Comparing Mfd- and UvrD-dependent models of transcription coupled DNA repair in live Escherichia coli using single-molecule tracking

During transcription-coupled DNA repair (TCR) the detection of DNA damage and initiation of nucleotide excision repair (NER) is performed by translocating RNA polymerases (RNAP), which are arrested upon encountering bulky DNA lesions. Two opposing models of the subsequent steps of TCR in bacteria exist. In the first model, stalled RNAPs are removed from the damage site by recruitment of Mfd which dislodges RNAP by pushing it forwards before recruitment of UvrA and UvrB. In the second model, UvrD helicase backtracks RNAP from the lesion site. Recent studies have proposed that both UvrD and UvrA continuously associate with RNAP before damage occurs, which forms the primary damage sensor for NER. To test these two models of TCR in living E. coli, we applied super-resolution microscopy (PALM) combined with single particle tracking to directly measure the mobility and recruitment of Mfd, UvrD, UvrA, and UvrB to DNA during ultraviolet-induced DNA damage. The intracellular mobilities of NER proteins in the absence of DNA damage showed that most UvrA molecules could in principle be complexed with RNAP, however, this was not the case for UvrD. Upon DNA damage, Mfd recruitment to DNA was independent of the presence of UvrA, in agreement with its role upstream of this protein in the TCR pathway. In contrast, UvrD recruitment to DNA was strongly dependent on the presence of UvrA. Inhibiting transcription with rifampicin abolished Mfd DNA-recruitment following DNA damage, whereas significant UvrD, UvrA, and UvrB recruitment remained, consistent with a UvrD and UvrA performing their NER functions independently of transcribing RNAP. Together, although we find that up to ∼8 UvrD-RNAP-UvrA complexes per cell could potentially form in the absence of DNA damage, our live-cell data is not consistent with this complex being the primary DNA damage sensor for NER.

Experimental examination of dipole-dipole cross-correlations by dielectric spectroscopy, depolarized dynamic light scattering, and computer simulations of molecular dynamics

The contribution of cross- and self-correlations to the dielectric and light-scattering spectra of supercooled polar glass formers has recently become a most challenging problem. Herein, we employ dielectric spectroscopy, depolarized dynamic light scattering (DDLS), and rheology to thoroughly examine the dynamics of van der Waals liquid 1,2-Diphenylvinylene. Carbonate (DVC), which is a polar counterpart of canonical glass former ortho-Terphenyl (OTP). We show that the light-scattering data correspond well with the dielectric permittivity function over a wide T range. This pattern is very different from the peaks' separation ω_{max}^{DDLS}/ω_{max}^{BDS}=3.7 reported recently for tributyl phosphate (TBP), despite the same dielectric characteristics of these two glass formers (β_{KWW}=0.75, Δɛ=20 for both TBP and DVC; KWW stands for Kohlrausch-Williams-Watts). This indicates different influence of orientational correlations in both methods for these two systems. We also show the results of the computer simulations of the model, polar molecules, which clearly indicate that the contribution of the cross-term to the correlation function probed in the DDLS experiment can be significant.

Control of Intermolecular Interactions toward the Production of Free-Standing Interfacial Polydopamine Films

Aggregation of the polydopamine (PDA) molecular building blocks at the air/water interface leads to obtaining large surface nanometric-thin films. This mechanism follows two possible pathways, namely, covalent or non-covalent self-assembly, which result in a different degree of structure order and, consequently, different structural properties. Control of this mechanism could be vital for applications that require true self-support PDA free-standing films, for example, electrochemical sensing or membrane technology. Here, we are considering the impact of boric acid (BA) and Cu²⁺ ions on the mentioned mechanism exclusively for the free-standing films from the air/water interface. We have employed and refined our own spectroscopic reflectometry method to achieve an exceptionally high real-time control over the thickness growth. It turned out that BA and Cu²⁺ ions significantly impact the film growth process. Reduction of the nanoparticles size and their number was examined via UV-vis spectroscopy and transmission electron microscopy, showing a colossal reduction in the mean diameter of nanoparticles in the case of BA and a moderate reduction in the case of Cu²⁺. This modification is leading to significant enhancement of the process efficiency through moderation of the topological properties of the films, as revealed by atomic force microscopy. Next, applying infrared, Raman, and X-ray photoelectron spectroscopy, we presented small amounts of metal (B or Cu) in the final structure of PDA and simultaneously their vital role in the oxidation mechanism and cross-linking through covalent or non-covalent bonds. Therefore, we revealed the possibility of synthesizing films via the expected self-assembly mechanism which has hitherto been out of control. Moreover, modification of mechanical properties toward exceptionally elastic films through the BA-assisted synthesis pathway was shown by achieving Young's modulus value up to 24.1 ± 5.6 and 18.3 ± 6.4 GPa, using nanoindentation and Brillouin light scattering, respectively.

