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Publications

SAXIER publications 2008-2009 on journal covers

2009 2008 2007

  1. Davies, R., Burghammer, M., & Riekel, C. (2009)
    A combined microRaman and microdiffraction setup at the European Synchrotron Radiation Facility ID13 beamline. J. of Synchrotron Radiation 16, 22-29.
  2. Pires, Ricardo, Bettina Hartlieb, Luca Signor, Guy Schoehn, Suman Lata, Manfred Roessle, Christine Moriscot, Sergei Popov, Andreas Hinz, Marc Jamin, Veronique Boyer, Remy Sadoul, Eric Forest, Dmitri I. Svergun, Heinrich G. Göttlinger and Winfried Weissenhorn (2009)
    A crescent-shaped ALIX dimer targets ESCRT-III CHMP4 filaments. Structure 17, 843-856.
  3. Bernadó, Pau, Yolanda Pérez, Jascha Blobel, Juan Fernández-Recio, Dmitri I. Svergun, and Miquel Pons (2009)
    Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scattering. Protein Science 18, 716-726.
  4. Gut, Heinz, Paola Dominici, Stefania Pilati, Alessandra Astegno, Maxim V. Petoukhov, Dmitri I. Svergun, Markus G. Grutter and Guido Capitani (2009)
    A Common Structural Basis for pH- and Calmodulin-mediated Regulation in Plant Glutamate Decarboxylase. J. Mol. Biol. 392, 334-351.
  5. Cheng, Zhihong, Kazuki Saito, Andrey V. Pisarev, et al. (2009)
    Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev. 23, 1106-1118.
  6. Cierpicki, Tomasz, Jakub Bielnicki, Meiying Zheng, Jakub Gruszczyk, Marta Kasterka, Maxim Petoukhov, Aming Zhang, Erik J. Fernandez, Dmitri I. Svergun, Urszula Derewenda, John H. Bushweller and Zygmunt S. Derewenda (2009)
    The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA. Protein Science 18, 2067-2079.
  7. Crowley, Peter B., Pedro M. Matias, Amir R. Khan, Manfred Roessle, and Dmitri I. Svergun (2009)
    Metal-Mediated Self-Assembly of a β-Sandwich Protein Chem. Eur. J., 15, 12672-12680.
  8. Franke, Daniel and Dmitri I. Svergun (2009)
    DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering J. Appl. Cryst. 42, 342-346.
  9. Heikkinen, Outi K., Salla Ruskamo, Peter V. Konarev, Dmitri I. Svergun, Tatu Iivanainen, Sami M. Heikkinen, Perttu Permi, Harri Koskela, Ilkka Kilpeläinen, and Jari Ylänne (2009)
    Atomic Structures of Two Novel Immunoglobulin-like Domain Pairs in the Actin Cross-linking Protein Filamin J. Biol. Chem. 284 (37), 25450-25458.
  10. Petoukhov, Maxim V., João B. Vicente, Peter B. Crowley, Maria Arménia Carrondo, Miguel Teixeira and Dmitri I. Svergun (2009)
    Quaternary Structure of Flavorubredoxin as Revealed by Synchrotron Radiation Small-Angle X-Ray Scattering Structure 16, 1428-1436.
  11. Taneva, Stefka G., Sonia Bañuelos, Jorge Falces, Igor Arregi, Arturo Muga, Petr V. Konarev, Dmitri I. Svergun, Adrián Velázquez-Campoy and Maria A. Urbaneja (2009)
    A Mechanism for Histone Chaperoning Activity of Nucleoplasmin: Thermodynamic and Structural Models J. Mol. Biol. 393 (2), 448-463.
  12. Werner, Arne, Petr V. Konarev, Dmitri I. Svergun, Ulrich Hahn (2009)
    Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering Analytical Biochemistry 389, 52-62.
  13. Zanchi, Dražen, Petr V. Konarev, Christophe Tribet, Alain Baron, Dmitri I. Svergun and Sylvain Guyot (2009)
    Rigidity, conformation, and solvation of native and oxidized tannin macromolecules in water-ethanol solution J. Chem. Phys. 130, 245103-1.

