMe)Ala-] are reported. The first crystallizes with two molecules of peptide and one of dioxane in the asymmetric unit: P2(1)2(1)2(1), a = 11.563(1), b = 21.863(2), c = 36.330(4) A. The second crystallizes with two molecules of peptide and one of water in the asymmetric unit: P2(1)2(1)2(1), a = 14.067(2), b = 16.695(1), c = 36.824(6) A. N-Methylation of four of the seven residues of ternatin appears to reduce the number of low-energy conformations the molecule can assume. The same H-bonded macrocyclic ring conformation is adopted by the backbone of each of the four molecules observed here. All the amino-acid side chains, with the exception of D-Ile2, have similar orientations in each of the four conformers. The heptapeptide macrocycle is characterized by: (i) a cis peptide between (NMe)Ala3 and (NMe)Leu4, (ii) a type II beta-bend, involving residues Leu5-(NMe)Ala6-D-(NMe)Ala7-beta-OH-D-Leu1, stabilized by two H-bonds, N1-->O5 and N5-->O1, between Leu5 and beta-OH-D-Leu1 residues, (iii) a third intramolecular H-bond, observed in each of the four molecules, between the hydroxyl group of beta-OH-D-Leu1 and the carbonyl oxygen of D-Ile2. PMID:8307686

  3. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

    NASA Astrophysics Data System (ADS)

    Gsponer, Jörg; Haberthür, Urs; Caflisch, Amedeo

    2003-04-01

    Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 μs. The simulations generate in-register parallel packing of GNNQQNY -strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel -sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.

  4. Specific high-affinity binding sites for a synthetic gliadin heptapeptide of human peripheral blood lymphocytes

    SciTech Connect

    Payan, D.G.; Horvath, K.; Graf, L.

    1987-03-23

    The synthetic peptide containing residues 43-49 of ..cap alpha..-gliadin, the major protein component of gluten, has previously been shown to inhibit the production of lymphokine activities by mononuclear leukocytes. The authors demonstrate using radiolabeled ..cap alpha..-gliadin(43-49) that human peripheral blood lymphocytes express approximately 20,000-25,000 surface receptors for this peptide, with a dissociation constant (K/sub D/) of 20 nM. In addition, binding is inhibited by naloxone and an enkephalin analog, thus confirming the functional correlate which demonstrates inhibition by these agents of ..cap alpha..-gliadin(43-49) functional effects. Furthermore, B-lymphocytes bind specifically a greater amount of (/sup 125/I)..cap alpha..-gliadin(43-49) than T-lymphocytes. The lymphocyte ..cap alpha..-gliadin(43-49) receptor may play an important role in mediating the immunological response to ..cap alpha..-gliadin. 16 references, 4 figures.

  5. A DECam Search for an Optical Counterpart to the LIGO Gravitational-wave Event GW151226

    NASA Astrophysics Data System (ADS)

    Cowperthwaite, P. S.; Berger, E.; Soares-Santos, M.; Annis, J.; Brout, D.; Brown, D. A.; Buckley-Geer, E.; Cenko, S. B.; Chen, H. Y.; Chornock, R.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Drout, M. R.; Farr, B.; Finley, D. A.; Foley, R. J.; Fong, W.; Fox, D. B.; Frieman, J.; Garcia-Bellido, J.; Gill, M. S. S.; Gruendl, R. A.; Herner, K.; Holz, D. E.; Kasen, D.; Kessler, R.; Lin, H.; Margutti, R.; Marriner, J.; Matheson, T.; Metzger, B. D.; Neilsen, E. H., Jr.; Quataert, E.; Rest, A.; Sako, M.; Scolnic, D.; Smith, N.; Sobreira, F.; Strampelli, G. M.; Villar, V. A.; Walker, A. R.; Wester, W.; Williams, P. K. G.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Cunha, C. E.; D’Andrea, C. B.; da Costa, L. N.; Desai, S.; Dietrich, J. P.; Evrard, A. E.; Fausti Neto, A.; Fosalba, P.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Johnson, M. W. G.; Johnson, M. D.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lima, M.; Maia, M. A. G.; Marshall, J. L.; Menanteau, F.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Smith, R. C.; Suchyta, E.; Tarle, G.; Thomas, D.; Thomas, R. C.; Tucker, D. L.; Weller, J.; The DES Collaboration

    2016-08-01

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg2 of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achieve 5σ point-source limiting magnitudes of i≈ 21.7 and z≈ 21.5, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with ≳ 3σ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of i-z≈ 0.3 mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.

  6. Role of monomer arrangement in the amyloid self-assembly

    PubMed Central

    Portillo, Alexander; Hashemi, Mohtadin; Zhang, Yuliang; Breydo, Leonid; Uversky, Vladimir N.; Lyubchenko, Yuri L.

    2015-01-01

    Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomers arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide-peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP--hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors. PMID:25542374

  7. The use of N-methylated peptides and depsipeptides to probe the binding of heptapeptide substrates to cAMP-dependent protein kinase.

    PubMed

    Bramson, H N; Thomas, N E; Kaiser, E T

    1985-12-15

    Peptide 1, Leu-Arg-Arg-Ala-Ser-Leu-Gly, is an excellent substrate for cAMP-dependent protein kinase. While the importance of both arginines for effective enzyme-substrate interactions has been shown, it has not been known whether the kinase will catalyze phosphorylation of substrates which contain other than peptide bonds. We report that analogs of peptide 1 which contain depsi linkages replacing selected amide bonds are good protein kinase substrates. Therefore, with the possible exception of the serine amide proton, no peptide 1 amide hydrogens are involved in peptide-peptide or peptide-enzyme hydrogen bonding crucial to defining the high substrate activity of this peptide. It is thus unlikely that peptide 1 is bound by the protein kinase while in an alpha-helical or a beta-turn structure. Three peptides were found to be very poor substrates for protein kinase, those containing N-methyl amino acids in place of Ser5 or Leu6 and a peptide containing Pro in place of Leu6. These peptides are poor substrates for the enzyme possibly because they are unable to adopt a conformation necessary for catalysis of phosphoryl group transfer to occur or due to steric effects in the enzymatic active site. PMID:4066678

  8. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  9. The Dark Energy Survey Camera

    NASA Astrophysics Data System (ADS)

    Flaugher, Brenna

    2012-03-01

    The Dark Energy Survey Collaboration has built the Dark Energy Camera (DECam), a 3 square degree, 520 Megapixel CCD camera which is being mounted on the Blanco 4-meter telescope at CTIO. DECam will be used to carry out the 5000 sq. deg. Dark Energy Survey, using 30% of the telescope time over a 5 year period. During the remainder of the time, and after the survey, DECam will be available as a community instrument. Construction of DECam is complete. The final components were shipped to Chile in Dec. 2011 and post-shipping checkout is in progress in Dec-Jan. Installation and commissioning on the telescope are taking place in 2012. A summary of lessons learned and an update of the performance of DECam and the status of the DECam installation and commissioning will be presented.

  10. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding

    PubMed Central

    Kirillova, Yuliya; Boyarskaya, Nataliya; Dezhenkov, Andrey; Tankevich, Mariya; Prokhorov, Ivan; Varizhuk, Anna; Eremin, Sergei; Esipov, Dmitry; Smirnov, Igor; Pozmogova, Galina

    2015-01-01

    New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA. PMID:26469337

  11. Evaluation of a High-Throughput Peptide Reactivity Format Assay for Assessment of the Skin Sensitization Potential of Chemicals

    PubMed Central

    Wong, Chin Lin; Lam, Ai-Leen; Smith, Maree T.; Ghassabian, Sussan

    2016-01-01

    The direct peptide reactivity assay (DPRA) is a validated method for in vitro assessment of the skin sensitization potential of chemicals. In the present work, we describe a peptide reactivity assay using 96-well plate format and systematically identified the optimal assay conditions for accurate and reproducible classification of chemicals with known sensitizing capacity. The aim of the research is to ensure that the analytical component of the peptide reactivity assay is robust, accurate, and reproducible in accordance with criteria that are used for the validation of bioanalytical methods. Analytical performance was evaluated using quality control samples (QCs; heptapeptides at low, medium, and high concentrations) and incubation of control chemicals (chemicals with known sensitization capacity, weak, moderate, strong, extreme, and non-sensitizers) with each of three synthetic heptapeptides, viz Cor1-C420 (Ac-NKKCDLF), cysteine- (Ac-RFAACAA), and lysine- (Ac-RFAAKAA) containing heptapeptides. The optimal incubation temperature for all three heptapeptides was 25°C. Apparent heptapeptide depletion was affected by vial material composition. Incubation of test chemicals with Cor1-C420, showed that peptide depletion was unchanged in polypropylene vials over 3-days storage in an autosampler but this was not the case for borosilicate glass vials. For cysteine-containing heptapeptide, the concentration was not stable by day 3 post-incubation in borosilicate glass vials. Although the lysine-containing heptapeptide concentration was unchanged in both polypropylene and borosilicate glass vials, the apparent extent of lysine-containing heptapeptide depletion by ethyl acrylate, differed between polypropylene (24.7%) and glass (47.3%) vials. Additionally, the peptide-chemical complexes for Cor1-C420-cinnamaldehyde and cysteine-containing heptapeptide-2, 4-dinitrochlorobenzene were partially reversible during 3-days of autosampler storage. These observations further highlight

  12. A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase II.

    PubMed Central

    Guilfoyle, T J

    1989-01-01

    A protein kinase from wheat germ that phosphorylates the largest subunit of RNA polymerase IIA has been partially purified and characterized. The kinase has a native molecular weight of about 200 kilodaltons. This kinase utilizes Mg2+ and ATP and transfers about 20 phosphates to the heptapeptide repeats Pro-Thr-Ser-Pro-Ser-Tyr-Ser in the carboxyl-terminal domain of the 220-kilodalton subunit of soybean RNA polymerase II. This phosphorylation results in a mobility shift of the 220-kilodalton subunits of a variety of eukaryotic RNA polymerases to polypeptides ranging in size from greater than 220 kilodaltons to 240 kilodaltons on sodium dodecyl sulfate-polyacrylamide gels. The phosphorylation is highly specific to the heptapeptide repeats since a degraded subunit polypeptide of 180 kilodaltons that lacks the heptapeptide repeats is poorly phosphorylated. Synthetic heptapeptide repeat multimers inhibit the phosphorylation of the 220-kilodalton subunit. PMID:2535525

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

    PubMed

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

    2012-10-17

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

  14. Fibronectin tetrapeptide is target for syphilis spirochete cytadherence

    SciTech Connect

    Thomas, D.D.; Baseman, J.B.; Alderete, J.F.

    1985-11-01

    The syphilis bacterium, Treponema pallidum, parasitizes host cells through recognition of fibronectin (Fn) on cell surfaces. The active site of the Fn molecule has been identified as a four-amino acid sequence, arg-gly-asp-ser (RGDS), located on each monomer of the cell-binding domain. The synthetic heptapeptide gly-arg-gly-asp-ser-pro-cys (GRGDSPC), with the active site sequence RGDS, specifically competed with SVI-labeled cell-binding domain acquisition by T. pallidum. Additionally, the same heptapeptide with the RGDS sequence diminished treponemal attachment to HEp-2 and HT1080 cell monolayers. Related heptapeptides altered in one key amino acid within the RGDS sequence failed to inhibit Fn cell-binding domain acquisition or parasitism of host cells by T. pallidum. The data support the view that T. pallidum cytadherence of host cells is through recognition of the RGDS sequence also important for eukaryotic cell-Fn binding.

  15. G-Protein-Coupled Receptor MrgD Is a Receptor for Angiotensin-(1-7) Involving Adenylyl Cyclase, cAMP, and Phosphokinase A.

    PubMed

    Tetzner, Anja; Gebolys, Kinga; Meinert, Christian; Klein, Sabine; Uhlich, Anja; Trebicka, Jonel; Villacañas, Óscar; Walther, Thomas

    2016-07-01

    Angiotensin (Ang)-(1-7) has cardiovascular protective effects and is the opponent of the often detrimental Ang II within the renin-angiotensin system. Although it is well accepted that the G-protein-coupled receptor Mas is a receptor for the heptapeptide, the lack in knowing initial signaling molecules stimulated by Ang-(1-7) prevented definitive characterization of ligand/receptor pharmacology as well as identification of further hypothesized receptors for the heptapeptide. The study aimed to identify a second messenger stimulated by Ang-(1-7) allowing confirmation as well as discovery of the heptapeptide's receptors. Ang-(1-7) elevates cAMP concentration in primary cells, such as endothelial or mesangial cells. Using cAMP as readout in receptor-transfected human embryonic kidney (HEK293) cells, we provided pharmacological proof that Mas is a functional receptor for Ang-(1-7). Moreover, we identified the G-protein-coupled receptor MrgD as a second receptor for Ang-(1-7). Consequently, the heptapeptide failed to increase cAMP concentration in primary mesangial cells with genetic deficiency in both Mas and MrgD Mice deficient in MrgD showed an impaired hemodynamic response after Ang-(1-7) administration. Furthermore, we excluded the Ang II type 2 receptor as a receptor for the heptapeptide but discovered that the Ang II type 2 blocker PD123319 can also block Mas and MrgD receptors. Our results lead to an expansion and partial revision of the renin-angiotensin system, by identifying a second receptor for Ang-(1-7), by excluding Ang II type 2 as a receptor for the heptapeptide, and by enforcing the revisit of such publications which concluded Ang II type 2 function by only using PD123319. PMID:27217404

  16. Periodic Distribution of a Putative Nucleosome Positioning Motif in Human, Nonhuman Primates, and Archaea: Mutual Information Analysis

    PubMed Central

    Sosa, Daniela; Miramontes, Pedro; Li, Wentian; Mireles, Víctor; Bobadilla, Juan R.; José, Marco V.

    2013-01-01

    Recently, Trifonov's group proposed a 10-mer DNA motif YYYYYRRRRR as a solution of the long-standing problem of sequence-based nucleosome positioning. To test whether this generic decamer represents a biological meaningful signal, we compare the distribution of this motif in primates and Archaea, which are known to contain nucleosomes, and in Eubacteria, which do not possess nucleosomes. The distribution of the motif is analyzed by the mutual information function (MIF) with a shifted version of itself (MIF profile). We found common features in the patterns of this generic decamer on MIF profiles among primate species, and interestingly we found conspicuous but dissimilar MIF profiles for each Archaea tested. The overall MIF profiles for each chromosome in each primate species also follow a similar pattern. Trifonov's generic decamer may be a highly conserved motif for the nucleosome positioning, but we argue that this is not the only motif. The distribution of this generic decamer exhibits previously unidentified periodicities, which are associated to highly repetitive sequences in the genome. Alu repetitive elements contribute to the most fundamental structure of nucleosome positioning in higher Eukaryotes. In some regions of primate chromosomes, the distribution of the decamer shows symmetrical patterns including inverted repeats. PMID:23841049

  17. A modification of the N-terminal amino acid in the eremomycin aglycone.

    PubMed

    Miroshnikova, O V; Berdnikova, T F; Olsufyeva, E N; Pavlov, A Y; Reznikova, M I; Preobrazhenskaya, M N; Ciabatti, R; Malabarba, A; Colombo, L

    1996-11-01

    An Edman degradation of the antibiotic eremomycin aglycone produced the corresponding hexapeptide, which was aminoacylated with D-lysine, D-histidine or D-tryptophan derivatives to give new heptapeptide analogs of the eremomycin aglycone. The aminoacylation of the eremomycin aglycone produced an octapeptide analog. The substitution of D-lysine for the N-terminal N-methyl-D-leucine does not seriously affect the in vitro antibacterial properties of the eremomycin aglycone whereas the heptapeptides with the N-terminal D-tryptophan or D-histidine moieties and the octapeptide with the N-terminal D-lysine are practically devoid of the antibacterial properties. PMID:8982345

  18. System Architecture of the Dark Energy Survey Camera Readout Electronics

    SciTech Connect

    Shaw, Theresa; Ballester, Otger; Cardiel-Sas, Laia; Castilla, Javier; Chappa, Steve; de Vicente, Juan; Holm, Scott; Huffman, Dave; Kozlovsky, Mark; Martinez, Gustavo; Moore, Todd; /Madrid, CIEMAT /Fermilab /Illinois U., Urbana /Fermilab

    2010-05-27

    The Dark Energy Survey makes use of a new camera, the Dark Energy Camera (DECam). DECam will be installed in the Blanco 4M telescope at Cerro Tololo Inter-American Observatory (CTIO). DECam is presently under construction and is expected to be ready for observations in the fall of 2011. The focal plane will make use of 62 2Kx4K and 12 2kx2k fully depleted Charge-Coupled Devices (CCDs) for guiding, alignment and focus. This paper will describe design considerations of the system; including, the entire signal path used to read out the CCDs, the development of a custom crate and backplane, the overall grounding scheme and early results of system tests.

  19. Design and status of the optical corrector for the DES survey instrument

    NASA Astrophysics Data System (ADS)

    Doel, P.; Abbott, T.; Antonik, M.; Bernstein, R.; Bigelow, B.; Brooks, D.; Cease, H.; DePoy, D. L.; Flaugher, B.; Gladders, M.; Gutierrez, G.; Kent, S.; Stefanik, A.; Walker, A.; Worswick, S.

    2008-07-01

    The DECam instrument, for the 4m Blanco telescope at CTIO, is a 5 lens element wide field camera giving a 2.2 degree diameter field of view. The lenses are large, with the biggest being 980mm in diameter, and this poses challenges in mounting and alignment. This paper reports the status of the production of the optics for the DECam wide field imager Also presented are the design and finite element modelling of the cell design for the 5 lenses of the imager along with the proposed alignment process.

  20. Molluscan mega-hemocyanin: an ancient oxygen carrier tuned by a ~550 kDa polypeptide

    PubMed Central

    2010-01-01

    Background The allosteric respiratory protein hemocyanin occurs in gastropods as tubular di-, tri- and multimers of a 35 × 18 nm, ring-like decamer with a collar complex at one opening. The decamer comprises five subunit dimers. The subunit, a 400 kDa polypeptide, is a concatenation of eight paralogous functional units. Their exact topology within the quaternary structure has recently been solved by 3D electron microscopy, providing a molecular model of an entire didecamer (two conjoined decamers). Here we study keyhole limpet hemocyanin (KLH2) tridecamers to unravel the exact association mode of the third decamer. Moreover, we introduce and describe a more complex type of hemocyanin tridecamer discovered in fresh/brackish-water cerithioid snails (Leptoxis, Melanoides, Terebralia). Results The "typical" KLH2 tridecamer is partially hollow, whereas the cerithioid tridecamer is almost completely filled with material; it was therefore termed "mega-hemocyanin". In both types, the staggering angle between adjoining decamers is 36°. The cerithioid tridecamer comprises two typical decamers based on the canonical 400 kDa subunit, flanking a central "mega-decamer" composed of ten unique ~550 kDa subunits. The additional ~150 kDa per subunit substantially enlarge the internal collar complex. Preliminary oxygen binding measurements indicate a moderate hemocyanin oxygen affinity in Leptoxis (p50 ~9 mmHg), and a very high affinity in Melanoides (~3 mmHg) and Terebralia (~2 mmHg). Species-specific and individual variation in the proportions of the two subunit types was also observed, leading to differences in the oligomeric states found in the hemolymph. Conclusions In cerithioid hemocyanin tridecamers ("mega-hemocyanin") the collar complex of the central decamer is substantially enlarged and modified. The preliminary O2 binding curves indicate that there are species-specific functional differences in the cerithioid mega-hemocyanins which might reflect different physiological

  1. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA BY LIQUID CHROMATOGRAPHY INTRODUCTION INTO A HYBRID LINEAR ION TRAP-FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETER

    EPA Science Inventory

    The cyclic heptapeptide microcystin toxins produced by a strain of Microcystis aeruginosa that has not been investigated previously were separated by liquid chromatography and identified by high-accuracy m/z measurements of their [M + H]+ ions and the fragment i...

  2. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA

    EPA Science Inventory

    Microcystin toxins are cyclic heptapeptides produced by several genera and species of cyanobacteria that are responsible for the "green scum" frequently observed on eutrophic surface waters. These toxins, which are a million times more toxic than cyanide ion, have caused deaths o...

  3. High affinity RGD-binding sites at the plasma membrane of Arabidopsis thaliana links the cell wall.

    PubMed

    Canut, H; Carrasco, A; Galaud, J P; Cassan, C; Bouyssou, H; Vita, N; Ferrara, P; Pont-Lezica, R

    1998-10-01

    The heptapeptide Tyr-Gly-Arg-Gly-Asp-Ser-Pro containing the sequence Arg-Gly-Asp (RGD--the essential structure recognised by animal cells in substrate adhesion molecules) was tested on epidermal cells of onion and cultured cells of Arabidopsis upon plasmolysis. Dramatic changes were observed on both types of cells following treatment: on onion cells, Hechtian strands linking the cell wall to the membrane were lost, while Arabidopsis cells changed from concave to convex plasmolysis. A control heptapeptide Tyr-Gly-Asp-Gly-Arg-Ser-Pro had no effect on the shape of plasmolysed cells. Protoplasts isolated from Arabidopsis cells agglutinate in the presence of ProNectinF, a genetically engineered protein of 72 kDa containing 13 RGD sequences: several protoplasts may adhere to a single molecule of ProNectinF. The addition of the RGD-heptapeptide disrupted the adhesion between the protoplasts. Purified plasma membrane from Arabidopsis cells exhibits specific binding sites for the iodinated RGD-heptapeptide. The binding is saturable, reversible, and two types of high affinity sites (Kd1 approximately 1 nM, and Kd2 approximately 40 nM) can be discerned. Competitive inhibition by several structurally related peptides and proteins noted the specific requirement for the RGD sequence. Thus, the RGD-binding activity of Arabidopsis fulfils the adhesion features of integrins, i.e. peptide specificity, subcellular location, and involvement in plasma membrane-cell wall attachments. PMID:9807828

  4. Sulfakinins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sulfakinins constitute a family of arthropod neuropeptides that typically contain the C-terminal heptapeptide Y(SO3H)GHMRFamide. They display structural and functional similarities to the vertebrate gastrin-cholecystokinin family of peptides. Sulfakinins are synthesized by a limited number of neuros...

  5. Mutations in RNA polymerase II enhance or suppress mutations in GAL4.

    PubMed Central

    Allison, L A; Ingles, C J

    1989-01-01

    The activation domains of eukaryotic DNA-binding transcription factors, such as GAL4, may regulate transcription by contacting RNA polymerase II. One potential site on RNA polymerase II for such interactions is the C-terminal tandemly repeated heptapeptide domain in the largest subunit (RPO21). We have changed the number of heptapeptide repeats in this yeast RPO21 C-terminal domain and have expressed these mutant RNA polymerase II polypeptides in yeast cells containing either wild-type or defective GAL4 proteins. Although the number of RPO21 heptapeptide repeats had no effect on the activity of wild-type GAL4, changing the length of the C-terminal domain modified the ability of mutant GAL4 proteins to activate transcription. Shorter or longer RPO21 C-terminal domains enhanced or partially suppressed, respectively, the effects of deletions in the transcriptional-activation domains of GAL4. The same RPO21 mutations also affected transcriptional activation by a GAL4-GCN4 chimera. These data suggest that the activation domains of DNA-binding transcription factors could interact, either directly or indirectly, with the heptapeptide repeats of RNA polymerase II. Images PMID:2495535

  6. Association Equilibrium for Cross-Associating Chains in a Good Solvent: Crowding and Other Nonideality Effects.

    PubMed

    Gotlib, Igor Yu; Malov, Ivan K; Victorov, Alexey I; Voznesenskiy, Mikhail A

    2016-07-28

    Association equilibrium has been studied by molecular dynamics (MD) for mixtures of cross-associating molecules (n-decamer+p-dimer and n-decamer+p-decamer) in a good solvent. Each monomer of n-decamers carries an associative site (n-sticker); each molecule of the second component contains two terminal associative sites (p-stickers). To model the univalent association between the n-sticker and the p-sticker, a technique based on introduction of dummy atoms has been used. We report MD data on the effects of temperature, chain flexibility, and location of the sticker within the chain on the association equilibrium. We find that the presence of nonassociating monomer units of p-chain has a substantial effect on the association equilibrium. This effect is similar to "crowding" in reactive mixtures known to be caused by the presence of inert molecules. Widely used mean field theories of associating chains (e.g., SAFT or Semenov-Rubinstein theory) do not account for the effect of crowding caused by the inert fragments of reactive chains. We introduce simple empirical corrections for crowding that describe association equilibrium in the presence of nonassociating fragment in a chain-like molecule. PMID:27359300

  7. Confronting JC virus and Homo sapiens biological signatures.

    PubMed

    Lucchese, Guglielmo

    2013-01-01

    The present report describes the peptide commonality between JC virus (JCV) and the human proteome at the heptamer level. In total, 53 viral heptapeptides occur in functionally important human proteins with potential consequences for host functions and JCV pathogenesis. A paradigmatic example of a crucial peptide match is the SGKTTLA sequence, shared by JCV LT antigen and human nicotinamide/nicotinic acid riboside kinase, an enzyme involved in myelination processes. In general, the JCV-versus-host heptapeptide overlap may result in a competition between viral sequences and identical motifs in host enzymic active sites, adhesive domains, regulatory signaling motifs, etc., thus interfering with essential reactions and posing disadvantages to the cell. Overall, this study provides a starting point for investigating the role of peptide commonality in host-pathogen interactions. PMID:23276955

  8. An enlarged largest subunit of Plasmodium falciparum RNA polymerase II defines conserved and variable RNA polymerase domains.

    PubMed Central

    Li, W B; Bzik, D J; Gu, H M; Tanaka, M; Fox, B A; Inselburg, J

    1989-01-01

    We have isolated the gene encoding the largest subunit of RNA polymerase II from Plasmodium falciparum. The RPII gene is expressed in the asexual erythrocytic stages of the parasite as a 9 kb mRNA, and is present as a single copy gene located on chromosome 3. The P. falciparum RPII subunit is the largest (2452 amino acids) eukaryotic RPII subunit, and it contains enlarged variable regions that clearly separate and define five conserved regions of the eukaryotic RPII largest subunits. A distinctive carboxyl-terminal domain contains a short highly conserved heptapeptide repeat domain which is bounded on its 5' side by a highly diverged heptapeptide repeat domain, and is bounded on its 3' side by a long carboxyl-terminal extension. Images PMID:2690004

  9. An enlarged largest subunit of Plasmodium falciparum RNA polymerase II defines conserved and variable RNA polymerase domains.