Nanomolar Nitric Oxide Concentrations in Living Cells Measured by Means of Fluorescence Correlation Spectroscopy

Measurement of the nitric oxide (NO) concentration in living cells in the physiological nanomolar range is crucial in understanding NO biochemical functions, as well as in characterizing the efficiency and kinetics of NO delivery by NO-releasing drugs. Here, we show that fluorescence correlation spectroscopy (FCS) is perfectly suited for these purposes, due to its sensitivity, selectivity, and spatial resolution. Using the fluorescent indicators, diaminofluoresceins (DAFs), and FCS, we measured the NO concentrations in NO-producing living human primary endothelial cells, as well as NO delivery kinetics, by an external NO donor to the immortal human epithelial living cells. Due to the high spatial resolution of FCS, the NO concentration in different parts of the cells were also measured. The detection of nitric oxide by means of diaminofluoresceins is much more efficient and faster in living cells than in PBS solutions, even though the conversion to the fluorescent form is a multi-step reaction.

On the nature of uncoupled chlorophylls in the extremophilic photosystem I-light harvesting I supercomplex

Photosystem I core-light-harvesting antenna supercomplexes (PSI-LHCI) were isolated from the extremophilic red alga Cyanidioschyzon merolae and studied by three fluorescence techniques in order to characterize chlorophylls (Chls) energetically uncoupled from the PSI reaction center (RC). Such Chls are observed in virtually all optical experiments of any PSI core and PSI-LHCI supercomplex preparations across various species and may influence the operation of PSI-based solar cells and other biohybrid systems. However, the nature of the uncoupled Chls (uChls) has never been explored deeply before. In this work, the amount of uChls was controlled by stirring the solution of C. merolae PSI-LHCI supercomplex samples at elevated temperature (~303 K) and was found to increase from <2% in control samples up to 47% in solutions stirred for 3.5 h. The fluorescence spectrum of uChls was found to be blue-shifted by ~20 nm (to ~680 nm) relative to the fluorescence band from Chls that are well coupled to PSI RC. This effect indicates that mechanical stirring leads to disappearance of some red Chls (emitting at above ~700 nm) that are present in the intact LHCI antenna associated with the PSI core. Comparative diffusion studies of control and stirred samples by fluorescence correlation spectroscopy together with biochemical analysis by SDS-PAGE and BN-PAGE indicate that energetically uncoupled Lhcr subunits are likely to be still physically attached to the PSI core, albeit with altered three-dimensional organization due to the mechanical stress.

Silver and ultrasmall iron oxides nanoparticles in hydrocolloids: effect of magnetic field and temperature on self-organization

Micro/nanostructures, which are assembled from various nanosized building blocks are of great scientific interests due to their combined features in the micro- and nanometer scale. This study for the first time demonstrates that ultrasmall superparamagnetic iron oxide nanoparticles can change the microstructure of their hydrocolloids under the action of external magnetic field. We aimed also at the establishment of the physiological temperature (39 °C) influence on the self-organization of silver and ultrasmall iron oxides nanoparticles (NPs) in hydrocolloids. Consequences of such induced changes were further investigated in terms of their potential effect on the biological activity in vitro. Physicochemical characterization included X-ray diffraction (XRD), optical microscopies (SEM, cryo-SEM, TEM, fluorescence), dynamic light scattering (DLS) techniques, energy dispersive (EDS), Fourier transform infrared (FTIR) and ultraviolet-visible (UV-Vis) spectroscopies, zeta-potential and magnetic measurements. The results showed that magnetic field affected the hydrocolloids microstructure uniformity, fluorescence properties and photodynamic activity. Likewise, increased temperature caused changes in NPs hydrodynamic size distribution and in hydrocolloids microstructure. Magnetic field significantly improved photodynamic activity that was attributed to enhanced generation of reactive oxygen species due to reorganization of the microstructure.

