Turbidity measurements in an analytical ultracentrifuge. Determinations of mass per length for filamentous viruses fd, Xf, and Pf3

Polyelectrolyte Complexes from Oppositely Charged Filamentous Viruses

Here, we present an explorative study on a new type of polyelectrolyte complex made from chemically modified filamentous fd viruses. The fd virus is a semiflexible rod-shaped bacteriophage with a length of 880 nm and a diameter of 6.6 nm, which has been widely used as a well-defined model system of colloidal rods to investigate phase, flow, and other behavior. Here, chemically modified viruses have been prepared to obtain two types with opposite electrical charges in addition to a steric stabilization layer by poly(ethylene glycol) (PEG) grafting. The complex formation of stoichiometric mixtures of these oppositely charged viruses is studied as a function of virus and salt concentration. Furthermore, static light scattering measurements show a varying, strong increase in scattering intensity in some samples without visual macroscopic complex formation. Finally, the results of the complex formation are rationalized by comparing to model calculations on the pair interaction potential between oppositely charged viruses.

The Applicability of Current Turbidimetric Approaches for Analyzing Fibrin Fibers and Other Filamentous Networks

Turbidimetry is an experimental technique often used to study the structure of filamentous networks. To extract structural properties such as filament diameter from turbidimetric data, simplifications to light scattering theory must be employed. In this work, we evaluate the applicability of three commonly utilized turbidimetric analysis approaches, each using slightly different simplifications. We make a specific application towards analyzing fibrin fibers, which form the structural scaffold of blood clots, but the results are generalizable. Numerical simulations were utilized to assess the applicability of each approach across a range of fiber lengths and diameters. Simulation results indicated that all three turbidimetric approaches commonly underestimate fiber diameter, and that the “Carr-Hermans” approach, utilizing wavelengths in the range of 500−800 nm, provided <10% error for the largest number of diameter/length combinations. These theoretical results were confirmed, under select conditions, via the comparison of fiber diameters extracted from experimental turbidimetric data, with diameters obtained using super-resolution microscopy.

Virus-poly(3,4-ethylenedioxythiophene) biocomposite films

Virus-poly(3,4-ethylenedioxythiophene) (virus-PEDOT) biocomposite films are prepared by electropolymerizing 3,4-ethylenedioxythiophene (EDOT) in aqueous electrolytes containing 12 mM LiClO(4) and the bacteriophage M13. The concentration of virus in these solutions, [virus](soln), is varied from 3 to 15 nM. A quartz crystal microbalance is used to directly measure the total mass of the biocomposite film during its electrodeposition. In combination with a measurement of the electrodeposition charge, the mass of the virus incorporated into the film is calculated. These data show that the concentration of the M13 within the electropolymerized film, [virus](film), increases linearly with [virus](soln). The incorporation of virus particles into the PEDOT film from solution is efficient, resulting in a concentration ratio of [virus](film):[virus](soln) ≈ 450. Virus incorporation into the PEDOT causes roughening of the film topography that is observed using scanning electron microscopy and atomic force microscopy (AFM). The electrical conductivity of the virus-PEDOT film, measured perpendicular to the plane of the film using conductive tip AFM, decreases linearly with virus loading, from 270 μS/cm for pure PEDOT films to 50 μS/cm for films containing 100 μM virus. The presence on the virus surface of displayed affinity peptides did not significantly influence the efficiency of incorporation into virus-PEDOT biocomposite films.

Guided selection of antibody fragments specific for human interferon gamma receptor 1 from a human VH- and VL-gene repertoire

OBJECTIVE

The guided selection strategy for isolation of human antibody (Ab) fragments specific for human interferon gamma receptor 1 (IFNGR-1) from a cloned Ab VH and VL repertoire has been investigated. In order to identify recombinant Abs binding to soluble antigen, a novel method termed affinity sedimentation was introduced here.

RESULTS AND CONCLUSIONS

The VH region of murine monoclonal Ab (IR gamma-1) against human IFNGR-1 was combined with human VL repertoire and used for selection of human VL regions. One of these human VL regions (kappa 2) possesses high homology to the murine template VL region, also in CDR3 (77%). A chimeric Fab consisting of kappa 2 and the murine IR gamma-1 VH region was highly IFNGR-1 specific and exerted the same epitope specificity and a comparable binding affinity as the parental murine Fab. In a further step, the selected human VL region kappa 2 was combined with a human VH repertoire and led by guided selection to the generation of a completely human Fab (1b5) specific for human IFNGR-1. The overall VH region homology of 1b5 compared to the parental antibody IR gamma-1 was 81%, with a rather low homology in CDR3. Binding competition studies revealed that the epitope recognized by 1b5 differs from the parental Ab IR gamma-1.