2008

  1. Schroer, C.G., Boye, P., Feldkamp, J., Patommel, J., Schropp, A. Schwab, A., Stephan, S., Burghammer, M., Schoeder, S. and Riekel, C.
    Coherent X-Ray Diffraction Imaging with Nanofocused Illumination. Phys. Rev. Lett. 101, 090801 (2008).
  2. Martel, A. Burghammer, M., Davies, RJ., Di Cola, E., Vendrely, C. & Riekel, C. (2008)
    Silk Fiber Assembly studied by Synchrotron Radiation SAXS/WAXS and Raman Spectroscopy. J. Am. Chem. Soc. 130 (50), 17070-4.
  3. Gebhardt, R., Vendrely, C., Hanfland, M., & Riekel, C. (2008)
    Silk Fiber Formation after High-Pressure Treatment of Fibroin Solution in a Diamond Anvil Cell. Macromolecules 41 (24) 9934-9936.
  4. Davies, R.J., Burghammer, M., & Riekel, C. (2008)
    Micro-Raman Spectroscopy as an in Situ Tool for Probing Radiation Damage during Microdiffraction Experiments in Soft Condensed Matter. Macromolecules 41 (19), 7251-7253.
  5. Martel, A. et al. (2008)
    A microfluidic cell for studying the formation of regenerated silk by synchrotron radiation small- and wide-angle X-ray scattering. Biomicrofluidics 2, 024104.
  6. Graceffa, R., Burghammer, M., Davies, R., & Riekel, C. (2008)
    Synchrotron radiation microdiffraction of ballistic molten wax microdrops. Rev. Sci. Instrum. 79, 086106-086101.
  7. Falcaro, P., S. Costacurta, L. Malfatti, M. Takahashi, T. Kidchob, M. F. Casula, M. Piccinini, A. Marcelli, B. Marmiroli, H. Amenitsch, P. Schiavuta, P. Innocenzi
    Fabrication of Mesoporous Functionalized Arrays by Integrating Deep X-Ray Lithography with Dip-Pen Writing, Advanced Materials, Vol.20, 1864-1869, (2008).
  8. Shyjumon, I., M. Rappolt, B. Sartori, H. Amenitsch & P. Laggner (2008)
    Novel in situ setup to study the formation of nanoparticles in the gas phase by small angle x-ray scattering Review of Scientific Instruments, 79, 043905.
  9. Youles, M., Holmes, O., Petoukhov, M. V., Nessen, M. A., Stivala, S., Svergun, D. I. & Gherardi, E. (2008).
    Engineering the NK1 fragment of hepatocyte growth factor/scatter factor as a MET receptor antagonist. J Mol Biol 377, 616-22.
  10. Xu, X. F., Reinle, W. G., Hannemann, F., Konarev, P. V., Svergun, D. I., Bernhardt, R. & Ubbink, M. (2008).
    Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy. Journal of the American Chemical Society 130, 6395-6403.
  11. Varga, A., Szabo, J., Flachner, B., Roy, B., Konarev, P., Svergun, D., Zavodszky, P., Perigaud, C., Barman, T., Lionne, C. & Vas, M. (2008).
    Interaction of human 3-phosphoglycerate kinase with l-ADP, the mirror image of d-ADP. Biochem Biophys Res Commun 366, 994-1000.
  12. Szabo, J., Varga, A., Flachner, B., Konarev, P. V., Svergun, D. I., Zavodszky, P. & Vas, M. (2008).
    Role of side-chains in the operation of the main molecular hinge of 3-phosphoglycerate kinase. Febs Letters 582, 1335-1340.
  13. Szabo, J., Varga, A., Flachner, B., Konarev, P., Svergun, D., Zavodszky, P. & Vas, M. (2008).
    Insight into the molecular details of domain movements of 3-phosphoglycerate kinase. Febs Journal 275, 466-466.
  14. Szabo, J., Varga, A., Flachner, B., Konarev, P. V., Svergun, D. I., Zavodszky, P. & Vas, M. (2008).
    Communication between the nucleotide site and the main molecular hinge of 3-phosphoglycerate kinase. Biochemistry 47, 6735-6744.