Acetate-Induced Disassembly of Spherical Iron Oxide Nanoparticle Clusters into Monodispersed Core-Shell Structures upon Nanoemulsion Fusion

It has been long known that the physical encapsulation of oleic acid-capped iron oxide nanoparticles (OA-IONPs) with the cetyltrimethylammonium (CTA+) surfactant induces the formation of spherical iron oxide nanoparticle clusters (IONPCs). However, the behavior and functional properties of IONPCs in chemical reactions have been largely neglected and are still not well-understood. Herein, we report an unconventional ligand-exchange function of IONPCs activated when dispersed in an ethyl acetate/acetate buffer system. The ligand exchange can successfully transform hydrophobic OA-IONP building blocks of IONPCs into highly hydrophilic, acetate-capped iron oxide nanoparticles (Ac-IONPs). More importantly, we demonstrate that the addition of silica precursors (tetraethyl orthosilicate and 3-aminopropyltriethoxysilane) to the acetate/oleate ligand-exchange reaction of the IONPs induces the disassembly of the IONPCs into monodispersed iron oxide-acetate-silica core-shell-shell (IONPs@acetate@SiO2) nanoparticles. Our observations evidence that the formation of IONPs@acetate@SiO2 nanoparticles is initiated by a unique micellar fusion mechanism between the Pickering-type emulsions of IONPCs and nanoemulsions of silica precursors formed under ethyl acetate buffered conditions. A dynamic rearrangement of the CTA+-oleate bilayer on the IONPC surfaces is proposed to be responsible for the templating process of the silica shells around the individual IONPs. In comparison to previously reported methods in the literature, our work provides a much more detailed experimental evidence of the silica-coating mechanism in a nanoemulsion system. Overall, ethyl acetate is proven to be a very efficient agent for an effortless preparation of monodispersed IONPs@acetate@SiO2 and hydrophilic Ac-IONPs from IONPCs.

EPR Oximetry Sensor-Developing a TAM Derivative for In Vivo Studies

Oxygenation is one of the most important physiological parameters of biological systems. Low oxygen concentration (hypoxia) is associated with various pathophysiological processes in different organs. Hypoxia is of special importance in tumor therapy, causing poor response to treatment. Triaryl methyl (TAM) derivative radicals are commonly used in electron paramagnetic resonance (EPR) as sensors for quantitative spatial tissue oxygen mapping. They are also known as magnetic resonance imaging (MRI) contrast agents and fluorescence imaging compounds. We report the properties of the TAM radical tris(2,3,5,6-tetrachloro-4-carboxy-phenyl)methyl, (PTMTC), a potential multimodal (EPR/fluorescence) marker. PTMTC was spectrally analyzed using EPR and characterized by estimation of its sensitivity to the oxygen in liquid environment suitable for intravenous injection (1 mM PBS, pH = 7.4). Further, fluorescent emission of the radical was measured using the same solvent and its quantum yield was estimated. An in vitro cytotoxicity examination was conducted in two cancer cell lines, HT-29 (colorectal adenocarcinoma) and FaDu (squamous cell carcinoma) and followed by uptake studies. The stability of the radical in different solutions (PBS pH = 7.4, cell media used for HT-29 and FaDu cells culturing and cytotoxicity procedure, full rat blood and blood plasma) was determined. Finally, a primary toxicity test of PTMTC was carried out in mice. Results of spectral studies confirmed the multimodal properties of PTMTC. PTMTC was demonstrated to be not absorbed by cancer cells and did not interfere with luciferin-luciferase based assays. Also in vitro and in vivo tests showed that it was non-toxic and can be freely administrated till doses of 250 mg/kg BW via both i.v. and i.p. injections. This work illustrated that PTMTC is a perfect candidate for multimodal (EPR/fluorescence) contrast agent in preclinical studies.

Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)

Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed.

Synthesis of fluorescein by a ship-in-a-bottle method in different zeolites

Composites consisting of fluorescein (F) entrapped inside various zeolite structures (i.e. FAU, LTL, MFI, and LTA) were prepared by catalytic synthesis of the dye from its precursors (phthalic anhydride and resorcinol) adsorbed in the zeolites.

Cytotoxicity and imaging studies of β-NaGdF4:Yb3+Er3+@PEG-Mo nanorods

Multimodal imaging based on nanostructures has become a subject of interest for numerous biomedical laboratories.

Synthesis, structure, EPR studies and up-conversion luminescence of ZnO:Er3+–Yb3+@Gd2O3 nanostructures

ZnO:Er³⁺–Yb³⁺@Gd₂O₃ nanostructures were obtained by “wet” chemistry methods – the sol–gel technique for the preparation of ZnO and ZnO:Er³⁺–Yb³⁺ nanoparticles (NPs), and the seed deposition method for obtaining Gd₂O₃.