    PubMed

    Li, W B; Bzik, D J; Gu, H M; Tanaka, M; Fox, B A; Inselburg, J

    1989-12-11

    We have isolated the gene encoding the largest subunit of RNA polymerase II from Plasmodium falciparum. The RPII gene is expressed in the asexual erythrocytic stages of the parasite as a 9 kb mRNA, and is present as a single copy gene located on chromosome 3. The P. falciparum RPII subunit is the largest (2452 amino acids) eukaryotic RPII subunit, and it contains enlarged variable regions that clearly separate and define five conserved regions of the eukaryotic RPII largest subunits. A distinctive carboxyl-terminal domain contains a short highly conserved heptapeptide repeat domain which is bounded on its 5' side by a highly diverged heptapeptide repeat domain, and is bounded on its 3' side by a long carboxyl-terminal extension. PMID:2690004

  10. Duck-billed platypus venom peptides induce Ca2+ influx in neuroblastoma cells.

    PubMed

    Kita, Masaki; Black, David StC; Ohno, Osamu; Yamada, Kaoru; Kigoshi, Hideo; Uemura, Daisuke

    2009-12-23

    The duck-billed platypus (Ornithorhynchus anatinus) is one of the few venomous Australian mammals. We previously found that its crude venom potently induces Ca(2+) influx in human neuroblastoma IMR-32 cells. Guided by this bioassay, we identified 11 novel peptides, including the heptapeptide H-His-Asp-His-Pro-Asn-Pro-Arg-OH (1). Compounds 1-4 and 5-11 coincided with the 6-9 N-terminal residues of Ornithorhynchus venom C-type natriuretic peptide (OvCNP) and the 132-150 part of OvCNP precursor peptide, respectively. Heptapeptide 1, which is one of the primary components of the venom fluid (approximately 200 ng/microL), induced a significant increase in [Ca(2+)](i) in IMR-32 cells at 75 microM. To the best of our knowledge, this is the first example of the isolation of the N-terminal linear fragments of CNPs in any mammal. PMID:19928958

  11. DEVD-Based Hydrogelator Minimizes Cellular Apoptosis Induction

    NASA Astrophysics Data System (ADS)

    Tang, An-Ming; Wang, Wei-Juan; Mei, Bin; Hu, Wang-Lai; Wu, Mian; Liang, Gao-Lin

    2013-05-01

    Herein, we report the rational design of a DEVD-based heptapeptide hydrogelator 1 which is susceptible to caspase-3 (CASP3), and its isomeric control hydrogelator 2 with a DEDV-based heptapeptide sequence. Self-assembly of 1 in water results in flexuous, long nanofibers to form supramolecular hydrogel I with higher mechanical strength than that of hydrogel II which is composed of rigid, short nanofibers of 2. In vitro enzymatic analysis indicated that 1 is susceptive to CASP3 while 2 is not. 3-(4,5-dimethylthiazol-2-yl) 2,5 diphenyl tetrazolium bromide (MTT) and Western blot analyses indicated that DEDV-based hydrogelator 2 induces cell death via apoptotic pathway while the DEVD-based hydrogelator 1 minimizes cellular apoptosis induction.

  12. A novel self-assembling peptide with UV-responsive properties.

    PubMed

    Wei, Ran; Jin, Cheng-Cheng; Quan, Jing; Nie, Hua-li; Zhu, Li-Min

    2014-03-01

    A novel heptapeptide comprising Ile-Gln-Ser-Pro-His-Phe-Phe (IQSPHFF) identified and found to undergo self-assembly into microparticles in solution. To understand the effects of ultraviolet (UV) irradiation on the self-assembly process, IQSPHFF solutions were exposed to the UV light of 365 nm at room temperature. This exposure was found to have a profound effect on the morphology of the self-assembled aggregates, converting the microparticles to nanorod shapes. Circular dichroism and FTIR studies indicated distinct structural differences in the arrangements of the peptide moieties before and after UV irradiation. However, Mass spectrum analysis and high performance liquid chromatography of the peptide molecules before and after UV irradiation demonstrated that the chemical structure of IQSPHFF was not changed. UV-visible spectroscopy and fluorescence spectroscopy studies showed that the absorption peak both increased after UV irradiation. Overall, our data show that the heptapeptide with UV-responsive properties. PMID:23828220

  13. Total synthesis of cyclomarins A, C and D, marine cyclic peptides with interesting anti-tuberculosis and anti-malaria activities.

    PubMed

    Barbie, Philipp; Kazmaier, Uli

    2016-07-01

    Cyclomarins are cyclic heptapeptides containing four unusual amino acids. New synthetic protocols toward their synthesis have been developed, leading to the synthesis and biological evaluation of three natural occurring cyclomarins. Interestingly, cyclomarins address two completely different targets: Clp C1, a subunit of the caseinolytic protease of Mycobacterium tuberculosis (MTB), as well as PfAp3Ase of Plasmodium falciparum. Therefore, cyclomarins are interesting lead structures for the development of drugs against tuberculosis and malaria. PMID:27241518

  14. Structure-based hybridization of the bioactive natural products rhizonin A and ternatin leading to a selective fat-accumulation inhibitor against 3T3-L1 adipocytes.

    PubMed

    Shimokawa, Kenichiro; Yamada, Kaoru; Uemura, Daisuke

    2009-02-01

    Based on the structural similarity between the naturally occurring cyclic heptapeptides rhizonin A and ternatin, two novel analogues were designed. The synthetic analogues were assessed with regard to their fat-accumulation inhibitory effect against 3T3-L1 adipocytes, and this led to the discovery of a potent and selective fat-accumulation inhibitor compared to the parent compound rhizonin A. PMID:19097891

  15. Structural development of stapled short helical peptides as vitamin D receptor (VDR)-coactivator interaction inhibitors.

    PubMed

    Misawa, Takashi; Demizu, Yosuke; Kawamura, Megumi; Yamagata, Nanako; Kurihara, Masaaki

    2015-03-01

    We developed several stabilized helical heptapeptides (DPI-01-10) composed of l-leucine residues, an α,α-disubstituted α-amino acid (α-aminoisobutyric acid [Aib] or hydroxymethylserine [Hms]), and a stapled side chain as inhibitors of vitamin D receptor (VDR)-coactivator interactions. The inhibitory activity of these peptides against VDR-coactivator interactions was evaluated using a receptor cofactor assay system, and DPI-08 demonstrated strong activity (IC50: 3.2μM). PMID:25637122

  16. Prediction of optimal peptide mixtures to induce broadly neutralizing antibodies to human immunodeficiency virus type 1.

    PubMed Central

    Holley, L H; Goudsmit, J; Karplus, M

    1991-01-01

    Sequences of the principal neutralizing determinant (PND) of the external envelope protein, gp120, from 245 isolates of human immunodeficiency virus type 1 are analyzed. The minimal set of peptides that would elicit antibodies to neutralize a majority of U.S. and European isolates of human immunodeficiency virus type 1 is determined with the assumption that peptides of a given length including the central Gly-Pro-Gly triad are required. In spite of the hypervariability of the PND, 90% of these 245 sequences include peptides from a set of 7 pentapeptides, 13 hexapeptides, or 17 heptapeptides. Tests of these peptide sets on 78 additional PND sequences show that 95% are covered by the 7 pentapeptides, 94% by the 13 hexapeptides, and 86% by the 17 heptapeptides. To anticipate variants not yet observed, single amino acid mutation frequencies from the 245 isolates are used to calculate an expanded set of the 10,000 most probable PND sequences. These sequences cover 86% of the total distribution expected for the central portion of the PND. Peptide lists derived from this expanded set when tested on the 78 additional sequences show that 7 pentapeptides cover 95%, 13 hexapeptides cover 94%, and 17 heptapeptides cover 94%. These results suggest that peptide cocktails of limited size with the potential to cover a large fraction of PND sequence variation may be feasible vaccine candidates. PMID:1862103

  17. Cyclic thrombospondin-1 mimetics: grafting of a thrombospondin sequence into circular disulfide-rich frameworks to inhibit endothelial cell migration

    PubMed Central

    Chan, Lai Yue; Craik, David J.; Daly, Norelle L.

    2015-01-01

    Tumour formation is dependent on nutrient and oxygen supply from adjacent blood vessels. Angiogenesis inhibitors can play a vital role in controlling blood vessel formation and consequently tumour progression by inhibiting endothelial cell proliferation, sprouting and migration. The primary aim of the present study was to design cyclic thrombospondin-1 (TSP-1) mimetics using disulfide-rich frameworks for anti-angiogenesis therapies and to determine whether these peptides have better potency than the linear parent peptide. A short anti-angiogenic heptapeptide fragment from TSP-1 (GVITRIR) was incorporated into two cyclic disulfide-rich frameworks, namely MCoTI-II (Momordica cochinchinensis trypsin inhibitor-II) and SFTI-1 (sunflower trypsin inhibitor-1). The cyclic peptides were chemically synthesized and folded in oxidation buffers, before being tested in a series of in vitro evaluations. Incorporation of the bioactive heptapeptide fragment into the cyclic frameworks resulted in peptides that inhibited microvascular endothelial cell migration, and had no toxicity against normal primary human endothelial cells or cancer cells. Importantly, all of the designed cyclic TSP-1 mimetics were far more stable than the linear heptapeptide in human serum. The present study has demonstrated a novel approach to stabilize the active region of TSP-1. The anti-angiogenic activity of the native TSP-1 active fragment was maintained in the new TSP-1 mimetics and the results provide a new chemical approach for the design of TSP-1 mimetics. PMID:26464514

  18. Cyclic thrombospondin-1 mimetics: grafting of a thrombospondin sequence into circular disulfide-rich frameworks to inhibit endothelial cell migration.

    PubMed

    Chan, Lai Yue; Craik, David J; Daly, Norelle L

    2015-01-01

    Tumour formation is dependent on nutrient and oxygen supply from adjacent blood vessels. Angiogenesis inhibitors can play a vital role in controlling blood vessel formation and consequently tumour progression by inhibiting endothelial cell proliferation, sprouting and migration. The primary aim of the present study was to design cyclic thrombospondin-1 (TSP-1) mimetics using disulfide-rich frameworks for anti-angiogenesis therapies and to determine whether these peptides have better potency than the linear parent peptide. A short anti-angiogenic heptapeptide fragment from TSP-1 (GVITRIR) was incorporated into two cyclic disulfide-rich frameworks, namely MCoTI-II (Momordica cochinchinensis trypsin inhibitor-II) and SFTI-1 (sunflower trypsin inhibitor-1). The cyclic peptides were chemically synthesized and folded in oxidation buffers, before being tested in a series of in vitro evaluations. Incorporation of the bioactive heptapeptide fragment into the cyclic frameworks resulted in peptides that inhibited microvascular endothelial cell migration, and had no toxicity against normal primary human endothelial cells or cancer cells. Importantly, all of the designed cyclic TSP-1 mimetics were far more stable than the linear heptapeptide in human serum. The present study has demonstrated a novel approach to stabilize the active region of TSP-1. The anti-angiogenic activity of the native TSP-1 active fragment was maintained in the new TSP-1 mimetics and the results provide a new chemical approach for the design of TSP-1 mimetics. PMID:26464514

  19. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures.

    PubMed

    Kang, Young Kee; Yoo, In Kee

    2016-09-01

    The propensities of peptides that contain the Asn-Gly segment to form β-turn and β-hairpin structures were explored using the density functional methods and the implicit solvation model in CH2 Cl2 and water. The populations of preferred β-turn structures varied depending on the sequence and solvent polarity. In solution, β-hairpin structures with βI' turn motifs were most preferred for the heptapeptides containing the Asn-Gly segment regardless of the sequence of the strands. These preferences in solution are consistent with the corresponding X-ray structures. The sequence, H-bond strengths, solvent polarity, and conformational flexibility appeared to interact to determine the preferred β-hairpin structure of each heptapeptide, although the β-turn segments played a role in promoting the formation of β-hairpin structures and the β-hairpin propensity varied. In the heptapeptides containing the Asn-Gly segment, the β-hairpin formation was enthalpically favored and entropically disfavored at 25°C in water. The calculated results for β-turns and β-hairpins containing the Asn-Gly segment imply that these structural preferences may be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics and the design of binding epitopes for protein-protein and protein-nucleic acid recognitions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 653-664, 2016. PMID:27122246

  20. Dark Energy Camera for Blanco

    SciTech Connect

    Binder, Gary A.; /Caltech /SLAC

    2010-08-25

    In order to make accurate measurements of dark energy, a system is needed to monitor the focus and alignment of the Dark Energy Camera (DECam) to be located on the Blanco 4m Telescope for the upcoming Dark Energy Survey. One new approach under development is to fit out-of-focus star images to a point spread function from which information about the focus and tilt of the camera can be obtained. As a first test of a new algorithm using this idea, simulated star images produced from a model of DECam in the optics software Zemax were fitted. Then, real images from the Mosaic II imager currently installed on the Blanco telescope were used to investigate the algorithm's capabilities. A number of problems with the algorithm were found, and more work is needed to understand its limitations and improve its capabilities so it can reliably predict camera alignment and focus.

  1. Toyz: A framework for scientific analysis of large datasets and astronomical images

    NASA Astrophysics Data System (ADS)

    Moolekamp, F.; Mamajek, E.

    2015-11-01

    As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it ​a convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images (>2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.

  2. Toyz: A framework for scientific analysis of large datasets and astronomical images

    NASA Astrophysics Data System (ADS)

    Moolekamp, F.; Mamajek, E.

    2015-11-01

    As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it ​a convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images (>2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.

  3. Low-energy electron scattering from DNA including structural water and base-pair irregularities

    SciTech Connect

    Caron, Laurent; Sanche, Leon; Tonzani, Stefano; Greene, Chris H.

    2009-07-15

    Elastic scattering of low-energy (0-13 eV) electrons from more realistic models of a DNA base-pair decamer is studied using multiple-scattering theory and T matrices obtained from ab initio R-matrix calculations. The models include two types of irregularities usually found in cellular DNA: base-pair mismatch and structural water molecules. Furthermore, we include in our calculation inelastic collisions. It is found that the basic interference patterns observed in the ideal and nonideal (i.e., more realistic) decamers are similar but have different amplitudes and are shifted in energy. Substantial inelastic losses, interestingly, cause pronounced local resonances, which could have an important influence in DNA strand breaks.

  4. Synthesis and hybridization properties of an acyclic achiral phosphonate DNA analogue.

    PubMed

    Kehler, J; Henriksen, U; Vejbjerg, H; Dahl, O

    1998-03-01

    Protected N-(2-hydroxyethyl)-N-(nucleobase-acetyl)aminomethanephosphonic+ ++ acid (6a-d) of all four DNA nucleobases have been prepared and oligomerized by solid-phase synthesis. Four DNA decamers containing 1-10 of these 'PPNA' monomers were prepared and evaluated by Tm measurements (medium salt) for binding to their DNA and RNA complements. One central modification reduced the binding strongly (delta Tm = -10 degrees C), but contiguous PPNA monomers gave smaller effects, and the all-PPNA decamer bound to RNA with a delta Tm of -1.2 degrees C per modification. Thus PPNA oligomers are inferior DNA and RNA binders compared to the closely related and strongly binding PNA oligomers. PMID:9568285

  5. NMR studies of the deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA)ter dot oligo(Dt) tract

    SciTech Connect

    Morden, K.M.; Gunn, B.M.; Maskos, K. )

    1990-09-18

    One- and two-dimensional NMR experiments were carried out on a decamer, d-(CGCTTTTCGC){center dot}d(GCGAAAAGCG), and on the same sequence with the addition of an unpaired thymidine, d(CGCTTTTCGC){center dot}d(GCGAATAAGCG), which will be referred to as the T-bulge decamer. Evidence from one-dimensional NOE experiments on the exchangeable protons indicates that the unpaired thymidine is extrahelical. This conclusion is also supported by numerous cross-peaks in the two-dimensional NOESY spectrum of the nonexchangeable protons. Assignments for all of the resonances, with the exception of the H5{prime} and H5{double prime} resonances, have been made for both oligonucleotide duplexes through the use of 2D NOESY, COSY, and relayed COSY experiments. Temperature dependence of the methyl resonance chemical shifts indicates that the unpaired thymidine shows unusual behavior compared to other thymidines in the duplex. Two-dimensional NOESY experiments carried out from 5 to 35{degree}C indicate the unpaired thymidine remains extrahelical throughout this temperature range. A similar temperature dependence for the methyl chemical shift is found in the corresponding single-strand d(GCGAATAAGCG). The oligo-(dA){center dot}oligo(dT) tracts in both the decamer and the T-bulge decamer have structures different from B-form DNA and exhibit NOEs similar to those observed in other oligonucleotides containing A{center dot}T tracts. The formation of this unusual A{center dot}T tract structure may induce the extrahelical conformation of the unpaired thymidine.

  6. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    SciTech Connect

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. F.; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-03-31

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. Additionally, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  7. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    SciTech Connect

    Melchior, P.; et al.

    2015-05-21

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modeling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modeling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1 degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  8. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    DOE PAGESBeta

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; et al

    2015-03-31

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Sciencemore » Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. Additionally, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.« less

  9. Presentation of Ligands on Hydroxylapatite

    NASA Technical Reports Server (NTRS)

    Chu, Barbara C. F.; Orgel, Leslie E.

    1997-01-01

    Conjugates of biotin with the decamer of glutamic acid (glu(sub 10)) and the trimer of D,L-2-amino-5-phosphonovaleric acid (I) have been synthesized, and it has been shown that they mediate the binding of avidin to hydroxylapatite. In a similar way a conjugate of methotrexate with glu(sub 10) mediates the binding of dihydrofolate reductase to the mineral. The presentation of ligands on the hydroxylapatite component of bone may find applications in clinical medicine.

  10. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    NASA Astrophysics Data System (ADS)

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. Fausti; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-05-01

    We measure the weak lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey (DES). This pathfinder study is meant to (1) validate the Dark Energy Camera (DECam) imager for the task of measuring weak lensing shapes, and (2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, point spread function (PSF) modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting Navarro-Frenk-White profiles to the clusters in this study, we determine weak lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1°(approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  11. UV Properties of High-Z Supernovae Found In Archival CFHTLS Data

    NASA Astrophysics Data System (ADS)

    Pritchard, Tyler A.; Cooke, Jeff

    2016-01-01

    Using a novel technique to detect z≥1.7 archival supernovae in the CFHT Legacy Survey (CFHTLS) we discuss rest-frame UV comparisons between a local sample comprised of Swift (photometric) and HST (spectroscopic) data and a high redshift CFHTLS (photometric) + Keck/LRIS (spectroscopic); as well as observations on the horizon for z≥2.5 Superluminous supernovae (SLSN) found through the Search for Superluminous Supernovae using DECam (SUDSS) and it's u-band companion program necessary for this technique.

  12. VizieR Online Data Catalog: Hydra I wide-field imaging and spectroscopy obs. (Hargis+, 2016)

    NASA Astrophysics Data System (ADS)

    Hargis, J. R.; Kimmig, B.; Willman, B.; Caldwell, N.; Walker, M. G.; Strader, J.; Sand, D. J.; Grillmair, C. J.; Yoon, J. H.

    2016-04-01

    Observations of Hydra I were obtained on 2014 March 20-23 using the DECam imager (ugri filters) installed on the CTIO Blanco 4m telescope. We used MMT/Hectochelle to target stars throughout the Hydra I overdensity. Spectroscopic observations were obtained over 7 nights using the Hectochelle spectrograph on the 6.5m MMT (R~38000). We complemented our Hectochelle data with archival spectroscopy from SDSS/SEGUE. (3 data files).

  13. Selective dispersion of single-walled carbon nanotubes with specific chiral indices by poly(N-decyl-2,7-carbazole).

    PubMed

    Lemasson, Fabien A; Strunk, Timo; Gerstel, Peter; Hennrich, Frank; Lebedkin, Sergei; Barner-Kowollik, Christopher; Wenzel, Wolfgang; Kappes, Manfred M; Mayor, Marcel

    2011-02-01

    Physico-chemical methods to sort single-walled carbon nanotubes (SWNTs) by chiral index are presently lacking but are required for in-depth experimental analysis and also for potential future applications of specific species. Here we report the unexpected selectivity of poly(N-decyl-2,7-carbazole) to almost exclusively disperse semiconducting SWNTs with differences of their chiral indices (n - m) ≥ 2 in toluene. The observed selectivity complements perfectly the dispersing features of the fluorene analogue poly(9,9-dialkyl-2,7-fluorene), which disperses semiconducting SWNTs with (n - m) ≤ 2 in toluene. The dispersed samples are further purified by density gradient centrifugation and analyzed by photoluminescence excitation spectroscopy. All-atom molecular modeling with decamer model compounds of the polymers and (10,2) and (7,6) SWNTs suggests differences in the π-π stacking interaction as origin of the selectivity. We observe energetically favored complexes between the (10,2) SWNT and the carbazole decamer and between the (7,6) SWNT and the fluorene decamer, respectively. These findings demonstrate that subtle structural changes of polymers lead to selective solvation of different families of carbon nanotubes. Furthermore, chemical screening of closely related polymers may pave the way toward simple, low-cost, and index-specific isolation of SWNTs. PMID:21171609

  14. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    NASA Astrophysics Data System (ADS)

    Soares-Santos, M.; Kessler, R.; Berger, E.; Annis, J.; Brout, D.; Buckley-Geer, E.; Chen, H.; Cowperthwaite, P. S.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Farr, B.; Finley, D. A.; Flaugher, B.; Foley, R. J.; Frieman, J.; Gruendl, R. A.; Herner, K.; Holz, D.; Lin, H.; Marriner, J.; Neilsen, E.; Rest, A.; Sako, M.; Scolnic, D.; Sobreira, F.; Walker, A. R.; Wester, W.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Benoit-Lévy, A.; Bernstein, R. A.; Bertin, E.; Brown, D. A.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Cenko, S. B.; Chornock, R.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Dietrich, J. P.; Drout, M. R.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Fairhurst, S.; Fernandez, E.; Fischer, J.; Fong, W.; Fosalba, P.; Fox, D. B.; Fryer, C. L.; Garcia-Bellido, J.; Gaztanaga, E.; Gerdes, D. W.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Karliner, I.; Kasen, D.; Kent, S.; Kuropatkin, N.; Kuehn, K.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; Margutti, R.; Martini, P.; Matheson, T.; McMahon, R. G.; Metzger, B. D.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Peoples, J.; Plazas, A. A.; Quataert, E.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, M.; Smith, N.; Smith, R. C.; Stebbins, A.; Sutton, P. J.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, R. C.; Tucker, D. L.; Vikram, V.; Wechsler, R. H.; Weller, J.; DES Collaboration

    2016-06-01

    We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg2 area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4–5, 7, and 24 days after the trigger. The median 5σ point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg2, corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4–5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i ‑ z) = 1, 0, ‑1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

  15. A dark energy camera search for an optical counterpart to the first advanced LIGO gravitational wave event GW150914

    DOE PAGESBeta

    Soares-Santos, M.

    2016-05-27

    We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg2 area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4–5, 7, and 24 days after the trigger. The median 5σ point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images throughmore » a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg2, corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4–5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i – z) = 1, 0, –1, respectively. Lastly, our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.« less

  16. Dark Energy Camera installation at CTIO: technical challenges

    NASA Astrophysics Data System (ADS)

    Muñoz A., Freddy; Montane, Andrés.; Tighe, Roberto; Warner, Michael; Abbott, Timothy M.

    2012-09-01

    The Dark Energy Camera (DECam) is a new prime focus, wide-field imager for the V. M. Blanco 4-m telescope at CTIO. Instrumentation includes large, five-lens optical corrector mounted on hexapod mechanism for fine adjustment, filters, and a 519 Megapixel camera vessel; all integrated in a cage similar to the existing telescope prime focus structure. Currently Blanco allows a flip of this structure such that the f/8 secondary mirror, mounted on the back of the cage, points towards the primary mirror for Ritchey-Chretien observations. DECam will maintain this capability by attaching the existing F/8 mirror cell to the front of the new cage. Installation of this 8,600 kg instrument required the removal from the telescope of the primary mirror, the removal of the old prime focus assembly, and fine adjustment of large, over-constrained mechanisms followed by reassembly. A large facility shutdown was scheduled for this upgrade and several tools, fixtures, monitoring systems and procedures were developed in order to identify and then recover the optical alignment of the system, to control the distribution of stresses during tuning of the installation and to maintain the balance of the telescope with significant added mass. The final goal has been to maintain high performance of the telescope for both the existing f/8 Ritchey-Chretien focus mounted instruments and the new DECam instrument now in commissioning. The challenges presented in handling large elements, real-time monitoring, alignment, verification and feedback are described.

  17. The Dark Energy Survey instrument design

    SciTech Connect

    Flaugher, B.; /Fermilab

    2006-05-01

    We describe a new project, the Dark Energy Survey (DES), aimed at measuring the dark energy equation of state parameter, w, to a statistical precision of {approx}5%, with four complementary techniques. The survey will use a new 3 sq. deg. mosaic camera (DECam) mounted at the prime focus of the Blanco 4m telescope at the Cerro-Tololo International Observatory (CTIO). DECam includes a large mosaic camera, a five element optical corrector, four filters (g,r,i,z), and the associated infrastructure for operation in the prime focus cage. The focal plane consists of 62 2K x 4K CCD modules (0.27''/pixel) arranged in a hexagon inscribed within the 2.2 deg. diameter field of view. We plan to use the 250 micron thick fully-depleted CCDs that have been developed at the Lawrence Berkeley National Laboratory (LBNL). At Fermilab, we will establish a packaging factory to produce four-side buttable modules for the LBNL devices, as well as to test and grade the CCDs. R&D is underway and delivery of DECam to CTIO is scheduled for 2009.

  18. Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry.

