D I Svergun

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi request reprint Molecular analysis and solution structure from small-angle X-ray scattering of the human natural killer inhibitory receptor IRp60 (CD300a)
    Nazzareno Dimasi
    Laboratorio di Medicina Molecolare, Istituto Giannina Gaslini, Largo Gerolamo Gaslini 5, 16147 Genova, Italy
    Int J Biol Macromol 40:193-200. 2007
  2. pmc X-ray scattering study of activated Arp2/3 complex with bound actin-WCA
    Malgorzata Boczkowska
    Department of Physiology, University of Pennsylvania School of Medicine, 3700 Hamilton Walk, A507 Richards Building, Philadelphia, PA 19104 6085, USA
    Structure 16:695-704. 2008
  3. doi request reprint Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody
    Sonia Covaceuszach
    Lay Line Genomics SpA, Via di Castel Romano 100, I 00128 Rome, Italy
    J Mol Biol 381:881-96. 2008
  4. pmc Structural analysis of influenza A virus matrix protein M1 and its self-assemblies at low pH
    Eleonora V Shtykova
    Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 8:e82431. 2013
  5. doi request reprint Small-angle X-ray scattering on biological macromolecules and nanocomposites in solution
    Clément E Blanchet
    European Molecular Biology Laboratory Hamburg, 22603 Hamburg, Germany
    Annu Rev Phys Chem 64:37-54. 2013
  6. ncbi request reprint Advances in structure analysis using small-angle scattering in solution
    Dmitri I Svergun
    EMBL, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    Curr Opin Struct Biol 12:654-60. 2002
  7. pmc Determination of domain structure of proteins from X-ray solution scattering
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, D 22603 Hamburg, Germany
    Biophys J 80:2946-53. 2001
  8. ncbi request reprint Conformation of the Drosophila motor protein non-claret disjunctional in solution from X-ray and neutron scattering
    D I Svergun
    Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospekt 59, 117333 Russia
    J Biol Chem 276:24826-32. 2001
  9. ncbi request reprint A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome
    D I Svergun
    European Molecular Biology Laboratory, EMBL c o DESY, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 275:14432-9. 2000
  10. ncbi request reprint Crystal versus solution structures of thiamine diphosphate-dependent enzymes
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, Deutsches Elektronen Synchrotron, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 275:297-302. 2000

Detail Information

Publications84

  1. ncbi request reprint Molecular analysis and solution structure from small-angle X-ray scattering of the human natural killer inhibitory receptor IRp60 (CD300a)
    Nazzareno Dimasi
    Laboratorio di Medicina Molecolare, Istituto Giannina Gaslini, Largo Gerolamo Gaslini 5, 16147 Genova, Italy
    Int J Biol Macromol 40:193-200. 2007
    ..The SAXS data revealed that IRp60 is monomeric in solution with a molecular shape characteristic of the immunoglobulin-like structures. A homology model of IRp60 was built and validated experimentally against the SAXS data...
  2. pmc X-ray scattering study of activated Arp2/3 complex with bound actin-WCA
    Malgorzata Boczkowska
    Department of Physiology, University of Pennsylvania School of Medicine, 3700 Hamilton Walk, A507 Richards Building, Philadelphia, PA 19104 6085, USA
    Structure 16:695-704. 2008
    ..The results support a model of activation that is consistent with most of the biochemical observations...
  3. doi request reprint Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody
    Sonia Covaceuszach
    Lay Line Genomics SpA, Via di Castel Romano 100, I 00128 Rome, Italy
    J Mol Biol 381:881-96. 2008
    ..The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor...
  4. pmc Structural analysis of influenza A virus matrix protein M1 and its self-assemblies at low pH
    Eleonora V Shtykova
    Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
    PLoS ONE 8:e82431. 2013
    ..In particular, this flexibility could allow M1 to structurally organise the viral membrane to maintain the integrity and the shape of the intact influenza virus. ..
  5. doi request reprint Small-angle X-ray scattering on biological macromolecules and nanocomposites in solution
    Clément E Blanchet
    European Molecular Biology Laboratory Hamburg, 22603 Hamburg, Germany
    Annu Rev Phys Chem 64:37-54. 2013
    ..The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles...
  6. ncbi request reprint Advances in structure analysis using small-angle scattering in solution
    Dmitri I Svergun
    EMBL, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    Curr Opin Struct Biol 12:654-60. 2002
    ..Substantial progress has also been made in the quantitative analysis and modelling of assembly and folding processes, and intermolecular interactions...
