The Experts below are selected from a list of 234 Experts worldwide ranked by ideXlab platform

Da Marvin - One of the best experts on this subject based on the ideXlab platform.

  • Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR
    European Biophysics Journal, 2011
    Co-Authors: S. K. Straus, W. R. P. Scott, Charles D Schwieters, Da Marvin
    Abstract:

    Filamentous bacteriophages (filamentous bacterial viruses or Inovirus ) are simple and well-characterised macromolecular assemblies that are widely used in molecular biology and biophysics, both as paradigms for studying basic biological questions and as practical tools in areas as diverse as immunology and solid-state physics. The strains fd, M13 and f1 are virtually identical filamentous phages that infect bacteria expressing F-pili, and are sometimes grouped as the Ff phages. For historical reasons fd has often been used for structural studies, but M13 and f1 are more often used for biological experiments. Many other strains have been identified that are genetically quite distinct from Ff and yet have a similar molecular structure and life cycle. One of these, Pf1, gives the highest resolution X-ray fibre diffraction patterns known for filamentous bacteriophage. These diffraction patterns have been used in the past to derive a molecular model for the structure of the phage. Solid-state NMR experiments have been used in separate studies to derive a significantly different model of Pf1. Here we combine previously published X-ray fibre diffraction data and solid-state NMR data to give a consensus structure model for Pf1 filamentous bacteriophage, and we discuss the implications of this model for assembly of the phage at the bacterial membrane.

  • The hand of the filamentous bacteriophage helix
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, Da Marvin
    Abstract:

    Filamentous bacteriophage ( Inovirus ) is a widely studied model system in molecular biophysics. The structure of the virion has been analysed by various methods, but the methods have seldom questioned the hand of the virion helix. The hand of the helix relating the protein subunits in the class II virus strain Pf1 was chosen by calculating an electron-density distribution from X-ray fibre diffraction data, using a maximum-entropy method, but to our knowledge this method has not been used for a similar purpose in any other system. Moreover, this same hand was extended only by analogy, with no direct analysis of the corresponding data, to the class I virus strain Ff (fd, f1, M13), which has a different helix symmetry. Here we use published solid-state NMR data to confirm the validity of the hand of Pf1 chosen by the maximum-entropy method, and to confirm the extension to Ff.

  • On the structures of filamentous bacteriophage Ff (fd, f1, M13)
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, M. F. Symmons, Da Marvin
    Abstract:

    The filamentous bacteriophage ( Inovirus ) strain Ff (fd, f1, M13) is widely used in molecular biophysics as a simple model system. A low resolution molecular model of the fd protein coat has been reported, derived from iterative helical real space reconstruction of cryo-electron micrographs (cryoEM). This model is significantly different from the model previously derived from X-ray fibre diffraction and solid-state NMR. We show that the cryoEM model agrees neither with solid-state NMR data nor with X-ray fibre diffraction data of fd, and has some puzzling structural features, for instance nanometre holes through the protein coat. We refine the cryoEM model against the X-ray data, and find that the model after refinement closely approximates the model derived directly from X-ray fibre diffraction and solid-state NMR data. We suggest possible reasons for the differences between the models derived from cryoEM and X-ray diffraction.

  • Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane.
    Journal of molecular biology, 2005
    Co-Authors: Da Marvin, W. R. P. Scott, Liam C. Welsh, Martyn F. Symmons, S. K. Straus
    Abstract:

    Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 A in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1 and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly.

  • The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus
    Journal of molecular biology, 2001
    Co-Authors: Dennis M Pederson, Da Marvin, Liam C. Welsh, Richard N. Perham, Matthew Sampson, Michael R. Slater
    Abstract:

