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Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

Bottom Line: These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus

From trimer to crystal. (a) Two views of a cypovirus trimer coloured by secondary structure. In the left panel (viewing the trimer from the ‘top’) each polyhedrin monomer is delineated by a different background colour. The arrow on the right panel goes through the threefold axis. The smaller green trimers are for orientation aids for panel (b). (b) Trimers can come together progressively. Trimers facing ‘inwards’ and ‘outwards’ have been coloured cyan and green respectively to aid interpretation and show the view. The unit cell is marked for clarity although it is unlikely that assembly will occur solely within it. (c) Multiple copies of the dodecamer are arrayed in the crystal. For one dodecamer each trimer is coloured individually. For clarity the dodecamers at the 1/2, 1/2, 1/2 position are coloured light pink. For all the panels the ‘core’ structure shown is that of CPV5 using just the residues which are aligned between all the 9 polyhedrin structures. Structural alignments were performed with SHP (Stuart et al., 1979). The surface maps have been progressively smoothed which results in a slightly coarse and stylised rendering but which helps to visualise the complicated interactions.
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f0010: From trimer to crystal. (a) Two views of a cypovirus trimer coloured by secondary structure. In the left panel (viewing the trimer from the ‘top’) each polyhedrin monomer is delineated by a different background colour. The arrow on the right panel goes through the threefold axis. The smaller green trimers are for orientation aids for panel (b). (b) Trimers can come together progressively. Trimers facing ‘inwards’ and ‘outwards’ have been coloured cyan and green respectively to aid interpretation and show the view. The unit cell is marked for clarity although it is unlikely that assembly will occur solely within it. (c) Multiple copies of the dodecamer are arrayed in the crystal. For one dodecamer each trimer is coloured individually. For clarity the dodecamers at the 1/2, 1/2, 1/2 position are coloured light pink. For all the panels the ‘core’ structure shown is that of CPV5 using just the residues which are aligned between all the 9 polyhedrin structures. Structural alignments were performed with SHP (Stuart et al., 1979). The surface maps have been progressively smoothed which results in a slightly coarse and stylised rendering but which helps to visualise the complicated interactions.

Mentions: To investigate whether the conservation of the molecular structure and crystal packing arises from conserved interactions, the inter- and intramolecular interactions made by residues were plotted against residue number (Fig. S4). This confirms that both the inter- and intramolecular interactions are broadly conserved across all nine polyhedra. The strongest intermolecular interactions define a trimer composed of a cluster of three β-barrels sandwiched by helices top and bottom (Fig. 2a). Strong hydrophobic interactions and large numbers of hydrogen bonds, mainly involving H3, H4, elements within V3 and sheet-CHE, bind the trimer around the body diagonal threefold axes. Some 38% of the amino acids in each subunit participate in the interface, which buries ∼3500 Å2 of surface area (Fig. S4a). Three outstretched arms, formed mainly by H1 mediate, in part, a complex higher-level assembly, with each trimer contacting eight others. These arms stretch to contact another trimer on the far side of the unit cell (translated in the direction of a cell edge). The strongest trimer-trimer interactions are also lateral, involving trimers tightly packed along a cell edge, forming contacts of ∼8000 Å2 per trimer (involving ∼55% of amino acids, Figs. 2b and S4b). A further interaction of ∼28% of the polyhedrin amino acids, burying ∼1500 Å2 of surface per trimer (Figs. 2b and S4b) is also formed. The net effect of these lateral interactions is to form layers of molecules in all three directions, stacked alternately (Fig. 2c). As the network of trimers builds up, four trimers are brought close together around (0, 0, 0) and (1/2, 1/2, 1/2), to form a dodecameric arrangement and there is interaction mainly between the base domains (Figs. 2b and S4b) (involving around 9% of amino acids, and burying ∼900–1800 Å2 per trimer). The sum of such interactions, from which the whole network of a polyhedron crystal can be constructed, involves the majority of the surface of the trimer (Fig. S4b).


Polyhedra structures and the evolution of the insect viruses.

Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI - J. Struct. Biol. (2015)

From trimer to crystal. (a) Two views of a cypovirus trimer coloured by secondary structure. In the left panel (viewing the trimer from the ‘top’) each polyhedrin monomer is delineated by a different background colour. The arrow on the right panel goes through the threefold axis. The smaller green trimers are for orientation aids for panel (b). (b) Trimers can come together progressively. Trimers facing ‘inwards’ and ‘outwards’ have been coloured cyan and green respectively to aid interpretation and show the view. The unit cell is marked for clarity although it is unlikely that assembly will occur solely within it. (c) Multiple copies of the dodecamer are arrayed in the crystal. For one dodecamer each trimer is coloured individually. For clarity the dodecamers at the 1/2, 1/2, 1/2 position are coloured light pink. For all the panels the ‘core’ structure shown is that of CPV5 using just the residues which are aligned between all the 9 polyhedrin structures. Structural alignments were performed with SHP (Stuart et al., 1979). The surface maps have been progressively smoothed which results in a slightly coarse and stylised rendering but which helps to visualise the complicated interactions.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4597613&req=5

f0010: From trimer to crystal. (a) Two views of a cypovirus trimer coloured by secondary structure. In the left panel (viewing the trimer from the ‘top’) each polyhedrin monomer is delineated by a different background colour. The arrow on the right panel goes through the threefold axis. The smaller green trimers are for orientation aids for panel (b). (b) Trimers can come together progressively. Trimers facing ‘inwards’ and ‘outwards’ have been coloured cyan and green respectively to aid interpretation and show the view. The unit cell is marked for clarity although it is unlikely that assembly will occur solely within it. (c) Multiple copies of the dodecamer are arrayed in the crystal. For one dodecamer each trimer is coloured individually. For clarity the dodecamers at the 1/2, 1/2, 1/2 position are coloured light pink. For all the panels the ‘core’ structure shown is that of CPV5 using just the residues which are aligned between all the 9 polyhedrin structures. Structural alignments were performed with SHP (Stuart et al., 1979). The surface maps have been progressively smoothed which results in a slightly coarse and stylised rendering but which helps to visualise the complicated interactions.
Mentions: To investigate whether the conservation of the molecular structure and crystal packing arises from conserved interactions, the inter- and intramolecular interactions made by residues were plotted against residue number (Fig. S4). This confirms that both the inter- and intramolecular interactions are broadly conserved across all nine polyhedra. The strongest intermolecular interactions define a trimer composed of a cluster of three β-barrels sandwiched by helices top and bottom (Fig. 2a). Strong hydrophobic interactions and large numbers of hydrogen bonds, mainly involving H3, H4, elements within V3 and sheet-CHE, bind the trimer around the body diagonal threefold axes. Some 38% of the amino acids in each subunit participate in the interface, which buries ∼3500 Å2 of surface area (Fig. S4a). Three outstretched arms, formed mainly by H1 mediate, in part, a complex higher-level assembly, with each trimer contacting eight others. These arms stretch to contact another trimer on the far side of the unit cell (translated in the direction of a cell edge). The strongest trimer-trimer interactions are also lateral, involving trimers tightly packed along a cell edge, forming contacts of ∼8000 Å2 per trimer (involving ∼55% of amino acids, Figs. 2b and S4b). A further interaction of ∼28% of the polyhedrin amino acids, burying ∼1500 Å2 of surface per trimer (Figs. 2b and S4b) is also formed. The net effect of these lateral interactions is to form layers of molecules in all three directions, stacked alternately (Fig. 2c). As the network of trimers builds up, four trimers are brought close together around (0, 0, 0) and (1/2, 1/2, 1/2), to form a dodecameric arrangement and there is interaction mainly between the base domains (Figs. 2b and S4b) (involving around 9% of amino acids, and burying ∼900–1800 Å2 per trimer). The sum of such interactions, from which the whole network of a polyhedron crystal can be constructed, involves the majority of the surface of the trimer (Fig. S4b).

Bottom Line: These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability.By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes.Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.

No MeSH data available.


Related in: MedlinePlus