Simple way to analyze Brillouin spectra from turbid liquids

The shape of the Brillouin light-scattering spectrum recorded from turbid liquids is distinctly distorted compared to that from a transparent sample. The reason for this is the multiple scattering of light within the medium. The usual expression for the Brillouin spectrum does not apply to the multiple scattering situation. In this Letter, we consider a Brillouin spectrum from opaque samples composed of a distribution of spectra resulting from elementary scattering events, each occurring in single scattering vector conditions. We introduce a one-parameter test function to define the probability distribution of scattering events occurring at a given value of the scattering vector. The proposed procedure was tested on model liquids that consisted of suspensions of sub-micrometer spherical particles of different size and concentration, dispersed in different carrier liquids and studied as a function of temperature. Our analysis made it possible to account for the effect of multiple scattering and to recover the values of mechanical parameters describing the pure solvents.

Successful FCS experiment in nonstandard conditions

Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13-0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS.

High-frequency propagating density fluctuations in deeply supercooled water: evidence of a single viscous relaxation

We performed a Brillouin scattering experiment on deeply supercooled water and compared the results with similar literature data obtained both at the same and at higher values of the exchanged wave vector. The whole set of available experimental data can be well reproduced with the use of the generalized hydrodynamic model where all the involved thermodynamic parameters are fixed to their literature values. On the contrary, the model based on the memory function approach generates the wrong estimates for measurables when the same values of the thermodynamic parameters are used. This result confirms our recent criticisms against the utilization of models originating from linear response theory [Phys. Rev. E 84, 051202 (2011)]. The inconsistency between models explains apparent discrepancies between the different conclusions on water acoustic behavior which may be found in the literature. We demonstrate that the observed behavior can be explained by assuming only a single relaxation process that is typical of any viscoelastic system. With all thermodynamics quantities fixed, the hydrodynamic description needs only two parameters to model the experimental data, namely, the relaxation time and the high-frequency limit of the sound velocity. The whole body of the experimental data can be well reproduced when the relaxation time behaves in an Arrhenian manner and the difference between the relaxed and not relaxed sound velocities is a constant. The high-frequency sound velocity is never higher than 2200 m/s. We conclude that, at least from experiments performed within the hydrodynamic regime, there is no indication for a fast sound close to the hypersonic velocity observed in ice.

Collective acoustic modes in liquids: a comparison between the generalized-hydrodynamics and memory-function approaches

The most familiar approaches used to describe the dynamical structure factor from adiabatic density fluctuations in liquids are based on generalized hydrodynamics and on the memory function, respectively. We show that, contrary to the common belief, the two approaches are not fully equivalent. In particular, models based on the memory function of a normalized damped oscillator fail in reproducing the correct experimental spectral profiles of systems close to the relaxation process. The discrepancy is due to misleading interpretation of the theoretical memory-function expressions, producing an unavoidable mixing of spectral contribution at different wave vectors when the theory is forced beyond its limits of validity.

Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale

We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length ξ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than ξ experienced matrix viscosity: η(matrix) ≈ 2.0 mPa·s for HeLa and 0.88 mPa·s for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, η(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Pa·s for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.

Size and shape of micelles studied by means of SANS, PCS, and FCS

The hexaethylene glycol monododecyl ether (C(12)E(6)) micelles at concentrations up to 10% have been studied in their isotropic phase (10-48 degrees C) by means of small angle neutron scattering (SANS) and photon correlation spectroscopy (PCS). The SANS data obtained at low temperatures could be unequivocally interpreted as a result of scattering from a suspension of compact globular micelles with the shape of a triaxial ellipsoid or a short end-capped elliptical rod. Different models have been applied to analyze the SANS data obtained at higher temperatures: (i) elongated rod-like micelles with purely sterical interactions, (ii) compact globular micelles with a weak attractive potential, and (iii) globular micelles influenced by the critical phenomena in the whole temperature range studied. The good quality of the experimental data indicated model (i) as the best fit for our data. The diffusion coefficients obtained from the PCS measurements have been compared to the diffusion coefficients calculated for the rod-like micelles--results of the SANS data analysis. A good agreement was achieved using the solvent viscosity, in agreement with the theoretical predictions for sterically interacting globular colloidal particles. Finally, the SANS results obtained at 24 degrees C were compared to the micelle self-diffusion coefficients previously measured by means of fluorescence correlation spectroscopy (FCS) at this temperature. The good agreement obtained after scaling the data with solution viscosity supports the validity of the generalized Stokes-Einstein relation in sterically interacting systems: the product of the colloidal particle self-diffusion coefficient and the macroscopic viscosity remains constant in a broad range of concentrations. It has been concluded that the FCS technique in combination with simple viscosity measurements might serve as a tool for estimating the micellar size and shape.

