Interparticle correlations due to electrostatic interactions: A small angle x-ray and dynamic light scattering study. I. Apoferritin

Electrostatically PEGylated DNA enables salt-free hybridization in water

Chemically modified nucleic acids have long served as a very important class of bio-hybrid structures. In particular, the modification with PEG has advanced the scope and performance of oligonucleotides in materials science, catalysis and therapeutics. Most of the applications involving pristine or modified DNA rely on the potential of DNA to form a double-stranded structure. However, a substantial requirement for metal-cations to achieve hybridization has restricted the range of applications. To extend the applicability of DNA in salt-free or low ionic strength aqueous medium, we introduce noncovalent DNA-PEG constructs that allow canonical base-pairing between individually PEGylated complementary strands resulting in a double-stranded structure in salt-free aqueous medium. This method relies on grafting of amino-terminated PEG polymers electrostatically onto the backbone of DNA, which results in the formation of a PEG-envelope. The specific charge interaction of PEG molecules with DNA, absolute absence of metal ions within the PEGylated DNA molecules and formation of a double helix that is significantly more stable than the duplex in an ionic buffer have been unequivocally demonstrated using multiple independent characterization techniques.

A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair

Uropathogenic E. coli experience a wide range of osmolarity conditions before and after successful infection. Stress-responsive regulatory proteins in bacteria, particularly proteins of the Hha family and H-NS, a transcription repressor, sense such osmolarity changes and regulate transcription through unknown mechanisms. Here we use an array of experimental probes complemented by molecular simulations to show that Cnu, a member of the Hha protein family, acts as an exquisite molecular sensor of solvent ionic strength. The osmosensory behavior of Cnu involves a fine-tuned modulation of disorder in the fourth helix and the three-dimensional structure in a graded manner. Order-disorder transitions in H-NS act synergistically with molecular swelling of Cnu contributing to a salt-driven switch in binding cooperativity. Thus, sensitivity to ambient conditions can be imprinted at the molecular level by tuning not just the degree of order in the protein conformational ensemble but also through population redistributions of higher-order molecular complexes.

The bacterial protein Cnu together with the transcription repressor H-NS regulate expression of virulence factors in an osmo-sensitive manner. Here authors show that the structure of Cnu swells with decreasing ionic strength driving the oligomerization of H-NS and regulating osmo-sensory response.

Self-Interaction of Human Serum Albumin: A Formulation Perspective

In the present study, small-angle X-ray scattering (SAXS) and static light scattering (SLS) have been used to study the solution properties and self-interaction of recombinant human serum albumin (rHSA) molecules in three pharmaceutically relevant buffer systems. Measurements are carried out up to high protein concentrations and as a function of ionic strength by adding sodium chloride to probe the role of electrostatic interactions. The effective structure factors (S _eff) as a function of the scattering vector magnitude q have been extracted from the scattering profiles and fit to the solution of the Ornstein-Zernike equation using a screened Yukawa potential to describe the double-layer force. Although only a limited q range is used, accurate fits required including an electrostatic repulsion element in the model at low ionic strength, while only a hard sphere model with a tunable diameter is necessary for fitting to high-ionic-strength data. The fit values of net charge agree with available data from potentiometric titrations. Osmotic compressibility data obtained by extrapolating the SAXS profiles or directly from SLS measurements has been fit to a 10-term virial expansion for hard spheres and an equation of state for hard biaxial ellipsoids. We show that modeling rHSA as an ellipsoid, rather than a sphere, provides a much more accurate fit for the thermodynamic data over the entire concentration range. Osmotic virial coefficient data, derived at low protein concentration, can be used to parameterize the model for predicting the behavior up to concentrations as high as 450 g/L. The findings are especially important for the biopharmaceutical sector, which require approaches for predicting concentrated protein solution behavior using minimal sample consumption.

Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion

We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers. The results suggest that BLG forms compact clusters that are static on the observation time scale of several nanoseconds. The presented analysis provides a general framework to access the structure and dynamics of macromolecular assemblies in solution.