    PubMed

    Nirudodhi, Sasidhar; Parsonage, Derek; Karplus, P Andrew; Poole, Leslie B; Maier, Claudia S

    2011-04-30

    This is the first comprehensive HX-MS study of a "robust" 2-Cys peroxiredoxin (Prx), namely Salmonella typhimurium AhpC (StAhpC). Prx proteins control intracellular peroxide levels and are abundant antioxidant proteins in eukaryotes, archaea and bacteria. Crystal structural analyses and structure/activity studies of several bacterial and mammalian 2-Cys Prxs have revealed that the activity of 2-Cys Prxs is regulated by redox-dependent oligmerization and a sensitivity of the active site cysteine residue to overoxidation. The propensity to overoxidation is linked to the conformational flexibility of the peroxidatic active site loop. The HX-MS results emphasize the modulation of the conformational motility of the active site loop by disulfide formation. To obtain information on the conformational impact of decamer formation on the active site loop motility, mutants with Thr77 substituted by Ile, a decamer-disrupting mutation or by Val, a decamer-stabilizing mutation, were studied. For the isoleucine mutant, enhanced mobility was observed for regions encompassing the α4 helix located in the dimer-dimer interface and regions surrounding the peroxidatic loop. In contrast, the T77V mutation resulted in an increase in conformational stability in most regions of the protein except for the active site loop and the region encompassing the resolving cysteine. PMID:21516234

  19. Embrace the Dark Side: Advancing the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Suchyta, Eric

    The Dark Energy Survey (DES) is an ongoing cosmological survey intended to study the properties of the accelerated expansion of the Universe. In this dissertation, I present work of mine that has advanced the progress of DES. First is an introduction, which explores the physics of the cosmos, as well as how DES intends to probe it. Attention is given to developing the theoretical framework cosmologists use to describe the Universe, and to explaining observational evidence which has furnished our current conception of the cosmos. Emphasis is placed on the dark sector - dark matter and dark energy - the content of the Universe not explained by the Standard Model of particle physics. As its name suggests, the Dark Energy Survey has been specially designed to measure the properties of dark energy. DES will use a combination of galaxy cluster, weak gravitational lensing, angular clustering, and supernovae measurements to derive its state of the art constraints, each of which is discussed in the text. The work described in this dissertation includes science measurements directly related to the first three of these probes. The dissertation presents my contributions to the readout and control system of the Dark Energy Camera (DECam); the name of this software is SISPI. SISPI uses client-server and publish-subscribe communication patterns to coordinate and command actions among the many hardware components of DECam - the survey instrument for DES, a 570 megapixel CCD camera, mounted at prime focus of the Blanco 4-m Telescope. The SISPI work I discuss includes coding applications for DECam's filter changer mechanism and hexapod, as well as developing the Scripts Editor, a GUI application for DECam users to edit and export observing sequence SISPI can load and execute. Next, the dissertation describes the processing of early DES data, which I contributed. This furnished the data products used in the first-completed DES science analysis, and contributed to improving the

  20. The upstream activator CTF/NF1 and RNA polymerase II share a common element involved in transcriptional activation.

    PubMed Central

    Xiao, H; Lis, J T; Xiao, H; Greenblatt, J; Friesen, J D

    1994-01-01

    The carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II consists of tandem repeats of a heptapeptide with the consensus YSPTSPS. It has been shown that the heptapeptide repeat interacts directly with the general transcription factor TFIID. We report here that the CTD activates transcription when fused to the DNA-binding domain of GAL4. More importantly, we find that the proline-rich transcriptional activation domain of the CCAAT-box-binding factor CTF/NF1 contains a sequence with striking similarity to the heptapeptide repeats of the CTD. We show that this CTD-like motif is essential for the transcriptional activator function of the proline-rich domain of CTF/NF1. Deletion of and point mutations in this CTD-like motif abolish the transcriptional activator function of the proline-rich domain, while natural CTD repeats from RNA polymerase II are fully functional in place of the CTD-like motif. We further show that the proline-rich activation domain of CTF/NF1 interacts directly with the TATA-box-binding protein (TBP), and that a mutation in the CTD-like motif that abolishes transcriptional activation reduces the affinity of the proline-rich domain for TBP. These results demonstrate that a class of proline-rich activator proteins and RNA polymerase II possess a common structural and functional component which can interact with the same target in the general transcription machinery. We discuss the implications of these results for the mechanisms of transcriptional activation in eucaryotes. Images PMID:8029001

  1. Angiotensin-(1–7) attenuates angiotensin II-induced cardiac remodeling associated with upregulation of dual-specificity phosphatase 1

    PubMed Central

    McCollum, LaTronya T.; Gallagher, Patricia E.

    2012-01-01

    Chronic hypertension induces cardiac remodeling, including left ventricular hypertrophy and fibrosis, through a combination of both hemodynamic and humoral factors. In previous studies, we showed that the heptapeptide ANG-(1–7) prevented mitogen-stimulated growth of cardiac myocytes in vitro, through a reduction in the activity of the MAPKs ERK1 and ERK2. In this study, saline- or ANG II-infused rats were treated with ANG-(1–7) to determine whether the heptapeptide reduces myocyte hypertrophy in vivo and to identify the signaling pathways involved in the process. ANG II infusion into normotensive rats elevated systolic blood pressure >50 mmHg, in association with increased myocyte cross-sectional area, ventricular atrial natriuretic peptide mRNA, and ventricular brain natriuretric peptide mRNA. Although infusion with ANG-(1–7) had no effect on the ANG II-stimulated elevation in blood pressure, the heptapeptide hormone significantly reduced the ANG II-mediated increase in myocyte cross-sectional area, interstitial fibrosis, and natriuretic peptide mRNAs. ANG II increased phospho-ERK1 and phospho-ERK2, whereas cotreatment with ANG-(1–7) reduced the phosphorylation of both MAPKs. Neither ANG II nor ANG-(1–7) altered the ERK1/2 MAPK kinase MEK1/2. However, ANG-(1–7) infusion, with or without ANG II, increased the MAPK phosphatase dual-specificity phosphatase (DUSP)-1; in contrast, treatment with ANG II had no effect on DUSP-1, suggesting that ANG-(1–7) upregulates DUSP-1 to reduce ANG II-stimulated ERK activation. These results indicate that ANG-(1–7) attenuates cardiac remodeling associated with a chronic elevation in blood pressure and upregulation of a MAPK phosphatase and may be cardioprotective in patients with hypertension. PMID:22140049

  2. Enzymatic Synthesis and Functional Characterization of Bioactive Microcin C-Like Compounds with Altered Peptide Sequence and Length

    PubMed Central

    Bantysh, Olga; Serebryakova, Marina; Zukher, Inna; Kulikovsky, Alexey; Tsibulskaya, Darya; Dubiley, Svetlana

    2015-01-01

    ABSTRACT Escherichia coli microcin C (McC) consists of a ribosomally synthesized heptapeptide attached to a modified adenosine. McC is actively taken up by sensitive Escherichia coli strains through the YejABEF transporter. Inside the cell, McC is processed by aminopeptidases, which release nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC is synthesized by the MccB enzyme, which terminally adenylates the MccA heptapeptide precursor MRTGNAN. Earlier, McC analogs with shortened peptide lengths were prepared by total chemical synthesis and were shown to have strongly reduced biological activity due to decreased uptake. Variants with longer peptides were difficult to synthesize, however. Here, we used recombinant MccB to prepare and characterize McC-like molecules with altered peptide moieties, including extended peptide lengths. We find that N-terminal extensions of E. coli MccA heptapeptide do not affect MccB-catalyzed adenylation and that some extended-peptide-length McC analogs show improved biological activity. When the peptide length reaches 20 amino acids, both YejABEF and SbmA can perform facilitated transport of toxic peptide adenylates inside the cell. A C-terminal fusion of the carrier maltose-binding protein (MBP) with the MccA peptide is also recognized by MccB in vivo and in vitro, allowing highly specific adenylation and/or radioactive labeling of cellular proteins. IMPORTANCE Enzymatic adenylation of chemically synthesized peptides allowed us to generate biologically active derivatives of the peptide-nucleotide antibiotic microcin C with improved bioactivity and altered entry routes into target cells, opening the way for development of various McC-based antibacterial compounds not found in nature. PMID:26195597

  3. Measurement of intrinsic properties of amyloid fibrils by the peak force QNM method

    NASA Astrophysics Data System (ADS)

    Adamcik, Jozef; Lara, Cecile; Usov, Ivan; Jeong, Jae Sun; Ruggeri, Francesco S.; Dietler, Giovanni; Lashuel, Hilal A.; Hamley, Ian W.; Mezzenga, Raffaele

    2012-07-01

    We report the investigation of the mechanical properties of different types of amyloid fibrils by the peak force quantitative nanomechanical (PF-QNM) technique. We demonstrate that this technique correctly measures the Young's modulus independent of the polymorphic state and the cross-sectional structural details of the fibrils, and we show that values for amyloid fibrils assembled from heptapeptides, α-synuclein, Aβ(1-42), insulin, β-lactoglobulin, lysozyme, ovalbumin, Tau protein and bovine serum albumin all fall in the range of 2-4 GPa.

  4. JBIR-78 and JBIR-95: phenylacetylated peptides isolated from Kibdelosporangium sp. AK-AA56.

    PubMed

    Izumikawa, Miho; Takagi, Motoki; Shin-Ya, Kazuo

    2012-02-24

    The search for metabolites of Kibdelosporangium sp. AK-AA56 resulted in the discovery of novel N-phenylacetylated peptides, JBIR-78 (1) and JBIR-95 (2). Compounds 1 and 2 were established to be N-phenylacetylated heptapeptides by extensive NMR and HRESIMS analyses. The absolute configuration of the standard amino acids including a cysteic acid moiety was determined using Marfey's method on the acid hydrolysates of 1 and 2. The relative and absolute configurations of a nonstandard amino acid, β-hydroxyleucine, were elucidated using the J-based and modified Mosher's methods, respectively. In an antimicrobial test, 1 showed antibacterial activity against Micrococcus luteus. PMID:22264203

  5. Effect of acute progestational hypoxia on the content of biogenic amines in the brain of albino rat pups: Peptide correction.

    PubMed

    Maslova, M V; Graf, A V; Sokolova, N A; Goncharenko, E N; Shestakova, S V; Kudryashova, N Yu; Andreeva, L A

    2003-08-01

    We studied the effect of exposure to acute hypobaric hypoxia in the progestational period on the content of biogenic amines in the brainstem and cerebral cortex in rat pups of different age. The possibility of correcting hypoxia-induced changes with regulatory peptides was evaluated. We found that early antenatal hypoxia disturbs maturation of catecholaminergic systems in the brain. It should be emphasized that the differences from the control varied depending on the age of rat pups. Single intranasal administration of Semax heptapeptides and beta-casomorphine-7 to pregnant females prevented changes in the content of biogenic amines in CNS of the offspring during postnatal ontogeny. PMID:14631488

  6. Unguisin F, a new cyclic peptide from the endophytic fungus Mucor irregularis.

    PubMed

    Akone, Sergi H; Daletos, Georgios; Lin, Wenhan; Proksch, Peter

    2016-01-01

    The new cyclic heptapeptide unguisin F (1) and the known congener unguisin E (2), were obtained from the endophytic fungus Mucor irregularis, isolated from the medicinal plant Moringa stenopetala, collected in Cameroon. The structure of the new compound was unambiguously determined on the basis of one- and two-dimensional NMR spectroscopy as well as by high-resolution mass spectrometry. The absolute configuration of the amino acid residues of 1 and 2 was determined using Marfey's analysis. Compounds 1 and 2 were evaluated for their antibacterial and antifungal potential, but failed to display significant activities. PMID:26812868

  7. Convergent synthesis and in vivo inhibitory effect on fat accumulation of (-)-ternatin, a highly N-methylated cyclic peptide.

    PubMed

    Shimokawa, Kenichiro; Yamada, Kaoru; Kita, Masaki; Uemura, Daisuke

    2007-08-15

    (-)-Ternatin (1), a highly N-methylated cyclic heptapeptide, is a potent inhibitor of fat accumulation against 3T3-L1 murine adipocytes (EC50 = 0.14 microg/mL) [Shimokawa, K.; Mashima, I.; Asai, A.; Yamada, K.; Kita, M.; Uemura, D. Tetrahedron Lett. 2006, 47, 4445]. Compound 1 was synthesized from Boc-protected amino acids in solution. Upon treatment with 1 at 5 mg/kg/day, increases in body weight and fat accumulation in high-fat-fed mice were both significantly suppressed. PMID:17590333

  8. Combining Classical MD and QM calculations to elucidate complex system nucleation: a twisted, three-stranded, parallel β-sheet seeds amyloid fibril conception.

    PubMed

    Mompeán, Miguel; González, Carlos; Lomba, Enrique; Laurents, Douglas V

    2014-07-01

    The crystal structure of the Sup35 prion segment, GNNQQNY, revealed precise side chain packing and an extensive H-bond network. However, the conformers and stabilizing interactions involved at nascent amyloid formation are still unclear. Here, long molecular dynamics simulations and quantum mechanical calculations have been utilized to study the conformation and energetics of the initial structure that acts to nucleate further growth. Considering all the plausible intermediates that may act as stepping stones, we find that the initial nucleus is a twisted single-layer, three-stranded parallel β-sheet. H-bonds between β-strands in this twisted sheet, some of which differ from those of the crystal structure's nontwisted β-strands, are key for the nucleus' formation and stability. High level theoretical calculations of these H-bonds' energetics can account for this amyloid-like trimer's remarkable stability. The intermeshing of facing sheets to form the dry interface provides less stability and would occur between two three-stranded β-sheets without metastable water nanowires. PMID:24918329

  9. The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

    SciTech Connect

    Langkilde, Annette E.; Morris, Kyle L.; Serpell, Louise C.; Svergun, Dmitri I.; Vestergaard, Bente

    2015-04-01

    The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.

  10. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

    SciTech Connect

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-02-01

    Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

  11. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    DOE PAGESBeta

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patternsmore » with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  12. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    SciTech Connect

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

  13. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

    PubMed Central

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-01

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented. PMID:25664747

  14. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

    NASA Astrophysics Data System (ADS)

    Tran, Thanh Thuy; Nguyen, Phuong H.; Derreumaux, Philippe

    2016-05-01

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  15. Survey of MAgellanic Stellar History - SMASH!

    NASA Astrophysics Data System (ADS)

    Nidever, D.; Smash Team

    2015-05-01

    Over the last several years, various discoveries have drastically altered our view of the iconic Magellanic Clouds (MCs), the nearest interacting galaxy system. The best evidence is now that they are on first infall into the Milky Way, that their stellar populations extend much further than previously thought, and that they suffered a close collision that tore out both the well-known Magellanic Stream and a large amount of still undetected stellar debris. Here we propose a community DECam survey of the Clouds mapping 480 deg2 (distributed over ˜2400 deg2 at ˜20% filling factor) to 24th mag in griz (and u 23 mag) that will supplement the 5000 deg2 Dark Energy Surveys partial coverage of the Magellanic periphery, allowing us to map the expected stellar debris and extended populations with unprecedented fidelity. We have already conducted a pilot project demonstrating that DECam will allow us to carry out the following: (1) Map the stellar periphery of the MCs with old main sequence turnoff stars to a surface brightness limit of ˜35 mag/arcsec2, revealing relics of their formation and past interactions. (2) Identify the stellar component of the Magellanic Stream and Leading Arm for the first time, if they exist, making them the only Galactic halo tracers with both gaseous and stellar components. (3) Derive spatially-resolved star formation histories covering all ages out to large radii of the MCs that will further complement our understanding of their formation. The combination of this survey and the DES data will allow us to uncover a multitude of stellar structure that will unveil the complex and dramatic history of these two dwarf galaxies, while enabling a broad spectrum of community-led projects. SMASH has obtained initial data through DECam Science Verification (data public now) and through first observing runs in 2013A. Subsequent observations to fulfill the science goals described below have been proposed through the NOAO Survey program.

  16. Modulation of TNF-α Secretion in Peripheral Blood Mononuclear Cells by Cocoa Flavanols and Procyanidins

    PubMed Central

    Mao, T. K.; van de Water, J.; Keen, C. L.; Schmitz, H. H.; Gershwin, M. E.

    2002-01-01

    Epidemiological reports have suggested that the consumption of foods rich in flavonoids is associated with a lower incidence of certain degenerative diseases, including cardiovascular disease. Flavanols and their related oligomers, the procyanidins CFP, isolated from cocoa can modulate the production and level of several signaling molecules associated with immune function and inflammation in vitro, including several cytokines and eicosanoids. To further elucidate the potential immuno-modulatory functions of flavanol-rich cocoa, the present investigation examined whether isolated CFP fractions (monomers through decamers) influence the secretion of tumor necrosis factor-α (TNF-α) from resting and phytohemagluttinin (PHA)-stimulated human peripheral blood mononuclear cells (PBMC). We used an in vitro culture system where PBMC from 14 healthy subjects were introduced to individual CFP fractions for 72 h prior to measuring the levels of TNF-α released. The intermediate-sized CFP fractions (tetramers through octamers) were the most active on resting cells, causing a 3–4 fold increase in TNF-α relative to media baseline. The monomers and dimers were the least stimulatory of the fractions tested, displaying a 42 and 31% increase, respectively, over media control, whereas the trimers, nonamers and decamers showed an intermediate stimulation of this cytokine. In the presence of PHA, the intermediate-sized CFP fractions again were the most active, enhancing TNF-α secretion in the range of 48–128% relative to the PHA control. The monomers and dimers were slightly inhibitory (–1.5 and –15%, respectively), while trimers, nonamers and decamers stimulated moderate increases in TNF-α levels (13, 19 and 15%, respectively). The above results lend support to the concept that CFP can be immunomodulatory. The stimulation of TNF-α secretion may contribute to the putative beneficial effects of dietary flavanoids against microbial infection and tumorigenesis. PMID:12885154

  17. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

    PubMed

    Tran, Thanh Thuy; Nguyen, Phuong H; Derreumaux, Philippe

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. PMID:27250331

  18. Genetic diversity in three populations of Avicennia marina along the eastcoast of India by RAPD markers.

    PubMed

    Hazarika, Dimendra; Thangaraj, M; Sahu, Sunil Kumar; Kathiresan, K

    2013-05-01

    Genetic diversity was analysed in three populations of the mangrove species, Avicennia marina by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Ten random decamer primers were used to score the diversity from three locations of eastcoast of India: Parangipettai (Tamil Nadu), Kakkinada (Andhra Pradesh) and Sundarbans (West Bengal). These primers produced 388 scorable DNA fragments, of which 252 (64.98%) were polymorphic, 182 (46.90%) were monomorphic, and 14 (3.61%) were unique. RAPD banding patterns displayed variations between and within the populations, while, there was no morphological variation. PMID:24617156

  19. VizieR Online Data Catalog: Galaxies in X-ray clusters with DES. I. Stellar mass (Zhang+, 2016)

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Miller, C.; McKay, T.; Rooney, P.; Evrard, A. E.; Romer, A. K.; Perfecto, R.; Song, J.; Desai, S.; Mohr, J.; Wilcox, H.; Bermeo-Hernandez, A.; Jeltema, T.; Hollowood, D.; Bacon, D.; Capozzi, D.; Collins, C.; Das, R.; Gerdes, D.; Hennig, C.; Hilton, M.; Hoyle, B.; Kay, S.; Liddle, A.; Mann, R. G.; Mehrtens, N.; Nichol, R. C.; Papovich, C.; Sahlen, M.; Soares-Santos, M.; Stott, J.; Viana, P. T.; Abbott, T.; Abdalla, F. B.; Banerji, M.; Bauer, A. H.; Benoit-Levy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Carnero Rosell, A.; Castander, F. J.; Diehl, H. T.; Doel, P.; Cunha, C. E.; Eifler, T. F.; Fausti Neto, A.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gruen, D.; Gruendl, R. A.; Honscheid, K.; James, D.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marshall, J. L.; Martini, P.; Miquel, R.; Ogando, R.; Plazas, A. A.; Roodman, A.; Rykoff, E. S.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla, I.; Smith, R. C.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Tucker, D.!; Vikram, V.; da Costa, L. N.

    2016-03-01

    The Dark Energy Survey (DES) is a ground-based optical survey that uses the wide-field DECam camera mounted on the 4m Blanco telescope to image 5000deg2 of the southern hemisphere sky (Sanchez et al. 2010JPhCS.259a2080S). The paper is based on 200deg2 DES Science Verification (SV) data. This data set was taken during the 2012B observing season before the main survey (Diehl et al. 2014SPIE.9149E..0VD) began. (1 data file).

  20. Interactions of nucleic acids with distamycins. Binding of Dst-3 to d(CGTTTAAACG)2 and d(CGTACGTACG)2.

    PubMed Central

    Capobianco, M L; Colonna, F P; Forni, A; Garbesi, A; Iotti, S; Moretti, I; Samori, B; Tondelli, L

    1991-01-01

    The binding between Distamycin 3 and the palindromic duplexes d(CGTTTAAACG)2 and d(CGTACGTACG)2 was investigated by two independent techniques: UV-Vis absorption in the Job's plot approach and Induced Circular Dichroism. Both decamers bind two molecules of peptide per duplex, with close overall affinities. This result indicates that a row of six A:T base pairs can accommodate two molecules of drug and that the minimal binding site of Distamycin 3 can consist of just two A:T base pairs. PMID:2027777

  1. Interactions of nucleic acids with distamycins. Binding of Dst-3 to d(CGTTTAAACG)2 and d(CGTACGTACG)2.

    PubMed

    Capobianco, M L; Colonna, F P; Forni, A; Garbesi, A; Iotti, S; Moretti, I; Samori, B; Tondelli, L

    1991-04-11

    The binding between Distamycin 3 and the palindromic duplexes d(CGTTTAAACG)2 and d(CGTACGTACG)2 was investigated by two independent techniques: UV-Vis absorption in the Job's plot approach and Induced Circular Dichroism. Both decamers bind two molecules of peptide per duplex, with close overall affinities. This result indicates that a row of six A:T base pairs can accommodate two molecules of drug and that the minimal binding site of Distamycin 3 can consist of just two A:T base pairs. PMID:2027777

  2. Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase.

    PubMed

    Yuan, Ye; Knaggs, Michael H; Poole, Leslie B; Fetrow, Jacquelyn S; Salsbury, Freddie R

    2010-08-01

    Typical 2-Cys peroxiredoxins (Prxs) are peroxidases which regulate cell signaling pathways, apoptosis, and differentiation. These enzymes are obligate homodimers, and can form decamers in solution. During catalysis, Prxs exhibit cysteine-dependent reactivity which requires the deprotonation of the peroxidatic cysteine (C(p)) supported by a lowered pK(a) in the initial step. We present the results of molecular dynamics simulations combined with pKa calculations on the monomeric, dimeric and decameric forms of one typical 2-Cys Prx, the tryparedoxin peroxidase from Trypanosoma cruzi (PDB id, 1uul). The calculations indicate that C(p) (C52) pK(a) values are highly affected by oligomeric state; an unshifted C(p) pK(a) (approximately 8.3, comparable to the pK(a) of isolated cysteine) is calculated for the monomer. In the dimers, starting with essentially identical structures, the C(p)s evolve dynamically asymmetric pK(a)s during the simulations; one subunit's C(p) pK(a) is shifted downward at a time, while the other is unshifted. However, when averaged over time, or multiple simulations, the two subunits within a dimer exhibit the same C(p), showing no preference for a lowered pK(a) in either subunit. Two conserved pathways that communicate the asymmetric pK(a)s between C(p)s of different subunits can be identified. In the decamer, all the C(p) pK(a)s are shifted downward, with slight asymmetry in the dimers which form the decamers. Structural analyses implicate oligomerization effects as responsible for these oligomeric state-dependent C(p) pK(a) shifts. The intra-dimer and the inter-dimer subunit contacts in the decamer restrict the conformations of the side chains of several residues (T49, T54 and E55) calculated to be key in shifting the C(p) pK(a). In addition, the backbone fluctuations of a few residues (M46, D47 and F48) result in a different electrostatic environment for the C(p) in dimers relative to the monomers. These side chain and backbone interactions

  3. Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD.

    PubMed

    Arakawa, Hirohumi; Kandadi, Machender R; Panzhinskiy, Evgeniy; Belmore, Kenneth; Deng, Ge; Love, Ebony; Robertson, Preshus M; Commodore, Juliette J; Cassady, Carolyn J; Nair, Sreejayan; Vincent, John B

    2016-06-01

    While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr(3+) to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media. PMID:26898644

  4. Hepatotoxic Seafood Poisoning (HSP) Due to Microcystins: A Threat from the Ocean?

    PubMed Central

    Vareli, Katerina; Jaeger, Walter; Touka, Anastasia; Frillingos, Stathis; Briasoulis, Evangelos; Sainis, Ioannis

    2013-01-01

    Cyanobacterial blooms are a major and growing problem for freshwater ecosystems worldwide that increasingly concerns public health, with an average of 60% of blooms known to be toxic. The most studied cyanobacterial toxins belong to a family of cyclic heptapeptide hepatotoxins, called microcystins. The microcystins are stable hydrophilic cyclic heptapeptides with a potential to cause cell damage following cellular uptake via organic anion-transporting proteins (OATP). Their intracellular biologic effects presumably involve inhibition of catalytic subunits of protein phosphatases (PP1 and PP2A) and glutathione depletion. The microcystins produced by cyanobacteria pose a serious problem to human health, if they contaminate drinking water or food. These toxins are collectively responsible for human fatalities, as well as continued and widespread poisoning of wild and domestic animals. Although intoxications of aquatic organisms by microcystins have been widely documented for freshwater ecosystems, such poisonings in marine environments have only occasionally been reported. Moreover, these poisonings have been attributed to freshwater cyanobacterial species invading seas of lower salinity (e.g., the Baltic) or to the discharge of freshwater microcystins into the ocean. However, recent data suggest that microcystins are also being produced in the oceans by a number of cosmopolitan marine species, so that Hepatotoxic Seafood Poisoning (HSP) is increasingly recognized as a major health risk that follows consumption of contaminated seafood. PMID:23921721

  5. How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic

    SciTech Connect

    Regni, Catherine A.; Roush, Rebecca F.; Miller, Darcie J.; Nourse, Amanda; Walsh, Christopher T.; Schulman, Brenda A.

    2009-09-11

    The 39-kDa Escherichia coli enzyme MccB catalyses a remarkable posttranslational modification of the MccA heptapeptide during the biosynthesis of microcin C7 (MccC7), a 'Trojan horse' antibiotic. The approximately 260-residue C-terminal region of MccB is homologous to ubiquitin-like protein (UBL) activating enzyme (E1) adenylation domains. Accordingly, MccB-catalysed C-terminal MccA-acyl-adenylation is reminiscent of the E1-catalysed activation reaction. However, unlike E1 substrates, which are UBLs with a C-terminal di-glycine sequence, MccB's substrate, MccA, is a short peptide with an essential C-terminal Asn. Furthermore, after an intramolecular rearrangement of MccA-acyl-adenylate, MccB catalyses a second, unique reaction, producing a stable phosphoramidate-linked analogue of acyl-adenylated aspartic acid. We report six-crystal structures of MccB in apo, substrate-, intermediate-, and inhibitor-bound forms. Structural and kinetic analyses reveal a novel-peptide clamping mechanism for MccB binding to heptapeptide substrates and a dynamic-active site for catalysing dual adenosine triphosphate-consuming reactions. The results provide insight into how a distinctive member of the E1 superfamily carries out two-step activation for generating the peptidyl-antibiotic MccC7.

  6. Identification of an epitope shared by the DNA-binding domain of glucocorticoid receptor and the B chain of insulin.

    PubMed Central

    Cayanis, E; Sarangarajan, R; Lombes, M; Nahon, E; Edelman, I S; Erlanger, B F

    1989-01-01

    A monoclonal antibody (8G11-C6) generated by an auto-anti-idiotypic route and directed to a site near the ligand-binding site of the glucocorticoid receptor also binds to native insulin and the B chain of insulin but not to the A chain of insulin. The glucocorticoid receptor and the B chain of insulin, therefore, share a cross-reacting epitope. Examination of the primary sequences of the two proteins revealed a limited number of regions of identity or close homology. Several peptides representative of those regions were synthesized. A heptapeptide sequence of the B chain of insulin with homology to a sequence in the first "zinc finger" of the DNA-binding domain of the glucocorticoid receptor was identified as the cross-reactive epitope. This heptapeptide sequence is restricted to and highly conserved among insulins of various species. Homologous sequences are found in the DNA-binding domains of most steroid receptors and related DNA-binding proteins. Consistent with this is the finding that 8G11-C6 inhibits the binding of glucocorticoid receptor to DNA-cellulose. PMID:2467302

  7. Protein interactions between the C-terminus of Aβ-peptide and phospholipase A2--a structure biology based approach to identify novel Alzheimer's therapeutics.