Excess compressibility in binary liquid mixtures

Brillouin scattering experiments have been carried out on some mixtures of molecular liquids. From the measurement of the hypersonic velocities we have evaluated the adiabatic compressibility as a function of the volume fraction. We show how the quadratic form of the excess compressibility dependence on the solute volume fraction can be derived by simple statistical effects and does not imply any interaction among the components of the system other than excluded volume effects. This idea is supported by the comparison of the experimental results with a well-established prototype model, consisting of a binary mixture of hard spheres with a nonadditive interaction potential. This naive model turns out to be able to produce a very wide spectrum of structural and thermodynamic features depending on values of its parameters. An attempt has made to understand what kind of structural information can be gained through the analysis of the volume fraction dependence of the compressibility.

Structuring Effects and Hydration Phenomena in Poly(Ethylene Glycol)/Water Mixtures Investigated by Brillouin Scattering

Aqueous solutions of poly(ethylene glycol) (PEG) of mean molecular mass of 600 g/mol (PEG600) are investigated by Brillouin scattering technique. At high PEG content, a relaxation phenomenon is observed, which is related to a local rearrangement of the polymer structure where the interaction, via hydrogen bonding, with the solvent molecules plays a role. The obtained values of the relaxation times match the literature data very well for a fast relaxation time revealed by dielectric relaxation measurements in very similar mixtures. The calculated concentration behaviors of the excess adiabatic compressibility turns out in good agreement with the previous findings from ultrasonic measurements at 3 MHz. The observed minimum in the adiabatic compressibility is interpreted as the result of the interaction between water and the EO units of the PEG chain, which results in a structure tighter then that typical of bulk water and of pure PEG600. Such a hypothesis is supported by the observation that volume fraction value of about 0.3 coincides with the concentration value at which full hydration of EO units takes place. The observation that at the same concentration, the polymer coils start to overlap each other further supports the idea that the adiabatic compressibility behavior is monitoring the structural evolution of the mixture. However, similar results are obtained for largely different binary mixture which suggests caution in taking this conclusion too literally. In particular, the hypothesis that the occurrence of an extreme in the excess adiabatic compressibility could be simply originated by statistical effects and that further work is required for disentangling entropic contribution from effects of hetero-association and self-aggregation of one or both the components.

Movement of Proteins in an Environment Crowded by Surfactant Micelles: Anomalous versus Normal Diffusion

Small proteins move in crowded cell compartments by anomalous diffusion. In many of them, e.g., the endoplasmic reticulum, the proteins move between lipid membranes in the aqueous lumen. Molecular crowding in vitro offers a systematic way to study anomalous and normal diffusion in a well controlled environment not accessible in vivo. We prepared a crowded environment in vitro consisting of hexaethylene glycol monododecyl ether (C(12)E(6)) nonionic surfactant and water and observed lysozyme diffusion between elongated micelles. We have fitted the data obtained in fluorescence correlation spectroscopy using an anomalous diffusion model and a two-component normal diffusion model. For a small concentration of surfactant (below 4 wt %) the data can be fitted by single-component normal diffusion. For larger concentrations the normal diffusion fit gave two components: one very slow and one fast. The amplitude of the slow component grows with C(12)E(6) concentration. The ratio of diffusion coefficients (slow to fast) is on the order of 0.1 for all concentrations of surfactant in the solution. The fast diffusion is due to free proteins while the slow one is due to the protein-micelle complexes. The protein-micelle interaction is weak since even in a highly concentrated solution (35% of C(12)E(6)) the amplitude of the slow mode is only 10%, despite the fact that the average distance between the micelles is the same as the size of the protein. The anomalous diffusion model gave the anomaly index (r(2)(t) approximately t(alpha)), alpha monotonically decreasing from alpha = 1 (at 4% surfactant) to alpha = 0.88 (at 37% surfactant). The fits for two-component normal diffusion and anomalous diffusion were of equally good quality, but the physical interpretation was only straightforward for the former.