Stealth Amphiphiles: Self-Assembly of Polyhedral Boron Clusters

This is the first experimental evidence that both self-assembly and surface activity are common features of all water-soluble boron cluster compounds. The solution behavior of anionic polyhedral boranes (sodium decaborate, sodium dodecaborate, and sodium mercaptododecaborate), carboranes (potassium 1-carba-dodecaborate), and metallacarboranes {sodium [cobalt bis(1,2-dicarbollide)]} was extensively studied, and it is evident that all the anionic boron clusters form multimolecular aggregates in water. However, the mechanism of aggregation is dependent on size and polarity. The series of studied clusters spans from a small hydrophilic decaborate-resembling hydrotrope to a bulky hydrophobic cobalt bis(dicarbollide) behaving like a classical surfactant. Despite their pristine structure resembling Platonic solids, the nature of anionic boron cluster compounds is inherently amphiphilic-they are stealth amphiphiles.

Hierarchical self-assembly and optical disassembly for controlled switching of magnetoferritin nanoparticle magnetism

Protein cages such as ferritin and viral capsids are interesting building blocks for nanotechnology due to their monodisperse structure and ability to encapsulate various functional moieties. Here we show that recombinant ferritin protein cages encapsulating Fe(3)O(4)-γ-Fe(2)O(3) iron oxide (magnetoferritin) nanoparticles and photodegradable Newkome-type dendrons self-assemble into micrometer-sized complexes with a face-centered-cubic (fcc) superstructure and a lattice constant of 13.1 nm. The magnetic properties of the magnetoferritin particles are affected directly by the hierarchical organization. Magnetoferritin nanoparticles dispersed in water exhibit typical magnetism of single domain noninteracting nanoparticles; however, the same nanoparticles organized into fcc superstructures show clearly the effects of the altered magnetostatic (e.g., dipole-dipole) interactions by exhibiting, for example, different hysteresis of the field-dependent magnetization. The magnetoferritin-dendron assemblies can be efficiently disassembled by a short optical stimulus resulting in release of free magnetoferritin particles. After the triggered release the nanomagnetic properties of the pristine magnetoferritin nanoparticles are regained.

pH-dependent structures of ferritin and apoferritin in solution: disassembly and reassembly

The pH-dependent structures of the ferritin shell (apoferritin, 24-mer) and the ferrihydrite core, under physiological conditions that permit enzymatic activity, were investigated by synchrotron small-angle X-ray scattering (SAXS). The solution structure of apoferritin was found to be nearly identical to the crystal structure. The shell thickness and hollow core volumes were estimated. The intact hollow spherical apoferritin was stable over a wide pH range, 3.40-10.0, and the ferrihydrite core was stable over the pH range 2.10-10.0. The apoferritin subunits underwent aggregation below pH 0.80, whereas the ferrihydrite cores aggregated below pH 2.10 as a result of the disassembly of the ferritin shell under the strongly acidic conditions. As the pH decreased from 3.40 to 0.80, apoferritin underwent stepwise disassembly by first forming a hollow sphere with two holes, then a headset-shaped structure, and, finally, rodlike oligomers. As the pH was increased from pH 1.96, the disassembled rodlike oligomers recovered only to the headset-shaped structure, and the disassembled headset-shaped intermediates recovered only to the hollow spherical structure with two hole defects. The apoferritin hole defects that formed during the disassembly process did not heal as the pH was increased to neutral or slightly basic conditions. The pH-induced apoferritin disassembly and reassembly processes were not fully reversible, although they were pseudoreversible over a limited pH range, between 10.0 and 2.66.

The sedimentation properties of ferritins. New insights and analysis of methods of nanoparticle preparation

BACKGROUND

Ferritin exhibits complex behavior in the ultracentrifuge due to variability in iron core size among molecules. A comprehensive study was undertaken to develop procedures for obtaining more uniform cores and assessing their homogeneity.