  7. pmc Determination of domain structure of proteins from X-ray solution scattering
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, D 22603 Hamburg, Germany
    Biophys J 80:2946-53. 2001
    ..The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins...
  8. ncbi request reprint Conformation of the Drosophila motor protein non-claret disjunctional in solution from X-ray and neutron scattering
    D I Svergun
    Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospekt 59, 117333 Russia
    J Biol Chem 276:24826-32. 2001
    ..The solution structure of the long ncd construct (MC1) including complete N-terminal coiled-coil and motor domains is modeled by adding a straight coiled-coil section to the model of MC5...
  9. ncbi request reprint A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome
    D I Svergun
    European Molecular Biology Laboratory, EMBL c o DESY, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 275:14432-9. 2000
    ..The protein-rRNA map enlarges the basis for the models of the rRNA folding and can further help to localize proteins in high-resolution crystallographic density maps...
  10. ncbi request reprint Crystal versus solution structures of thiamine diphosphate-dependent enzymes
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, Deutsches Elektronen Synchrotron, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 275:297-302. 2000
    ..58 and 1.53 nm, respectively) were required. A clear correlation was observed between the magnitude of the distortions induced by the crystal environment and the interfacial area between subunits...
  11. pmc Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    D I Svergun
    European Molecular Biology Laboratory, Hamburg, Germany and Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia
    Biophys J 76:2879-86. 1999
    ..Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data...
  12. pmc Protein hydration in solution: experimental observation by x-ray and neutron scattering
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    Proc Natl Acad Sci U S A 95:2267-72. 1998
    ..Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces...
  13. doi request reprint Small-angle X-ray and neutron scattering as a tool for structural systems biology
    Dmitri I Svergun
    EMBL, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    Biol Chem 391:737-43. 2010
    ..Possibilities of synergistic use of the method with other techniques are considered...
  14. ncbi request reprint Synergistic use of synchrotron radiation techniques for biological samples in solution: a case study on protein-ligand recognition by the peroxisomal import receptor Pex5p
    W A Stanley
    EMBL Hamburg, c o DESY, Notkestrasse 85, 22603 Hamburg, Germany
    J Synchrotron Radiat 11:490-6. 2004
    ..Implications of the combined use of synchrotron-based circular dichroism spectropolarimetry and X-ray scattering in structural biology and proteomics are discussed...
  15. ncbi request reprint Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, EMBL c o DESY, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 275:4210-4. 2000
    ..Potential DNA binding surfaces of sigma54 are also predicted by comparison with the sigma54 core binding fragment...
  16. ncbi request reprint Solution structure of bacteriophage PRD1 vertex complex
    A Sokolova
    Institute of Crystallography, Russian Academy of Sciences, Moscow 117333, Russia
    J Biol Chem 276:46187-95. 2001
    ..The constructed models of these assemblies provided support for a model of vertex assembly onto the virion. Although similar in overall architecture, clear differences between PRD1 and adenovirus spike assemblies have been revealed...
  17. ncbi request reprint Biochemical and structural characterization of recombinant copper-metallothionein from Saccharomyces cerevisiae
    Z Sayers
    European Molecular Biology Laboratory, Hamburg, Germany
    Eur J Biochem 262:858-65. 1999
    ..2 nm for the recombinant protein, indicating a more extended structure in solution than that derived from the recent NMR data [Peterson, C.W., Narula, S.S. & Armitage, I.A. (1996) FEBS Lett. 379, 85-93]...
  18. ncbi request reprint A novel quaternary structure of the dimeric alpha-crystallin domain with chaperone-like activity
    I K Feil
    European Molecular Biology Laboratory EMBL, EMBL Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 276:12024-9. 2001
    ..This flexibility may be important for biological activity and for the formation of alphaB-crystallin complexes of variable sizes and compositions...
  19. pmc Addition of missing loops and domains to protein models by x-ray solution scattering
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg Outstation, D 22603 Hamburg, Germany
    Biophys J 83:3113-25. 2002
    ..After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available...
  20. ncbi request reprint Analysis of X-ray and neutron scattering from biomacromolecular solutions
    Maxim V Petoukhov
    EMBL, Hamburg Outstation, Germany
    Curr Opin Struct Biol 17:562-71. 2007
    ....