Evidences of Nonideal Mixing in Poly(ethylene Glycol)/Organic Solvent Mixtures by Brillouin Scattering

The concentration dependence of the hypersonic properties of solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in benzene and toluene has been investigated by Brillouin scattering. The two solvents are very similar in structure and chemical properties, but while benzene is nonpolar, toluene possess a modest dipole. In both solvents a high-frequency relaxation process has been observed at high concentrations which has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. In both cases, the concentration dependence of the adiabatic compressibility deviates significantly from linearity, indicating the existence of nonideal mixing phenomena driven by aggregation processes taking place in the systems. However, there is no temperature dependence for solutions of PEG600 in benzene; on the contrary, the results obtained for solutions of PEG600 in toluene are noticeably dependent on the temperature. The comparison of the experimental data with the results of previous experiments on similar systems allows a general picture for weakly interacting mixtures of hydrogen-bonded systems and organic solvents to be developed. In particular, in the presence of a nonpolar solvent molecule the local structure of the mixture is dominated by solute self-association processes and any resulting solute-solvent correlation is barely induced by excluded volume effects. At high enough dilution the self-aggregation of solute molecules produces a variety of new local topologies that cannot be observed in bulk solute, and as a consequence, the concentration evolution of the system is too rich to be described in terms of a linear combination of a few components over the whole concentration range. The situation seems to be simpler for the polar toluene solvent molecules, where a three-component model seems able to fit the experimental concentration dependence of the hypersonic velocity. This result is interpreted to imply that the interaction between the solvent dipoles and the active sites of the solute produces a relatively stable heterocoordination, while the relevance of self-association is partially reduced.

Hidden Minima of the Gibbs Free Energy Revealed in a Phase Separation in Polymer/Surfactant/Water Mixture

We observed a very unusual kinetic pathway in a separating C(12)E(6)/PEG/H(2)O ternary mixture. We let the mixture separate above the spinodal temperature (cloud point temperature) for some time and next cool it into a metastable region of a phase diagram, characterized by two minima of the Gibbs potential, one corresponding to the homogeneous mixture and one to the fully separated PEG-rich and C(12)E(6)-rich phases. Despite the fact that in the metastable region the thermodynamic equilibrium corresponds to the separated phases (global minimum of the Gibbs free energy), we observe perfect mixing of the initially separated phase. The homogeneous state, obtained in this way, does not separate, if left undisturbed. However, many cooling-heating cycles or full separation with visible meniscus above the cloud point temperature induce the phase separation in the metastable region. The metastable region can exist tens of degrees below the cloud point temperature. This effect is not observed in the binary mixture of C(12)E(6)/H(2)O.

Structural Relaxation Processes in Polyethylene Glycol/CCl4 Solutions by Brillouin Scattering

We present results of a Brillouin scattering experiment on solutions of poly(ethylene glycol) of mean molecular mass 600 g/mol (PEG600) in CCl4. The relaxation process detected has been assigned to conformational rearrangements of the polymeric chains, triggered by reorientation of the side groups. The concentration dependencies of the hypersound velocity and normalized absorption are compared against the indications from several models proposed in the literature. The concentration evolution of the system is described in terms of two distinct regimes. At high polymer content, the system is dominated by the structure of the dense polymer, where polymer-polymer interactions, together with excluded volume effects, induce the existence of a preferred local arrangement resulting in a narrow distribution of the relaxation times, with the average value of the relaxation time following a simple Arrhenius temperature dependence. As the concentration decreases, the original structure of the hydrogen bonded polymer network is destroyed, and a number of different local configuration coexist, giving rise to a wider distribution of relaxation times or to a multiple relaxation. At low concentrations, the experimental data are well fitted assuming a Vogel-Fulker-Tammon behavior for the average relaxation time. In addition, the observed deviation from the ideal behavior for the refractive index and the density suggests that CCl4 does not behave as an inert solvent, and due to polarization effects, it can develop local hetero-associated structures via electrostatic interaction with the O-H end groups of the polymeric chains. The hypothesis has been successfully tested by fitting the concentration behavior of the hypersonic velocity to a recent three-component model, suitable to describe the concentration dependence of sound velocity in moderately interacting fluids. The indication of the model furnishes a very high value for the association constant of the PEG600, confirming the literature indication that, in polymeric systems capable of developing long liner aggregates via hydrogen bonding interaction, the Brillouin probe is insensitive to the true length of the polymeric chains. The Brillouin scattering experiment just sees an effective hydrogen bonded aggregate that is huge relative to the length of the single polymeric chain and becomes sensitive only to the density fluctuations of the local segmental motions.