METHODS

Analytical ultracentrifugation was used to measure the mineral core size distributions obtained by adding iron under high- and low-flux conditions to horse spleen (apoHoSF) and human H-chain (apoHuHF) apoferritins.

RESULTS

More uniform core sizes are obtained with the homopolymer human H-chain ferritin than with the heteropolymer horse spleen HoSF protein in which subpopulations of HoSF molecules with varying iron content are observed. A binomial probability distribution of H- and L-subunits among protein shells qualitatively accounts for the observed subpopulations. The addition of Fe(2+) to apoHuHF produces iron core particle size diameters from 3.8 + or - 0.3 to 6.2 + or - 0.3 nm. Diameters from 3.4 + or - 0.6 to 6.5 + or - 0.6 nm are obtained with natural HoSF after sucrose gradient fractionation. The change in the sedimentation coefficient as iron accumulates in ferritin suggests that the protein shell contracts approximately 10% to a more compact structure, a finding consistent with published electron micrographs. The physicochemical parameters for apoHoSF (15%/85% H/L subunits) are M=484,120 g/mol, nu=0.735 mL/g, s(20,w)=17.0 S and D(20,w)=3.21 x 10(-)(7) cm(2)/s; and for apoHuHF M=506,266 g/mol, nu=0.724 mL/g, s(20,w)=18.3S and D(20,w)=3.18 x 10(-)(7) cm(2)/s.

SIGNIFICANCE

The methods presented here should prove useful in the synthesis of size controlled nanoparticles of other minerals.

Linear and nonlinear magneto-optics of ferritin

Measurements of Rayleigh light scattering and Cotton-Mouton (CM) effect are carried out at room temperature for 100 mM NaCl solutions of apoferritin/ferritin loaded with 0, 90, 100, 500, 700, and 1500 Fe atoms/molecule. Because of the spherical shape, ferritin macromolecule should not manifest magnetic anisotropy; however, in solution it shows the induced magnetic birefringence (CM effect) and changes in intensity of the scattered light components. The newly obtained data support the previously reported conclusions indicating that the deformation of linear optical polarizability induced in the ferritin by a magnetic field and the orientation of the induced magnetic dipole moment by this field are the main sources of the magneto-optical phenomena observed. Nevertheless, it is also found that the orientation of the permanent magnetic dipole moment contributes to both effects. The magnetic field induced changes in the light scattering and the CM effect theoretically depend on the linear magneto-optical polarizability, chi, on the nonlinear magneto-optical polarizability, eta, and square of the permanent magnetic dipole moment value of the macromolecule, mu(2). On the basis of the theory describing both effects as well as the experimental data, the values of the anisotropy of linear magneto-optical polarizabilities components, the values of the linear optical polarizability and its anisotropy, nonlinear magneto-optical polarizability and its anisotropy, are estimated. Also the magnetic dipole moment of the ferritin macromolecule is found. Interestingly, not all iron atoms in the ferritin are indicated to be in the superparamagnetic state, some of them occur in the diamagnetic form.

Structure analysis using acoustically levitated droplets

Synchrotron diffraction with a micrometer-sized X-ray beam permits the efficient characterization of micrometer-sized samples, even in time-resolved experiments, which is important because often the amount of sample available is small and/or the sample is expensive. In this context, we will present acoustic levitation as a useful sample handling method for small solid and liquid samples, which are suspended in a gaseous environment (air) by means of a stationary ultrasonic field. A study of agglomeration and crystallization processes in situ was performed by continuously increasing the concentration of the samples by evaporating the solvent. Absorption and contamination processes on the sample container walls were suppressed strongly by this procedure, and parasitic scattering such as that observed when using glass capillaries was also absent. The samples investigated were either dissolved or dispersed in water droplets with diameters in the range of 1 micrometer to 2 millimeters. Initial results from time-resolved synchrotron small- and wide-angle X-ray scattering measurements of ascorbic acid, acetylsalicylic acid, apoferritin, and colloidal gold are presented.