  21. ncbi request reprint Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state
    D I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, Germany
    Proteins 27:110-7. 1997
    ..14 nm away from the molecular center along this axis...
  22. ncbi request reprint Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution
    Michel H Koch
    European Molecular Biology Laboratory Hamburg Outstation, EMBL c o DESY, Notkestrasse 85, D 22603 Hamburg, Germany
    Q Rev Biophys 36:147-227. 2003
    ....
  23. ncbi request reprint The impact of protein characterization in structural proteomics
    Arie Geerlof
    EMBL Hamburg Outstation, Notkestrasse 85, Hamburg, Germany
    Acta Crystallogr D Biol Crystallogr 62:1125-36. 2006
    ..Examples of the application of the various methods are given...
  24. ncbi request reprint Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens
    T V Tikhonova
    Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
    Biochemistry (Mosc) 73:164-70. 2008
    ..Thermostability of the hexameric form of the nitrite reductase is characterized in terms of thermoinactivation and thermodenaturation...
  25. ncbi request reprint Structural features of the single-stranded DNA-binding protein of Epstein-Barr virus
    E Mumtsidu
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    J Struct Biol 161:172-87. 2008
    ..One major difference is the tendency of Balf2DeltaC to dimerize on different surfaces to that used for oligomerization when binding to ssDNA, and this may have implications for the mechanism of replication initiation...
  26. ncbi request reprint Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg Outstation, c o DESY, Notkestrasse 85, 22603, Hamburg, Germany
    Eur Biophys J 35:567-76. 2006
    ..The efficiency of the methods is demonstrated in model examples, and potential sources of ambiguity are discussed...
  27. ncbi request reprint Structural characterization of flexible proteins using small-angle X-ray scattering
    Pau Bernado
    European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
    J Am Chem Soc 129:5656-64. 2007
    ..In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts...
  28. pmc Solution structure of human Pex5.Pex14.PTS1 protein complexes obtained by small angle X-ray scattering
    Kumiko Shiozawa
    European Molecular Biology Laboratory Hamburg Outstation, c o DESY, Notkestrasse 85, 22603 Hamburg, Germany
    J Biol Chem 284:25334-42. 2009
    ..These results suggest that the extended structure of Pex5p may play a role in interactions with other substrates such as lipids and membrane proteins during the formation of functional multiprotein complexes...
  29. doi request reprint A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly
    Meikel Diepholz
    EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Structure 16:1789-98. 2008
    ..However, the relative arrangement of the EG and C subunits in solution is more open than that in the holoenzyme, suggesting a conformational change of EGC during regulatory assembly and disassembly...
  30. ncbi request reprint Conformation of polypyrimidine tract binding protein in solution
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
    Structure 14:1021-7. 2006
    ..Domains 3 and 4 were found to be in close contact, whereas domains 2 and especially 1 had loose contacts with the rest of the protein...
  31. doi request reprint Domain conformation of tau protein studied by solution small-angle X-ray scattering
    Efstratios Mylonas
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
    Biochemistry 47:10345-53. 2008
    ....
  32. pmc Global rigid body modeling of macromolecular complexes against small-angle scattering data
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg, Germany
    Biophys J 89:1237-50. 2005
    ..The methods described are implemented in publicly available computer programs running on major hardware platforms...
  33. pmc Low resolution structural models of the basic helix-loop-helix leucine zipper domain of upstream stimulatory factor 1 and its complexes with DNA from small angle X-ray scattering data
    Ekaterina P Lamber
    European Molecular Biology Laboratory, Hamburg Outstation, D 22603 Hamburg, Germany
    Biophys J 94:193-7. 2008
    ....
  34. ncbi request reprint Solution scattering suggests cross-linking function of telethonin in the complex with titin
    Peijian Zou
    European Molecular Biology Laboratory EMBL, Hamburg Outstation, EMBL c o Deutsches Electronen Synchrotron DESY, Notkestrasse 85, Germany
    J Biol Chem 278:2636-44. 2003
    ..These results suggest a possible role of telethonin in linking titin filaments at the Z-disk periphery...
  35. pmc Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates
    Anna V Sokolova
    Shemyakin Ovchinnikov Institute of Bioorganic Chemistry and Institute of Crystallography, Russian Academy of Sciences, Moscow 119991, Russia
    Proc Natl Acad Sci U S A 103:16206-11. 2006
    ..2-3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section...
