Solution structure of bacteriophage T4D and icosahedral capsid geometry visualized in freeze-fractured, deep-etched replicas

The prolate icosahedral capsid geometry of wild type bacteriophage T4D has been determined by direct visualization of the triangular faces in stereoimages of transmission electron micrographs of phage particles. Bacteriophage T4 was prepared for transmission electron microscopy (TEM) following a protocol of freeze-fracturing, deep-etching (FDET) and replication by vertical deposition (80 degrees angle) of a thin platinum-carbon (Pt-C) metal layer of 1.01 nm. From direct statistical measurements of the ratio of the head length to width and of stereometric angles on T4 heads, we have estimated a Q number of 21. This confirms previous indirect studies on T4 and agrees with determinations on bacteriophage T2. Many of the structural features of T4 observed in FDET preparations differ significantly from those observed by classical negative staining methods for TEM imaging. Most important among the differences are the conformation of the baseplate (a closed rosebud) and the positioning of the tail fibers (retracted). The retracted position of the tail fibers in the FDET preparations has been confirmed by negatively staining phage previously fixed suspended in solution with 2% glutaraldehyde. The FDET protocols appear to reveal important structural features not seen in negative stained preparations. These have implications for bacteriophage T4 conformation in solution, viral assembly and phage conformation states prior to tail contraction and DNA ejection.     

Solution Structure of Bacteriophage T4D and Icosahedral Capsid Geometry Visualized in Freeze-Fractured,Deep-Etched Replicas

Abstract

The prolate icosahedral capsid geometry of wild type bacteriophage T4D has been determined by direct visualization of the triangular faces in stereoimages of transmission electron micrographs of phage particles. Bacteriophage T4 was prepared for transmission electron microscopy (TEM) following a protocol of freeze-fracturing, deep-etching (FDET) and replication by vertical deposition (80° angle) of a thin platinum-carbon (Pt-C) metal layer of 1.01 nm. From direct statistical measurements of the ratio of the head length to width and of stereometric angles on T4 heads, we have estimated a Q number of 21. This confirms previous indirect studies on T4 and agrees with determinations on bacteriophage T2. Many of the structural features of T4 observed in FDET preparations differ significantly from those observed by classical negative staining methods for TEM imaging. Most important among the differences are the conformation of the baseplate (a closed rosebud) and the positioning of the tail fibers (retracted). The retracted position of the tail fibers in the FDET preparations has been confirmed by negatively staining phage previously fixed suspended in solution with 2% glutaraldehyde. The FDET protocols appear to reveal important structural features not seen in negative stained preparations. These have implications for bacteriophage T4 conformation in solution, viral assembly and phage conformation states prior to tail contraction and DNA ejection.     

Hydrodynamics,size, and shape of bacteriophage T4D tails and baseplates

We have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to be D = 8.56 × 10^?8 cm²/s. For the tail, we found D = 5.88 × 10^?8 cm²/s by QLS, and D = 6.02 × 10^?8 cm²/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex-to-vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320-Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube-sheath-connector complex 1050-Å long and 240 Å in diameter, the calculated D is 5.93 × 10^?8 cm²/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the structure of biomolecular complexes.     

Joining of bacteriophage T4D heads and tails: A kinetic study by inelastic light scattering

We have used inelastic laser light scattering to study the kinetics of the spontaneous assembly of heads and tails of bacteriophage T4D to form noninfectious tail fiberless particles. For interpretation of the kinetics, it was first necessary to determine the physical properties of the strongly scattering phage parts. For heads, these are D_{20,w = 3.60 × 10⁻⁸cm²/s, 820,w = 1025 S, M = 1.76 × 10⁸}. For tail fiberless particles, D_20,w = 3.14 × 10⁻⁸cm²/s, 8_20,w = 968 S, and M = 1.95 × 10⁸. The kinetics of the head-tail joining process was followed by measuring the time variation of the homodyne scattering autocorrelation function. This was interpreted as a sum of exponentials whose decay constants were known from the scattering angle and the diffusion coefficients, and whose amplitudes were related to the concentrations of reactants and products. Scattering experiments at 22 °C gave a bimolecular rate constant of 1.02 × 10⁷m⁻¹ s⁻¹, while infectivity assays at 30 °C gave a rate constant of 1.28 × 10⁷. Adjustment of both rate constants to 20 °C, assuming diffusion controlled reaction, gave 0.97 × 10⁷ and 0.98 × 10⁷m⁻¹ s⁻¹, respectively. This rate is about $\text{1}\text{500}$ that predicted by Smoluchowski theory for a diffusion controlled reaction between two spherical particles; the discrepancy is largely explicable from orientational factors.     

Ionic strength effects on macroion diffusion and excess light-scattering intensities of short DNA rods

Quasielastic and static light-scattering measurements were made on DNA isolated from chicken erythrocyte mononucleosomes as a function of ionic strength between 6 × 10^?4 and 1.0M. A transition from single-exponential autocorrelation functions to markedly non-single-exponential decays was observed around 10^?2M ionic strength and was accompanied by a large decrease in the excess light-scattering intensity. Autocorrelation functions recorded below 10^?2M salt were well fit by the sum of two exponential relaxation which differed by as much as 100-fold in time constants. Apparent diffusion coefficients for the fast and slow processes plateaued around 10^?3M with numerical values approximately 10-fold and 1/10, respectively, of the translational diffusion coefficient for mononucleosome DNA at high ionic strength. This behavior is similar to that observed with poly(L -lysine), for which the slow decay has been associated with a transition to an extraordinary phase. The strong and complex salt dependence observed here illustrates potential difficulties in deriving structural information from scattering by polyions at low ionic strength.