    PubMed

    Mirza, Zeenat; Pillai, Vikram G; Kamal, Mohammad A

    2014-01-01

    Amyloid β (Aβ) polypeptide plays a key role in determining the state of protein aggregation in Alzheimer's disease. The hydrophobic C-terminal part of the Aβ peptide is critical in triggering the transformation from α-helical to β- sheet structure. We hypothesized that phospholipase A2 (PLA2) may inhibit the aggregation of Aβ peptide by interacting with the peptide and keeping the two peptide chains apart. In order to examine the nature of interactions between PLA2 and Aβ peptide, we prepared and crystallized complex of Naja naja sagittifera PLA2 with the C-terminal hepta-peptide Val-Gly-Gly-Val-Val-Ile-Ala. The X-ray intensity data were collected to 2.04 A resolution and the structure was determined by molecular replacement and refined to the crystallographic R factor of 0.186. The structural analysis revealed that the peptide binds to PLA2 at the hydrophobic substrate binding cavity forming at least eight hydrogen bonds and approximately a two dozen Van der Waals interactions. The number and nature of interactions indicate that the affinity between PLA2 and the hepta-peptide is greater than the affinity between two Aβ peptide chains. Therefore, PLA2 is proposed as a probable ligand to prevent the aggregation of Aβ peptides. PMID:25230229

  8. A radiometric assay for HIV-1 protease

    SciTech Connect

    Hyland, L.J.; Dayton, B.D.; Moore, M.L.; Shu, A.Y.; Heys, J.R.; Meek, T.D. )

    1990-08-01

    A rapid, high-throughput radiometric assay for HIV-1 protease has been developed using ion-exchange chromatography performed in 96-well filtration plates. The assay monitors the activity of the HIV-1 protease on the radiolabeled form of a heptapeptide substrate, (tyrosyl-3,5-3H)Ac-Ser-Gln-Asn-Tyr-Pro-Val-Val-NH2, which is based on the p17-p24 cleavage site found in the viral polyprotein substrate Pr55gag. Specific cleavage of this uncharged heptapeptide substrate by HIV-1 protease releases the anionic product (tyrosyl-3,5-3H)Ac-Ser-Gln-Asn-Tyr, which is retained upon minicolumns of the anion-exchange resin AG1-X8. Protease activity is determined from the recovery of this radiolabeled product following elution with formic acid. This facile and highly sensitive assay may be utilized for steady-state kinetic analysis of the protease, for measurements of enzyme activity during its purification, and as a routine assay for the evaluation of protease inhibitors from natural product or synthetic sources.

  9. Structure and potential C-terminal dimerization of a recombinant mutant of surfactant-associated protein C in chloroform/methanol.

    PubMed

    Luy, Burkhard; Diener, Alexander; Hummel, Rolf-Peter; Sturm, Ernst; Ulrich, Wolf-Rüdiger; Griesinger, Christian

    2004-06-01

    The solution structure of a recombinant mutant [rSP-C (FFI)] of the human surfactant-associated protein C (hSP-C) in a mixture of chloroform and methanol was determined by high-resolution NMR spectroscopy. rSP-C (FFI) contains a helix from Phe5 to the C-terminal Leu34 and is thus longer by two residues than the helix of porcine SP-C (pSP-C), which is reported to start at Val7 in the same solvent. Two sets of resonances at the C-terminus of the peptide were observed, which are explained by low-order oligomerization, probably dimerization of rSP-C (FFI) in its alpha-helical form. The dimerization may be induced by hydrogen bonding of the C-terminal carboxylic groups or by the strictly conserved C-terminal heptapeptide segment with a motif similar to the GxxxG dimerization motif of glycophorin A. Dimerization at the heptapeptide segment would be consistent with findings based on electrospray ionization MS data, chemical cross-linking studies, and CNBr cleavage data. PMID:15153097

  10. A few atoms make the difference: synthetic, CD, NMR and computational studies on antiviral and antibacterial activities of glycopeptide antibiotic aglycon derivatives.

    PubMed

    Bereczki, Ilona; Mándi, Attila; Rőth, Erzsébet; Borbás, Anikó; Fizil, Ádám; Komáromi, István; Sipos, Attila; Kurtán, Tibor; Batta, Gyula; Ostorházi, Eszter; Rozgonyi, Ferenc; Vanderlinden, Evelien; Naesens, Lieve; Sztaricskai, Ferenc; Herczegh, Pál

    2015-04-13

    Despite the close structural similarity between the heptapeptide cores of the glycopeptide antibiotics teicoplanin and ristocetin, synthetically modified derivatives of their aglycons show significantly different antibacterial and antiviral properties. The teicoplanin aglycon derivatives with one exception proved to be potent antibacterials but they did not exhibit anti-influenza virus activity. In contrast, the aglycoristocetin derivatives generally showed high anti-influenza virus activity and possessed moderate antibacterial activity. A systematic structure-activity relationship study has been carried out on ristocetin and teicoplanin aglycon derivatives, to explore which structural differences are responsible for these markedly different biological activities. According to electronic circular dichroism and in silico conformational studies, it was found that the differences in anti-influenza virus activity are mainly determined by the conformation of the heptapeptide core of the antibiotics controlled by the presence or absence of chloro substituents. Knowledge of the bioactive conformation will help to design new analogs with improved anti-influenza virus activity. For the teicoplanin derivatives, it was shown that derivatization to improve the antiviral efficacy was accompanied by a significant decrease in antibacterial activity. PMID:25752526

  11. A Hero's Little Horse: Discovery of a Dissolving Star Cluster in Pegasus

    NASA Astrophysics Data System (ADS)

    Kim, Dongwon; Jerjen, Helmut

    2015-01-01

    We report the discovery of an ultra-faint stellar system in the constellation of Pegasus. This concentration of stars was detected by applying our overdensity detection algorithm to the Sloan Digital Sky Survey Data Release 10 and confirmed with deeper photometry from the Dark Energy Camera (DECam) at the 4 m Blanco telescope. The best-fitting model isochrone indicates that this stellar system, Kim 1, features an old (12 Gyr) and metal-poor ([Fe/H] ~ -1.7) stellar population at a heliocentric distance of 19.8 ± 0.9 kpc. We measure a half-light radius of 6.9 ± 0.6 pc using a Plummer profile. The small physical size and the extremely low luminosity are comparable to the faintest known star clusters Segue 3, Koposov 1 and 2, and Muñoz 1. However, Kim 1 exhibits a lower star concentration and is lacking a well-defined center. It also has an unusually high ellipticity and irregular outer isophotes, which suggests that we are seeing an intermediate mass star cluster being stripped by the Galactic tidal field. An extended search for evidence of an associated stellar stream within the 3 \\deg 2 DECam field remains inconclusive. The finding of Kim 1 is consistent with current overdensity detection limits and supports the hypothesis that there are still a substantial number of extreme low-luminosity star clusters undetected in the wider Milky Way halo.

  12. Inhibition of Key Digestive Enzymes by Cocoa Extracts 1 and Procyanidins

    PubMed Central

    Gu, Yeyi; Hurst, William J.; Stuart, David A.; Lambert, Joshua D.

    2011-01-01

    We determined the in vitro inhibitory effects of cocoa extracts and procyanidins against pancreatic α-amylase (PA), pancreatic lipase (PL) and secreted phospholipase A2 (PLA2), and characterized the kinetics of such inhibition. Lavado, regular and Dutch-processed cocoa extracts as well as cocoa procyanidins (degree of polymerization (DP) = 2 to 10) were examined. Cocoa extracts and procyanidins dose-dependently inhibited PA, PL and PLA2. Lavado cocoa extract was the most potent inhibitor (IC50 = 8.5 – 47 μg/mL). An inverse correlation between Log IC50 and DP (R2 > 0.93) was observed. Kinetic analysis suggested that regular cocoa extract, the pentamer and decamer inhibited PL activity in a mixed mode. The pentamer and decamer non-competitively inhibited PLA2 activity, whereas regular cocoa extract inhibited PLA2 competitively. Our study demonstrates that cocoa polyphenols can inhibit digestive enzymes in vitro, and may, in conjunction with a low calorie diet, play a role in body weight management. PMID:21495725

  13. The development of a cryogenic over-pressure pump

    NASA Astrophysics Data System (ADS)

    Alvarez, M.; Cease, H.; Flaugher, B.; Flores, R.; Garcia, J.; Lathrop, A.; Ruiz, F.

    2014-01-01

    A cryogenic over-pressure pump (OPP) was tested in the prototype telescope liquid nitrogen (LN2) cooling system for the Dark Energy Survey (DES) Project. This OPP consists of a process cylinder (PC), gas generator, and solenoid operated valves (SOVs). It is a positive displacement pump that provided intermittent liquid nitrogen (LN2) flow to an array of charge couple devices (CCDs) for the prototype Dark Energy Camera (DECam). In theory, a heater submerged in liquid would generate the drive gas in a closed loop cooling system. The drive gas would be injected into the PC to displace that liquid volume. However, due to limitations of the prototype closed loop nitrogen system (CCD cooling system) for DECam, a quasiclosed-loop nitrogen system was created. During the test of the OPP, the CCD array was cooled to its designed set point temperature of 173K. It was maintained at that temperature via electrical heaters. The performance of the OPP was captured in pressure, temperature, and flow rate in the CCD LN2 cooling system at Fermi National Accelerator Laboratory (FNAL).

  14. The development of a cryogenic over-pressure pump

    SciTech Connect

    Alvarez, M.; Cease, H.; Flaugher, B.; Flores, R.; Lathrop, A.; Garcia, J.; Ruiz, F.

    2014-01-29

    A cryogenic over-pressure pump (OPP) was tested in the prototype telescope liquid nitrogen (LN2) cooling system for the Dark Energy Survey (DES) Project. This OPP consists of a process cylinder (PC), gas generator, and solenoid operated valves (SOVs). It is a positive displacement pump that provided intermittent liquid nitrogen (LN2) flow to an array of charge couple devices (CCDs) for the prototype Dark Energy Camera (DECam). In theory, a heater submerged in liquid would generate the drive gas in a closed loop cooling system. The drive gas would be injected into the PC to displace that liquid volume. However, due to limitations of the prototype closed loop nitrogen system (CCD cooling system) for DECam, a quasiclosed-loop nitrogen system was created. During the test of the OPP, the CCD array was cooled to its designed set point temperature of 173K. It was maintained at that temperature via electrical heaters. The performance of the OPP was captured in pressure, temperature, and flow rate in the CCD LN2 cooling system at Fermi National Accelerator Laboratory (FNAL)

  15. Crystal Structure and Function of Human Nucleoplasmin (Npm2): A Histone Chaperone in Oocytes and Embryos

    SciTech Connect

    O Platonova; I Akey; J Head; C Akey

    2011-12-31

    Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9 {angstrom} resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits. This feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.

  16. Light Echoes of Galactic Explosions and Eruptions

    NASA Astrophysics Data System (ADS)

    Rest, Armin; Bianco, Federica; Chornock, Ryan; Foley, Ryan; Matheson, Thomas; Narayan, Gautham; Olsen, Knut; Prieto, Jose Luis; Smith, Chris; Smith, Nathan; Suntzeff, Nick; Welch, Doug; Zenteno, Alfredo

    2014-02-01

    We propose to continue our search for the first light echoes (LEs) associated with historical Galactic supernovae and LBV outbursts: SN 1006, Kepler's SN, RCW 86, Crab Nebula, and P Cygni. In previously granted NOAO time, we have discovered LEs of three ancient SNe in the LMC as well as from the historic SN events of Cas A and Tycho [2, 3], which allowed their spectroscopic classification [6, 7, 10] and 3D spectroscopy [8, 9]. Most recently, we discovered light echoes of the mid-19th-century Great Eruption of η Carinae using CTIO 4m Mosaic images [11]. Subsequent spectroscopic follow-up of Eta Carinae revealed that its outburst spectral type was most similar to those of G-type supergiants, rather than reported LBV outburst spectral types of F-type (or earlier) [11]. We propose to continue our search for light echoes of the remaining historical events. With DECam, we have a 10-15 fold improvement in efficiency over the retired CTIO-Mosaic camera, which allows us to cover the bigger search areas of most of the remaining targets. With the KPNO 4-m, we will observe fields too far north for CTIO/DECam. The study of scattered-light echoes from these Galactic supernovae and eruptions will give us the opportunity to directly compare the original outburst and its current remnant, and in favorable cases (like Eta Carinae), it provides a three-dimensional view of the event and/or a spectral time series.

  17. Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA

    PubMed Central

    Kandiah, Eaazhisai; Carriel, Diego; Perard, Julien; Malet, Hélène; Bacia, Maria; Liu, Kaiyin; Chan, Sze W. S.; Houry, Walid A.; Ollagnier de Choudens, Sandrine; Elsen, Sylvie; Gutsche, Irina

    2016-01-01

    The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions. PMID:27080013

  18. Fractionation of polymeric procyanidins from lowbush blueberry and quantification of procyanidins in selected foods with an optimized normal-phase HPLC-MS fluorescent detection method.

    PubMed

    Gu, Liwei; Kelm, Mark; Hammerstone, John F; Beecher, Gary; Cunningham, David; Vannozzi, Sarah; Prior, Ronald L

    2002-08-14

    The polymeric procyanidins were fractionated from lowbush blueberry on a Sephadex LH-20 column. The degree of polymerization (DP) for the polymers was determined by thiolysis to be in a range of 19.9 to 114.1. Normal-phase HPLC analysis indicated that the polymeric procyanidins did not contain oligomeric procyanidins with DP < 10. The polymers eluted as a single peak at the end of the chromatogram. The normal-phase HPLC gradient was modified to improve the separation of procyanidin monomers through decamers and to elute all the polymers beyond those as a distinct peak. Monomers through decamers were quantified individually. All the polymers (DP > 10) were quantified using a mixture of purified polymers as an external standard. Polymers were found to be the dominant procyanidins in brown sorghum bran, cranberry, and blueberry. Thiolysis of the polymer peaks indicated that epicatechin was present as extension units in these foods, however, the composition of terminal units varied considerably between catechin and epicatechin, or an A-type dimer linkage in the case of cranberry. PMID:12166971

  19. In vivo parameters influencing 2-Cys Prx oligomerization: The role of enzyme sulfinylation.

    PubMed

    Noichri, Y; Palais, G; Ruby, V; D'Autreaux, B; Delaunay-Moisan, A; Nyström, T; Molin, M; Toledano, M B

    2015-12-01

    2-Cys Prxs are H2O2-specific antioxidants that become inactivated by enzyme hyperoxidation at elevated H2O2 levels. Although hyperoxidation restricts the antioxidant physiological role of these enzymes, it also allows the enzyme to become an efficient chaperone holdase. The critical molecular event allowing the peroxidase to chaperone switch is thought to be the enzyme assembly into high molecular weight (HMW) structures brought about by enzyme hyperoxidation. How hyperoxidation promotes HMW assembly is not well understood and Prx mutants allowing disentangling its peroxidase and chaperone functions are lacking. To begin addressing the link between enzyme hyperoxidation and HMW structures formation, we have evaluated the in vivo 2-Cys Prxs quaternary structure changes induced by H2O2 by size exclusion chromatography (SEC) on crude lysates, using wild type (Wt) untagged and Myc-tagged S. cerevisiae 2-Cys Prx Tsa1 and derivative Tsa1 mutants or genetic conditions known to inactivate peroxidase or chaperone activity or altering the enzyme sensitivity to hyperoxidation. Our data confirm the strict causative link between H2O2-induced hyperoxidation and HMW formation/stabilization, also raising the question of whether CP hyperoxidation triggers the assembly of HMW structures by the stacking of decamers, which is the prevalent view of the literature, or rather, the stabilization of preassembled stacked decamers. PMID:26335398

  20. Mass Substructure in Abell 3128

    NASA Astrophysics Data System (ADS)

    McCleary, J.; dell'Antonio, I.; Huwe, P.

    2015-05-01

    We perform a detailed two-dimensional weak gravitational lensing analysis of the nearby (z = 0.058) galaxy cluster Abell 3128 using deep ugrz imaging from the Dark Energy Camera (DECam). We have designed a pipeline to remove instrumental artifacts from DECam images and stack multiple dithered observations without inducing a spurious ellipticity signal. We develop a new technique to characterize the spatial variation of the point-spread function that enables us to circularize the field to better than 0.5% and thereby extract the intrinsic galaxy ellipticities. By fitting photometric redshifts to sources in the observation, we are able to select a sample of background galaxies for weak-lensing analysis free from low-redshift contaminants. Photometric redshifts are also used to select a high-redshift galaxy subsample with which we successfully isolate the signal from an interloping z = 0.44 cluster. We estimate the total mass of Abell 3128 by fitting the tangential ellipticity of background galaxies with the weak-lensing shear profile of a Navarro-Frenk-White (NFW) halo and also perform NFW fits to substructures detected in the 2D mass maps of the cluster. This study yields one of the highest resolution mass maps of a low-z cluster to date and is the first step in a larger effort to characterize the redshift evolution of mass substructures in clusters.

  1. Protein self-association induced by macromolecular crowding: a quantitative analysis by magnetic relaxation dispersion.

    PubMed

    Snoussi, Karim; Halle, Bertil

    2005-04-01

    In the presence of high concentrations of inert macromolecules, the self-association of proteins is strongly enhanced through an entropic, excluded-volume effect variously called macromolecular crowding or depletion attraction. Despite the predicted large magnitude of this universal effect and its far-reaching biological implications, few experimental studies of macromolecular crowding have been reported. Here, we introduce a powerful new technique, fast field-cycling magnetic relaxation dispersion, for investigating crowding effects on protein self-association equilibria. By recording the solvent proton spin relaxation rate over a wide range of magnetic field strengths, we determine the populations of coexisting monomers and decamers of bovine pancreatic trypsin inhibitor in the presence of dextran up to a macromolecular volume fraction of 27%. Already at a dextran volume fraction of 14%, we find a 30-fold increase of the decamer population and 510(5)-fold increase of the association constant. The analysis of these results, in terms of a statistical-mechanical model that incorporates polymer flexibility as well as the excluded volume of the protein, shows that the dramatic enhancement of bovine pancreatic trypsin inhibitor self-association can be quantitatively rationalized in terms of hard repulsive interactions. PMID:15665132

  2. Investigating interactions of the pentraxins serum amyloid P component and C-reactive protein by mass spectrometry.

    PubMed

    Aquilina, J Andrew; Robinson, Carol V

    2003-10-15

    The oligomeric state of human SAP (serum amyloid P component) in the absence and presence of known ligands has been investigated using nanoelectrospray ionization MS. At pH 8.0, in the absence of Ca2+, SAP has been shown to consist of pentameric and decameric forms. In the presence of physiological levels of Ca2+, SAP was observed to exist primarily as a pentamer, reflecting its in vivo state. dAMP was shown not only to promote decamerization, but also to lead to decamer stacking involving up to 30 monomers. A mechanism for this finding is proposed. CRP (C-reactive protein), a pentraxin closely related to SAP, exists as a pentamer in the presence or absence of Ca2+. Pentamers of CRP and SAP were shown to form mixed decamers in Ca2+-free buffer; however, in the presence of Ca2+, this interaction was not observed. Furthermore, no exchange of monomeric subunits was observed between the SAP and CRP oligomers, suggesting a remarkable stability of the individual pentameric complexes. PMID:12892563

  3. DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC).

    PubMed

    Thirugnanasambandam, Arunachalam; Karthik, Selvam; Artheswari, Gunanithi; Gautham, Namasivayam

    2016-06-01

    High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs. PMID:27303798

  4. Preparing for the Kepler K2 Microlensing Survey: A Call to Arms

    NASA Astrophysics Data System (ADS)

    Penny, Matthew

    2015-01-01

    In 2016 the ninth campaign of K2 (the extended, two-wheel Kepler mission) will be targeted towards the Galactic bulge, where it will perform the first wide-field, space-based microlensing survey. This survey will discover tens of both bound and free-floating planets by itself, but its real value will come from simultaneous ground-based observations that will provide parallax measurements enabling both mass and distance measurements for the majority of these planets and their hosts. These will include the first ever measurements of free-floating planet masses.K2's immediate public data release policy offers a huge one-time-only opportunity to build up the US's expertise in exoplanetary microlensing surveys in preparation for the WFIRST mission. Unbeknownst to most astronomers at home and abroad, the US also owns the best instrument in the world for conducting ground-based microlensing surveys -- DECam on the Blanco 4m, whose etendue is a factor of 20 larger than OGLE's at equal resolution. A simultaneous survey using ~80 half nights on DECam (as part of a NOAO large survey program) could also make its data immediately public, catapulting US astronomers to the forefront of planetary microlensing surveys, measuring masses of and distances to microlensing exoplanets on a never-before-possible scale. This is an opportunity that should not be missed and I will outline ways in which you can get involved.

  5. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site.

    PubMed

    Collins, E J; Garboczi, D N; Wiley, D C

    1994-10-13

    Class I major histocompatibility complex (MHC) molecules present peptides to CD8+ T cells for immunological surveillance (reviewed in ref. 1). The structures of complexes of class I MHC molecules with octamer, nonamer and decamer peptides determined until now show a common binding mode, with both peptide termini bound in conserved pockets at the ends of the peptide binding site. Length variations were accommodated by the peptide bulging or zig-zagging in the middle. Here we describe the structure of a decamer peptide which binds with the carboxy-terminal residue positioned outside the peptide binding site. Several protein side chains have rearranged to allow the peptide to exit. The structure suggests that even longer peptides could bind. The energetic effect of the altered mode of binding has been assessed by measuring the stability of the complex to thermal denaturation. Peptides bound in this novel manner are stable at physiological temperature, raising questions about their role in T-cell recognition and their production by proteolytic processing. PMID:7935798

  6. Evidence That Hydra I is a Tidally Disrupting Milky Way Dwarf Galaxy

    NASA Astrophysics Data System (ADS)

    Hargis, Jonathan R.; Kimmig, Brian; Willman, Beth; Caldwell, Nelson; Walker, Matthew G.; Strader, Jay; Sand, David J.; Grillmair, Carl J.; Yoon, Joo Heon

    2016-02-01

    The Eastern Banded Structure (EBS) and Hydra I halo overdensities are very nearby (d ˜ 10 kpc) objects discovered in Sloan Digital Sky Survey (SDSS) data. Previous studies of the region have shown that EBS and Hydra I are spatially coincident, cold structures at the same distance, suggesting that Hydra I may be the EBS's progenitor. We combine new wide-field Dark Energy Camera (DECam) imaging and MMT/Hectochelle spectroscopic observations of Hydra I with SDSS archival spectroscopic observations to quantify Hydra I's present-day chemodynamical properties, and to infer whether it originated as a star cluster or dwarf galaxy. While previous work using shallow SDSS imaging assumed a standard old, metal-poor stellar population, our deeper DECam imaging reveals that Hydra I has a thin, well-defined main sequence turnoff of intermediate age (˜5-6 Gyr) and metallicity ([Fe/H] = -0.9 dex). We measure statistically significant spreads in both the iron and alpha-element abundances of {σ }[{Fe/{{H}}]}=0.13+/- 0.02 dex and {σ }[α /{{Fe}]}=0.09+/- 0.03 dex, respectively, and place upper limits on both the rotation and its proper motion. Hydra I's intermediate age and [Fe/H]—as well as its low [α/Fe], apparent [Fe/H] spread, and present-day low luminosity—suggest that its progenitor was a dwarf galaxy, which has subsequently lost more than 99.99% of its stellar mass.

  7. The readout and control system of the Dark Energy Camera

    NASA Astrophysics Data System (ADS)

    Honscheid, Klaus; Elliott, Ann; Annis, James; Bonati, Marco; Buckley-Geer, Elizabeth; Castander, Francisco; daCosta, Luiz; Fausti, Angelo; Karliner, Inga; Kuhlmann, Steve; Neilsen, Eric; Patton, Kenneth; Reil, Kevin; Roodman, Aaron; Thaler, Jon; Serrano, Santiago; Soares Santos, Marcelle; Suchyta, Eric

    2012-09-01

    The Dark Energy Camera (DECam) is a new 520 Mega Pixel CCD camera with a 3 square degree field of view designed for the Dark Energy Survey (DES). DES is a high precision, multi-bandpass, photometric survey of 5000 square degrees of the southern sky. DECam is currently being installed at the prime focus of the Blanco 4-m telescope at the Cerro- Tololo International Observatory (CTIO). In this paper we describe SISPI, the data acquisition and control system of the Dark Energy Camera. SISPI is implemented as a distributed multi-processor system with a software architecture based on the Client-Server and Publish-Subscribe design patterns. The underlying message passing protocol is based on PYRO, a powerful distributed object technology system written entirely in Python. A distributed shared variable system was added to support exchange of telemetry data and other information between different components of the system. We discuss the SISPI infrastructure software, the image pipeline, the observer console and user interface architecture, image quality monitoring, the instrument control system, and the observation strategy tool.

  8. Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide.