  36. ncbi request reprint Quaternary structure of Azospirillum brasilense NADPH-dependent glutamate synthase in solution as revealed by synchrotron radiation x-ray scattering
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D 22603 Hamburg, Germany
    J Biol Chem 278:29933-9. 2003
    ..The holoenzyme model allows for independent catalytic activity of the alpha beta protomers, which is consistent with the available biochemical evidence...
  37. pmc Solution structure of poly(ethylene) glycol-conjugated hemoglobin revealed by small-angle X-ray scattering: implications for a new oxygen therapeutic
    Dmitri I Svergun
    European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
    Biophys J 94:173-81. 2008
    ..The proposed methodology for assessment of low-resolution structures and interactions is a powerful means for rational design of PEGylated therapeutic agents...
  38. ncbi request reprint Structural variations in the catalytic and ubiquitin-associated domains of microtubule-associated protein/microtubule affinity regulating kinase (MARK) 1 and MARK2
    Alexander Marx
    Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany
    J Biol Chem 281:27586-99. 2006
    ..Notably, the UBA domain has the same unusual conformation as in MARK2, and it binds at the same site. Remarkable differences occur in the catalytic domain at helix C, the catalytic loop, and the activation segment...
  39. ncbi request reprint The structure of a full-length response regulator from Mycobacterium tuberculosis in a stabilized three-dimensional domain-swapped, activated state
    Jack King-Scott
    EMBL Hamburg Outstation, c o DESY, Notkestrasse 85, D 22603, Hamburg, Germany
    J Biol Chem 282:37717-29. 2007
    ..The dimer in solution differs from the active form observed in the crystal, resembling instead the model of the inactive full-length response regulator PhoB...
  40. doi request reprint Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering
    Maxim V Petoukhov
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
    Structure 16:1428-36. 2008
    ..This finding suggests that Rd behaves as an independent domain and is freely available to participate in redox reactions with protein partners...
  41. doi request reprint The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation
    Simone Weyand
    EMBL Hamburg Outstation, c o DESY, Hamburg, Germany
    J Struct Funct Genomics 10:209-17. 2009
    ..Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme...
  42. doi request reprint Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy
    Xingfu Xu
    Institute of Chemistry, Leiden University, P O Box 9502, NL 2300RA Leiden, The Netherlands
    J Am Chem Soc 130:6395-403. 2008
    ..Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex...
  43. doi request reprint Small angle X-ray studies reveal that Aspergillus niger glucoamylase has a defined extended conformation and can form dimers in solution
    Anders Dysted Jørgensen
    Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark
    J Biol Chem 283:14772-80. 2008
    ..Our results suggest that glucoamylase functions via transient dimer formation during hydrolysis of insoluble substrates and address the question of the cooperative effect of starch binding and hydrolysis...
  44. ncbi request reprint Low resolution structure determination shows procollagen C-proteinase enhancer to be an elongated multidomain glycoprotein
    Simonetta Bernocco
    Institut de Biologie et Chimie des Proteines, UMR 5086 CNRS UCBL1, 69367 Lyon Cedex 07, France
    J Biol Chem 278:7199-205. 2003
    ..Bernocco, S., Font, B., Moali, C., Eichenberger, D., Farjanel, J., Burchardt, E. R., van der Rest, M., Kessler, E., and Hulmes, D. J. S. (2002) J. Biol. Chem. 277, 33864-33869) for the mechanism of action of PCPE...
  45. ncbi request reprint The crystal and solution studies of glucosamine-6-phosphate synthase from Candida albicans
    Joanna Raczynska
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul Noskowskiego 12 14, 61 704 Poznan, Poland
    J Mol Biol 372:672-88. 2007
    ..This study of Gfa1p focuses on the features that distinguish it from the prokaryotic homologue in terms of quaternary structure, control of the enzymatic activity and details of the isomerase active site...
  46. pmc Evidence for an elongated dimeric structure of heparin-binding hemagglutinin from Mycobacterium tuberculosis
    Carla Esposito
    Istituto di Biostrutture e Bioimmagini, C N R, I 80134, Napoli, Italy
    J Bacteriol 190:4749-53. 2008
    ..These data, together with the low-resolution structures of a full-length form and a truncated form of HBHA obtained by small-angle X-ray scattering, have unambiguously indicated that HBHA has a dimeric structure with an elongated shape...