  15. Shtykova, E. V., Huang, X. L., Gao, X. F., Dyke, J. C., Schmucker, A. L., Dragnea, B., Remmes, N., Baxter, D. V., Stein, B., Konarev, P. V., Svergun, D. I. & Bronstein, L. M. (2008).
    Hydrophilic Monodisperse Magnetic Nanoparticles Protected by an Amphiphilic Alternating Copolymer. Journal of Physical Chemistry C 112, 16809-16817.
  16. She, M., Decker, C. J., Svergun, D. I., Round, A., Chen, N., Muhlrad, D., Parker, R. & Song, H. (2008).
    Structural basis of Dcp2 recognition and activation by Dcp1. Molecular Cell 29, 337-349.
  17. Round, A. R., Franke, D., Moritz, S., Huchler, R., Fritsche, M., Malthan, D., Klaering, R., Svergun, D. I. & Roessle, M. (2008).
    Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. Journal of Applied Crystallography 41, 913-917.
  18. Petoukhov, M. V., Vicente, J. B., Crowley, P. B., Carrondo, M. A., Teixeira, M. & Svergun, D. I. (2008).
    Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering. Structure 16, 1428-1436.
  19. Niemann, H. H., Petoukhov, M. V., Hartlein, M., Moulin, M., Gherardi, E., Timmins, P., Heinz, D. W. & Svergun, D. I. (2008).
    X-ray and neutron small-angle scattering analysis of the complex formed by the Met receptor and the Listeria monocytogenes invasion protein InlB. J Mol Biol 377, 489-500.
  20. Mumtsidu, E., Makhov, A. M., Konarev, P. V., Svergun, D. I., Griffith, J. D. & Tucker, P. A. (2008).
    Structural features of the single-stranded DNA-binding protein of Epstein-Barr virus. Journal of Structural Biology 161, 172-187.
  21. Majava, V., Petoukhov, M. V., Hayashi, N., Pirila, P., Svergun, D. I. & Kursula, P. (2008).
    Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure. BMC Struct Biol 8, 10.
  22. Gabel, F., Simon, B., Nilges, M., Petoukhov, M., Svergun, D. & Sattler, M. (2008).
    A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints. Journal of Biomolecular Nmr 41, 199-208.
  23. Esposito, C., Petoukhov, M. V., Svergun, D. I., Ruggiero, A., Pedone, C., Pedone, E. & Berisio, R. (2008).
    Evidence for an elongated dimeric structure of heparin-binding hemagglutinin from Mycobacterium tuberculosis. J Bacteriol 190, 4749-53.
  24. Covaceuszach, S., Cassetta, A., Konarev, P. V., Gonfloni, S., Rudolph, R., Svergun, D. I., Lamba, D. & Cattaneo, A. (2008).
    Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody. Journal of Molecular Biology 381, 881-896.
  25. Cottevieille, M., Larquet, E., Jonic, S., Petoukhov, M. V., Caprini, G., Paravisi, S., Svergun, D. I., Vanoni, M. A. & Boisset, N. (2008).
    The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications. J Biol Chem 283, 8237-49.
  26. Bronstein, L. M., Kostylev, M., Shtykova, E., Vlahu, T., Huang, X., Stein, B. D., Bykov, A., Remmes, N. B., Baxter, D. V. & Svergun, D. I. (2008).
    Mixed Co/Fe Oxide Nanoparticles in Block Copolymer Micelles. Langmuir 24, 12618-12626.
  27. Boczkowska, M., Rebowski, G., Petoukhov, M. V., Hayes, D. B., Svergun, D. I. & Dominguez, R. (2008).
    X-ray scattering study of activated Arp2/3 complex with bound actin-WCA. Structure 16, 695-704.
  28. Aliprandi P, Sizun C, Perez J, Mareuil F, Caputo S, Leroy JL, Odaert B, Laalami S, Uzan M. & Bontems F. (2008).
    S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis. J Biol Chem. 283, 13289-301.