    PubMed

    Diaz-Avalos, Ruben; Long, Chris; Fontano, Eric; Balbirnie, Melinda; Grothe, Robert; Eisenberg, David; Caspar, Donald L D

    2003-07-25

    The seven-residue peptide GNNQQNY from the N-terminal region of the yeast prion protein Sup35, which forms amyloid fibers, colloidal aggregates and highly ordered nanocrystals, provides a model system for characterizing the elusively protean cross-beta conformation. Depending on preparative conditions, orthorhombic and monoclinic crystals with similar lath-shaped morphology have been obtained. Ultra high-resolution (<0.5A spacing) electron diffraction patterns from single nanocrystals show that the peptide chains pack in parallel cross-beta columns with approximately 4.86A axial spacing. Mosaic striations 20-50 nm wide observed by electron microscopy indicate lateral size-limiting crystal growth related to amyloid fiber formation. Frequently obtained orthorhombic forms, with apparent space group symmetry P2(1)2(1)2(1), have cell dimensions ranging from /a/=22.7-21.2A, /b/=39.9-39.3A, /c/=4.89-4.86A for wet to dried states. Electron diffraction data from single nanocrystals, recorded in tilt series of still frames, have been mapped in reciprocal space. However, reliable integrated intensities cannot be obtained from these series, and dynamical electron diffraction effects present problems in data analysis. The diversity of ordered structures formed under similar conditions has made it difficult to obtain reproducible X-ray diffraction data from powder specimens; and overlapping Bragg reflections in the powder patterns preclude separated structure factor measurements for these data. Model protofilaments, consisting of tightly paired, half-staggered beta strands related by a screw axis, can be fit in the crystal lattices, but model refinement will require accurate structure factor measurements. Nearly anhydrous packing of this hydrophilic peptide can account for the insolubility of the crystals, since the activation energy for rehydration may be extremely high. Water-excluding packing of paired cross-beta peptide segments in thin protofilaments may be characteristic

  9. Angiotensin antagonists with increased specificity for the renal vasculature.

    PubMed Central

    Taub, K J; Caldicott, W J; Hollenberg, N K

    1977-01-01

    This study was designed to ascertain whether renal vascular angiotensin receptors differ from other systemic angiotensin receptors and whether, on that basis, antagonists with greater specificity for the renal vasculature can be defined. Femoral and renal blood flow and their responses to angiotensin II (AII) and its heptapeptide analogue, 1-des Asp AII (AIII), were measured with an electromagnetic flowmeter in 26 dogs. For the kidney, the threshold doses of AII and AIII were identical (2.5+/-0.27 vs. 2.3+/-0.35 pmol/100 ml renal blood flow, with similar dose-response curves. In contrast, AII had a greater pressor effect (P less than 0.001) and produced more femoral vasoconstriction (P less than 0.001) than AIII. All four antagonists studied (1-Sar, 8-Ala AII [P113]; 8-Ala AII; 1-des Asp, 8-Ala AII; 1-des Asp, 8-Ile AII) induced parallel shifts in the renal blood flow response to AII and AIII. P113 induced greater blockade than 8-Ala AII (P less than 0.001) which, in turn, was more effective than 1-des Asp, 8-Ala AII (P less than 0.001). 1-des Asp, 8-Ile AII was as effective as P113. Each analogue induced an identical inhibition of the renal vascular response to AII and AIII. In addition, AII and AIII induced cross-tachyphylaxis. All lines of evidence suggested that AII and AIII act on a single receptor in the kidney, which differs at least functionally from other systemic vascular receptors. The possibility that heptapeptide analogues represent angiotensin antagonists with greater specificity for the renal vasculature was pursued in a model in which the renin-angiotensin system is activated. Acute, partial thoracic inferior vena caval occlusion was induced in an additional 16 dogs. P113 induced progressive, dose-related hypotension and a limited increase in renal blood flow in this model. The 1-des Asp, 8-Ile AII analogue, conversely, induced a consistent, larger, dose-related renal blood flow increase, with significantly less hypotension over a wide dose range

  10. Synthesis of a Cytotoxic Amanitin for Biorthogonal Conjugation.

    PubMed

    Zhao, Liang; May, Jonathan P; Blanc, Antoine; Dietrich, David J; Loonchanta, Anastak; Matinkhoo, Kaveh; Pryyma, Alla; Perrin, David M

    2015-07-01

    Alpha-amanitin is an exceedingly toxic, naturally occurring, bicyclic octapeptide that inhibits RNA polymerase and results in cellular and organismal death. Here we report the straightforward synthesis of an amanitin analogue that exhibited near-native toxicity. A pendant alkyne was readily installed to enable copper-catalyzed alkyne-azide cycloaddition (CuAAC) to azido-rhodamine and two azide-bearing versions of the RGD peptide. The fluorescent toxin analogue entered cells and provoked morphological changes consistent with cell death. The latter two conjugates are as toxic as the parent alkyne precursor, which demonstrates that conjugation does not diminish toxicity. In addition, we showed that toxicity depends on a single diastereomer of the unnatural amino acid, dihydroxyisoleucine (DHIle), at position 3. The convenient synthesis of a heptapeptide precursor now provides access to bioactive amanitin analogues that may be readily conjugated to biomolecules of interest. PMID:26043184

  11. Effect of methylene group insertions on the structural rigidity of Aib containing helices.

    PubMed

    Duley, Anju; Gowda, Vasantha; Ganjiwale, Anjali; Raghothama, Srinivasarao; Ramanathan, Gurunath

    2015-11-01

    Nonprotein amino acids are being extensively used in the design of synthetic peptides to create new structure mimics. In this study we report the effect of methylene group insertions in a heptapeptide Boc-Ala1-Leu2-Aib3-Xxx4-Ala5-Leu6-Aib7-OMe which nicely folds into a mixed 310 -/α-helical structure when Xxx= Ala. Analogs of this peptide have been made and studied by replacing central Xxx4 residue with Glycine (α-residue), β-Alanine (β-Αla), γ-aminobutyric acid (Gaba), and ε-aminocaproic acid (ε-Aca). NMR and circular dichroism were used to study the solution structure of these peptides. Crystals of the peptides containing alanine, β-Αla, and Gaba reveal that increasing the number of central methylene (-CH2 -) groups introduces local perturbations even as the helical structure is retained. PMID:26152771

  12. The proteolytic action of Arvin on human fibrinogen

    PubMed Central

    Ewart, M. R.; Hatton, M. W. C.; Basford, J. M.; Dodgson, K. S.

    1970-01-01

    1. Human fibrinogen was subjected to proteolysis by enzyme preparations (clinical Arvin and IRC-50 Arvin) from the venom of Agkistrodon rhodostoma. 2. IRC-50 Arvin releases three peptides from fibrinogen, and these were identified as fibrinopeptides AP, AY and A. 3. The less purified `clinical' Arvin releases, in addition to fibrinopeptides AP, AY and A, small amounts of two heptapeptides derived from fibrinopeptides AP and A, probably because it contains another enzyme as well as Arvin. 4. No fibrinopeptide B is released by either Arvin preparation. 5. Thus, although Arvin is known to differ from `reptilase' from Bothrops jararaca in that it does not activate the enzyme that cross-links fibrin (fibrin-stabilizing factor), it is identical with reptilase with respect to the peptides that it liberates from fibrinogen. PMID:5529716

  13. An N-terminal pro-atrial natriuretic peptide (NT-proANP) 'aggregation-prone' segment involved in isolated atrial amyloidosis.

    PubMed

    Louros, Nikolaos N; Iconomidou, Vassiliki A; Tsiolaki, Paraskevi L; Chrysina, Evangelia D; Baltatzis, Georgios E; Patsouris, Efstratios S; Hamodrakas, Stavros J

    2014-01-01

    Isolated atrial amyloidosis (IAA) is a common localized form of amyloid deposition within the atria of the aging heart. The main constituents of amyloid fibrils are atrial natriuretic peptide (ANP) and the N-terminal part of its precursor form (NT-proANP). An 'aggregation-prone' heptapeptide ((114)KLRALLT(120)) was located within the NT-proANP sequence. This peptide self-assembles into amyloid-like fibrils in vitro, as electron microscopy, X-ray fiber diffraction, ATR FT-IR spectroscopy and Congo red staining studies reveal. Consequently, remedies/drugs designed to inhibit the aggregation tendency of this 'aggregation-prone' segment of NT-proANP may assist in prevention/treatment of IAA, congestive heart failure (CHF) or atrial fibrillation (AF). PMID:24220659

  14. Hepatitis B virus and Homo sapiens proteome-wide analysis: A profusion of viral peptide overlaps in neuron-specific human proteins

    PubMed Central

    Ricco, Rosalia; Kanduc, Darja

    2010-01-01

    The primary amino acid sequence of the hepatitis B virus (HBV) proteome was searched for identity spots in the human proteome by using the Protein Information Resource database. We find that the HBV polyprotein shares sixty-five heptapeptides, one octapeptide, and one nonapeptide with the human proteins. The viral matches are disseminated among fundamental human proteins such as adhesion molecules, leukocyte differentiation antigens, enzymes, proteins associated with spermatogenesis, and transcription factors. As a datum of special interest, a number of peptide motifs are shared between the virus- and brain-specific antigens involved in neuronal protection. This study may help to evaluate the potential cross reactions and side effects of HBV antigen-based vaccines. PMID:20531967

  15. Elucidating the Locking Mechanism of Peptides onto Growing Amyloid Fibrils through Transition Path Sampling

    PubMed Central

    Schor, Marieke; Vreede, Jocelyne; Bolhuis, Peter G.

    2012-01-01

    We investigate the molecular mechanism of monomer addition to a growing amyloid fibril composed of the main amyloidogenic region from the insulin peptide hormone, the LVEALYLLVEALYL heptapeptide. Applying transition path sampling in combination with reaction coordinate analysis reveals that the transition from a docked peptide to a locked, fully incorporated peptide can occur in two ways. Both routes involve the formation of backbone hydrogen bonds between the three central amino acids of the attaching peptide and the fibril, as well as a reorientation of the central Glu side chain of the locking peptide toward the interface between two β-sheets forming the fibril. The mechanisms differ in the sequence of events. We also conclude that proper docking is important for correct alignment of the peptide with the fibril, as alternative pathways result in misfolding. PMID:22995502

  16. The primary structure of the aridicin aglycon as revealed by long-range J values

    NASA Astrophysics Data System (ADS)

    Mueller, Luciano; Jeffs, Peter W.

    The aglycon of aridicin, which is a member of the vancomycin class of antibiotics, was analyzed by utilizing J spin-spin interactions in two-dimensional NMR experiments.This unusual heptapeptide with the molecular formula C 59H 45N 7O 19Cl 4 (MW 1296.160) has a large number of quateernary carbons in aromatic side chains. For that reason most information was obtained from delayed COSY and COLOC spectra which reveal homo- and heteronuclear connectivities via long-range J couplings. The carbon-13 spectrum was assigned completely. In addition, the primary structure of the aridicin aglycon could be deduced, with the exception of the ether linkages between the side chains A, B, and C, by solely relying on J-connectivity maps.

  17. Sub-lethal cadmium exposure increases phytochelatin concentrations in the aquatic snail Lymnaea stagnalis.

    PubMed

    Sf, Gonçalves; Sk, Davies; Bennett, M; Raab, A; Feldmann, J; Kille, P; Loureiro, S; Dj, Spurgeon; Jg, Bundy

    2016-10-15

    Phytochelatins are metal-binding metabolites found in almost all plant species and some animal groups, including nematodes and annelids, where they can play an important role in detoxifying metals such as cadmium. Species from several other taxa contain a phytochelatin synthase (PCS) gene orthologue, including molluscs, indicating they may have the potential to synthesize phytochelatins. However, the presence of a gene alone does not demonstrate that it plays a functional role in metal detoxification. In the present study, we show that the aquatic snail Lymnaea stagnalis produced both penta- and heptapeptide phytochelatins (i.e. phytochelatin-2 and phytochelatin-3), and their levels increased in response to sub-lethal levels of cadmium. PMID:27358197

  18. Emerging Views on the CTD Code

    PubMed Central

    Zhang, David W.; Rodríguez-Molina, Juan B.; Tietjen, Joshua R.; Nemec, Corey M.; Ansari, Aseem Z.

    2012-01-01

    The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the “CTD code” hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. Here, we highlight the role of CTD modifications in directing transcription initiation, elongation, and termination. We examine the major readers, writers, and erasers of the CTD code and examine the relevance of describing patterns of posttranslational modifications as a “code.” Finally, we discuss major questions regarding the function of the newly discovered CTD modifications and the fundamental insights into transcription regulation that will necessarily emerge upon addressing those challenges. PMID:22567385

  19. Chromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groups. [Mastigocladus laminosus; Anabaena variabilis

    SciTech Connect

    Bishop, J.E.; Rapoport, H.; Klotz, A.V.; Chan, C.F.; Glazer, A.N.; Fueglistaller, P.; Zuber, H.

    1987-01-01

    Phycoerythrocyanin carries two covalently attached phycocyanobilin (PCB) groups on the ..beta.. subunit and a phycobiliviolinoid (PXB) group on the ..cap alpha.. subunit. Three distinct bilipeptides were obtained by proteolytic digestion of this protein: Asn-Gln-Ala-Ala-Cys(PCB)-Ile-Arg, Gly-Asp-Cys(PCB)-Ser-Gln, and Cys(PXB)-Val-Arg. Correlation 500-MHz /sup 1/H NMR analyses showed that the heptapeptide and pentapeptide were attached by cysteinyl thioether linkage to the A ring of the PCB moiety. /sup 1/H NMR and mass spectrometry determinations led to structural assignment for the hitherto uncharacterized PXB moiety, with peptide-thioether bonding possible to either ring A or D. Amino acid sequence homologies strongly favor A-ring linkage.

  20. A Functional Interaction between the Carboxy-Terminal Domain of RNA Polymerase II and Pre-mRNA Splicing

    PubMed Central

    Du, Lei; Warren, Stephen L.

    1997-01-01

    In the preceding study we found that Sm snRNPs and SerArg (SR) family proteins co-immunoprecipitate with Pol II molecules containing a hyperphosphorylated CTD (Kim et al., 1997). The association between Pol IIo and splicing factors is maintained in the absence of pre-mRNA, and the polymerase need not be transcriptionally engaged (Kim et al., 1997). The latter findings led us to hypothesize that a phosphorylated form of the CTD interacts with pre-mRNA splicing components in vivo. To test this idea, a nested set of CTD-derived proteins was assayed for the ability to alter the nuclear distribution of splicing factors, and to interfere with splicing in vivo. Proteins containing heptapeptides 1-52 (CTD52), 1-32 (CTD32), 1-26 (CTD26), 1-13 (CTD13), 1-6 (CTD6), 1-3 (CTD3), or 1 (CTD1) were expressed in mammalian cells. The CTD-derived proteins become phosphorylated in vivo, and accumulate in the nucleus even though they lack a conventional nuclear localization signal. CTD52 induces a selective reorganization of splicing factors from discrete nuclear domains to the diffuse nucleoplasm, and significantly, it blocks the accumulation of spliced, but not unspliced, human β-globin transcripts. The extent of splicing factor disruption, and the degree of inhibition of splicing, are proportional to the number of heptapeptides added to the protein. The above results indicate a functional interaction between Pol II's CTD and pre-mRNA splicing. PMID:9008699

  1. A Carboxyl-terminal Sequence in the Lutropin β Subunit Contributes to the Sorting of Lutropin to the Regulated Pathway*

    PubMed Central

    Jablonka-Shariff, Albina; Pearl, Christopher A.; Comstock, Anna; Boime, Irving

    2008-01-01

    Although synthesized in the same pituitary gonadotropes, the secretion profiles of lutropin (LH) and follitropin (FSH) differ. LH is secreted through a regulated pathway and associated with a bolus release at mid-estrous cycle. In contrast, the majority of FSH is secreted constitutively with an incremental increase until ovulation. Both share an identicalα subunit, and thus theβ subunit contains determinants for sorting into the regulated pathway. Previously, we demonstrated that a hydrophobic carboxyl-terminal heptapeptide of the LHβ subunit (Leu-Ser-Gly-Leu-Leu-Phe-Leu), not found in the FSHβ subunit, influences the intracellular behavior of the LH dimer. To test the hypothesis that the peptide contributes to differential sorting, we monitored the fates of LH and LHΔT (LHβ subunit lacking the carboxyl-terminal seven amino acids) dimers in the rat somatotrope-derived GH3 cell line in which both the regulated and constitutive secretory pathways operate. Pulse-chase labeling demonstrated that the LHΔT dimer was diverted to the constitutive pathway, resulting in a significant decrease in the corresponding intracellular pool. Forskolin stimulated LH dimer release 3-fold, which was accompanied by a parallel decrease of intracellular LH; only marginal forskolin stimulation of LHΔT was seen. Immunofluorescence after cycloheximide treatment demonstrated decreased retention of LHΔT compared with LH, consistent with increased constitutive secretion of LHΔT. We also demonstrated that fusing the heptapeptide to the carboxyl terminus of the FSHβ subunit resulted in an increased regulated secretion of this FSH analog compared with wild-type FSH. These data are the first to identify a novel structural determinant responsible for the sorting of a member of the glycoprotein hormone family into the regulated secretory pathway. PMID:18292086

  2. A biocompatible cobaltporphyrin-based complex micelle constructed via supramolecular assembly for oxygen transfer.

    PubMed

    Shen, Liangliang; Qu, Rui; Shi, Hejin; Huang, Fan; An, Yingli; Shi, Linqi

    2016-05-26

    Herein, a complex micelle as an oxygen nano-carrier is constructed through the hierarchical assembly of the diblock copolymer poly(ethylene glycol)-block-poly(l-lysine) (PEG-b-PLys), tetrakis(4-sulfonatophenyl)porphinato cobalt(ii) (Co(ii)TPPS), a heptapeptide (Cys-His-His-His-His-His-His) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TM-β-CD). Co(ii)TPPS was encapsulated into the cavities of TM-β-CDs driven by the host-guest interaction so that the irreversible formation of a μ-oxo-dimer of Co(ii)TPPS can be effectively prevented. The imidazole groups of the heptapeptide were selected as good axial ligands coordinating to the centric cobalt of Co(ii)TPPS, which subtly constituted the five-coordinated precursor serving as an active functional centre for oxygen binding. The sixth position of Co(ii)TPPS can bind oxygen. Furthermore, the host-guest inclusion (TM-β-CD/Co(ii)TPPS) was loaded into the hydrophobic core of the complex micelle and tightly fixed with PLys chains. The hydrophilic PEG blocks stretched in the aqueous solution constitute the shells which stabilize the structure of the complex micelle as well as impart the complex micelle sufficient blood circulation time. Moreover, the complex micelle exhibited excellent biocompatibility and cellular uptake. Therefore, the rationally designed amphiphilic structure can work as promising artificial O2 carriers in vivo. Potentially, the complex micelle can be expected to change the anaerobic microenvironment and find applications in the repair of the cells damaged by cellular hypoxia. PMID:27009911

  3. Identification of the polypeptides encoded in the unassigned reading frames 2, 4, 4L, and 5 of human mitochondrial DNA

    SciTech Connect

    Mariottini, P.; Chomyn, A.; Riley, M.; Cottrell, B.; Doolittle, R.F.; Attardi, G.

    1986-03-01

    In previous work, antibodies prepared against chemically synthesized peptides predicted from the DNA sequence were used to identify the polypeptides encoded in three of the eight unassigned reading frames (URFs) of human mitochondrial DNA (mtDNA). In the present study, this approach has been extended to other human mtDNA URFs. In particular, antibodies directed against the NH/sub 2/-terminal octapeptide of the putative URF2 product specifically precipitated component 11 of the HeLa cell mitochondrial translation products, the reaction being inhibited by the specific peptide. Similarly, antibodies directed against the COOH-terminal nonapeptide of the putative URF4 product reacted specifically with components 4 and 5, and antibodies against a COOH-terminal heptapeptide of the presumptive URF4L product reacted specifically with component 26. Antibodies against the NH/sub 2/-terminal heptapeptide of the putative product of URF5 reacted with component 1, but only to a marginal extent; however, the results of a trypsin fingerprinting analysis of component 1 point strongly to this component as being the authentic product of URF5. The polypeptide assignments to the mtDNA URFs analyzed here are supported by the relative electrophoretic mobilities of proteins 11, 4-5, 26, and 1, which are those expected for the molecular weights predicted from the DNA sequence for the products of URF2, URF4, URF4L, and URF5, respectively. With the present assignment, seven of the eight human mtDNA URFs have been shown to be expressed in HeLa cells.

  4. Extension of the AMBER force field to cyclic α,α dialkylated peptides.

    PubMed

    Grubišić, Sonja; Brancato, Giuseppe; Pedone, Alfonso; Barone, Vincenzo

    2012-11-28

    The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing α,α dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and α-helical structures is established in aqueous solution, in agreement with EPR data. PMID:23051698

  5. Classifying X-ray Sources from the Chandra Galactic Bulge Survey

    NASA Astrophysics Data System (ADS)

    Hynes, Robert

    2012-09-01

    The completion of the Galactic Bulge Survey (GBS) by Chandra in AO-13 identified 400 new X-ray sources (on top of the 1200 already known), many of which are expected to have accessible optical counterparts. Wide-field variability studies can be an extremely powerful tool to classify these sources. In two nights with the new NOAO DECam we can obtain lightcurves of ALL of the optically accessible objects, together with another 400 GBS sources from earlier AOs, and about 1700 additional fainter objects from the Chandra Source Catalog. We therefore propose a joint Archival-NOAO study to obtain these lightcurves, use them to classify the X-ray sources, and pick out ellipsoidal variations and eclipses from the many quiescent low-mass X-ray binaries predicted to be accessible.

  6. Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.

    PubMed

    Maita, Nobuo; Okada, Kengo; Hatakeyama, Kazuyuki; Hakoshima, Toshio

    2002-02-01

    In the presence of phenylalanine, GTP cyclohydrolase I feedback regulatory protein (GFRP) forms a stimulatory 360-kDa complex with GTP cyclohydrolase I (GTPCHI), which is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin. The crystal structure of the stimulatory complex reveals that the GTPCHI decamer is sandwiched by two GFRP homopentamers. Each GFRP pentamer forms a symmetrical five-membered ring similar to beta-propeller. Five phenylalanine molecules are buried inside each interface between GFRP and GTPCHI, thus enhancing the binding of these proteins. The complex structure suggests that phenylalanine-induced GTPCHI x GFRP complex formation enhances GTPCHI activity by locking the enzyme in the active state. PMID:11818540

  7. Identification of Turkish and standard apple rootstocks by morphological and molecular markers.

    PubMed

    Koc, A; Akbulut, M; Orhan, E; Celik, Z; Bilgener, S; Ercisli, S

    2009-01-01

    Two local (Vezir-1 and Vezir-2) and two standard (M9 and MM106) clonal apple rootstocks were compared using both morphological and molecular markers. International Union for the Protection of New Varieties of Plants criteria were used for morphological evaluation, which did not clearly separate these rootstocks. We tested 47 random decamer primers for random amplified polymorphic DNA analysis; 15 of them gave reproducible polymorphic patterns, yielding 109 bands, which showed 78% polymorphism. Based on a dendrogram obtained by unweighted pair group method using arithmetic average analysis, three clusters were obtained. The highest genetic similarities were found between M9 and Vezir-2 (0.670). The random amplified polymorphic DNA markers proved to be more efficient than the standard morphological markers for the identification of rootstocks. PMID:19551628

  8. Synthesis and properties of oligonucleotides containing aminodeoxythymidine units.

    PubMed Central

    Gryaznov, S M; Letsinger, R L

    1992-01-01

    Procedures are described for synthesis via solid support methodology of oligonucleotide analogues derived in part from 3'-amino-3'-deoxythymidine or 5'-amino-5'-deoxythymidine. Oligothymidylate decamers terminated with a 3'-amino group or containing a 3'-NHP(O)(O-)O-5' internucleoside link are found to form unusually stable complexes with poly(dA), poly(A), and oligo(dA). For related derivatives of 5'-amino-5'-deoxythymidine enhancement is less or absent, and in the case of multiple substitution destabilization of the heteroduplex may be observed. That the effect of the 3'-amino group is general for oligonucleotide derivatives is indicated by enhanced Tm values for heteroduplex complexes of the mixed-base oligomer, d(TATTCAGTCAT(NH2)), and the methyl phosphonate derivatives, TmTmTmTmTmTmTmTmTmT(NH2) and d(TmAmTmTmCmAmGmTmCmAmT(NH2)). PMID:1630911

  9. Variable Stars in the Field of the Hydra II Ultra-Faint Dwarf Galaxy

    NASA Astrophysics Data System (ADS)

    Vivas, Anna Katherina; Olsen, Knut A.; Blum, Robert D.; Nidever, David L.; Walker, Alistair R.; Martin, Nicolas; Besla, Gurtina; Gallart, Carme; Van Der Marel, Roeland P.; Majewski, Steven R.; Munoz, Ricardo; Kaleida, Catherine C.; Saha, Abhijit; Conn, Blair; Jin, Shoko

    2016-06-01

    We searched for variable stars in Hydra II, one of the recently discovered ultra-faint dwarf satellites of the Milky Way, using gri time-series obtained with the Dark Energy Camera (DECam) at Cerro Tololo Inter-American Observatory, Chile. We discovered one RR Lyrae star in the galaxy which was used to derive a distance of 154±8 kpc to this system and to re-calculate its absolute magnitude and half-light radius.A comparison with other RR Lyrae stars in ultra-faint systems indicates similar pulsational properties among them, which are different to those found among halo field stars and those in the largest of the Milky Way satellites. We also report the discovery of 31 additional short period variables in the field of view (RR Lyrae, SX Phe, eclipsing binaries, and a likely anomalous cepheid) which are likely not related with Hydra II.

  10. DNA binding studies of Vinca alkaloids: experimental and computational evidence.

    PubMed

    Pandya, Prateek; Gupta, Surendra P; Pandav, Kumud; Barthwal, Ritu; Jayaram, B; Kumar, Surat

    2012-03-01

    Fluorescence studies on the indole alkaloids vinblastine sulfate, vincristine sulfate, vincamine and catharanthine have demonstrated the DNA binding ability of these molecules. The binding mode of these molecules in the minor groove of DNA is non-specific. A new parameter of the purine-pyrimidine base sequence specificty was observed in order to define the non-specific DNA binding of ligands. Catharanthine had shown 'same' pattern of 'Pu-Py' specificity while evaluating its DNA binding profile. The proton resonances of a DNA decamer duplex were assigned. The models of the drug:DNA complexes were analyzed for DNA binding features. The effect of temperature on the DNA binding was also evaluated. PMID:22545401

  11. Gravitational wave triggered searches for failed supernovae

    NASA Astrophysics Data System (ADS)

    Annis, James; Dark Energy Survey Collaboration

    2016-03-01

    Stellar core collapses occur to all stars of sufficiently high mass and often result in supernovae. A small fraction of supergiant stars, however, are thought to collapse directly into black holes without producing supernovae. A survey of such ``failed'' supernovae would require monitoring millions of supergiants for several years. That is very challenging even for current surveys. With the start of the Advanced LIGO science run, we investigate the possibility of detecting failed supernovae by looking for missing supergiants associated with gravitational wave triggers. We use the Dark Energy Camera (DECam). Our project is a joint effort between the community and the Dark Energy Survey (DES) collaboration. In this talk we report on our ongoing efforts and discuss prospects for future searches.

  12. Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.

    PubMed

    Mattagajasingh, Ilwola; Mukherjee, Arup Kumar; Das, Premananda

    2006-01-01

    Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species. PMID:16989321

  13. The DES Science Verification Weak Lensing Shear Catalogs

    SciTech Connect

    Jarvis, M.

    2015-07-20

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.

  14. The DES Science Verification weak lensing shear catalogues

    NASA Astrophysics Data System (ADS)

    Jarvis, M.; Sheldon, E.; Zuntz, J.; Kacprzak, T.; Bridle, S. L.; Amara, A.; Armstrong, R.; Becker, M. R.; Bernstein, G. M.; Bonnett, C.; Chang, C.; Das, R.; Dietrich, J. P.; Drlica-Wagner, A.; Eifler, T. F.; Gangkofner, C.; Gruen, D.; Hirsch, M.; Huff, E. M.; Jain, B.; Kent, S.; Kirk, D.; MacCrann, N.; Melchior, P.; Plazas, A. A.; Refregier, A.; Rowe, B.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Suchyta, E.; Troxel, M. A.; Vikram, V.; Abbott, T.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Clampitt, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Fausti Neto, A.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nord, B.; Ogando, R.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Wechsler, R. H.

    2016-08-01

    We present weak lensing shear catalogues for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogues of 2.12 million and 3.44 million galaxies, respectively. We detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. We also discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogues for the full 5-yr DES, which is expected to cover 5000 square degrees.

  15. The Canarias Einstein ring: a newly discovered optical Einstein ring

    NASA Astrophysics Data System (ADS)

    Bettinelli, M.; Simioni, M.; Aparicio, A.; Hidalgo, S. L.; Cassisi, S.; Walker, A. R.; Piotto, G.; Valdes, F.