  47. doi request reprint X-ray and neutron small-angle scattering analysis of the complex formed by the Met receptor and the Listeria monocytogenes invasion protein InlB
    Hartmut H Niemann
    Division of Structural Biology, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D 38124 Braunschweig, Germany
    J Mol Biol 377:489-500. 2008
    ....
  48. doi request reprint Structural characterization of the active and inactive states of Src kinase in solution by small-angle X-ray scattering
    Pau Bernado
    Institute for Research in Biomedicine, Parc Cientific de Barcelona, Josep Samitier, 1 5, 08028 Barcelona, Spain
    J Mol Biol 376:492-505. 2008
    ..The regulation model emerging from this study, including at least three different conformational states, allows the tight regulation of the enzyme without compromising fast response in the presence of natural targets...
  49. ncbi request reprint Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway
    Anja Schütz
    Institut fur Biochemie, Fachbereich Biochemie Biotechnologie, Martin Luther Universitat Halle Wittenberg, Halle, Germany
    Eur J Biochem 270:2322-31. 2003
    ..Chem.16, 1207-1216] and comparison with indole-3-pyruvic acid conversion by pyruvate decarboxylases from Saccharomyces cerevisiae and Zymomonas mobilis provided some insight into the catalytic mechanism of indolepyruvate decarboxylase...
  50. ncbi request reprint The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure
    Bente Vestergaard
    Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Copenhagen
    Mol Cell 20:929-38. 2005
    ..These conclusions obviate the need for assuming large conformational changes in RFs during termination...
  51. pmc Structural basis of hepatocyte growth factor/scatter factor and MET signalling
    Ermanno Gherardi
    Medical Research Council Centre and Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Proc Natl Acad Sci U S A 103:4046-51. 2006
    ....
  52. ncbi request reprint Molecular insights into the self-assembly mechanism of dystrophia myotonica kinase
    Pilar Garcia
    Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstr 70, Basel CH 4056, Switzerland
    FASEB J 20:1142-51. 2006
    ..Our findings support a shared pattern of assembly across DMPK, ROCKs, and MRCK members of this family...
  53. pmc Conformation of full-length Bruton tyrosine kinase (Btk) from synchrotron X-ray solution scattering
    Jose A Marquez
    European Molecular Biology Laboratory, Grenoble Outstation, 6, rue Jules Horowitz, BP181 38042 Grenoble Cedex 9, France
    EMBO J 22:4616-24. 2003
    ..Taken together, our results indicate that, contrary to Src and Abl, Btk might not require an assembled conformation for the regulation of its activity...
  54. ncbi request reprint Looking behind the beamstop: X-ray solution scattering studies of structure and conformational changes of biological macromolecules
    Patrice Vachette
    LURE Bat 209d, University Paris Sud, F 91898 Orsay, France
    Methods Enzymol 374:584-615. 2003
  55. ncbi request reprint The active conformation of glutamate synthase and its binding to ferredoxin
    Robert H H van den Heuvel
    Department of Genetics and Microbiology, University of Pavia, via Abbiategrasso 207, Italy
    J Mol Biol 330:113-28. 2003
    ..A fundamental consequence of this result is that two Fd molecules bind consecutively to Fd-GltS to yield the reduced FMN cofactor during catalysis...
  56. ncbi request reprint Structural analysis of the stalk subunit Vma5p of the yeast V-ATPase in solution
    Andrea Armbruster
    Universitat des Saarlandes, Fachrichtung 2 5 Biophysik, Universitätsbau 76, D 66421 Homburg, Germany
    FEBS Lett 570:119-25. 2004
    ..Vma5p is an elongated boot-shaped particle consisting of two distinct domains. Co-reconstitution of Vma5p to V1 without C from Manduca sexta resulted in a V1-Vma5p hybrid complex and a 20% increase in ATPase hydrolysis activity...
  57. ncbi request reprint Structural characterization of the nonameric assembly of an Archaeal alpha-L-fucosidase by synchrotron small angle X-ray scattering
    Camillo Rosano
    X ray Structural Biology Unit National Institute for Cancer Research IST, Largo R Benzi 10, 16132 Genoa, Italy
    Biochem Biophys Res Commun 320:176-82. 2004
    ....
  58. ncbi request reprint The HC fragment of tetanus toxin forms stable, concentration-dependent dimers via an intermolecular disulphide bond
    Omar Qazi
    Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
    J Mol Biol 365:123-34. 2007
    ..We propose a possible mechanism for H(C) oligomerisation and discuss how this may relate to toxicity...