    Abstract The PH75 strain of filamentous bacteriophage (Inovirus) grows in the thermophilic bacterium Thermus thermophilus at 70 °C. We have characterized the viral DNA and determined the amino acid sequence of the major coat protein, p8. The p8 protein is synthesized without a leader sequence, like that of bacteriophage Pf3 but unlike that of bacteriophage Pf1, both of which grow in the mesophile Pseudomonas aeruginosa. X-ray diffraction patterns from ordered fibres of the PH75 virion are similar to those from bacteriophages Pf1 and Pf3, indicating that the protein capsid of the PH75 virion has the same helix symmetry and subunit shape, even though the primary structures of the major coat proteins are quite different and the virions assemble at very different temperatures. We have used this information to build a molecular model of the PH75 protein capsid based on that of Pf1, and refined the model by simulated annealing, using fibre diffraction data extending to 2.4 A resolution in the meridional direction and to 3.1 A resolution in the equatorial direction. The common design may reflect a fundamental motif of α-helix packing, although differences exist in the DNA packaging and in the means of insertion of the major coat protein of these filamentous bacteriophages into the membrane of the host bacterial cell. These may reflect differences in the assembly mechanisms of the virions.

S. K. Straus - One of the best experts on this subject based on the ideXlab platform.

  • Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR
    European Biophysics Journal, 2011
    Co-Authors: S. K. Straus, W. R. P. Scott, Charles D Schwieters, Da Marvin
    Abstract:

    Filamentous bacteriophages (filamentous bacterial viruses or Inovirus ) are simple and well-characterised macromolecular assemblies that are widely used in molecular biology and biophysics, both as paradigms for studying basic biological questions and as practical tools in areas as diverse as immunology and solid-state physics. The strains fd, M13 and f1 are virtually identical filamentous phages that infect bacteria expressing F-pili, and are sometimes grouped as the Ff phages. For historical reasons fd has often been used for structural studies, but M13 and f1 are more often used for biological experiments. Many other strains have been identified that are genetically quite distinct from Ff and yet have a similar molecular structure and life cycle. One of these, Pf1, gives the highest resolution X-ray fibre diffraction patterns known for filamentous bacteriophage. These diffraction patterns have been used in the past to derive a molecular model for the structure of the phage. Solid-state NMR experiments have been used in separate studies to derive a significantly different model of Pf1. Here we combine previously published X-ray fibre diffraction data and solid-state NMR data to give a consensus structure model for Pf1 filamentous bacteriophage, and we discuss the implications of this model for assembly of the phage at the bacterial membrane.

  • The hand of the filamentous bacteriophage helix
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, Da Marvin
    Abstract:

    Filamentous bacteriophage ( Inovirus ) is a widely studied model system in molecular biophysics. The structure of the virion has been analysed by various methods, but the methods have seldom questioned the hand of the virion helix. The hand of the helix relating the protein subunits in the class II virus strain Pf1 was chosen by calculating an electron-density distribution from X-ray fibre diffraction data, using a maximum-entropy method, but to our knowledge this method has not been used for a similar purpose in any other system. Moreover, this same hand was extended only by analogy, with no direct analysis of the corresponding data, to the class I virus strain Ff (fd, f1, M13), which has a different helix symmetry. Here we use published solid-state NMR data to confirm the validity of the hand of Pf1 chosen by the maximum-entropy method, and to confirm the extension to Ff.

  • On the structures of filamentous bacteriophage Ff (fd, f1, M13)
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, M. F. Symmons, Da Marvin
    Abstract:

    The filamentous bacteriophage ( Inovirus ) strain Ff (fd, f1, M13) is widely used in molecular biophysics as a simple model system. A low resolution molecular model of the fd protein coat has been reported, derived from iterative helical real space reconstruction of cryo-electron micrographs (cryoEM). This model is significantly different from the model previously derived from X-ray fibre diffraction and solid-state NMR. We show that the cryoEM model agrees neither with solid-state NMR data nor with X-ray fibre diffraction data of fd, and has some puzzling structural features, for instance nanometre holes through the protein coat. We refine the cryoEM model against the X-ray data, and find that the model after refinement closely approximates the model derived directly from X-ray fibre diffraction and solid-state NMR data. We suggest possible reasons for the differences between the models derived from cryoEM and X-ray diffraction.

  • Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane.
    Journal of molecular biology, 2005
    Co-Authors: Da Marvin, W. R. P. Scott, Liam C. Welsh, Martyn F. Symmons, S. K. Straus
    Abstract:

    Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 A in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1 and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly.

Liam C. Welsh - One of the best experts on this subject based on the ideXlab platform.

  • Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane.
    Journal of molecular biology, 2005
    Co-Authors: Da Marvin, W. R. P. Scott, Liam C. Welsh, Martyn F. Symmons, S. K. Straus
    Abstract:

    Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 A in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1 and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly.

  • The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus
    Journal of molecular biology, 2001
    Co-Authors: Dennis M Pederson, Da Marvin, Liam C. Welsh, Richard N. Perham, Matthew Sampson, Michael R. Slater
    Abstract:

    Abstract The PH75 strain of filamentous bacteriophage (Inovirus) grows in the thermophilic bacterium Thermus thermophilus at 70 °C. We have characterized the viral DNA and determined the amino acid sequence of the major coat protein, p8. The p8 protein is synthesized without a leader sequence, like that of bacteriophage Pf3 but unlike that of bacteriophage Pf1, both of which grow in the mesophile Pseudomonas aeruginosa. X-ray diffraction patterns from ordered fibres of the PH75 virion are similar to those from bacteriophages Pf1 and Pf3, indicating that the protein capsid of the PH75 virion has the same helix symmetry and subunit shape, even though the primary structures of the major coat proteins are quite different and the virions assemble at very different temperatures. We have used this information to build a molecular model of the PH75 protein capsid based on that of Pf1, and refined the model by simulated annealing, using fibre diffraction data extending to 2.4 A resolution in the meridional direction and to 3.1 A resolution in the equatorial direction. The common design may reflect a fundamental motif of α-helix packing, although differences exist in the DNA packaging and in the means of insertion of the major coat protein of these filamentous bacteriophages into the membrane of the host bacterial cell. These may reflect differences in the assembly mechanisms of the virions.

  • The molecular structure and structural transition of the alpha-helical capsid in filamentous bacteriophage Pf1.
    Acta Crystallographica Section D Biological Crystallography, 2000
    Co-Authors: Liam C. Welsh, Martyn F. Symmons, Da Marvin
    Abstract:

    The major coat protein in the capsid of Pf1 filamentous bacteriophage (Inovirus) forms a helical assembly of about 7000 identical protein subunits, each of which contains 46 amino-acid residues and can be closely approximated by a single gently curved alpha-helix. Since the viral DNA occupies the core of the tubular capsid and appears to make no significant specific interactions with the capsid proteins, the capsid is a simple model system for the study of the static and dynamic properties of alpha-helix assembly. The capsid undergoes a reversible temperature-induced structural transition at about 283 K between two slightly different helix forms. The two forms can coexist without an intermediate state, consistent with a first-order structural phase transition. The molecular model of the higher temperature form was refined using improved X-ray fibre diffraction data and new refinement and validation methods. The refinement indicates that the two forms are related by a change in the orientation of the capsid subunits within the virion, without a significant change in local conformation of the subunits. On the higher temperature diffraction pattern there is a region of observed intensity that is not consistent with a simple helix of identical subunits; it is proposed that the structure involves groups of three subunits which each have a slightly different orientation within the group. The grouping of subunits suggests that a change in subunit libration frequency could be the basis of the Pf1 structural transition; calculations from the model are used to explore this idea.

  • Analysis of X-ray diffraction from fibres of Pf1 Inovirus (filamentous bacteriophage) shows that the DNA in the virion is not highly ordered.
    Journal of molecular biology, 1998
    Co-Authors: Liam C. Welsh, Da Marvin, Richard N. Perham
    Abstract:

    X-ray fibre diffraction patterns of well-aligned Pf1 filamentous bacteriophage show sharp layer-lines attributable to an ordered helical array of protein subunits. Electron density maps calculated from the intensity on these layer-lines show no evidence for DNA following the symmetry of the protein, nor is there evidence on the diffraction patterns for the additional layer-lines expected if ordered DNA follows a symmetry different from that of the protein. We conclude that the interactions between DNA and protein in the Pf1 virion, like those in the Ff virion, are delocalized rather than specific, and the DNA structure in the virion is less regular than the protein structure. This conclusion has implications for the process of virion assembly, and we suggest a possible model for the change in the viral DNA symmetry as the DNA is passed to the virion from the intracellular complex with the viral gene 5 single-stranded DNA-binding protein.

  • Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution.
    Journal of molecular biology, 1998
    Co-Authors: Liam C. Welsh, Da Marvin, Martyn F. Symmons, Julian M. Sturtevant, Richard N. Perham
    Abstract:

    Abstract We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of α-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely α-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.

W. R. P. Scott - One of the best experts on this subject based on the ideXlab platform.

  • Consensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR
    European Biophysics Journal, 2011
    Co-Authors: S. K. Straus, W. R. P. Scott, Charles D Schwieters, Da Marvin
    Abstract:

    Filamentous bacteriophages (filamentous bacterial viruses or Inovirus ) are simple and well-characterised macromolecular assemblies that are widely used in molecular biology and biophysics, both as paradigms for studying basic biological questions and as practical tools in areas as diverse as immunology and solid-state physics. The strains fd, M13 and f1 are virtually identical filamentous phages that infect bacteria expressing F-pili, and are sometimes grouped as the Ff phages. For historical reasons fd has often been used for structural studies, but M13 and f1 are more often used for biological experiments. Many other strains have been identified that are genetically quite distinct from Ff and yet have a similar molecular structure and life cycle. One of these, Pf1, gives the highest resolution X-ray fibre diffraction patterns known for filamentous bacteriophage. These diffraction patterns have been used in the past to derive a molecular model for the structure of the phage. Solid-state NMR experiments have been used in separate studies to derive a significantly different model of Pf1. Here we combine previously published X-ray fibre diffraction data and solid-state NMR data to give a consensus structure model for Pf1 filamentous bacteriophage, and we discuss the implications of this model for assembly of the phage at the bacterial membrane.

  • The hand of the filamentous bacteriophage helix
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, Da Marvin
    Abstract:

    Filamentous bacteriophage ( Inovirus ) is a widely studied model system in molecular biophysics. The structure of the virion has been analysed by various methods, but the methods have seldom questioned the hand of the virion helix. The hand of the helix relating the protein subunits in the class II virus strain Pf1 was chosen by calculating an electron-density distribution from X-ray fibre diffraction data, using a maximum-entropy method, but to our knowledge this method has not been used for a similar purpose in any other system. Moreover, this same hand was extended only by analogy, with no direct analysis of the corresponding data, to the class I virus strain Ff (fd, f1, M13), which has a different helix symmetry. Here we use published solid-state NMR data to confirm the validity of the hand of Pf1 chosen by the maximum-entropy method, and to confirm the extension to Ff.

  • On the structures of filamentous bacteriophage Ff (fd, f1, M13)
    European Biophysics Journal, 2008
    Co-Authors: S. K. Straus, W. R. P. Scott, M. F. Symmons, Da Marvin
    Abstract:

    The filamentous bacteriophage ( Inovirus ) strain Ff (fd, f1, M13) is widely used in molecular biophysics as a simple model system. A low resolution molecular model of the fd protein coat has been reported, derived from iterative helical real space reconstruction of cryo-electron micrographs (cryoEM). This model is significantly different from the model previously derived from X-ray fibre diffraction and solid-state NMR. We show that the cryoEM model agrees neither with solid-state NMR data nor with X-ray fibre diffraction data of fd, and has some puzzling structural features, for instance nanometre holes through the protein coat. We refine the cryoEM model against the X-ray data, and find that the model after refinement closely approximates the model derived directly from X-ray fibre diffraction and solid-state NMR data. We suggest possible reasons for the differences between the models derived from cryoEM and X-ray diffraction.

  • Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane.
    Journal of molecular biology, 2005
    Co-Authors: Da Marvin, W. R. P. Scott, Liam C. Welsh, Martyn F. Symmons, S. K. Straus
    Abstract:

    Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 A in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1 and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly.

Richard N. Perham - One of the best experts on this subject based on the ideXlab platform.