Unfolding and refolding of juvenile hormone binding protein

Juvenile hormone (JH) regulates insect development. JH present in the hemolymph is bound to a specific glycoprotein, juvenile hormone binding protein (JHBP), which serves as a carrier to deploy the hormone to target tissues. In this report structural changes of JHBP from Galleria mellonella induced by guanidine hydrochloride have been investigated by a combination of size-exclusion chromatography, protein activity measurements, and spectroscopic methods. Molecules of JHBP change their conformation from a native state via two unstable intermediates to a denatured state. The first intermediate appears in a compact state, because it slightly changes its molecular size and preserves most of the JHBP secondary structure of the native state. Although the second intermediate also preserves a substantial part of the secondary structure, it undergoes a change into a noncompact state changing its Stokes radius from approximately 30 to 39 A. Refolding experiments showed that JHBP molecules recover their full protein structure, as judged from the CD spectrum, fluorescence experiments, and JH binding activity measurements. The free energy of unfolding in the absence of the denaturant, DeltaG(D-N), is calculated to be 4.1 kcal mol(-1).

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.

Magneto-optics of Ferritin

Measurements of Rayleigh light scattering, nonlinear light scattering in DC magnetic fields, and the Cotton-Mouton effect were carried out for 15 mM NaCl and water solutions of ferritin at room temperature. The spherical geometry of the molecule implies that it is optically isotropic. Such a macromolecule should not manifest magnetic anisotropy; however, in solution it shows induced magnetic birefringence (Cotton-Mouton effect) and changes in the intensity of the scattered light components. The analysis of the obtained results indicates the deformation of linear optical polarizability induced in the ferritin by a magnetic field as the main source of the magneto-optical phenomena observed. Light scattering and the CM effects theoretically depend on the linear magneto-optical polarizability, chi, and the nonlinear magneto-optical polarizability, eta. Using the theory describing the phenomena as well as the experimental data, the values of the anisotropy of linear magneto-optical polarizability components, chi(parallel) - chi(perpendicular) = -(1.3 +/- 0.7) x 10(-22) [cm3] (in SI units chi(parallel) - chi(perpendicular) = -(2.0 +/- 1.2) x 10(-33) [m3]), the linear optical polarizability, alpha = (alpha(parallel) + 2alpha(perpendicular))/3 = (3.9 +/- 1.0) x 10(-20) [cm3] (in SI units alpha = (3.52 +/- 0.09)x10(-4) [Cm2 V(-1)]), and its anisotropy, kappa(alpha) = (alpha(parallel) - alpha(perpendicular))/3alpha = -(0.06+/-0.03), nonlinear magneto-optical polarizability, eta = (eta(parallel) + 2eta(perpendicular))/3 = -(4.7 +/- 0.9) x 10(-30) [cm3 Oe(-2)] (in SI units eta = -(6.7 +/- 1.3) x 10(-18) [Cm4 V(-1) A(-2)]) and its anisotropy, kappa(eta) = (eta[parallel) - eta(perpendicular))/3eta = -(0.15 +/- 0.10), were deduced. Here alpha(parallel), eta(parallel), alpha(perpendicular), eta(perpendicular) are the optical and magneto-optical polarizability components along the parallel and the perpendicular axes of the axially symmetric molecule, respectively.

Correlation between nonexponential relaxation and non-Arrhenius behavior under conditions of high compression

Photon correlation spectroscopy was used to investigate the behavior of the dynamical properties of 1,1'-di(4-methoxy-5-methyl-phenyl)cyclohexane (BMMPC) at elevated pressures. The fragility of BMMPC measured by the steepness index m(T) is decreasing and the nonexponentiality parameter beta(KWW) is increasing with increasing pressure. This result strongly suggests that the phenomenological correlation between the steepness index and nonexponentionality is also preserved under high compression. The pressure dependence of the structural relaxation times is well characterized by a simple activation volume form. The activation volume continuously increases with decreasing temperature, which is probably due to the increase of cooperativity of the structural relaxation process. Moreover, we found that the glass-transition temperature exhibits a significant dependence on pressure.