  59. pmc Biophysical characterization of the unstructured cytoplasmic domain of the human neuronal adhesion protein neuroligin 3
    Aviv Paz
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Biophys J 95:1928-44. 2008
    ..However, several of these techniques indicate that it is not fully extended, but becomes significantly more extended under denaturing conditions...
  60. ncbi request reprint Poly-Ig tandems from I-band titin share extended domain arrangements irrespective of the distinct features of their modular constituents
    Marco Marino
    Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056, Basel, Switzerland
    J Muscle Res Cell Motil 26:355-65. 2005
    ..It can be expected that this principle is generally applicable to all Ig-tandems from I-band titin...
  61. doi request reprint Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12
    Ivano Bertini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Am Chem Soc 130:7011-21. 2008
    ..Hints on the probable conformations are also obtained. This experimental finding opens new perspectives for the often hypothesized active role of the hemopexin-like domain in the enzymatic activity of MMPs...
  62. doi request reprint Communication between the nucleotide site and the main molecular hinge of 3-phosphoglycerate kinase
    Judit Szabo
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H 1518 Budapest, PO Box 7, Hungary, Germany
    Biochemistry 47:6735-44. 2008
    ..The transmission path of the nucleotide effect toward the main hinge of PGK is described for the first time at the level of interactions existing in the tertiary structure...
  63. doi request reprint The structure and binding behavior of the bacterial cell surface layer protein SbsC
    Tea Pavkov
    Institute of Molecular Biosciences, Structural Biology, University of Graz, Humboldtsrasse 50 3, 8010 Graz, Austria
    Structure 16:1226-37. 2008
    ....
  64. pmc Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies
    Gabriel Zoldak
    Department of Biochemistry, P J Safarik University Kosice, Slovakia
    Nucleic Acids Res 35:1343-53. 2007
    ..thermophilus and E. coli. Thermodynamic analyses and the X-ray scattering results for T. thermophilus RF2 in solution suggest that the compact conformation of RF2 resembles a physiological state in absence of the ribosome...
  65. ncbi request reprint Structure and RNA interactions of the N-terminal RRM domains of PTB
    Peter J Simpson
    Department of Biological Sciences, Imperial College, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
    Structure 12:1631-43. 2004
    ..These new insights into the structure and RNA binding properties of PTB suggest revised models of its mechanism of action...
  66. ncbi request reprint The crystal and solution structure of a putative transcriptional antiterminator from Mycobacterium tuberculosis
    J Preben Morth
    EMBL Hamburg Outstation, c o DESY, Notkestrasse 85, Germany
    Structure 12:1595-605. 2004
    ....
  67. ncbi request reprint A key structural role for active site type 3 copper ions in human ceruloplasmin
    Patrice Vachette
    LURE, Bat 209D, Universite Paris Sud, B P 34, F91898 Orsay Cedex, France
    J Biol Chem 277:40823-31. 2002
    ..Our results demonstrate that, beyond catalytic activity, the three-copper cluster at the N-terminal-C-terminal interface plays a crucial role in the structural stability of human ceruloplasmin...
  68. ncbi request reprint Structure validation of the Josephin domain of ataxin-3: conclusive evidence for an open conformation
    Giuseppe Nicastro
    National Institute for Medical Research, The Ridgeway, London, NW7 1AA, UK
    J Biomol NMR 36:267-77. 2006
    ..Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners...
  69. pmc Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain
    Mark Wells
    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 105:5762-7. 2008
    ..The core domains enveloped the response element in the center of the molecule, with the Taz2-bound TADs projecting outward from the core...
  70. pmc Absence of equilibrium cluster phase in concentrated lysozyme solutions
    Anuj Shukla
    European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F 38043 Grenoble Cedex 9, France
    Proc Natl Acad Sci U S A 105:5075-80. 2008
    ..Within the decoupling approximation, the experimental data can be fitted using an effective interparticle interaction potential involving short-range attraction and long-range repulsion...
  71. pmc A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils
    Bente Vestergaard
    Department of Medicinal Chemistry, University of Copenhagen, Copenhagen, Denmark
    PLoS Biol 5:e134. 2007
    ..The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases...