    2016-09-01

    We report the discovery of an optical Einstein ring in the Sculptor constellation, IAC J010127-334319, in the vicinity of the Sculptor dwarf spheroidal galaxy. It is an almost complete ring (˜300°) with a diameter of ˜4.5 arcsec. The discovery was made serendipitously from inspecting Dark Energy Camera (DECam) archive imaging data. Confirmation of the object nature has been obtained by deriving spectroscopic redshifts for both components, lens and source, from observations at the 10.4 m Gran Telescopio CANARIAS (GTC) with the spectrograph OSIRIS. The lens, a massive early-type galaxy, has a redshift of z = 0.581, while the source is a starburst galaxy with redshift of z = 1.165. The total enclosed mass that produces the lensing effect has been estimated to be Mtot = (1.86 ± 0.23) × 1012 M⊙.

  16. Green fluorescent protein nanopolygons as monodisperse supramolecular assemblies of functional proteins with defined valency

    NASA Astrophysics Data System (ADS)

    Kim, Young Eun; Kim, Yu-Na; Kim, Jung A.; Kim, Ho Min; Jung, Yongwon

    2015-05-01

    Supramolecular protein assemblies offer novel nanoscale architectures with molecular precision and unparalleled functional diversity. A key challenge, however, is to create precise nano-assemblies of functional proteins with both defined structures and a controlled number of protein-building blocks. Here we report a series of supramolecular green fluorescent protein oligomers that are assembled in precise polygonal geometries and prepared in a monodisperse population. Green fluorescent protein is engineered to be self-assembled in cells into oligomeric assemblies that are natively separated in a single-protein resolution by surface charge manipulation, affording monodisperse protein (nano)polygons from dimer to decamer. Several functional proteins are multivalently displayed on the oligomers with controlled orientations. Spatial arrangements of protein oligomers and displayed functional proteins are directly visualized by a transmission electron microscope. By employing our functional protein assemblies, we provide experimental insight into multivalent protein-protein interactions and tools to manipulate receptor clustering on live cell surfaces.

  17. A Radiometric All-Sky Infrared Camera (RASICAM) for DES/CTIO

    SciTech Connect

    Lewis, Peter M.; Rogers, Howard; Schindler, Rafe H.; /SLAC

    2010-08-25

    A novel radiometric all-sky infrared camera [RASICAM] has been constructed to allow automated real-time quantitative assessment of night sky conditions for the Dark Energy Camera [DECam] located on the Blanco Telescope at the Cerro Tololo Inter-American Observatory in Chile. The camera is optimized to detect the position, motion and optical depth of thin, high (8-10km) cirrus clouds and contrails by measuring their apparent temperature above the night sky background. The camera system utilizes a novel wide-field equiresolution catadioptic mirror system that provides sky coverage of 2{pi} azimuth and 14-90{sup o} from zenith. Several new technological and design innovations allow the RASICAM system to provide unprecedented cloud detection and IR-based photometricity quantification. The design of the RASICAM system is presented.

  18. Investigation of Reddening in Fields of the SMASH Survey

    NASA Astrophysics Data System (ADS)

    Juelfs, Elizabeth A.; Olsen, Knut A.; SMASH Team

    2016-01-01

    We present dust extinction maps derived from eight fields in the Survey of the MAgellanic Stellar History (SMASH), a survey that is imaging 480 deg^2 of the southern sky in DES-ugriz with the CTIO 4-m Blanco telescope and the Dark Energy Camera (DECam). We derive the extinction due to dust using fits to the stellar locus of stars brighter than g=21 in color-color diagrams, and explore the spatial distribution of the extinction within each of the fields. We compare our results to the extinction map of Schlegel, Finkbeiner, & Davis (1998), and find generally good agreement. We describe plans to measure the three-dimensional distribution of extinction in these fields using fainter stars and background galaxies as tracers. Juelfs was supported by the NOAO/KPNO Research Experiences for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program (AST-1262829).

  19. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOEpatents

    Studier, F. William

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

  20. The DES Science Verification weak lensing shear catalogues

    NASA Astrophysics Data System (ADS)

    Jarvis, M.; Sheldon, E.; Zuntz, J.; Kacprzak, T.; Bridle, S. L.; Amara, A.; Armstrong, R.; Becker, M. R.; Bernstein, G. M.; Bonnett, C.; Chang, C.; Das, R.; Dietrich, J. P.; Drlica-Wagner, A.; Eifler, T. F.; Gangkofner, C.; Gruen, D.; Hirsch, M.; Huff, E. M.; Jain, B.; Kent, S.; Kirk, D.; MacCrann, N.; Melchior, P.; Plazas, A. A.; Refregier, A.; Rowe, B.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Suchyta, E.; Troxel, M. A.; Vikram, V.; Abbott, T.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Clampitt, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Fausti Neto, A.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nord, B.; Ogando, R.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Wechsler, R. H.

    2016-08-01

    We present weak lensing shear catalogues for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogues of 2.12 million and 3.44 million galaxies respectively. We detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. We also discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogues for the full 5-year DES, which is expected to cover 5000 square degrees.

  1. The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

    SciTech Connect

    Diaz, Z.; Xavier, K; Miller, S

    2009-01-01

    Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (??)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.

  2. PreCam

    SciTech Connect

    Allam, Sahar S.; Tucker, Douglas L.

    2015-01-01

    The Dark Energy Survey (DES) will be taking the next step in probing the properties of Dark Energy and in understanding the physics of cosmic acceleration. A step towards the photometric calibration of DES is to have a quick, bright survey in the DES footprint (PreCam), using a pre-production set of the Dark Energy Camera (DECam) CCDs and a set of 100 mm×100 mm DES filters. The objective of the PreCam Survey is to create a network of calibrated DES grizY standard stars that will be used for DES nightly calibrations and to improve the DES global relative calibrations. Here, we describe the first year of PreCam observation, results, and photometric calibrations.

  3. Identification and DNA fingerprinting of Legionella strains by randomly amplified polymorphic DNA analysis.

    PubMed Central

    Bansal, N S; McDonell, F

    1997-01-01

    The randomly amplified polymorphic DNA (RAPD) technique was used in the development of a fingerprinting (typing) and identification protocol for Legionella strains. Twenty decamer random oligonucleotide primers were screened for their discriminatory abilities. Two candidate primers were selected. By using a combination of these primers, RAPD analysis allowed for the differentiation between all different species, between the serogroups, and further differentiation between subtypes of the same serogroup. The usefulness of RAPD analysis was also evaluated with outbreak-related clinical and environmental isolates previously typed by the restriction fragment length polymorphism technique. RAPD analysis proved to be as accurate as other genotypic methods, reproducible, and highly discriminatory and is a valuable new alternative to traditional fingerprinting and identification of Legionella species and strains. PMID:9276408

  4. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOEpatents

    Studier, F.W.

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

  5. PreCam: A Step Towards the Photometric Calibration of the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Allam, S. S.; Tucker, D. L.; PreCam Team; DES Collaboration

    2016-05-01

    The Dark Energy Survey (DES) will be taking the next step in probing the properties of Dark Energy and in understanding the physics of cosmic acceleration. A step towards the photometric calibration of DES is to have a quick, bright survey in the DES footprint (PreCam), using a pre-production set of the Dark Energy Camera (DECam) CCDs and a set of 100 mm×100 mm DES filters. The objective of the PreCam Survey is to create a network of calibrated DES grizY standard stars that will be used for DES nightly calibrations and to improve the DES global relative calibrations. Here, we describe the first year of PreCam observation, results, and photometric calibrations.

  6. High-Molecular-Weight Proanthocyanidins in Foods: Overcoming Analytical Challenges in Pursuit of Novel Dietary Bioactive Components.

    PubMed

    Neilson, Andrew P; O'Keefe, Sean F; Bolling, Bradley W

    2016-01-01

    Proanthocyanidins (PACs) are an abundant but complex class of polyphenols found in foods and botanicals. PACs are polymeric flavanols with a variety of linkages and subunits. Connectivity and degree of polymerization (DP) determine PAC bioavailability and bioactivity. Current quantitative and qualitative methods may ignore a large percentage of dietary PACs. Subsequent correlations between intake and activity are hindered by a lack of understanding of the true PAC complexity in many foods. Additionally, estimates of dietary intakes are likely inaccurate, as nutrient databank values are largely based on standards from cocoa (monomers to decamers) and blueberries (mean DP of 36). Improved analytical methodologies are needed to increase our understanding of the biological roles of these complex compounds. PMID:26735794

  7. Crystallization and preliminary X-ray characterization of 1,3-propanediol dehydrogenase from the human pathogen Klebsiella pneumoniae

    PubMed Central

    Marçal, D.; Rego, A. T.; Fogg, M. J.; Wilson, K. S.; Carrondo, M. A.; Enguita, F. J.

    2007-01-01

    1,3-Propanediol dehydrogenase (1,3-PD-DH), encoded by the dhaT gene, is a key enzyme in the dissimilation process for converting glycerol to 1,3-propanediol in the human pathogen Klebsiella pneumoniae. Single colourless crystals were obtained from a recombinant preparation of 1,3-propanediol dehydrogenase overexpressed in Escherichia coli. The crystals belong to space group P21, with unit-cell parameters a = 91.9, b = 226.6, c = 232.6 Å, β = 92.9°. The crystals probably contain two decamers in the asymmetric unit, with a V M value of 3.07 Å3 Da−1 and an estimated solvent content of 59%. Diffraction data were collected to 2.7 Å resolution using synchrotron radiation at the ID14-4 beamline of the European Synchrotron Radiation Facility. PMID:17329826

  8. Caterpillar Track Complexes in Template‐Directed Synthesis and Correlated Molecular Motion†

    PubMed Central

    Liu, Shiqi; Kondratuk, Dmitry V.; Rousseaux, Sophie A. L.; Gil‐Ramírez, Guzmán; O'Sullivan, Melanie C.; Cremers, Jonathan; Claridge, Tim D. W.

    2015-01-01

    Abstract Small alterations to the structure of a star‐shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8‐ and 10‐porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10‐porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.

  9. The DES Science Verification Weak Lensing Shear Catalogues

    NASA Astrophysics Data System (ADS)

    Jarvis, M.; Sheldon, E.; Zuntz, J.; Kacprzak, T.; Bridle, S. L.; Amara, A.; Armstrong, R.; Becker, M. R.; Bernstein, G. M.; Bonnett, C.; Chang, C.; Das, R.; Dietrich, J. P.; Drlica-Wagner, A.; Eifler, T. F.; Gangkofner, C.; Gruen, D.; Hirsch, M.; Huff, E. M.; Jain, B.; Kent, S.; Kirk, D.; MacCrann, N.; Melchior, P.; Plazas, A. A.; Refregier, A.; Rowe, B.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Suchyta, E.; Troxel, M. A.; Vikram, V.; Abbott, T.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Carretero, J.; Castander, F. J.; Clampitt, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Neto, A. Fausti; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nord, B.; Ogando, R.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Wechsler, R. H.

    2016-05-01

    We present weak lensing shear catalogues for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogues of 2.12 million and 3.44 million galaxies respectively. We detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. We also discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogues for the full 5-year DES, which is expected to cover 5000 square degrees.

  10. RAPD-inferred genetic variability of some indigenous Rhizobium leguminosarum isolates from red clover (Trifolium pratense L.) nodules.

    PubMed

    Stefan, Andrei; Rosu, Craita M; Stedel, Catalina; Gorgan, Lucian D; Efrose, Rodica C

    2015-09-01

    The application of commercial rhizobial inoculants to legume crops is proving to be an alternative to synthetic fertilizer use. The challenge for sustainable agriculture resides in the compatibility between crop, inoculants and environmental conditions. The evaluation of symbiotic efficiency and genetic diversity of indigenous rhizobial strains could lead to the development of better inoculants and increased crop production. The genetic variability of 32 wild indigenous rhizobial isolates was assessed by RAPD (Random Amplified Polymorphic DNA). The strains were isolated from red clover (Trifolium pratense L.) nodules from two distinct geographical regions of Northern and Eastern Romania. Three decamer primers were used to resolve the phylogenetic relationships between the investigated isolates. Cluster analysis revealed a high diversity; most strains clustered together based on their geographical location. PMID:26344027

  11. 2-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analog of 2-O-[2-(Methoxy)ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA

    SciTech Connect

    Prakash, T.P.; Manoharan, M.; Fraser, A.S.; Kawasaki, A.M.; Lesnik, E.; Sioufi, N.; Leeds, J.M.; Teplova, M.; Egli, M.

    2010-03-08

    A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

  12. Observation of two new L4 Neptune Trojans in the Dark Energy Survey supernova fields

    DOE PAGESBeta

    Gerdes, D. W.

    2016-01-28

    We report the discovery of the eighth and ninth known Trojans in stable orbits around Neptune's leading Lagrange point, L4. The objects 2014 QO441 and 2014 QP441 were detected in data obtained during the 2013-14 and 2014-15 observing seasons by the Dark Energy Survey, using the Dark Energy Camera (DECam) on the 4-meter Blanco telescope at Cerro Tololo Inter- American Observatory. Both are in high-inclination orbits (18.8° and 19.4° respectively). Furthermore, with an eccentricity of 0.104, 2014 QO441 has the most eccentric orbit of the eleven known stable Neptune Trojans. We describe the search procedure and investigate the objects' long-termmore » dynamical stability and physical properties.« less

  13. Identification of Anoectochilus formosanus and Anoectochilus koshunensis species with RAPD markers.

    PubMed

    Cheng, K T; Fu, L C; Wang, C S; Hsu, F L; Tsay, H S

    1998-02-01

    RAPD (random amplified polymorphic DNA) markers were developed to distinguish Anoectochilus formosanus from Anoectochilus koshunensis and their putative hybrids. Morphological differentiation of these two species beyond the flowering period is difficult. RAPD markers provide a rapid and easy tool for identification of the two Anoectochilus species. In the study, forty arbitrary decamer primers were screened, and nineteen species-specific RAPD markers generated from polymerase chain reactions (PCR) with eight random primers were obtained. Nine were specific to A. formosanus and ten to A. koshunensis. Two primers, OPC-08 and OPL-07, produced two markers, one specific to A. formosanus and the other specific to A. koshunensis, which simultaneously appeared in the hybrids pattern. The RAPD markers can be applied both to identification of A. formosanus and A. koshunensis species and to assessment of the extent fo hybridization in hybrids between them. This information facilitates the breeding program process. PMID:17253217

  14. The DES Science Verification Weak Lensing Shear Catalogs

    DOE PAGESBeta

    Jarvis, M.

    2016-05-01

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SVmore » data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.« less

  15. The Inner Oort Cloud Population

    NASA Astrophysics Data System (ADS)

    Sheppard, Scott; Trujillo, Chad

    2014-08-01

    The Kuiper Belt population has an outer edge at about 50 AU. Sedna and our recent discovery, 2012 VP113, are the only known objects with perihelion significantly beyond this edge at about 80 AU. These inner Oort cloud objects obtained their orbits when the solar system was vastly different from now. There are several theories as to the origin of these objects that can only be tested by finding several more. This population is likely larger than the Kuiper Belt but previous surveys did not go faint enough, did not have the required long cadence, or covered too small of sky area to find them. The dynamical and physical properties of objects in this region offer key constraints on the formation and evolution of our solar system. We propose to continue our survey with DECam in order to find several more inner Oort cloud objects to further constrain formation theories and thus learn about our Sun's formation environment and evolution.

  16. Functional analysis of the murine T-cell receptor beta enhancer and characteristics of its DNA-binding proteins.

    PubMed Central

    Takeda, J; Cheng, A; Mauxion, F; Nelson, C A; Newberry, R D; Sha, W C; Sen, R; Loh, D Y

    1990-01-01

    The minimal T-cell receptor (TCR) beta-chain (TCR beta) enhancer has been identified by transfection into lymphoid cells. The minimal enhancer was active in T cells and in some B-lineage cells. When a larger fragment containing the minimal enhancer was used, its activity was apparent only in T cells. Studies with phytohemagglutinin and 4 beta-phorbol-12,13-dibutyrate revealed that the enhancer activity was increased by these agents. By a combination of DNase I footprinting, gel mobility shift assay, and methylation interference analysis, seven different motifs were identified within the minimal enhancer. Furthermore, competition experiments showed that some of these elements bound identical or similar factors that are known to bind to the TCR V beta promoter decamer or to the immunoglobulin enhancer kappa E2 or muEBP-E motif. These shared motifs may be important in the differential gene activity among the different lymphoid subsets. Images PMID:2144608

  17. Decameric uracil complexes around Li+.

    PubMed

    Zins, Emilie-Laure; Pepe, Claude; Schröder, Detlef

    2010-07-01

    Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings. PMID:20564575

  18. Deep Surveys for Inner Oort Cloud Objects

    NASA Astrophysics Data System (ADS)

    Trujillo, Chadwick A.; Tholen, David J.; Sheppard, Scott S.

    2015-11-01

    We are undertaking two deep wide-field surveys to discover extremely distant solar system objects. While our target solar system population is the Inner Oort Cloud objects such as 2012 VP113 and Sedna, we are also sensitive to other populations with high perihelia such as the Scattered Kuiper Belt Objects and the highest perihelion Kuiper Belt Objects which have similar arguments of perihelion to the Inner Oort Cloud Objects. These unusual populations are thought to consist primarily of highly eccentric objects which spend most of their orbits hundreds or thousands of AU from the sun. Large aperture telescopes are needed to reach the faintness limits, red magnitudes of 23.5 to 25, required for detection of even the large members of the population. In addition, wide fields of view are also needed since the sky density of the detectable members of the populations approach 1 in 100 square degrees even with large telescopes.Our primary discovery instruments are the Dark Energy Camera (DECam) on the 4 meter Blanco Telescope at the Cerro Tololo Inter-American Observatory and Hyper Suprime-Cam (HSC) on Subaru Telescope at Maunakea. Each of these instruments has a tremendously wide field of view considering the size of the telescope they are mounted on. DECam has a field of view of about 3 square degrees and HSC has a field of view of about 1.75 square degrees. We will present our survey progress in terms of sky area covered and new objects discovered and highlight some of our more interesting findings.

  19. Genetic relatedness of artichoke (Cynara scolymus L.) hybrids using random amplified polymorphic DNA (RAPD) fingerprinting.

    PubMed

    Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R

    2015-01-01

    The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level. PMID:26782491

  20. Readout electronics for the Dark Energy Camera

    NASA Astrophysics Data System (ADS)

    Castilla, Javier; Ballester, Otger; Cardiel, Laia; Chappa, Steve; de Vicente, Juan; Holm, Scott; Huffman, David; Kozlovsky, Mark; Martinez, Gustavo; Olsen, Jamieson; Shaw, Theresa; Stuermer, Walter

    2010-07-01

    The goal of the Dark Energy Survey (DES) is to measure the dark energy equation of state parameter with four complementary techniques: galaxy cluster counts, weak lensing, angular power spectrum and type Ia supernovae. DES will survey a 5000 sq. degrees area of the sky in five filter bands using a new 3 deg2 mosaic camera (DECam) mounted at the prime focus of the Blanco 4-meter telescope at the Cerro-Tololo International Observatory (CTIO). DECam is a ~520 megapixel optical CCD camera that consists of 62 2k x 4k science sensors plus 4 2k x 2k sensors for guiding. The CCDs, developed at the Lawrence Berkeley National Laboratory (LBNL) and packaged and tested at Fermilab, have been selected to obtain images efficiently at long wavelengths. A front-end electronics system has been developed specifically to perform the CCD readout. The system is based in Monsoon, an open source image acquisition system designed by the National Optical Astronomy Observatory (NOAO). The electronics consists mainly of three types of modules: Control, Acquisition and Clock boards. The system provides a total of 132 video channels, 396 bias levels and around 1000 clock channels in order to readout the full mosaic at 250 kpixel/s speed with 10 e- noise performance. System configuration and data acquisition is done by means of six 0.8 Gbps optical links. The production of the whole system is currently underway. The contribution will focus on the testing, calibration and general performance of the full system in a realistic environment.

  1. Crystal structure of decameric fructose-6-phosphate aldolase from Escherichia coli reveals inter-subunit helix swapping as a structural basis for assembly differences in the transaldolase family.

    PubMed

    Thorell, Stina; Schürmann, Melanie; Sprenger, Georg A; Schneider, Gunter

    2002-05-24

    Fructose-6-phosphate aldolase from Escherichia coli is a member of a small enzyme subfamily (MipB/TalC family) that belongs to the class I aldolases. The three-dimensional structure of this enzyme has been determined at 1.93 A resolution by single isomorphous replacement and tenfold non-crystallographic symmetry averaging and refined to an R-factor of 19.9% (R(free) 21.3%). The subunit folds into an alpha/beta barrel, with the catalytic lysine residue on barrel strand beta 4. It is very similar in overall structure to that of bacterial and mammalian transaldolases, although more compact due to extensive deletions of additional secondary structural elements. The enzyme forms a decamer of identical subunits with point group symmetry 52. Five subunits are arranged as a pentamer, and two ring-like pentamers pack like a doughnut to form the decamer. A major interaction within the pentamer is through the C-terminal helix from one monomer, which runs across the active site of the neighbouring subunit. In classical transaldolases, this helix folds back and covers the active site of the same subunit and is involved in dimer formation. The inter-subunit helix swapping appears to be a major determinant for the formation of pentamers rather than dimers while at the same time preserving importing interactions of this helix with the active site of the enzyme. The active site lysine residue is covalently modified, by forming a carbinolamine with glyceraldehyde from the crystallisation mixture. The catalytic machinery is very similar to that of transaldolase, which together with the overall structural similarity suggests that enzymes of the MipB/TALC subfamily are evolutionary related to the transaldolase family. PMID:12051943

  2. Static and statistical bending of DNA evaluated by Monte Carlo simulations.

    PubMed Central

    Zhurkin, V B; Ulyanov, N B; Gorin, A A; Jernigan, R L

    1991-01-01

    To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5.T5 and A4.T4 blocks. Monte Carlo simulations have confirmed the DNA bending anisotropy: B-DNA bends most easily in a groove direction (roll). The A5.T5 block is more rigid than the other sequences; the pyrimidine-purine dimers are found to be the most flexible. For A5TCTCT, A5CTCTC, and A5GAGAG, the average bend angle per decamer is 20-25 degrees in a direction toward the minor groove in the center of the A5.T5 tract, which is consistent with both the "junction" and "wedge AA" models. However, in A5T5, A4T4CG, and T4A4GC, bending is directed into the grooves at the 5' and 3' ends of purine tracts. Thus, directionality of bending caused by An.Tn blocks strongly depends on their neighboring sequences. These calculations demonstrate that the sequence-dependent variation of the minor-groove width mimics the observed hydroxyl radical cleavage pattern. To estimate the effect of fluctuations on the overall shape of curved DNA fragments, longer pieces of DNA (up to 200 base pairs) were generated. For sequences with strong curvature (A5X5 and A4T4CG), the static model and Monte Carlo ensemble give similar results but, for moderately and slightly curved sequences (A5T5 or T4A4GC), the static model predicts a much smaller degree of bending than does the statistical representation. Considering fluctuations is important for quantitative interpretation of the gel electrophoresis measurements of DNA curvature, where both the static and statistical bends are operative. PMID:1871119

  3. Unique actinomycin D binding to self-complementary d(CXYGGCCY′X′G) sequences: duplex disruption and binding to a nominally base-paired hairpin

    PubMed Central

    Chen, Fu-Ming; Sha, Feng; Chin, Ko-Hsin; Chou, Shan-Ho

    2003-01-01

    Actinomycin D (ACTD) has been shown to bind weakly to the sequence -GGCC-, despite the presence of a GpC site. It was subsequently found, however, that d(CATGGCCATG) binds relatively well to ACTD but exhibits unusually slow association kinetics, contrary to the strong-binding -XGCY- sites. In an effort to elucidate the nature of such binding and to delineate the origin of its interesting kinetic behavior, studies have now been extended to include oligomers with the general sequence motifs of d(CXYGGCCY′X′G)2. It was found that analogous binding characteristics are observed for these self-duplex decamers and comparative studies with progressively base-truncated oligomers from the 5′-end led to the finding that d(GGCCY′X′G) oligomers bind ACTD considerably stronger than their parent decamers and exhibit 1:1 drug/strand binding stoichiometry. Melting profiles monitored at the drug spectral region indicated additional drug binding prior to the onset of eventual complex disruptions with near identical melting temperatures for all the oligomers studied. These results are consistent with the notion that the related oligomers share a common strong binding mode of a hairpin-type, with the 3′-terminus G folding back to base-pair with the C base of GGC. A binding scheme is proposed in which the oligomers d(CXYGGCCY′X′G) exist predominantly in the duplex form and bind ACTD initially at the central GGCC weak site but subsequently disrupt to accommodate the stronger hairpin binding and thus the slow association kinetics. Such a mechanism is supported by the observation of distinct biphasic fluorescence kinetic traces in the binding of 7-amino-ACTD to these duplexes. PMID:12853642

  4. An identification in fish of the genus Puntius Hamilton 1822 (Cypriniformes: Cyprinidae) of some wetlands in northeast Thailand with the use of random amplified polymorphic DNA technique.

    PubMed

    Champasri, T; Rapley, R; Duangjinda, M; Suksri, A

    2008-02-15

    The experiment was carried out during the 2003 to 2006 at the Department of Fisheries, Khon Kaen University, Khon Kaen, Thailand in collaboration with the Department of Biosciences, the University of Hertfordshire, College Land, Hatfield, Herts, UK. Molecular RAPD technique was used for the determinations of DNA patterns of the fish genus Puntius Hamilton 1822. The fish samples of 1,500 individual fish were collected from fifteen wetlands in Northeast Thailand and they were used for DNA extraction. Before the experiment was carried out the fish samples were morphologically identified and it was found that the collected fish consisted of 9 species i.e., Puntius altus, P. aurotaeniatus, P. binotatus, P. gonionotus, (e) P. leiacanthus, P. orphoides, P. partipentazona, P. schwanenfeldi and P. wetmorei. Genomic DNAs were extracted from 5 mg of muscle tissues (skeleton muscles) with the use of PUREGENE DNA Isolation Kit for Laboratory Use, Gentra Systems, USA. Eighty decamer primers from four kits were subjected to a preliminary test. It was found that only 10 decamer primers were most suited for this PCR amplification. The results showed that genetic distant values being established among and between pairs of the fishes of the 9 fish species ranged from 0.191 to 0.456 for a pair between Puntius gonionotus and Puntius altus and a pair between Puntius schwanenfeldi and Puntius leiacanthus, respectively. Similarity coefficient values within the 9 fish species ranged from 0.109 to 0.231. The results on a Dendrogram of clusters showed that there were 5 minor groups of the 9 fish species but the 9 species could not be split or shifted into other genera of the fish due to small differences found within the values of similarity coefficients. PMID:18817121

  5. The Mayall z-band Legacy Survey

    NASA Astrophysics Data System (ADS)

    Silva, David R.; Blum, Robert D.; Allen, Lori; Dey, Arjun; Schlegel, David J.; Lang, Dustin; Moustakas, John; Meisner, Aaron M.; Valdes, Francisco; Patej, Anna; Myers, Adam D.; Sprayberry, David; Saha, Abi; Olsen, Knut A.; Safonova, Sasha; Yang, Qian; Burleigh, Kaylan J.; MzLS Team

    2016-06-01

    The Mayall z-band Legacy Survey (MzLS) is conducting a deep z-band imaging survey covering 5000 square degrees in the north Galactic cap as part of the Legacy Survey, which is associated with the Dark Energy Spectroscopic Instrument (DESI) redshift survey. The Legacy Survey covers 14000 square degrees in the g, r, and z bands and is being executed on the Blanco 4-m, Mayall 4-m, and Bok 2.3-m telescopes. The MzLS footprint will be observed in the g and r bands using the Bok 2.3-m telescope also on Kitt Peak. The Beijing Arizona Sky Survey (BASS) is being conducted by a parallel team from Beijing and the University of Arizona. MzLS will cover the sky north of declination 30 degrees and reach a depth of z=23.0. The survey began in January 2016 and will run through June 2017 comprising approximately 230 nights on the Mayall telescope. The data are being obtained with an upgraded Mosaic camera that deploys with newred-sensitive CCDs from Lawrence Berkeley Lab (LBL) whose throughput is in excess of 80% at 8000 to approximately 9800 Angstrom. The upgrade project was a collaboration of Yale, LBL, and NOAO. MzLS images are public as soon as they are taken and delivered to the NOAO archive. Catalogs based on Tractor photometry for all available Legacy Survey images are released soon after they are constructed and MzLS sources will be included in next release planned for summer 2016. The Dark Energy Spectroscopic Instrument (DESI) will observe 30+ million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these MzLS data, DECam data from the DECam Legacy Survey, and data from the BASS survey.

