The ionic properties of the filamentous bacteriophages Pf1 and fd.

Zimmermann, Karel; Hagedorn, H; Heuck, C C; Hinrichsen, M; Ludwig, H.

doi:10.1016/s0021-9258(17)35990-2

Cited by 125 publications

(66 citation statements)

References 21 publications

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“…A similar observation has been made for the coat proteins that assemble on its DNA to form a complete fd bacteriophage, extracted from E. coli bacteria (Marvin and Hohn 1969;Marvin et al 1994), where the dissociation of condensed ions is responsible for the binding of DNA strands (Kang 2021;Zimmermann et al 1986). To conclude, the system of hydrophobic-salt-induced reversible DNA strand fluctuations is able both experimentally and theoretically to provide an understand of their active motions.…”

Section: Discussionsupporting

confidence: 62%

Direct visualization of local activities of long DNA strands via image–time correlation

Kang

Sadakane

2021

Eur Biophys J

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Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5–10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of $$\upmu m$$ μ m ) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image–time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.

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Section: Discussionsupporting

confidence: 62%

Direct visualization of local activities of long DNA strands via image–time correlation

Kang

Sadakane

2021

Eur Biophys J

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“…For bacteriophage Pf1 a cylinder radius of 3.35 nm, a density of 1.46 g/ cm 3 , a surface charge density of ÿ0.475 e/nm 2 , and a liquid crystal order parameter of 0.9 was used (Zimmermann et al, 1986). The static dielectric constant of water was set to 78.29.…”

Section: Calculation Of Electrostatic Interactionsmentioning

confidence: 99%

Prediction of Charge-Induced Molecular Alignment of Biomolecules Dissolved in Dilute Liquid-Crystalline Phases

Zweckstetter

Hummer

Bax

2004

Biophysical Journal

116

123

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Alignment of macromolecules in nearly neutral aqueous lyotropic liquid-crystalline media such as bicelles, commonly used in macromolecular NMR studies, can be predicted accurately by a steric obstruction model (Zweckstetter and Bax, 2000). A simple extension of this model is described that results in improved predictions for both the alignment orientation and magnitude of protein and DNA solutes in charged nematic media, such as the widely used medium of filamentous phage Pf1. The extended model approximates the electrostatic interaction between a solute and an ordered phage particle as that between the solute's surface charges and the electric field of the phage. The model is evaluated for four different proteins and a DNA oligomer. Results indicate that alignment in charged nematic media is a function not only of the solute's shape, but also of its electric multipole moments of net charge, dipole, and quadrupole. The relative importance of these terms varies greatly from one macromolecule to another, and evaluation of the experimental data indicates that these terms scale differently with ionic strength. For several of the proteins, the calculated alignment is sensitive to the precise position of the charged groups on the protein surface. This suggests that NMR alignment measurements can potentially be used to probe protein electrostatics. Inclusion of electrostatic interactions in addition to steric effects makes the extended model applicable to all liquid crystals used in biological NMR to date.

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“…Another versatile colloidal rod-like model system that has been investigated [34][35][36] is semi-flexible filamentous fd-virus. The viruses have an aspect ratio ≈ 130 and are charge stabilized at values of pH > 4.2 due to the negative surface charge of the coat proteins 37 . In several studies, fd-virus has been used to mediate an attraction between single spherical particles and a fixed wall and to determine the corresponding depletion potential 17,[19][20][21] .…”

Section: Introductionmentioning

confidence: 99%

Phase stability of colloidal mixtures of spheres and rods

Opdam

Guu

Schelling

et al. 2021

The Journal of Chemical Physics

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We determined the phase boundaries of aqueous mixtures containing colloidal rod-like fd-viruses and polystyrene spheres using diffusing-wave spectroscopy and compared the results with free volume theory predictions. Excluded volume interactions in mixtures of colloidal rods and spheres lead to mediated depletion interactions. The strength and range of this attractive interaction depend on the concentrations of the particles, the length L and diameter D of the rods and the radius R of the spheres. At strong enough attraction, this depletion interaction leads to phase separation. We experimentally determined the rod and sphere concentrations where these phase transitions occur by systematically varying the size ratios L/R and D/R and the aspect ratio L/D. This was done by using spheres with different radii and modifying the effective diameter of the rods through either the ionic strength of the buffer or anchoring a polymeric brush to the surface of the rods. The observed phase transitions were from a binary fluid to a colloidal gas/liquid phase coexistence which occurred already at very low concentrations due to the depletion efficiency of highly anisotropic rods. The experimentally measured phase transitions were compared to phase boundaries obtained using free volume theory (FVT), a well established theory for calculating the phase behaviour of colloidal particles mixed with depletants. We find good correspondence between the experimental phase transitions and the theoretical FVT model where the excluded volume of the rod-like depletants was explicitly accounted for in both the reservoir and the system.

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The ionic properties of the filamentous bacteriophages Pf1 and fd.

Cited by 125 publications

References 21 publications

Direct visualization of local activities of long DNA strands via image–time correlation

Direct visualization of local activities of long DNA strands via image–time correlation

Prediction of Charge-Induced Molecular Alignment of Biomolecules Dissolved in Dilute Liquid-Crystalline Phases

Phase stability of colloidal mixtures of spheres and rods

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