  72. pmc Fine-tuning of intrinsic N-Oct-3 POU domain allostery by regulatory DNA targets
    Robert Alazard
    Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, 31077 Toulouse, France
    Nucleic Acids Res 35:4420-32. 2007
    ..Finally, we suggest that a specific pair of glycine residues in the linker might act as a major conformational switch...
  73. ncbi request reprint Crystal structure and activity of Kunjin virus NS3 helicase; protease and helicase domain assembly in the full length NS3 protein
    Eloise Mastrangelo
    Department of Biomolecular Sciences and Biotechnology, CNR INFM, University of Milano, Via Celoria 26, 20133, Milano, Italy
    J Mol Biol 372:444-55. 2007
    ....
  74. ncbi request reprint Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis
    Elzbieta Nowak
    European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22 603 Hamburg, Germany
    Structure 14:275-85. 2006
    ..We also describe the high-resolution crystal structure of the catalytic domain alone, and we show that, in solution, it binds ATP. The conformational flexibility of this domain is discussed and related to other structural information...
  75. ncbi request reprint Multiple assembly states of lumazine synthase: a model relating catalytic function and molecular assembly
    Xiaofeng Zhang
    Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry, S 14157 Huddinge, Sweden
    J Mol Biol 362:753-70. 2006
    ..The data show that multiple assembly forms are a general feature of lumazine synthases...
  76. ncbi request reprint Metalated diblock and triblock poly(ethylene oxide)-block-poly(4-vinylpyridine) copolymers: understanding of micelle and bulk structure
    Lyudmila M Bronstein
    Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, USA
    J Phys Chem B 109:18786-98. 2005
    ..This model reveals that nearly spherical micellar cores of about 10 nm in diameter (filled with Pt nanoparticles) aggregate forming slightly oblate hollow bodies with an outer diameter of about 40 nm...
  77. ncbi request reprint X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum
    Peter Goettig
    Max Planck Institut fur Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Biol Chem 280:33387-96. 2005
    ..Moreover, small angle x-ray scattering measurements for tricorn and inhibited F1 have been interpreted as formation of transient and substrate-induced complexes...
  78. ncbi request reprint Structural and mutational analysis of substrate complexation by anthranilate phosphoribosyltransferase from Sulfolobus solfataricus
    Marco Marino
    Division of Structural Biology, Biozentrum, University of Basel, Switzerland
    J Biol Chem 281:21410-21. 2006
    ..Results allow the comparative analysis of PRT and pyrimidine NP families and expose related structural motifs involved in nucleotide/nucleoside recognition by these enzyme families...
  79. doi request reprint The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications
    Magali Cottevieille
    Département de Biologie Structurale, IMPMC UMR 7590, CNRS, Universités Paris 6 et Paris 7, IPGP, Paris, France
    J Biol Chem 283:8237-49. 2008
    ....
  80. pmc A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain
    Eleonore von Castelmur
    Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH 4056 Basel, Switzerland
    Proc Natl Acad Sci U S A 105:1186-91. 2008
    ..We propose a mechanistic model based on freely jointed rigid segments that rationalizes the response to stretch of titin Ig-tandems according to molecular features...
  81. doi request reprint Fab MOR03268 triggers absorption shift of a diagnostic dye via packaging in a solvent-shielded Fab dimer interface
    Roman C Hillig
    Bayer Schering Pharma AG, Global Drug Discovery, 13342 Berlin, Germany
    J Mol Biol 377:206-19. 2008
    ....
  82. pmc Structural basis of dcp2 recognition and activation by dcp1
    Meipei She
    Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, Proteos, 138673 Singapore
    Mol Cell 29:337-49. 2008
    ..Notably, the interface of Dcp1 and Dcp2 is not fully conserved, explaining why the Dcp1-Dcp2 interaction in higher eukaryotes requires an additional factor...
  83. pmc 19 A solution structure of the filarial nematode immunomodulatory protein, ES-62
    Claire J Ackerman
    Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, United Kingdom
    Biophys J 84:489-500. 2003
    ..This study represents the first attempt to understand the multifunctional properties of this important parasite-derived molecule by studying its structure...
  84. doi request reprint Engineering the NK1 fragment of hepatocyte growth factor/scatter factor as a MET receptor antagonist
    Mark Youles
    Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, UK
    J Mol Biol 377:616-22. 2008
    ..These NK1 variants have no detectable agonistic activity on, behave as bona fide receptor antagonists by blocking cell migration and DNA synthesis in target cells and have strong prospects as therapeutics for human cancer...