<i>Ab initio</i>phase determination for spherical viruses: parameter determination for spherical-shell models

Chapman, Michael S.; Tsao, Jun; Rossmann, Michael G.

doi:10.1107/s0108767391013211

Cited by 26 publications

(15 citation statements)

References 7 publications

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“…The feasibility of ab initio phase determination has been demonstrated for spherical viruses (Tsao et al, 1992). The initial phases of canine parvovirus (CPV), calculated at 20 Å resolution using a spherical hollowshell model of the virus, were successfully refined and extended to 13.5 Å resolution (Chapman et al, 1992). As CPV particles are located at general positions exhibiting non-centrosymmetry, the initial phases deviate from the centre of symmetry.…”

Section: Introductionmentioning

confidence: 99%

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Ab initiocrystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

et al. 2005

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Ab initio phasing by non-crystallographic symmetry averaging coupled with solvent flattening has previously been used to determine the structure of canine parvovirus. As CPV particles were located at general positions, initial phases were generated with a spherical shell deviating from the centre of symmetry. In many virus crystals, the viral particles are located at positions with a centre of symmetry in the unit cell. Thus, the initial phases calculated with a spherical shell model have a centre of symmetry. The inherent difficulty in structural determination was breaking the centre of symmetry in the initial phase. The centric nature of the initial phases of the rice dwarf virus crystal, however, was successfully broken at low resolution by iteration of the density-modification method described by Tsao et al. (1992). In this study, ab initio phasing was tested for seven viruses ranging from 82 to 344 A in radius. Although the crystal structures of the initial spherical shell models for each virus had a centre of symmetry, the centric natures of the initial phases were successfully broken by non-crystallographic symmetry averaging coupled with solvent flattening at a low resolution; these phases were then successfully extended to high-resolution measurements. A novel procedure of ab initio phasing for spherical virus crystals is proposed.

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Section: Introductionmentioning

confidence: 99%

“…Ab initio phasing by non-crystallographic symmetry averaging coupled with solvent flattening has previously been used to determine the structure of canine parvovirus [CPV; Tsao et al (1992), Acta Cryst. A48, 293-301; Chapman et al (1992), Acta Cryst. A48, [301][302][303][304][305][306][307][308][309][310][311][312].…”

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Ab initiocrystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

et al. 2005

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“…In the absence of any phase information, the overall particle dimensions could be estimated using dynamic light scattering (DLS), small angle X-ray solution scattering (SAXS) or transmission electron microscopy (TEM). Chapman et al [2] describe methods for estimating the overall virus dimensions from the diffraction data. We assume 220 here only that initial estimates of the capsid inner and outer radii are available.…”

Section: Envelope Definition and Refinementmentioning

confidence: 99%

Iterative projection algorithms for ab initio phasing in virus crystallography

Kingston

Millane

2016

Journal of Structural Biology

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“…In determining the structure of canine parvovirus, it was possible to extend the phases from a 12 Å, low-resolution hollow spherical shell to high resolution. [70,71] The structure of HRV14 provided a lot of fascinating and unexpected information. [24] First and foremost, the structure of the HRV14 capsid was similar to that of the plant viruses such as TBSV and SBMV although the three independent subunits in the icosahedral asymmetric unit, viral protein 1 (VP1), VP2 and VP3, had quite different amino acid sequences ( Figure 12).…”

Section: Picornavirusesmentioning

confidence: 99%

Virus crystallography and structural virology: a personal perspective

Rossmann

2014

Crystallography Reviews

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My first experiences with crystallography were as a graduate student at the University of Glasgow determining the structure of aromatic hydrocarbons using only primitive hand calculation techniques. I had my first experience using electronic computers as a post-doc in the lab of William Lipscomb in Minnesota. That gave me a good preparation for the structure determination of haemoglobin with Max Perutz in Cambridge. The discovery of the conserved globin fold had a major impact on my subsequent activities. It also provided the foundation for the development of the molecular replacement method and non-crystallographic symmetry electron density averaging that was essential for the structure determination of simple icosahedral viruses. The structure determination of a common cold virus was also a major stimulus for the study of more complex viruses and the development of the use of cryoelectron microscopy. This provided the basis for the investigation of lipid-enveloped viruses such as Sindbis virus and dengue virus. It also provided the technology for the study of bacteriophage DNA packaging motors and the mechanisms of infection by tailed and untailed phages. Downloaded by [University of Connecticut] at 02:51 03 February 2015 58 M.G. Rossmann The beginnings of protein crystallographyThe most common types of crystals encountered in daily life are primarily inorganic substances such as common salt and minerals. Thus, it is not surprising that these substances were the first to be analysed in the first decade or two after the discovery of X-ray diffraction in 1912 by P. Ewald and M. von Laue in Germany and by W.H. Bragg and W.L. Bragg in England. This was most fortunate because many of these structures could be described in terms of a few atoms sitting at special positions on symmetry axes. Even so, it took a great deal of ingenuity and talent to solve these early structures as represented dramatically in the writings of C.P. Snow.[1] Gradually, with increasing experience, crystalized organic substances became within technical range. Kathleen Lonsdale, working in London, determined the structure of some benzene derivatives in 1929 and verified what chemists had suspected, that a benzene ring is planar.[2] The complexity of structures being determined increased steadily. This was aided by the introduction of Fourier syntheses by W.L. Bragg,[3] of the heavy-atom method by J.M. Robertson [4,5] and by the F 2 function by A.L. Patterson.[6] Initially, most organic structures were limited to the analysis of only the principal projections because of the large and tedious experimental procedures and the large computational tasks. Various time-saving devices had been introduced both for collecting data, such as the Weissenbeg camera, and for the computational tasks, such as Beevers-Lipson strips.[7] The power of crystallography was being demonstrated more and more in the 1930s by, for instance, J. Desmond Bernal, Dorothy Crowfoot Hodgkin and Isidor Fankuchen [8] in their work on steroids and by Dorothy Crowfoot Hodgkin in the ...

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Ab initiophase determination for spherical viruses: parameter determination for spherical-shell models

Cited by 26 publications

References 7 publications

Ab initiocrystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

Ab initiocrystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell

Iterative projection algorithms for ab initio phasing in virus crystallography

Virus crystallography and structural virology: a personal perspective

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