Determination of the concentration dependence of polyelectrolyte diffusion coefficients by application of the Boltzmann gradient method

The concentration dependence of a polyelectrolyte diffusion coefficient in aqueous low salt solution (KCl, 1 mM) is determined from a single dynamic gradient experiment. The Boltzmann method is applied to calculate the diffusion coefficient. A special diffusion cell is constructed that minimizes aberrations in the optical detection of the polyion concentration profile. Bovine serum albumin (BSA) is chosen as a model polyion. To get information about the diffusion process down to very small polyion concentrations, the BSA molecule is fluorescently labeled. The fluorescence intensity is used as a measure of the polyion concentration. The change of the polyion net charge caused by labeling is discussed. The cell is illuminated by an LED, and the fluorescence intensity profile is detected by a CCD camera. Experiments at 5 and 17 degrees C show that the diffusion coefficient of labeled BSA remains constant in the very low polyion concentration range below a threshold of about 1.5 g/l. This is in contradiction to the linear concentration dependence of polyion diffusion coefficients at very low concentrations often postulated in the literature without reference to direct experimental evidence. Our finding is confirmed by dynamic light scattering experiments published recently. An explanation for this behavior based on a modified Donnan osmotic compressibility approach is given.

Neutron spin echo studies on ferritin: free-particle diffusion and interacting solutions

The dynamics of proteins are often studied by means of quasielastic neutron scattering (QENS), for example by time-of-flight methods. The spatial dimensions (10-20 nm) present in protein solutions are accessible by neutron scattering. In this article, a systematic study of diffusive dynamics of ferritin and apoferritin (=ferritin without iron core) is presented. Apoferritin consists of a spherical shell built of 24 protein units and carries net negative charge at pH 5. We have studied diffusive dynamics of ferritin solutions by neutron spin echo (NSE). We pay attention to an important feature of this technique compared to other QENS methods, which being the usage of a broad wavelength band. Using a more sophisticated fit function than usually used in NSE, we find as expected in low concentrated systems that the diffusion coefficient approaches the free-particle value of apoferritin and coincides with the diameter of the apoferritin shell (12.2 nm). In interacting solutions, the NSE results reveal that the dynamic picture of this complex liquid is dominated by slowing down of the dynamics. In low-salt solutions, a structure factor peak appears due to ordering of the ferritin molecules on the length scale of several intermolecular distances. We discuss the usage of different NSE fit functions for interacting solutions near the structure factor peak. Comparison of the dependence of elastic and dynamic data on the scattering vector value shows the influence of indirect interactions on the dynamic picture, irrespective of the way of data analysis, which being necessary due to the broad wavelength spectrum.

Diffusion of spheres in isotropic and nematic networks of rods: electrostatic interactions and hydrodynamic screening

Translational diffusion of a small charged tracer sphere in isotropic and nematic suspensions of long and thin charged rods is investigated as a function of ionic strength and rod concentration. A theory for the diffusive properties of a small sphere is developed, where both (screened) hydrodynamic interactions and charge interactions between the tracer sphere and the rod network are analyzed. Hydrodynamic interactions are formulated in terms of the hydrodynamic screening length. As yet, there are no independent theoretical predictions for the hydrodynamic screening length for rod networks. Experimental tracer-diffusion data are presented for various ionic strengths as a function of the rod concentration, both in the isotropic and nematic states. Orientational order parameters are measured for the same ionic strengths as a function of the rod concentration. The hydrodynamic screening length is determined from these experimental data and scaling relations obtained from the above mentioned theory. For the isotropic networks, a master curve is found for the hydrodynamic screening length as a function of the rod concentration. For the nematic networks the screening length turns out to be a very sensitive function of the orientational order parameter.