  6. A HERO'S LITTLE HORSE: DISCOVERY OF A DISSOLVING STAR CLUSTER IN PEGASUS

    SciTech Connect

    Kim, Dongwon; Jerjen, Helmut E-mail: helmut.jerjen@anu.edu.au

    2015-01-20

    We report the discovery of an ultra-faint stellar system in the constellation of Pegasus. This concentration of stars was detected by applying our overdensity detection algorithm to the Sloan Digital Sky Survey Data Release 10 and confirmed with deeper photometry from the Dark Energy Camera (DECam) at the 4 m Blanco telescope. The best-fitting model isochrone indicates that this stellar system, Kim 1, features an old (12 Gyr) and metal-poor ([Fe/H] ∼ -1.7) stellar population at a heliocentric distance of 19.8 ± 0.9 kpc. We measure a half-light radius of 6.9 ± 0.6 pc using a Plummer profile. The small physical size and the extremely low luminosity are comparable to the faintest known star clusters Segue 3, Koposov 1 and 2, and Muñoz 1. However, Kim 1 exhibits a lower star concentration and is lacking a well-defined center. It also has an unusually high ellipticity and irregular outer isophotes, which suggests that we are seeing an intermediate mass star cluster being stripped by the Galactic tidal field. An extended search for evidence of an associated stellar stream within the 3 deg{sup 2} DECam field remains inconclusive. The finding of Kim 1 is consistent with current overdensity detection limits and supports the hypothesis that there are still a substantial number of extreme low-luminosity star clusters undetected in the wider Milky Way halo.

  7. Early Science Results from the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Ross, Ashley

    2015-04-01

    The Dark Energy Survey (DES) is a next-generation large galaxy survey designed to unravel the mystery of the nature of the dark energy that powers the current accelerated expansion of the Universe. The DES collaboration built and participated in the installation and commissioning of DECam, a 570 mega-pixel optical and near-infrared camera with a large 3 deg2 field of view, set at the prime focus of the Víctor M. Blanco 4-meter telescope in at the Cerro Tololo Inter-American Observatory in Chile. Using DECam, DES will map 5000 deg2 to a depth IAB ~ 24 and observe designated supernova survey fields at high cadence. These data will allow DES to measure positions, approximate redshifts, and shapes for 300 million galaxies, the light-curves of several thousand supernovae, and the masses of tens of thousands of galaxy clusters. Using these data, DES will use four main probes to study the properties of dark energy: galaxy clustering on large scales, weak gravitational lensing, galaxy-cluster abundance, and supernova distances. I describe the early progress of the survey and provide highlights of the science analyses that have been completed so far. These include: large-scale galaxy clustering measurements; significant detection of a cross-correlation with SPT CMB lensing maps; galaxy-shear and shear-shear correlation function measurements; discoveries of super-luminous supernovae, dozens of strong lenses, and redshift > 6 quasars; and characterization of DES galaxy clusters and SNe1a light-curves.

  8. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16-22 and Sup357-13 in AOT reverse micelles

    NASA Astrophysics Data System (ADS)

    Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.

    2014-12-01

    Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results

  9. Effect of electrostatics on aggregation of prion protein Sup35 peptide

    NASA Astrophysics Data System (ADS)

    Portillo, Alexander M.; Krasnoslobodtsev, Alexey V.; Lyubchenko, Yuri L.

    2012-04-01

    Self-assembly of misfolded proteins into ordered fibrillar structures is a fundamental property of a wide range of proteins and peptides. This property is also linked with the development of various neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Environmental conditions modulate the misfolding and aggregation processes. We used a peptide, CGNNQQNY, from yeast prion protein Sup35, as a model system to address effects of environmental conditions on aggregate formation. The GNNQQNY peptide self-assembles in fibrils with structural features that are similar to amyloidogenic proteins. Atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence assay were employed to follow the aggregation process at various pHs and ionic strengths. We also used single molecule AFM force spectroscopy to probe interactions between the peptides under various conditions. The ThT fluorescence data showed that the peptide aggregates fast at pH values approaching the peptide isoelectric point (pI = 5.3) and the kinetics is 10 times slower at acidic pH (pH 2.0), suggesting that electrostatic interactions contribute to the peptide self-assembly into aggregates. This hypothesis was tested by experiments performed at low (11 mM) and high (150 mM) ionic strengths. Indeed, the aggregation lag time measured at pH 2 at low ionic strength (11 mM) is 195 h, whereas the lag time decreases ˜5 times when the ionic strength is increased to 150 mM. At conditions close to the pI value, pH 5.6, the aggregation lag time is 12 ± 6 h under low ionic strength, and there is minimal change to the lag time at 150 mM NaCl. The ionic strength also influences the morphology of aggregates visualized with AFM. In pH 2.0 and at high ionic strength, the aggregates are twofold taller than those formed at low ionic strength. In parallel, AFM force spectroscopy studies revealed minimal contribution of electrostatics to dissociation of transient peptide dimers.

  10. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16−22 and Sup357−13 in AOT reverse micelles

    PubMed Central

    Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.

    2014-01-01

    Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16−22, and the GNNQQNY subsequence, Sup357−13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16−22 and Sup357−13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results

  11. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.

    PubMed

    Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E

    2014-12-14

    Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results

  12. Secretory Trafficking Signal Encoded in the Carboxyl-Terminal Region of the CGβ-Subunit

    PubMed Central

    Jablonka-Shariff, Albina; Boime, Irving

    2009-01-01

    Although the LHβ- and chorionic gonadotropin-β- (CGβ) subunits share a high degree of sequence identity (>85%) in the first 114 amino acids, there is considerable sequence divergence at their carboxy ends. The CGβ-subunit terminates with a unique carboxyl-terminal extension (115–145; carboxyl-terminal peptide), which contains four O-linked oligosaccharides, whereas the LHβ-subunit bears a hydrophobic heptapeptide (115–121) at its carboxy terminus. LH is released through the regulated pathway in the pituitary, whereas CG is secreted constitutively from the placenta. We previously demonstrated in rat somatotroph-derived GH3 cells that the LH is associated primarily with a regulated routing, and although the majority of CG was released constitutively from the cells, there was a fraction that was segregated through the regulated pathway. Moreover, we showed that the LHβ heptapeptide is a determinant for the regulated secretion of LH. Given that the primary evolutionary change between LHβ and CGβ occurred at the carboxy terminus, these data suggested that the presence of the CGβ carboxyl-terminal peptide region is responsible for the constitutive secretion of CG. A CG114 mutant (CGΔT) was constructed and expressed in GH3 cells. Steady-state labeling and pulse-chase experiments demonstrated that the CGΔT entered the regulated pathway resulting in over 4-fold increase in the intracellular pool. The secretagogue, forskolin, stimulated CGΔT release over 3-fold, which was accompanied by a parallel intracellular decrease, and only marginal stimulation of CG was seen. Immunofluorescence demonstrated a unique membrane pattern of staining for CGΔT compared with dispersed cytoplasmic puncta for CG. Stimulation with forskolin caused a significant reduction in the relative fluorescence of CGΔT cells compared with a minor reduction for CG. These data show that the CGΔT analog resembles LH in its intracellular trafficking, further supporting the hypothesis that

  13. Screening a phage display library for a novel FGF8b-binding peptide with anti-tumor effect on prostate cancer

    SciTech Connect

    Wang, Wenhui; Chen, Xilei; Li, Tao; Li, Yanmei; Wang, Ruixue; He, Dan; Luo, Wu; Li, Xiaokun; Wu, Xiaoping

    2013-05-01

    Fibroblast growth factor 8b (FGF8b) is the major isoform of FGF8 expressed in prostate cancer and it correlates with the stage and grade of the disease. FGF8b has been considered as a potential target for prostate cancer therapy. Here we isolated 12 specific FGF8b-binding phage clones by screening a phage display heptapeptide library with FGF8b. The peptide (HSQAAVP, named as P12) corresponding to one of these clones showed high homology to the immunoglobulin-like (Ig-like) domain II(D2) of high-affinity FGF8b receptor (FGFR3c), contained 3 identical amino acids (AVP) to the authentic FGFR3 D2 sequence aa 163–169 (LLAVPAA) directly participating in ligand binding, carried the same charges as its corresponding motif (aa163–169) in FGFR3c, suggesting that P12 may have a greater potential to interrupt FGF8b binding to its receptors than other identified heptapeptides do. Functional analysis indicated that synthetic P12 peptides mediate significant inhibition of FGF8b-induced cell proliferation, arrest cell cycle at the G0/G1 phase via suppression of Cyclin D1 and PCNA, and blockade of the activations of Erk1/2 and Akt cascades in both prostate cancer cells and vascular endothelial cells. The results demonstrated that the P12 peptide acting as an FGF8b antagonist may have therapeutic potential in prostate cancer. - Highlights: ► A novel FGF8b-binding peptide P12 was isolated from a phage display library. ► The mechanisms for P12 peptide inhibiting cell proliferation were proposed. ► P12 caused cell cycle arrest at G0/G1 phase via suppression of Cyclin D1 and PCNA. ► P12 suppressed FGF8b-induced activations of Akt and MAP kinases. ► P12 acting as an FGF8b antagonist may have therapeutic potential in prostate cancer.

  14. Measuring the Flatness of Focal Plane for Very Large Mosaic CCD Camera

    SciTech Connect

    Hao, Jiangang; Estrada, Juan; Cease, Herman; Diehl, H.Thomas; Flaugher, Brenna L.; Kubik, Donna; Kuk, Keivin; Kuropatkine, Nickolai; Lin, Huan; Montes, Jorge; Scarpine, Vic; /Fermilab

    2010-06-08

    Large mosaic multiCCD camera is the key instrument for modern digital sky survey. DECam is an extremely red sensitive 520 Megapixel camera designed for the incoming Dark Energy Survey (DES). It is consist of sixty two 4k x 2k and twelve 2k x 2k 250-micron thick fully-depleted CCDs, with a focal plane of 44 cm in diameter and a field of view of 2.2 square degree. It will be attached to the Blanco 4-meter telescope at CTIO. The DES will cover 5000 square-degrees of the southern galactic cap in 5 color bands (g, r, i, z, Y) in 5 years starting from 2011. To achieve the science goal of constraining the Dark Energy evolution, stringent requirements are laid down for the design of DECam. Among them, the flatness of the focal plane needs to be controlled within a 60-micron envelope in order to achieve the specified PSF variation limit. It is very challenging to measure the flatness of the focal plane to such precision when it is placed in a high vacuum dewar at 173 K. We developed two image based techniques to measure the flatness of the focal plane. By imaging a regular grid of dots on the focal plane, the CCD offset along the optical axis is converted to the variation the grid spacings at different positions on the focal plane. After extracting the patterns and comparing the change in spacings, we can measure the flatness to high precision. In method 1, the regular dots are kept in high sub micron precision and cover the whole focal plane. In method 2, no high precision for the grid is required. Instead, we use a precise XY stage moves the pattern across the whole focal plane and comparing the variations of the spacing when it is imaged by different CCDs. Simulation and real measurements show that the two methods work very well for our purpose, and are in good agreement with the direct optical measurements.

  15. Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1

    PubMed Central

    Jerebtsova, Marina; Klotchenko, Sergei A.; Artamonova, Tatiana O.; Ammosova, Tatiana; Washington, Kareem; Egorov, Vladimir V.; Shaldzhyan, Aram A.; Sergeeva, Maria V.; Zatulovskiy, Evgeny A.; Temkina, Olga A.; Petukhov, Mikhail G.; Vasin, Andrei V.; Khodorkovskii, Mikhail A.; Orlov, Yuri N.

    2011-01-01

    Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxyterminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription. PMID:20941529

  16. Alteration in the Expression of Cytochrome P450s (CYP1A1, CYP2E1, and CYP3A11) in the Liver of Mouse Induced by Microcystin-LR

    PubMed Central

    Zhang, Bangjun; Liu, Yang; Li, Xiaoyu

    2015-01-01

    Microcystins (MCs) are cyclic heptapeptide toxins and can accumulate in the liver. Cytochrome P450s (CYPs) play an important role in the biotransformation of endogenous substances and xenobiotics in animals. It is unclear if the CYPs are affected by MCs exposure. The objective of this study was to evaluate the effects of microcystin-LR (MCLR) on cytochrome P450 isozymes (CYP1A1, CYP2E1, and CYP3A11) at mRNA level, protein content, and enzyme activity in the liver of mice the received daily, intraperitoneally, 2, 4, and 8 µg/kg body weight of MCLR for seven days. The result showed that MCLR significantly decreased ethoxyresorufin-O-deethylase (EROD) (CYP1A1) and erythromycin N-demthylase (ERND) (CYP3A11) activities and increased aniline hydroxylase (ANH) activity (CYP2E1) in the liver of mice during the period of exposure. Our findings suggest that MCLR exposure may disrupt the function of CYPs in liver, which may be partly attributed to the toxicity of MCLR in mice. PMID:25831226

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

    PubMed

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

    2004-06-01

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

  18. Degradation and transport of AVP by proximal tubule

    SciTech Connect

    Carone, F.A.; Christensen, E.I.; Flouret, G. Univ. of Aarhus )

    1987-12-01

    High-performance liquid chromatography (HPLC) analysis revealed that (3,4,5-{sup 3}H-Phe{sup 3},Arg{sup 8})vasopressin (({sup 3}H)AVP) was not degraded by isolated renal brush-border membranes or by a cortical lysosomal fraction in vitro; however, in the presence of 1 mM reduced glutathione, ({sup 3}H)AVP was degraded by both preparations. Renal cortical homogenates in vitro and luminal peptidases of proximal tubule in vivo degraded ({sup 3}H)AVP and in both instances yielded phenylalanine, hexapeptide AVP 1-6, heptapeptide AVP 1-7, octapeptide AVP 1-8, and two uncharacterized products X and Y. These data suggest that filtered AVP is reduced in the proximal tubule by a reduced glutathione-dependent transhydrogenase and subsequently cleaved to ({sup 3}H)Phe by tubular aminopeptidases. Following microinfusion of ({sup 3}H)AVP into proximal tubules, 15.7% of the label was absorbed. Five and fifteen minutes after infusion of ({sup 3}H)AVP, sequestration of total label in proximal tubules was 4.5 and 2.1%, respectively, and quantitative electron microscope autoradiography revealed accumulation of grains over apical endocytic vacuoles and lysosomes consistent with endocytic uptake and rapid lysosomal degradation of AVP and/or a large metabolite. Thus, enzymatic cleavage of AVP by luminal and lysosomal peptidases in proximal tubules could involve disulfide bond, C-terminal, and N-terminal loci.

  19. Intestinal transport of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg through a Caco-2 Bbe monolayer.

    PubMed

    Vermeirssen, V; Deplancke, B; Tappenden, K A; Van Camp, J; Gaskins, H R; Verstraete, W

    2002-03-01

    ACE inhibitory peptides are biologically active peptides that play a role in blood pressure regulation. When derived from food proteins during food processing or gastrointestinal digestion, these peptides could function as efficient agents in treating and preventing hypertension. However, in order to exert an antihypertensive effect by inhibition of the ACE enzyme, they have to reach the bloodstream intact. The aim of this research was to assess if the known ACE inhibitory peptide Ala-Leu-Pro-Met-His-Ile-Arg, derived from a tryptic digest of beta-lactoglobulin, could be absorbed through a Caco-2 Bbe cell monolayer in an Ussing chamber and reach the serosal side undegraded. Samples of the mucosal compartment showed high ACE inhibitory activity. No or only little ACE inhibitory activity was detected in the serosal compartment. However, when the serosal sample was concentrated three-fold, a substantial ACE inhibitory activity was registered. Concomitantly, HPLC and MS clearly showed the presence of Ala-Leu-Pro-Met-His-Ile-Arg in the mucosal compartment, whereas in the serosal compartment only MS was able to detect the heptapeptide. In conclusion. under the observed experimental conditions, the ACE inhibitory peptide Ala-Leu-Pro-Met-His-Ile-Arg was transported intact through the Caco-2 Bbe monolayer, but in concentrations too low to exert an ACE inhibitory activity. PMID:11931586

  20. A novel post-translational modification involving bromination of tryptophan. Identification of the residue, L-6-bromotryptophan, in peptides from Conus imperialis and Conus radiatus venom.

    PubMed

    Craig, A G; Jimenez, E C; Dykert, J; Nielsen, D B; Gulyas, J; Abogadie, F C; Porter, J; Rivier, J E; Cruz, L J; Olivera, B M; McIntosh, J M

    1997-02-21

    We report a novel post-translational modification involving halogenation of tryptophan in peptides recovered from the venom of carnivorous marine cone snails (Conus). The residue, L-6-bromotryptophan, was identified in the sequence of a heptapeptide, isolated from Conus imperialis, a worm-hunting cone. This peptide does not elicit gross behavioral symptoms when injected centrally or peripherally in mice. L-6-Bromotryptophan was also identified in a 33-amino acid peptide from Conus radiatus; this peptide has been shown to induce a sleep-like state in mice of all ages and is referred to as bromosleeper peptide. The sequences of the two peptides and were determined using a combination of mass spectrometry, amino acid, and chemical sequence analyses, where Pca = pyroglutamic acid, Hyp = hydroxyproline, Gla = gamma-carboxyglutamate, and Trp* = L-6-bromotryptophan. The precise structure and stereochemistry of the modified residue were determined as L-6-bromotryptophan by synthesis, co-elution, and enzymatic hydrolysis experiments. To our knowledge this is the first documentation of tryptophan residues in peptides/proteins being modified in a eukaryotic system and the first report of halogenation of tryptophan in vivo. PMID:9030520

  1. Cyanobacterial Cyclopeptides as Lead Compounds to Novel Targeted Cancer Drugs

    PubMed Central

    Sainis, Ioannis; Fokas, Demosthenes; Vareli, Katerina; Tzakos, Andreas G.; Kounnis, Valentinos; Briasoulis, Evangelos

    2010-01-01

    Cyanobacterial cyclopeptides, including microcystins and nodularins, are considered a health hazard to humans due to the possible toxic effects of high consumption. From a pharmacological standpoint, microcystins are stable hydrophilic cyclic heptapeptides with a potential to cause cellular damage following uptake via organic anion-transporting polypeptides (OATP). Their intracellular biological effects involve inhibition of catalytic subunits of protein phosphatase 1 (PP1) and PP2, glutathione depletion and generation of reactive oxygen species (ROS). Interestingly, certain OATPs are prominently expressed in cancers as compared to normal tissues, qualifying MC as potential candidates for cancer drug development. In the era of targeted cancer therapy, cyanotoxins comprise a rich source of natural cytotoxic compounds with a potential to target cancers expressing specific uptake transporters. Moreover, their structure offers opportunities for combinatorial engineering to enhance the therapeutic index and resolve organ-specific toxicity issues. In this article, we revisit cyanobacterial cyclopeptides as potential novel targets for anticancer drugs by summarizing existing biomedical evidence, presenting structure-activity data and discussing developmental perspectives. PMID:20411119

  2. Stress Induces Changes in the Phosphorylation of Trypanosoma cruzi RNA Polymerase II, Affecting Its Association with Chromatin and RNA Processing

    PubMed Central

    Rocha, Antônio Augusto; Moretti, Nilmar Silvio

    2014-01-01

    The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the trans-splicing of all mRNAs transcribed on long polycistronic units. We found that Trypanosoma cruzi RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing. PMID:24813189

  3. Comparison of the level of residual coagulant activity in different cheese varieties.

    PubMed

    Bansal, Nidhi; Fox, Patrick F; McSweeney, Paul L H

    2009-08-01

    The coagulant retained in cheese curd is a major contributor to proteolysis during ripening. The objective of this study was to quantify residual coagulant in 9 cheese varieties by measuring its activity on a synthetic heptapeptide (Pro-Thr-Glu-Phe-[NO2-Phe]-Arg-Leu) assayed using reversed-phase HPLC. The level of residual coagulant activity was highest in Camembert cheese, probably due to its low pH at whey drainage and the high moisture content of the cheese, followed in order by Feta=Port du Salut=Cheddar>Gouda>Emmental=Parmigiano Reggiano=low-moisture part-skim Mozzarella=Mozzarella di Bufala Campana. The high cooking temperature (50-54 degrees C) used during the manufacture of Emmental and Parmigiano Reggiano cheeses and the cooking and stretching step in hot water during the manufacture of Mozzarella cheese may be the reasons for the lowest residual coagulant activity in these cheeses. The level of residual coagulant activity was higher in Feta cheese made from milk concentrated by ultrafiltration than in conventional Feta. PMID:19445824

  4. A protein kinase that phosphorylates the C-terminal repeat domain of the largest subunit of RNA polymerase II.

    PubMed Central

    Lee, J M; Greenleaf, A L

    1989-01-01

    The unique C-terminal repeat domain (CTD) of the largest subunit (IIa) of eukaryotic RNA polymerase II consists of multiple repeats of the heptapeptide consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The number of repeats ranges from 26 in yeast to 42 in Drosophila to 52 in mouse. The CTD is essential in vivo, but its structure and function are not yet understood. The CTD can be phosphorylated at multiple serine and threonine residues, generating a form of the largest subunit (II0) with markedly reduced mobility in NaDodSO4/polyacrylamide gels. To investigate this extensive phosphorylation, which presumably modulates functional properties of RNA polymerase II, we began efforts to purify a specific CTD kinase. Using CTD-containing fusion proteins as substrates, we have purified a CTD kinase from the yeast Saccharomyces cerevisiae. The enzyme extensively phosphorylates the CTD portion of both the fusion proteins and intact subunit IIa, producing products with reduced electrophoretic mobilities. The properties of the CTD kinase suggest that it is distinct from previously described protein kinases. Analogous activities were also detected in Drosophila and HeLa cell extracts. Images PMID:2657724

  5. A carboxyl-terminal-domain kinase associated with RNA polymerase II transcription factor delta from rat liver.

    PubMed Central

    Serizawa, H; Conaway, R C; Conaway, J W

    1992-01-01

    We previously purified RNA polymerase II transcription factor delta from rat liver and found that it has an associated DNA-dependent ATPase (dATPase) activity. In this report, we show that delta is also closely associated with a protein kinase activity that catalyzes phosphorylation of the largest subunit of RNA polymerase II. Kinase activity copurifies with transcription and DNA-dependent ATPase (dATPase) activities when delta is analyzed by anion- and cation-exchange HPLC as well as by sucrose gradient sedimentation, arguing that delta possesses all three activities. Phosphorylation of the largest subunits of both rat and yeast RNA polymerase II is stimulated by DNA, whereas phosphorylation of a synthetic peptide containing multiple copies of the carboxyl-terminal heptapeptide repeat is not. Although both ATP and GTP appear to function as phosphate donors, GTP is utilized less than 10% as well as ATP. These findings suggest that delta may exert its action in transcription at least in part through a mechanism involving phosphorylation of the largest subunit of RNA polymerase II. Images PMID:1386928

  6. pH-replica exchange molecular dynamics in proteins using a discrete protonation method.

    PubMed

    Sabri Dashti, Danial; Meng, Yilin; Roitberg, Adrian E

    2012-08-01

    Protonation equilibria in biological molecules modulates structure, dynamics, and function. A pH-replica exchange molecular dynamics (pH-REMD) method is described here to improve the coupling between conformational and protonation sampling. Under a Hamiltonian replica exchange setup, conformations are swapped between two neighboring replicas, which themselves are at different pHs. The method has been validated on a series of biological systems. We applied pH-REMD to a series of model compounds, to an terminally charged ADFDA pentapeptide, and to a heptapeptide derived from the ovomucoid third domain (OMTKY3). In all of those systems, the predicted pK(a) by pH-REMD is very close to the experimental value and almost identical to the ones obtained by constant pH molecular dynamics (CpH MD). The method presented here, pH-REMD, has the advantage of faster convergence properties due to enhanced sampling of both conformation and protonation spaces. PMID:22694266

  7. Genotoxicity of microcystin-LR in human lymphoblastoid TK6 cells.

    PubMed

    Zhan, Li; Sakamoto, Hiroko; Sakuraba, Mayumi; Wu, De Sheng; Zhang, Li Shi; Suzuki, Takayoshi; Hayashi, Makoto; Honma, Masamitsu

    2004-01-10

    Toxic cyanobacteria (blue-green algae) water blooms have become a serious problem in several industrialized areas of the world. Microcystin-LR (MCLR) is a cyclic heptapeptidic toxin produced by the cyanobacteria. In the present study, we used human lymphoblastoid cell line TK6 to investigate the in vitro genotoxicity of MCLR. In a standard 4h treatment, MCLR did not induce a significant cytotoxic response at <80 microg/ml. In a prolonged 24h treatment, in contrast, it induced cytotoxic as well as mutagenic responses concentration-dependently starting at 20 microg/ml. At the maximum concentration (80 microg/ml), the micronucleus frequency and the mutation frequency at the heterozygous thymidine kinase (TK) locus were approximately five-times the control values. Molecular analysis of the TK mutants revealed that MCLR specifically induced loss of heterozygosity at the TK locus, but not point mutations or other small structural changes. These results indicate that MCLR had a clastogenic effect. We discuss the mechanisms of MCLR genotoxicity and the possibility of its being a hepatocarcinogen. PMID:14706513

  8. [Regulation of cell activity by the extracellular matrix: the concept of matrikines].