Turbidimetric studies of Limulus coagulin gel formation

The turbidity during trypsin-induced coagulin gel formation was studied over a range of wavelengths. The range of wavelengths used (686-326 nm) also made it possible to investigate the dependence of turbidity on wavelength (the wavelength exponent). Using the results from that work, and structural information on coagulin and the coagulin gel from other studies, a model gel-forming system was designed that consists of species for which the turbidity can be calculated relatively simply. These species include small particles (small in all dimensions relative to the wavelength of incident light); long rods and long random coils (particles that are large in just one dimension relative to the wavelength of incident light); and reflective regions (aggregated material that is large in more than one dimension relative to the wavelength of incident light). The turbidimetric characteristics of the real coagulin gel-forming system are compared with those of the model system.

Interchangeability of the adsorption proteins of bacteriophages Ff and IKe

The wild-type adsorption protein (g3p) of filamentous phage IKe cannot be exchanged with its analogous protein in the related Ff (M13, fd, and f1) phage particles. Deletion mutants of the protein, however, are assembled into Ff phage particles. These hybrid Ff phage particles bearing deleted IKe g3p attach to N pili, thus conserving the host attachment property of the protein but not its infection-initiating function. This means that the attachment specificity is determined by IKe g3p independently of other phage components in contact with it. Infection initiation function, the process in which phage DNA is released into the host, in contrast seems to require either more complex structural features of the protein (for example, a certain oligomeric structure) provided only in the original particle, or a concerted action of g3p with another particle component, not replaceable by its homologous counterpart in the related phage.

The adsorption protein of phage IKe. Localization by deletion mutagenesis of domains involved in infectivity

We constructed a set of plasmid-encoded internal deletion mutants within the gene for the adsorption protein (g3p) of phage IKe. All mutant proteins still contain the signal and membrane anchor sequence, as those are known to be indispensable for proper localization and hence assembly of the g3p into phage. These various deletions comprise all internal parts of the protein and are properly incorporated into phage, which remarkably shows that signal and anchor sequence are sufficient for incorporation of g3p. The data furthermore reveal that two separate sections within the IKe g3p are essential for infection: one amino-terminal, preceding the glycine-rich stretch, and the other carboxy-terminal. We conclude that this latter domain is involved in penetration because mutants lacking it are not infectious, but still bind to the receptor. The amino-terminal region, essential for infection, bears the receptor-recognizing domain and a sequence homologous to the penetration domain of the evolutionary related Ff phages, which is probably also involved in penetration of phage IKe. The prominent glycine-rich stretch of the IKe g3p is not essential for infection but significantly promotes it.

A theory of the symmetries of filamentous bacteriophages

A mathematical model is presented which explains the symmetries observed for the protein coats of filamentous bacterial viruses. Three viruses (Ff, IKe, and If1) all have five-start helices with rotation angles of 36 degrees and axial translations of 16 A (Type I symmetry), and three other viruses (Pf1, Xf, and Pf3) all have one-start helices with rotation angles of approximately equal to 67 degrees and translations of approximately 3 A (Type II symmetry). The coat protein subunits in each group diverge from each other in amino acid sequence, and Type II viruses differ dramatically in DNA structure. Regardless of the differences, both Type I and Type II symmetry can be understood as direct, natural consequences of the close-packing of alpha-helical protein subunits. In our treatment, an alpha-helical subunit is modeled as consisting of two interconnected, flexible tubular segments that follow helical paths around the DNA, one in an inner layer and the other in an outer layer. The mathematical model is a set of algebraic equations describing the disposition of the flexible segments. Solutions are described by newly introduced symmetry indices and other parameters. An exhaustive survey over the range of indices has produced a library of all structures that are geometrically feasible within our modeling scheme. Solutions which correspond in their rotation angles to Type I and Type II viruses occur over large ranges of the parameter space. A few solutions with other symmetries are also allowed, and viruses with these symmetries may exist in nature. One solution to the set of equations, obtained without any recourse to the x-ray data, yields a calculated x-ray diffraction pattern for Pf1 which compares reasonably with experimental patterns. The close-packing geometry we have used helps explain the near constant linear mass density of known filamentous phages. Helicoid, rigid cylinder, and maximum entropy structure models proposed by others for Pf1 are reconciled with the flexible tube models and with one another.