  • The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus
    Journal of molecular biology, 2001
    Co-Authors: Dennis M Pederson, Da Marvin, Liam C. Welsh, Richard N. Perham, Matthew Sampson, Michael R. Slater
    Abstract:

    Abstract The PH75 strain of filamentous bacteriophage (Inovirus) grows in the thermophilic bacterium Thermus thermophilus at 70 °C. We have characterized the viral DNA and determined the amino acid sequence of the major coat protein, p8. The p8 protein is synthesized without a leader sequence, like that of bacteriophage Pf3 but unlike that of bacteriophage Pf1, both of which grow in the mesophile Pseudomonas aeruginosa. X-ray diffraction patterns from ordered fibres of the PH75 virion are similar to those from bacteriophages Pf1 and Pf3, indicating that the protein capsid of the PH75 virion has the same helix symmetry and subunit shape, even though the primary structures of the major coat proteins are quite different and the virions assemble at very different temperatures. We have used this information to build a molecular model of the PH75 protein capsid based on that of Pf1, and refined the model by simulated annealing, using fibre diffraction data extending to 2.4 A resolution in the meridional direction and to 3.1 A resolution in the equatorial direction. The common design may reflect a fundamental motif of α-helix packing, although differences exist in the DNA packaging and in the means of insertion of the major coat protein of these filamentous bacteriophages into the membrane of the host bacterial cell. These may reflect differences in the assembly mechanisms of the virions.

  • Analysis of X-ray diffraction from fibres of Pf1 Inovirus (filamentous bacteriophage) shows that the DNA in the virion is not highly ordered.
    Journal of molecular biology, 1998
    Co-Authors: Liam C. Welsh, Da Marvin, Richard N. Perham
    Abstract:

    X-ray fibre diffraction patterns of well-aligned Pf1 filamentous bacteriophage show sharp layer-lines attributable to an ordered helical array of protein subunits. Electron density maps calculated from the intensity on these layer-lines show no evidence for DNA following the symmetry of the protein, nor is there evidence on the diffraction patterns for the additional layer-lines expected if ordered DNA follows a symmetry different from that of the protein. We conclude that the interactions between DNA and protein in the Pf1 virion, like those in the Ff virion, are delocalized rather than specific, and the DNA structure in the virion is less regular than the protein structure. This conclusion has implications for the process of virion assembly, and we suggest a possible model for the change in the viral DNA symmetry as the DNA is passed to the virion from the intracellular complex with the viral gene 5 single-stranded DNA-binding protein.

  • Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution.
    Journal of molecular biology, 1998
    Co-Authors: Liam C. Welsh, Da Marvin, Martyn F. Symmons, Julian M. Sturtevant, Richard N. Perham
    Abstract:

    Abstract We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of α-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely α-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.

  • Evidence for Tilted Smectic Liquid Crystalline Packing of fd Inovirus from X-ray Fiber Diffraction
    Macromolecules, 1996
    Co-Authors: Liam C. Welsh, Martyn F. Symmons, C. Nave, Richard N. Perham, E. A. Marseglia, Da Marvin
    Abstract:

    Fibers of the fd strain of Inovirus (filamentous bacteriophage) prepared above its isoelectric point (about pH 4) give X-ray diffraction patterns, higher pH patterns, that differ from the patterns of fd fibers below the isoelectric point, lower pH patterns. The overall distribution of intensity on higher and lower pH patterns is substantially the same, indicating that the virion structure is substantially the same, but the crystalline reflections that define the packing of the virions in crystallites are different. For the lower pH patterns, the crystalline reflections can be indexed on a conventional hexagonal lattice. However, for the higher pH patterns, the crystalline reflections on the equator and first layer line are spread out in a broad, angular, but specific fashion (layer-line fanning), unlike disorientation spreading. We interpret this observation to mean that the crystallites in the higher pH fiber are tilted with respect to the fiber axis. This interpretation is supported by simulated fiber diffraction patterns calculated from models of the packing of tilted virions. The diffraction patterns from fibers of some mutants of fd, and from other wild-type strains of Inovirus (M13, IKe, If1), do not show layer-line fanning. We propose that the tilting of crystallites that gives rise to layer-line fanning in fd fibers is due both to a specific pattern of charge on the surface of the fd virion at higher pH and to the presence of a specific inter-subunit hydrogen bond. Apparently these features of the fd virion structure require a strict 2-fold screw axis along the virion axis that affects the packing between neighboring virions, resulting in the formation of a tilted smectic liquid crystal phase.