    PubMed

    Maquart, F X; Siméon, A; Pasco, S; Monboisse, J C

    1999-01-01

    The activity of connective tissue cells is modulated by a number of factors present in their environment. In addition to the soluble factors such as hormones, cytokines or growth factors, cells also receive signals from the surrounding extracellular matrix (ECM) macromolecules. Moreover, they may degrade the ECM proteins and liberate peptides which may by themselves constitute new signals for the surrounding cells. Therefore, an actual regulation loop exists in connective tissue, constituted by peptides generated by ECM degradation and connective tissue cells. The term of "matrikine" has been proposed to designate such ECM-derived peptides able to regulate cell activity. In this review, we summarize some data obtained in our laboratory with two different matrikines: the tripeptide glycyl-histidyl-lysine (GHK) and the heptapeptide cysteinyl-asparaginyl-tyrosyl-tyrosyl-seryl-asparaginyl-serine (CNYYSNS). GHK is a potent activator of ECM synthesis and remodeling, whereas CNYYSNS is able to inhibit polymorphonuclear leukocytes activation and decrease the invasive capacities of cancer cells. PMID:10689625

  9. Early endosomal escape of a cyclic cell-penetrating peptide allows effective cytosolic cargo delivery.

    PubMed

    Qian, Ziqing; LaRochelle, Jonathan R; Jiang, Bisheng; Lian, Wenlong; Hard, Ryan L; Selner, Nicholas G; Luechapanichkul, Rinrada; Barrios, Amy M; Pei, Dehua

    2014-06-24

    Cyclic heptapeptide cyclo(FΦRRRRQ) (cFΦR4, where Φ is l-2-naphthylalanine) was recently found to be efficiently internalized by mammalian cells. In this study, its mechanism of internalization was investigated by perturbing various endocytic events through the introduction of pharmacologic agents and genetic mutations. The results show that cFΦR4 binds directly to membrane phospholipids, is internalized into human cancer cells through endocytosis, and escapes from early endosomes into the cytoplasm. Its cargo capacity was examined with a wide variety of molecules, including small-molecule dyes, linear and cyclic peptides of various charged states, and proteins. Depending on the nature of the cargos, they may be delivered by endocyclic (insertion of cargo into the cFΦR4 ring), exocyclic (attachment of cargo to the Gln side chain), or bicyclic approaches (fusion of cFΦR4 and cyclic cargo rings). The overall delivery efficiency (i.e., delivery of cargo into the cytoplasm and nucleus) of cFΦR4 was 4-12-fold higher than those of nonaarginine, HIV Tat-derived peptide, or penetratin. The higher delivery efficiency, coupled with superior serum stability, minimal toxicity, and synthetic accessibility, renders cFΦR4 a useful transporter for intracellular cargo delivery and a suitable system for investigating the mechanism of endosomal escape. PMID:24896852

  10. Gold nanoparticles-peptide based gas sensor arrays for the detection of food aromas.

    PubMed

    Compagnone, D; Fusella, G C; Del Carlo, M; Pittia, P; Martinelli, E; Tortora, L; Paolesse, R; Di Natale, C

    2013-04-15

    A gas sensor array based on peptide modified gold nanoparticles deposited onto 20MHz quartz crystal microbalances has been realized. Glutathione and its constituting aminoacids and dipeptides have been used as ligands. A great increase in sensitivity (2 orders of magnitude) was achieved using gold nanoparticles versus monolayer modified QCMs. The sensors have been characterised in terms of sensitivity for hexane, water, trimethylammine and ethanol. Highest sensitivity was found for water. The ability to discriminate typical food aromas as cis-3-hexenol, isopentylacetate, ethylacetate, and terpinen-4-ol dissolved in different solvents was studied using a gas sensor array constituted by gold nanoparticles modified with the glutathione peptides, thioglycolic acid and an heptapeptide. The array was found able to discriminate the food aromas, the response being dependent on the polarity of the solvent used. Tests on real olive oil samples gave a satisfactory separation among samples having defects versus non defected samples demonstrating that this approach has high potential for the development of gas sensor arrays to be used in real samples. PMID:23261699

  11. Colocalization of amanitin and a candidate toxin-processing prolyl oligopeptidase in Amanita basidiocarps.

    PubMed

    Luo, Hong; Hallen-Adams, Heather E; Scott-Craig, John S; Walton, Jonathan D

    2010-12-01

    Fungi in the basidiomycetous genus Amanita owe their high mammalian toxicity to the bicyclic octapeptide amatoxins such as α-amanitin. Amatoxins and the related phallotoxins (such as the heptapeptide phalloidin) are encoded by members of the "MSDIN" gene family and are synthesized on ribosomes as short (34- to 35-amino-acid) proproteins. Antiamanitin antibodies and confocal microscopy were used to determine the cellular and subcellular localizations of amanitin accumulation in basidiocarps (mushrooms) of the Eastern North American destroying angel (Amanita bisporigera). Consistent with previous studies, amanitin is present throughout the basidiocarp (stipe, pileus, lamellae, trama, and universal veil), but it is present in only a subset of cells within these tissues. Restriction of amanitin to certain cells is especially marked in the hymenium. Several lines of evidence implicate a specific prolyl oligopeptidase, A. bisporigera POPB (AbPOPB), in the initial processing of the amanitin and phallotoxin proproteins. The gene for AbPOPB is restricted taxonomically to the amatoxin-producing species of Amanita and is clustered in the genome with at least one expressed member of the MSDIN gene family. Immunologically, amanitin and AbPOPB show a high degree of colocalization, indicating that toxin biosynthesis and accumulation occur in the same cells and possibly in the same subcellular compartments. PMID:20889720

  12. Application of mimotope peptides of fumonisin b1 in Peptide ELISA.

    PubMed

    Liu, Xing; Xu, Yang; He, Qing-hua; He, Zhen-yun; Xiong, Zheng-ping

    2013-05-22

    Anti-fumonisin B(1) (FB(1)) McAb 1D11 was used as the target for biopanning from a phage random loop-constrained heptapeptide library. After three cycles of panning, seven phages with three mimotope peptides were selected to mimic the binding of FB(1) to 1D11. After the identification of phage ELISA, the phage clone that showed the best linear range of detection was chosen for further research. One peptide with the inserted peptide sequence of the phage was synthetized, named CT-452. An indirect competitive ELISA (peptide ELISA) for detecting FB(1) was established using the CT-452-bovine serum albumin conjugate as coating antigen. The linear range of the inhibition curve was 1.77-20.73 ng/mL. The half inhibitory concentration (IC50) was 6.06 ng/mL, and the limit of detection was 1.18 ng/mL. This method was compared with conventional indirect ELISA (commercial ELISA kit) and high-performance liquid chromatography (HPLC), and the results showed the reliability of the peptide ELISA for the determination of FB(1) in cereal samples. The relationship between the CT-452 and FB(1) standard concentrations in peptide ELISA was evaluated. The results indicated that synthetic peptide CT-452 can replace the FB(1) standard to establish an immunoassay free of FB(1). PMID:23692446

  13. Structural Basis for Microcin C7 Inactivation by the MccE Acetyltransferase

    SciTech Connect

    Agarwal, Vinayak; Metlitskaya, Anastasiya; Severinov, Konstantin; Nair, Satish K.

    2015-10-15

    The antibiotic microcin C7 (McC) acts as a bacteriocide by inhibiting aspartyl-tRNA synthetase and stalling the protein translation machinery. McC is synthesized as a heptapeptide-nucleotide conjugate, which is processed by cellular peptidases within target strains to yield the biologically active compound. As unwanted processing of intact McC can result in self-toxicity, producing strains utilize multiple mechanisms for autoimmunity against processed McC. We have shown previously that the mccE gene within the biosynthetic cluster can inactivate processed McC by acetylating the antibiotic. Here, we present the characterization of this acetylation mechanism through biochemical and structural biological studies of the MccE acetyltransferase domain (MccE{sup AcTase}). We have also determined five crystal structures of the MccE-acetyl-CoA complex with bound substrates, inhibitor, and reaction product. The structural data reveal an unexpected mode of substrate recognition through p-stacking interactions similar to those found in cap-binding proteins and nucleotidyltransferases. These studies provide a rationale for the observation that MccE{sup AcTase} can detoxify a range of aminoacylnucleotides, including those that are structurally distinct from microcin C7.

  14. Interactions between lipid-free apolipoprotein-AI and a lipopeptide incorporating the RGDS cell adhesion motif

    NASA Astrophysics Data System (ADS)

    Castelletto, V.; Hamley, I. W.; Reza, M.; Ruokolainen, J.

    2014-11-01

    The interaction of a designed bioactive lipopeptide C16-GGGRGDS, comprising a hexadecyl lipid chain attached to a functional heptapeptide, with the lipid-free apoliprotein, Apo-AI, is examined. This apolipoprotein is a major component of high density lipoprotein and it is involved in lipid metabolism and may serve as a biomarker for cardiovascular disease and Alzheimers' disease. We find via isothermal titration calorimetry that binding between the lipopeptide and Apo-AI occurs up to a saturation condition, just above equimolar for a 10.7 μM concentration of Apo-AI. A similar value is obtained from circular dichroism spectroscopy, which probes the reduction in α-helical secondary structure of Apo-AI upon addition of C16-GGGRGDS. Electron microscopy images show a persistence of fibrillar structures due to self-assembly of C16-GGGRGDS in mixtures with Apo-AI above the saturation binding condition. A small fraction of spheroidal or possibly ``nanodisc'' structures was observed. Small-angle X-ray scattering (SAXS) data for Apo-AI can be fitted using a published crystal structure of the Apo-AI dimer. The SAXS data for the lipopeptide/Apo-AI mixtures above the saturation binding conditions can be fitted to the contribution from fibrillar structures coexisting with flat discs corresponding to Apo-AI/lipopeptide aggregates.

  15. Agrobacterium-Mediated Disruption of a Nonribosomal Peptide Synthetase Gene in the Invertebrate Pathogen Metarhizium anisopliae Reveals a Peptide Spore Factor▿ †

    PubMed Central

    Moon, Yong-Sun; Donzelli, Bruno G. G.; Krasnoff, Stuart B.; McLane, Heather; Griggs, Mike H.; Cooke, Peter; Vandenberg, John D.; Gibson, Donna M.; Churchill, Alice C. L.

    2008-01-01

    Numerous secondary metabolites have been isolated from the insect pathogenic fungus Metarhizium anisopliae, but the roles of these compounds as virulence factors in disease development are poorly understood. We targeted for disruption by Agrobacterium tumefaciens-mediated transformation a putative nonribosomal peptide synthetase (NPS) gene, MaNPS1. Four of six gene disruption mutants identified were examined further. Chemical analyses showed the presence of serinocyclins, cyclic heptapeptides, in the extracts of conidia of control strains, whereas the compounds were undetectable in ΔManps1 mutants treated identically or in other developmental stages, suggesting that MaNPS1 encodes a serinocyclin synthetase. Production of the cyclic depsipeptide destruxins, M. anisopliae metabolites also predicted to be synthesized by an NPS, was similar in ΔManps1 mutant and control strains, indicating that MaNPS1 does not contribute to destruxin biosynthesis. Surprisingly, a MaNPS1 fragment detected DNA polymorphisms that correlated with relative destruxin levels produced in vitro, and MaNPS1 was expressed concurrently with in vitro destruxin production. ΔManps1 mutants exhibited in vitro development and responses to external stresses comparable to control strains. No detectable differences in pathogenicity of the ΔManps1 mutants were observed in bioassays against beet armyworm and Colorado potato beetle in comparison to control strains. This is the first report of targeted disruption of a secondary metabolite gene in M. anisopliae, which revealed a novel cyclic peptide spore factor. PMID:18502925

  16. Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.

    PubMed

    Morris, Katherine; Kuo, Byron; Wilkinson, Mark D; Davison, Joseph S; Befus, A Dean; Mathison, Ronald D

    2007-06-01

    The recently emerged Vcsa1 gene is one member of the variable coding sequence (VCS) multigene family of Rattus norvegicus. This gene encodes the precursor prohormone SMR1 (submandibular rat-1), which on enzymatic processing gives rise to several 5 to 11 amino acid peptides that modulate a variety of physiological functions. The analgesic pentapeptide sialorphin and anti-inflammatory heptapeptide submandibular gland peptide-T (TDIFEGG) are the most intensively studied. Although the Vcsa1 gene and its protein product are unique to rats, TDIFEGG or a derivative acts on all species examined to date, including human cells, in functions related to allergic reactions and inflammation. In this review, the patent and academic literature on SMR1 and its natural peptides and their derivatives are reviewed for consideration of biological targets and relevance to the development of novel therapeutic agents. The VCS gene family is discussed and we speculate on possible human homologs of these potent anti-inflammatory rat-derived peptides. The biologically active peptide products of SMR1 are considered and the mechanism of action and structure-activity relationships of the anti-inflammatory submandibular gland peptide-T and its derivatives are discussed. PMID:19075974

  17. Conjugation of Microcystins with Thiols Is Reversible: Base-Catalyzed Deconjugation for Chemical Analysis.

    PubMed

    Miles, Christopher O; Sandvik, Morten; Nonga, Hezron E; Ballot, Andreas; Wilkins, Alistair L; Rise, Frode; Jaabaek, J Atle H; Loader, Jared I

    2016-05-16

    Microcystins are potent cyclic heptapeptide toxins found in many freshwater cyanobacteria. Most microcystins contain an α,β-unsaturated amide that can react with thiol-containing amino acids, peptides, and proteins in vivo and in vitro. While soluble conjugates formed from small peptides can be extracted and analyzed directly by LC-MS, microcystins conjugated to proteins are analyzed after oxidative cleavage of their Adda side chains, but information on which microcystin analogues were present is lost. Observations during the development of thiol-derivatization-based LC-MS methods for microcystin analysis indicated that the reaction of thiols with microcystins was reversible. The kinetics of deconjugation was investigated with mercaptoethanol as a model thiol to identify suitable reaction conditions. A range of microcystins conjugated to mercaptoethanol, methanethiol, cysteine, and glutathione were then successfully deconjugated, demonstrating the feasibility of releasing conjugated forms of microcystins for chemical analysis. Reagents for removing the released thiols or for trapping the released microcystins increased the reaction rate. Optimization of methodologies based on this reaction should increase the method's utility for measuring free and conjugated microcystins. The results also indicate that thiol-conjugated microcystins slowly release free microcystins, even at neutral pH, with consequences for assessment of toxin exposure, metabolism, and trophic transfer. A range of other common natural and environmental toxins, such as deoxynivalenol and acrylamide, also contain α,β-unsaturated carbonyl groups and can be expected to behave in a similar manner. PMID:26999366

  18. Could angiotensin-(1-7) be connected with improvement of microvascular function in diabetic patients? Angiotensin-(1-7) iontophoresis may provide the answer.

    PubMed

    Kibel, Aleksandar

    2016-08-01

    Diabetes mellitus, a metabolic disorder with significant global health care burden, causes chronic microvascular and macrovascular complications that still comprise a therapeutic challenge. Angiotensin-(1-7), a heptapeptide with vasodilatory properties, has been found to restore vascular reactivity and endothelial cell function, mostly in experiments on larger isolated animal vessels and in cell cultures. The presented hypothesis suggests that angiotensin-(1-7) might have beneficial effects on microvascular function that is damaged in diabetic patients, alleviating endothelial dysfunction and increasing microvascular reactivity to various vasoactive agents in diabetes. It is further proposed that iontophoresis with angiotensin-(1-7) might be used to explore this potential beneficial effect, as well as provide a possible future therapeutic delivery method for angiotensin-(1-7). Since other peptides and proteins have been previously tested and used in iontophoretic transdermal delivery, it is plausible that angiotensin-(1-7) would be a suitable candidate for transdermal iontophoretic application for research (and potentially therapeutic) purposes. If confirmed, the delineated hypothesis would have immense implications for more effective care of diabetic patients, as well as for better understanding of microcirculatory pathophysiological mechanisms in diabetes. PMID:27372850

  19. The Periplasmic Bacterial Molecular Chaperone SurA Adapts Its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues

    SciTech Connect

    Xu, X.; Wang, S.; Hu, Y.-X.; McKay, D.B.

    2009-06-04

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

  20. Stability of microcystins from cyanobacteria--IV. Effect of chlorination on decomposition.

    PubMed

    Tsuji, K; Watanuki, T; Kondo, F; Watanabe, M F; Nakazawa, H; Suzuki, M; Uchida, H; Harada, K

    1997-07-01

    Microcystins, the cyclic heptapeptide toxins produced by cyanobacteria such as Microcystis, show tumor-promoting activity through inhibition of protein phosphatases 1 and 2A. They potentially threaten human health, and are increasing the world-wide interest in the health risk associated with cyanobacterial toxins. In this study, the effect of chlorination on the decomposition of microcystins-LR and -RR was examined. The toxins were easily decomposed by chlorination with sodium hypochlorite, and the decomposition depended on the free chlorine dose. In this operation, many reaction products were formed, one of which was determined to be dihydroxymicrocystin formed through the chloronium ion at the conjugated diene of Adda [3-amino-9-methoxy-10-phenyl-2,6,8-trimethyl-deca-4(E), 6(E)-dienoic acid], followed by hydrolysis. Other products may be its stereoisomers and/or regioismers. No noxious products were detected from the chlorination process of microcystin-LR. Although these results suggested that chlorination at an adequate chlorine dose is very effective for the removal of microcystin in raw water, preoxidation of the cell itself with chlorine must be avoided, because it frequently causes toxin release from algae and produce trihalomethanes during water treatment. PMID:9248002

  1. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S.; Dewdney, Tamaria G.; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  2. Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Brunzelle, Joseph; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-03-27

    Under drug selection pressure, emerging mutations render HIV-1 protease drug resistant, leading to the therapy failure in anti-HIV treatment. It is known that nine substrate cleavage site peptides bind to wild type (WT) HIV-1 protease in a conserved pattern. However, how the multidrug-resistant (MDR) HIV-1 protease binds to the substrate cleavage site peptides is yet to be determined. MDR769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) was selected for present study to understand the binding to its natural substrates. MDR769 HIV-1 protease was co-crystallized with nine substrate cleavage site hepta-peptides. Crystallographic studies show that MDR769 HIV-1 protease has an expanded substrate envelope with wide open flaps. Furthermore, ligand binding energy calculations indicate weaker binding in MDR769 HIV-1 protease-substrate complexes. These results help in designing the next generation of HIV-1 protease inhibitors by targeting the MDR HIV-1 protease.

  3. Circular permutation as a tool to reduce surface entropy triggers crystallization of the signal recognition particle receptor beta subunit.

    PubMed

    Schwartz, Thomas U; Walczak, Rudolf; Blobel, Günter

    2004-10-01

    The production of diffraction-quality crystals remains a difficult obstacle on the road to high-resolution structural characterization of proteins. This is primarily a result of the empirical nature of the process. Although crystallization is not predictable, factors inhibiting it are well established. First, crystal formation is always entropically unfavorable. Reducing the entropic cost of crystallizing a given protein is thus desirable. It is common practice to map boundaries and remove unstructured regions surrounding the folded protein domain. However, a problem arises when flexible regions are not at the boundaries but within a domain. Such regions cannot be deleted without adding new restraints to the domain. We encountered this problem during an attempt to crystallize the beta subunit of the eukaryotic signal recognition particle (SRbeta), bearing a long and flexible internal loop. Native SRbeta did not crystallize. However, after circularly permuting the protein by connecting the spatially close N and C termini with a short heptapeptide linker GGGSGGG and removing 26 highly flexible loop residues within the domain, we obtained diffraction-quality crystals. This protein-engineering method is simple and should be applicable to other proteins, especially because N and C termini of protein domains are often close in space. The success of this method profits from prior knowledge of the domain fold, which is becoming increasingly common in today's postgenomic era. PMID:15340174

  4. Mechanical unfolding pathway of a model β-peptide foldamer

    NASA Astrophysics Data System (ADS)

    Uribe, Lalita; Jaschonek, Stefan; Gauss, Jürgen; Diezemann, Gregor

    2015-05-01

    Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function of the helix elongation. It is thus demonstrated that even with the rather large pulling velocities employed in the force ramp simulations relevant information about the equilibrium kinetics can be obtained. The smallness of the system allows a detailed analysis of the unfolding pathway, which is characterized by an opening of the terminal loops followed by the unfolding of the center. This sequence is in accord with the configurational preferences of the system that also are responsible for the stability of the 314-helix. From an analysis of the distributions of rupture forces and the force spectra, the kinetic rates for both transitions were determined and common models were used to extract geometric quantities describing the free energy landscape of the system.

  5. Peptide inhibitors of the Escherichia coli DsbA oxidative machinery essential for bacterial virulence.

    PubMed

    Duprez, Wilko; Premkumar, Lakshmanane; Halili, Maria A; Lindahl, Fredrik; Reid, Robert C; Fairlie, David P; Martin, Jennifer L

    2015-01-22

    One approach to address antibiotic resistance is to develop drugs that interfere with bacterial virulence. A master regulator of virulence in Gram-negative bacteria is the oxidative folding machinery comprising DsbA and DsbB. A crystal structure at 2.5 Å resolution is reported here for Escherichia coli DsbA complexed with PFATCDS, a heptapeptide derived from the partner protein Escherichia coli DsbB. Details of the peptide binding mode and binding site provide valuable clues for inhibitor design. Structure-activity relationships for 30 analogues were used to produce short peptides with a cysteine that bind tightly to EcDsbA (Kd = 2.0 ± 0.3 μM) and inhibit its activity (IC50 = 5.1 ± 1.1 μM). The most potent inhibitor does not bind to or inhibit human thioredoxin that shares a similar active site. This finding suggests that small molecule inhibitors can be designed to exploit a key interaction of EcDsbA, as the basis for antivirulence agents with a novel mechanism of action. PMID:25470204

  6. Ribosomal Biosynthesis of the Cyclic Peptide Toxins of Amanita Mushrooms

    PubMed Central

    Walton, Jonathan D.; Hallen-Adams, Heather E.; Luo, Hong

    2014-01-01

    Some species of mushrooms in the genus Amanita are extremely poisonous and frequently fatal to mammals including humans and dogs. Their extreme toxicity is due to amatoxins such as α- and β-amanitin. Amanita mushrooms also biosynthesize a chemically related group of toxins, the phallotoxins, such as phalloidin. The amatoxins and phallotoxins (collectively known as the Amanita toxins) are bicyclic octa- and heptapeptides, respectively. Both contain an unusual Trp-Cys cross-bridge known as tryptathionine. We have shown that, in Amanita bisporigera, the amatoxins and phallotoxins are synthesized as proproteins on ribosomes and not by nonribosomal peptide synthetases. The proproteins are 34–35 amino acids in length and have no predicted signal peptides. The genes for α-amanitin (AMA1) and phallacidin (PHA1) are members of a large family of related genes, characterized by highly conserved amino acid sequences flanking a hypervariable “toxin” region. The toxin regions are flanked by invariant proline (Pro) residues. An enzyme that could cleave the proprotein of phalloidin was purified from the phalloidin-producing lawn mushroom Conocybe apala. The enzyme is a serine protease in the prolyl oligopeptidase (POP) subfamily. The same enzyme cuts at both Pro residues to release the linear hepta- or octapeptide. PMID:20564017

  7. Discovery of selective hexapeptide agonists to human neuromedin U receptors types 1 and 2.

    PubMed

    Takayama, Kentaro; Mori, Kenji; Taketa, Koji; Taguchi, Akihiro; Yakushiji, Fumika; Minamino, Naoto; Miyazato, Mikiya; Kangawa, Kenji; Hayashi, Yoshio

    2014-08-14

    Neuromedin U (NMU) are bioactive peptides with a common C-terminal heptapeptide sequence (FLFRPRN-amide, 1a) among mammals, which is responsible for receptor activation, namely NMU receptor types 1 (NMUR1) and 2 (NMUR2). Among the various physiological actions of NMU, the anorexigenic effect has recently attracted attention in drug discovery efforts for treating obesity. Although several structure-activity relationship (SAR) studies have been reported, receptor-selective small peptide agonists have yet to be disclosed. Herein a SAR study of 1a-derived peptide derivatives is described. We initially screened both human NMUR1- and NMUR2-selective peptides in calcium-mobilization assays with cells transiently expressing receptors. Then we performed a precise assay with a stable expression system of receptors and consequently discovered hexapeptides 8d and 6b possessing selective agonist activity toward each respective receptor. Hexapeptide 6b, which selectively activates NMUR2 without significant NMUR1 activation, should aid in the development of anorexigenic drugs as well as advance NMU-related endocrinological research. PMID:24999562

  8. Discovery of potent hexapeptide agonists to human neuromedin u receptor 1 and identification of their serum metabolites.

    PubMed

    Takayama, Kentaro; Mori, Kenji; Sohma, Yuko; Taketa, Koji; Taguchi, Akihiro; Yakushiji, Fumika; Minamino, Naoto; Miyazato, Mikiya; Kangawa, Kenji; Hayashi, Yoshio

    2015-03-12

    Neuromedin U (NMU) and S (NMS) display various physiological activities, including an anorexigenic effect, and share a common C-terminal heptapeptide-amide sequence that is necessary to activate two NMU receptors (NMUR1 and NMUR2). On the basis of this knowledge, we recently developed hexapeptide agonists 2 and 3, which are highly selective to human NMUR1 and NMUR2, respectively. However, the agonists are still less potent than the endogenous ligand, hNMU. Therefore, we performed an additional structure-activity relationship study, which led to the identification of the more potent hexapeptide 5d that exhibits similar NMUR1-agonistic activity as compared to hNMU. Additionally, we studied the stability of synthesized agonists, including 5d, in rat serum, and identified two major biodegradation sites: Phe(2)-Arg(3) and Arg(5)-Asn(6). The latter was more predominantly cleaved than the former. Moreover, substitution with 4-fluorophenylalanine, as in 5d, enhanced the metabolic stability at Phe(2)-Arg(3). These results provide important information to guide the development of practical hNMU agonists. PMID:25815150

  9. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue.

    PubMed

    Harlen, Kevin M; Trotta, Kristine L; Smith, Erin E; Mosaheb, Mohammad M; Fuchs, Stephen M; Churchman, L Stirling

    2016-06-01

    Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD) and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7), we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3' end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3' splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes. PMID:27239037

  10. UV-B Exposure Affects the Biosynthesis of Microcystin in Toxic Microcystis aeruginosa Cells and Its Degradation in the Extracellular Space.

    PubMed

    Yang, Zhen; Kong, Fanxiang

    2015-10-01

    Microcystins (MCs) are cyclic hepatotoxic heptapeptides produced by cyanobacteria that can be toxic to aquatic and terrestrial organisms. MC synthesis and degradation are thought to be influenced by several different physical and environmental parameters. In this study, the effects of different intensities of UV-B radiation on MC biosynthesis in Microcystis cells and on its extracellular degradation were investigated by mRNA analysis and degradation experiments. Exposure to UV-B at intensities of 1.02 and 1.45 W/m² not only remarkably inhibited the growth of Microcystis, but also led to a decrease in the MC concentration. In addition, mcyD transcription was decreased under the same UV-B intensities. These results demonstrated that the effects of UV-B exposure on the biosynthesis of MCs in Microcystis cells could be attributed to the regulation of mcy gene transcription. Moreover, the MC concentration was decreased significantly after exposure to different intensities of UV-B radiation. Of the three MC variants (MC-LR, -RR and -YR, L, R and Y are abbreviations of leucine, arginine and tyrosine), MC-LR and MC-YR were sensitive to UV-B radiation, whereas MC-RR was not. In summary, our results showed that UV-B radiation had a negative effect on MC production in Microcystis cells and MC persistence in the extracellular space. PMID:26492272