Diffusion of spheres in isotropic and nematic suspensions of rods

Diffusion of a small tracer sphere (apoferritin) in isotropic and nematic networks [of fd virus] is discussed. For a tracer sphere that is smaller than the mesh size of the network, screened hydrodynamic interactions between the sphere and the network determine its diffusion coefficient. A theory is developed for such interactions as well as their relation to the long-time self-diffusion coefficient. Fluorescence correlation spectroscopy measurements on mixtures of apoferritin and fd virus are presented. The long-time self-diffusion coefficient of apoferritin is measured as a function of the fd-virus concentration, both in the isotropic and nematic state, in directions parallel and perpendicular to the nematic director. The hydrodynamic screening length of the fd-virus network as a function of fd concentration is obtained by combining these experimental data with the theory. Surprisingly, the screening length increases with increasing concentration in nematic networks. This is due to the increase in the degree of alignment, which apparently leads to a strong increase of the screening length. Hydrodynamic screening is thus strongly diminished by alignment. A self-consistent calculation of the screening length does not work at higher concentrations, probably due to the strong variation of the typical incident flow fields over the contour of a rod.

Diffusion and microstructural properties of solutions of charged nanosized proteins: Experiment versus theory

We have reanalyzed our former static small-angle x-ray scattering and photon correlation spectroscopy results on dense solutions of charged spherical apoferritin proteins using theories recently developed for studies of colloids. The static structure factors S(q), and the small-wave-number collective diffusion coefficient D(c) determined from those experiments are interpreted now in terms of a theoretical scheme based on a Derjaguin-Landau-Verwey-Overbeek-type continuum model of charged colloidal spheres. This scheme accounts, in an approximate way, for many-body hydrodynamic interactions. Stokesian dynamics computer simulations of the hydrodynamic function have been performed for the first time for dense charge-stabilized dispersions to assess the accuracy of the theoretical scheme. We show that the continuum model allows for a consistent description of all experimental results, and that the effective particle charge is dependent upon the protein concentration relative to the added salt concentration. In addition, we discuss the consequences of small ions dynamics for the collective protein diffusion within the framework of the coupled-mode theory.

Self-Diffusion and Collective Diffusion of Charged Colloids Studied by Dynamic Light Scattering

A microemulsion of decane droplets stabilized by a nonionic surfactant film is progressively charged by substitution of a nonionic surfactant molecule by a cationic surfactant. We check that the microemulsion droplets remain identical within the explored range of volume fraction (0.02-0.18) and of the number of charges per droplet (0-40). We probe the dynamics of these microemulsions by dynamic light scattering. Despite the similar structures of the uncharged and charged microemulsions, the dynamics are very different. In the neutral microemulsion, the fluctuations of polarization relax, as is well-known, via the collective diffusion of the droplets. In the charged microemulsions, two modes of relaxation are observed. The fast one is ascribed classically to the collective diffusion of the charged droplets coupled to the diffusion of the counterions. The slow one has, to our knowledge, not been observed previously neither in similar microemulsions nor in charged spherical colloids. We show that the slow mode is also diffusive and suggest that its possible origin is the relaxation of local charge fluctuations via the local exchange of droplets bearing different numbers of charges. The diffusion coefficient associated with this mode is then the self-diffusion coefficient of the droplets.

Structural similarity ofE. coli 5S rRNA in solution and within the ribosome

The article presents translational and rotational diffusion coefficients of 5S rRNA determined experimentally by the method of dynamic light scattering (DLS) and its comparison with the values predicted for different models of this molecule. The tertiary structure of free 5S rRNA was proposed on the basis of the atomic structures of the 5S rRNA from E. coli and H. marismortui extracted from the ribosome. A comparison of the values of DT, tauR, and Rg predicted for different models with experimental results for the free molecule in solution suggests that free 5S rRNA is less compact than that in the complex with ribosomal proteins. In general, the molecules of 5S rRNA consist of three domains: a short one and two longer ones. As follows from a comparison of the results of our simulations with experimental values, in the molecule in solution the two closest helical fragments of the longer domains remain collinear, whereas the short domain takes a position significantly deviated from them.