Two forms of Pf1Inovirus: X-ray diffraction studies on a structural phase transition and a calculated libration normal mode of the asymmetric unit

The molecular structure and structural transition of the α-helical capsid in filamentous bacteriophage Pf1

“…We de®ned the shape of the protein capsid model and then calculated the transform of uniform density solvent inside this volume, which we subtracted from the transform of the molecule (including all H atoms) calculated relative to vacuum, as described by and Marvin et al (1992). We applied a temperature factor B = 200 A Ê 2 to the solvent transform to ensure that any false detail in the solvent correction did not affect the higher resolution data.…”

“…The data in PDB entry r4ifmsf are oversampled along the layer-lines by about a factor of three, but if we use only every third data point, there are 1183 independent data points in the resolution range 12±2.6 A Ê . We calculated free R values from ten independent simulated-annealing re®nements, omitting randomly about 10% of the 1183 independent data points as for single-crystal data (Bru È nger, 1997), rather than blocks of layer-lines as described by Welsh, Symmons et al (1998) (Marvin et al, 1992;Gonzalez et al, 1995). We also calculated transforms of our Pf1 H model for |n| max = 30 and for |n| max = 60 and could detect no difference between these two transforms within the accuracy of the experimental data.…”

“…The Pf1 virion undergoes a reversible temperature-induced structural transition between the canonical higher temperature form (Pf1 H ) above about 283 K and a lower temperature form (Pf1 L ) below this temperature; bacteriophages fd and Pf3 do not show such a transition (Wachtel et al, , 1977Nave et al, 1979;Hinz et al, 1980;Marvin et al, 1981Marvin et al, , 1992Welsh, Symmons et al, 1998). As a consequence of the transition, a small change in the relationship between one subunit and the next is ampli®ed over the 2000 nm length of the Pf1 virion, such that one end of the virion rotates by about 15 turns with respect to the other end and the length of the virion changes by about 100 nm.…”

“…The ambiguities were eventually fully resolved using higher resolution diffraction data from native virions and heavy-atom derivatives, and using a maximumentropy method to calculate a model-independent electrondensity distribution (Nave et al, 1979Marvin et al, 1981Marvin et al, , 1987Bryan et al, 1983;, enabling a molecular model to be built and re®ned against the quantitative X-ray data (Bryan et al, 1983;Marvin, 1990a,b;Marvin et al, 1992;Gonzalez et al, 1995). The canonical class II Pf1 virion has 27 subunits in ®ve turns of a right-handed helix with an axial repeat c of about 75±80 A Ê (c varies slightly with the water content of the ®bre; Marvin et al, 1974).…”

Intersubunit Hydrophobic Interactions in Pf1 Filamentous Phage

“…The transition is clearly a property of a single virion particle, as shown by studies done at varying concentrations of 100 mg/ml by Raman optical activity (16), 50 mg/ml by NMR (17), 20 mg/ml by diffraction from oriented gels (10), and 0.5 mg/ml and lower by calorimetry and CD (18). However, the transition is apparently blocked at the very high concentrations of 400 mg/ml or more in fibers; dry fibers made at the high temperature exhibit the same diffraction pattern when the temperature is lowered to 4°C and vice versa (9,19). The electronic and vibrational spectroscopies revealed little if any change in protein conformation, although changes involving DNA have been observed by CD and Raman optical activity (16,20).…”