Mechanism of assembly of sea urchin egg tubulin

Tubulin purified from eggs of the sea urchin Strongylocentrotus purpuratus assembles efficiently in vitro to form microtubules at physiological (18 degrees C) and nonphysiological (37 degrees C) temperatures. MAPs, ring oligomers, and high concentrations of nonphysiological solvents are not required for the assembly reaction. At concentrations above 1.2 mg/ml at 18 degrees C and 0.5 mg/ml at 37 degrees C a concentration-dependent overshoot in turbidity and in light scattering at small angles was observed: turbidity and scattering increased rapidly to a peak, then decreased asymptotically toward a steady-state value. Electron microscopic analysis demonstrated that tubulin sheets were prevalent during the initial stages of overshoot assembly, whereas complete microtubules were present at steady state. Qualitative observations of solution birefringence suggested that the polymer became progressively more aligned during assembly. The overshoot cannot be explained by proteolysis or denaturation of tubulin, by depletion of GTP, by a decrease in assembled mass, or by redistribution of polymer lengths. Taken together, the results suggest that changes in the form and/or in the organization of the assembling polymer are responsible for the overshoots in turbidity and in light scattering at small angles. Our results are consistent with models of microtubule assembly that postulate nucleation by tubulin sheets and subsequent folding of the sheets to form mature microtubules.

The precursor complex of Pf3 bacteriophage

Filamentous bacteriophage infections give rise to intracellular filamentous precursor complexes composed of a circular single-stranded DNA molecule and on the order of 10(3) copies of a viral-encoded, single-stranded DNA binding protein. A protocol was developed for the purification of the precursor complex from Pf3 phage-infected Pseudomonas aeruginosa cells, and existing protocols for Ff and Pf1 complexes were amended by the introduction of a molecular sieving column step. The Pf3 precursor complex has an average contour length of 500 nm, which is shorter than that of the mature Pf3 virus. M/L (mass/length) values were obtained from turbidity measurements, from scanning-transmission electron microscopy, and from the total particle mass divided by its length. The average M/L obtained was 19,300 Da/nm which is close to that of the Pf3 virion. The complex has a nucleotide/subunit ratio of 6.0. The protein component of the precursor complex has less than 10% alpha-helicity, whereas the protein component of the virus is greater than 90% alpha-helical. The DNA structure in the precursors is very different from that in the virus, so that during virus assembly the DNA structure must change dramatically. The results for the Pf3 system, together with the available information for the Ff and Pf1 filamentous virus systems, indicate that different DNA-protein interactions and packing arrangements are involved in performing equivalent functions.

Major coat protein and single-stranded DNA-binding protein of filamentous virus Pf3

The region of the Pf3 virus genome encoding its major coat protein and its single-stranded DNA-binding protein is organized somewhat like the corresponding region of the fd (M13, f1) genome. Nevertheless, the major coat protein is unique among the major coat proteins of fd and the other filamentous phages studied in that it lacks a signal sequence and appears to be a direct translation product and in that it has fewer basic amino acid residues than its equivalent of DNA phosphates in the virion. These features are relevant to considerations of both protein insertion into membranes and DNA structure in filamentous viruses. The single-stranded DNA-binding protein also has a sequence that is different from the sequences of single-stranded DNA-binding proteins from other filamentous viruses.

Cloning of Pf3, a filamentous bacteriophage of Pseudomonas aeruginosa, into the pBD214 vector of Bacillus subtilis

The genome of Pf3, a filamentous single-stranded DNA bacteriophage of Pseudomonas aeruginosa (a gram-negative organism) was cloned into pBD214, a plasmid cloning vector of Bacillus subtilis (a gram-positive organism). Cloning in the gram-positive organism was done to avoid anticipated lethal effects. The entire Pf3 genome was inserted in each orientation at a unique Bc/I site within a thymidylate synthetase gene (from B. subtilis phage beta 22) on the plasmid. Additional clones were made by inserting EcoRI fragments of Pf3 DNA into a unique EcoRI site within this gene.

DNA and protein lattice-lattice interactions in the filamentous bacteriophages

The relations between the protein coats and DNAs of the four filamentous bacteriophages fd, Xf, Pf1, and Pf3 are considered. These viruses have similar morphologies, yet show a diversity of detailed structure, having different protein coat symmetries (helical and rotational), different coat protein sizes (44-50 amino acids per subunit) and sequences, different nucleotide axial translations (2.3-5.5 A), and different ratios of nucleotides per coat protein subunit (integers 1.0 and 2.0, and nonintegers approximately 2.4). These divergences are all reconciled quantitatively by means of two theoretical concepts: the pitch connection and the restricted pitch connection. The pitch connection relates protein and DNA surface lattices with arbitrary, nonintegral nucleotide/subunit ratios in a nonrandom way. The restricted pitch connection selects a preferred set of n/s values. Both relations are derived formally in a mathematical appendix. The available structural data are explained, including the fd DNA pitch indicated by x-ray diffraction photos and the similar DNA morphologies of Xf and fd. Predictions are made for the existence of nonclassical inverted DNA structures (I-DNA) in Pf1 and Pf3.

