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  • 1
    Electronic Resource
    Electronic Resource
    A Genetic Algorithm for the Ab Initio Phasing of Icosahedral Viruses (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 235-251 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Genetic algorithms have been investigated as computational tools for the de novo phasing of low-resolution X-ray diffraction data from crystals of icosahedral viruses. Without advance knowledge of the shape of the virus and only approximate knowledge of its size, the virus can be modeled as the symmetry expansion of a short list of nearly tetrahedrally arranged lattice points which coarsely, but uniformly, sample the icosahedrally unique volume. The number of lattice points depends on an estimate of the non-redundant information content at the working resolution limit. This parameterization permits a simple matrix formulation of the model evaluation calculation, resulting in a highly efficient survey of the space of possible models. Initially, one bit per parameter is sufficient, since the assignment of ones and zeros to the lattice points yields a physically reasonable low-resolution image of the virus. The best candidate solutions identified by the survey are refined to relax the constraints imposed by the coarseness of the modeling, and then trials whose intensity-based statistics are comparatively good in all resolution ranges are chosen. This yields an acceptable starting point for symmetry-based direct phase extension about half the time. Improving efficiency by incorporating the selection criterion directly into the genetic algorithm's fitness function is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995011620
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  • 2
    Electronic Resource
    Electronic Resource
    A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 693-711 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several strains of poliovirus, focus on an arbitrary-sized parallelepiped (termed the `protomer' box) containing a single complete averaged copy of the structural motif which forms the protein capsid, together with the fragments of other symmetry-related copies of the motif which are located in its immediate neighborhood. The Fourier transform of the protomer box provides reference structure factors for stereochemically restrained crystallographic refinement of the atomic model parameters. The phases of the reference structure factors are based on the averaged map, and are not permitted to change during the refinement. It is demonstrated that models refined using the protomer box methods do not differ significantly from models refined by more expensive full-cell calculations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996001060
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Binding of the antiviral drug WIN51711 to the sabin strain of type 3 poliovirus: structural comparison with drug binding in rhinovirus 14 (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 473-489 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The crystal structure of the Sabin strain of type 3 poliovirus (P3/Sabin) complexed with the antiviral drug WIN51711 has been determined at 2.9 Å resolution. Drugs of this kind are known to inhibit the uncoating of the virus during infection, by stabilizing the capsid against receptor-induced conformational changes. The electron density for the bound drug is very well defined so that its position and orientation are unambiguous. The drug binds in a nearly extended conformation, slightly bent in the middle, in a blind pocket formed predominantly by hydrophobic residues in the core of the β-barrel of capsid protein VP1. Comparisons between this structure, the corresponding drug complex in human rhinovirus 14 (HRV 14), and the native structures of both viruses demonstrate that the binding of WIN51711 has markedly different effects on the structures of these two viruses. Unlike HRV14, wherein large conformational changes are observed in the coat protein after drug binding, the binding of this drug in poliovirus does not induce any significant conformational changes in the structure of the capsid protein, though the drug has a greater inhibitory effect in P3/Sabin than in HRV14. The implications of this result for the mechanism of capsid stabilization are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499401084X
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  • 4
    Electronic Resource
    Electronic Resource
    Ligand-Induced Conformational Changes in Poliovirus–Antiviral Drug Complexes (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 558-570 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystal structures of the Mahoney strain of type 1 poliovirus complexed with the antiviral compounds R80633 and R77975 were determined at 2.9 Å resolution. These compounds block infection by preventing conformational changes required for viral uncoating. In various drug–poliovirus complexes reported earlier, no significant conformational changes were found in the structures of the capsid proteins. In the structures reported here, the strain of virus is relatively insensitive to these antivirals. Correspondingly, significant conformational changes are necessary to accommodate the drug. These conformational changes affect both the immediate vicinity of the drug binding site, and more distant loops located near the fivefold axis. In addition, small but concerted shifts of the centers of mass of the major capsid proteins consistently have been detected whose magnitudes are correlated inversely with the effectiveness of the drugs. Collectively, the drug complexes appear to sample the conformational repertoire of poliovirus near equilibrium, and thus provide a possible model for the earliest stages of viral uncoating during infection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997000954
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  • 5
    Electronic Resource
    Electronic Resource
    Structure Determination of Echovirus 1 (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1261-1272 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 Å resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 Å. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 Å resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998002790
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  • 6
    Electronic Resource
    Electronic Resource
    Myristylation of picornavirus capsid protein VP4 and its structural significance (1987)
    [s.l.] : Nature Publishing Group
    Nature 327 (1987), S. 482-486 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] We have obtained evidence that poliovirus and other picornavirus particles are specifically modified by having myristic acid covalently bound to a capsid protein. The electron density map ofpoliovirus confirms the position of the myristate molecule and defines its location in the virus particle. ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/327482a0
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