Structural polymorphism of telomeres studied by photon correlation spectroscopy

Photon Correlation Spectroscopy (PCS) was used to study the dynamics and structure of Tetrahymena telomeric sequence d(5'-TGGGGT-3')4. Two different modes were observed, corresponding to the following structures: intermolecular (tetramolecular) G-quadruplex and intramolecular (monomeric) G-quartet. Experimental values of translational diffusion coefficients DT were obtained for each structural form. The value of DT for the monomer equals to 1.4 x 10(6) (cm2/s), while for the tetramolecular structure, to 0.8 x 10(6) (cm2/s). The relative weight concentrations of these two forms were analyzed versus the concentration of NaCl varied from 10 mM to 500 mM. The values of experimentally determined diffusion coefficients were compared with those calculated assuming the "bead model" and with the atomic coordinates from the NMR and X-ray crystallographic data. For both structures the experimental and calculated values of DT were in reasonable agreement. In the entire NaCl concentration range studied, the contribution of the relative weight concentration of the monomeric telomere form changed from 85% for 10 mM NaCl to 60% for 500 mM NaCl.

Solution structure of biopolymers: a new method of constructing a bead model

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma = 5.0 A was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (tau(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and tau(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger sigma = 5.7 A. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of sigma = 4.5 A for amino acids. The lack of experimental data on tau(R) for proteins restricted the tests to the translational diffusion properties.

Structural polymorphism of telomeres studied by photon correlation spectroscopy

Photon Correlation Spectroscopy (PCS) was used to study the dynamics and structure of Tetrahymena telomeric sequence d(5'-TGGGGT-3')4. Two different modes were observed, corresponding to the following structures: intermolecular (tetramolecular) G-quadruplex and intramolecular (monomeric) G-quartet. Experimental values of translational diffusion coefficients DT were obtained for each structural form. The value of DT for the monomer equals to 1.4 x 10(6) (cm2/s), while for the tetramolecular structure, to 0.8 x 10(6) (cm2/s). The relative weight concentrations of these two forms were analyzed versus the concentration of NaCl varied from 10 mM to 500 mM. The values of experimentally determined diffusion coefficients were compared with those calculated assuming the "bead model" and with the atomic coordinates from the NMR and X-ray crystallographic data. For both structures the experimental and calculated values of DT were in reasonable agreement. In the entire NaCl concentration range studied, the contribution of the relative weight concentration of the monomeric telomere form changed from 85% for 10 mM NaCl to 60% for 500 mM NaCl.

Effect of acrylamide on aldolase structure. II. Characterization of aldolase unfolding intermediates

Molecules of muscle aldolase A exposed to acrylamide change their conformation via I1, T, I2, D intermediates [1] and undergo a slow irreversible chemical modification of thiol groups. There is no direct correlation between activity loss and thiol groups modification. In the native enzyme two classes of Trp residues of 1. 8 ns and 4.9 ns fluorescence lifetime have been found. Acrylamide (0. 2-0.5 M) increases lifetime of longer-lived component, yet the transfer of aldolase molecules even from higher (1.0 M) perturbant concentration to a buffer, allows regain original Trp fluorescence lifetime. I1, detected at about 0.2 M acrylamide, represents low populated tetramers of preserved enzyme activity. T, of maximum population at about 0.7-1.0 M acrylamide, consists of meta-stable tetramers of partial enzymatic activity. These molecules are able to exchange their subunits with aldolase C in opposition to the native molecules. At transition point for I2 appearance (1.8 M acrylamide), aldolase becomes highly unstable: part of molecules dissociate into subunits which in the absence of perturbant are able to reassociate into active tetramers, the remaining part undergoes irreversible denaturation and aggregation. Some expansion of aldolase tetramers takes place prior to dissociation. D, observed above 3.0 M acrylamide, consists of irreversibly denatured enzyme molecules.

Light gradients in spherical photosynthetic vesicles

Light-gradient photovoltage measurements were performed on EDTA-treated thylakoids and on osmotically swollen thylakoids (blebs), both of spherical symmetry but of different sizes. In the case of EDTA vesicles, a negative polarity (due to the normal light gradient) was observed in the blue range of the absorption spectrum, and a positive polarity, corresponding to an inverse light gradient, was observed at lambda = 530 and lambda = 682 nm. The sign of the photovoltage polarity measured in large blebs (swollen thylakoids) is the same as that obtained for whole chloroplasts, although differences in the amplitudes are observed. An approach based on the use of polar coordinates was adapted for a theoretical description of these membrane systems of spherical symmetry. The light intensity distribution and the photovoltage in such systems were calculated. Fits to the photovoltage amplitudes, measured as a function of light wavelength, made it possible to derive the values of the dielectric constant of the protein, epsilons = 3, and the refractive index of the photosynthetic membrane for light propagating perpendicular and parallel to the membrane surface, nt = 1.42 and nn = 1.60, respectively. The latter two values determine the birefringence of the biological membrane, Deltan = nn - nt = 0.18.