Structure similarity, difference and variability in the filamentous viruses fd, If1, IKe, Pf1 and Xf. Investigation by laser Raman spectroscopy

The filamentous bacteriophages fd, If1, IKe, Pf1, Xf and Pf3 in aqueous solutions of low, moderate and high ionic strength have been investigated as a function of temperature by laser Raman difference spectroscopy. By analogy with Raman spectra of model compounds and viruses of known structure, the data reveal the following structural features: the predominant secondary structure of the coat protein subunit in each virus is the alpha-helix, but the amount of alpha-helix differs from one virus to another, ranging from an estimated high of 100% in Pf1 to a low of approximately 50% in Xf. The molecular environment and intermolecular interactions of tyrosine, tryptophan and phenylalanine residues differ among the different viruses, as do the conformations of aliphatic amino acid side-chains. The foregoing features of coat protein structure are highly sensitive to changes in Na+ concentration, temperature or both. The backbones of A-DNA and B-DNA structures do not occur in any of the viruses, and unusual DNA structures are indicated for all six viruses. The alpha-helical protein subunits of Pf1, like those of Pf3 and Xf, can undergo reversible transitions to beta-sheet structures while retaining their association with DNA; yet fd, IKe and If1 do not undergo such transitions. Raman intensity changes with ionic strength or temperature suggest that transgauche rotations of aliphatic amino acid side-chains and stacking of aromatic side-chains are important structural variables in each virus.

Hydrodynamic determination of molecular weight, dimensions, and structural parameters of Pf3 virus

Measurements of the translational, DT, and rotational, DR, diffusion coefficients of Pf3 virus by low-angle polarized intensity fluctuation spectroscopy and field-free transient electric birefringence, respectively, give a length of 720 +/- 25 nm and diameter of 6.5 +/- 1.5 nm upon simultaneous solution of the Broersma equations for rigid rods. Sedimentation coefficient and density increment values obtained under solvent conditions identical with those of DT give a molecular weight of (13.4 +/- 0.8) x 10(6) g mol-1, which gives a mass per length of 18 600 +/- 1300 g mol-1 nm-1. Combining these results with the molecular weight of Pf3 DNA yields a number of protein subunits of 2500 +/- 160 and 2.38 +/- 0.14 nucleotides/protein subunit. Sedimentation coefficient and density increment values of Xf virus when combined with a value for the Xf translational diffusion coefficient [Chen, F. C., Koopmans, G., Wiseman, R. L., Day, L. A., & Swinney, H. L. (1980) Biochemistry 19, 1373] yield a molecular weight of (17.9 +/- 1.0) x 10(6) g mol-1, a number of protein subunits of 3590 +/- 230, 2.07 +/- 0.15 nucleotides/protein subunit, and a mass per length of 18 300 +/- 1200 g mol-1 nm-1. Thus, despite major differences in the DNA-protein packing between these viruses, as well as fd virus, the mass per lengths are surprisingly similar.

DNA packing in the filamentous viruses fd, Xf, Pf1 and Pf3

Spectral data for filamentous viruses in the presence and absence of Ag+, together with other parameters, indicate that the DNA structures in two of the viruses, fd and Xf, are similar to each other but that these differ from two quite unusual and different DNA structures in Pf1 and Pf3.

The molecular weight of Artemia ribosomes, as determined from their refractive-index increment and light-scattering intensity

Cytoplasmic ribosomes were isolated from the cryptobiotic embryos of the brine shrimp Artemia salina. Measurements of their refractive-index increments and light-scattering intensities give a value for their molecular weight of (3.4+/-0.2)x10(6).

Conformational transitions in Pf3 and their implications for the structure and assembly of filamentous bacterial viruses

Laser Raman and circular dichroism spectra of filamentous bacteriophage Pf3 show that its coat protein is predominantly alpha-helical, similar to the subunits of bacteriophages Pf1 and fd. Unlike Pf1 and fd, however, the subunits of Pf3 are converted to beta-sheet structures by raising the temperature, the transition temperature depending upon phage and NaCl concentrations. On cooling, the beta structure reverts to an alpha structure the same as or similar to the native structure. On further heating it converts irreversibly to a second alpha-helical form different from the original one. The spectra also show that aromatic amino acid residues of Pf3 undergo dramatic changes in molecular environment during the alpha leads to beta transition. Similar transitions are observed to take place in the filamentous bacteriophage Xf.

Aggregation of small oligonucleosomal chains into 300-A globular particles

Chicken erythrocyte oligonucleosomes (trimers to about 20-mers) are able to interact with each other through the very lysine-rich histones (H1 and H5) and form heterogeneous globular particles with a mean diameter of about 300 A. These particles assemble spontaneously during micrococcal nuclease digestion of chromatin in the presence of 30 mM NaCl and contain approximately 25 nucleosomes. They are sensitive to ionic strength and unfold at lower salt concentrations but can be reconstituted by restoring the initial salt concentration. Even at 30 mM NaCl, the particles remain dynamic structures, being in equilibrium with their oligonucleosomal components as revealed by the fact that particle stability depends on the concentration of oligonucleosomes.