2007

  1. Bernado, P., Mylonas, E., Petoukhov, M.V., Blackledge, M. & Svergun, D.I. (2007)
    Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc, 129, 5656-5664.
  2. Petoukhov, M.V., Konarev, P.V., Kikhney, A.G. & Svergun, D.I. (2007)
    ATSAS 2.1 - towards automated and web-supported small-angle scattering data analysis. J. Appl. Cryst., 40, s223-s228.
  3. Petoukhov, M.V. & Svergun, D.I. (2007)
    Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr Opin Struct Biol, 17, 562-571.
  4. Roessle, M.W., Klaering, R., Ristau, U., Robrahn, B., Jahn, D., Gehrmann, T., Konarev, P., Round, A., Fiedler, S., Hermes, C. & Svergun, D. (2007)
    Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J. Appl. Cryst., 40, s190-s194.
  5. Tidow, H., Melero, R., Mylonas, E., Freund, S.M., Grossmann, J.G., Carazo, J.M., Svergun, D.I., Valle, M. & Fersht, A.R. (2007)
    Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proc Natl Acad Sci U S A. 104, 12324-12329.
  6. Mastrangelo, E., Milani, M., Bollati, M., Selisko, B., Peyrane, F., Pandini, V., Sorrentino, G., Canard, B., Konarev, P.V., Svergun, D.I., de Lamballerie, X., Coutard, B., Khromykh, A.A. & Bolognesi, M. (2007)
    Crystal Structure and Activity of Kunjin Virus NS3 Helicase; Protease and Helicase Domain Assembly in the Full Length NS3 Protein. J Mol Biol. 372, 444-55.
  7. Svergun, D.I. (2007)
    Small-angle scattering studies of macromolecular solutions. J. Appl. Crystallogr. 40, s10-s17.
  8. Sjekloca, L., Pudas, R., Sjoblom, B., Konarev, P., Carugo, O., Rybin, V., Kiema, T.R., Svergun, D., Ylanne, J. & Carugo, K.D. (2007)
    Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer. J Mol Biol. 368, 1011-1023.
  9. Vestergaard, B., Groenning, M., Roessle, M., Kastrup, J.S., de Weert, M.V., Flink, J.M., Frokjaer, S., Gajhede, M. & Svergun, D.I. (2007)
    A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils. PLoS Biol. 5, e134.
  10. Németh-Pongrácz, V., Barabás, O., Fuxreiter, M., Simon, I., Pichová, I., Rumlová, M., Zábranská, H., Svergun, D., Petoukhov, M., Harmat, V., Klement, É., Hunyadi-Gulyás, É., Medzihradszky, K., Kónya, E. & Vértessy B. (2007)
    Flexible segments modulate co-folding of dutpase and nucleocapsid proteins. Nucleic Acid Res. 35, 495-505.
  11. F. Mareuil, C. Sizun, J. Perez, M. Schoenauer, J.-Y. Lallemand & F. Bontems (2007)
    A simple genetic algorithm for the optimization of multidomain protein homology models driven by NMR residual dipolar coupling and small angle X -ray scattering data, Eur. Biophys. J. 37, 95-104.
  12. Moukhametzianov, R. et al. (2007)
    Protein crystallography with a micron-sized synchrotron radiation beam. Acta Cryst D.
  13. Roth, S.V. et al. (2007)
    In-situ observation of nanoparticle ordering at the air-water-substrate boundary in colloidal solutions using x-ray nanobeams. APL 91, 081915-1 - 081915-3.
  14. Mueller-Buschbaum, P., Gebhardt, R., Roth, S., Metwalli, E., & Doster, W., Effect of Calcium Concentration on the Structure of Casein Micelles in Thin Films. Biophys. J. 93, 960-968 (2007).
The list of publications might be incomplete. Let us know if something is missing.