Ultrasonic study of the kinetics of counterion site binding in aqueous solutions of polyelectrolytes

The excess ultrasonic absorption due to counterion binding has been studied as a function of frequency for a series of polysalts in the range 1–150 MHz. All the relaxation spectra can be represented by a relaxation equation with two relaxation terms. The relaxation frequencies appear concentration independent and the relaxation amplitudes seem proportional to concentration. The low frequency relaxation process appears to depend mainly on the nature of the counterion while the high frequency relaxation process seems to be mostly dependent on the nature of the polyion. These results are quite similar to those obtained in ultrasonic studies of ion-pairing in solutions of divalent sulfates. The kinetic model used for the quantitative analysis of these results has been modified for polysalts through introducing the concept of“counterion condensation”. In this modified model the excess absorption is assigned to the perturbation by the ultrasonic waves of the equilibria between the three states of hydration of ths complex formed by a counterion and that part of the polyion where it is bound. Analytical expressions of the relaxation amplitudes have been derived using classical procedures for this modified kinetic model. In the case of cobalt-polyphosphate (Co-PP), the ultrasonic data together with the results of NMR measurements on either Co²⁺ or Co-PP have been used for the evaluation of the volume changes, the rate constants and the fractions of counterions in the three states of hydration involved in the binding equilibria. The volume changes obtained in this manner depend only slightly on the method of calculation and appear to be consistent with volume changes for outer-sphere and inner-sphere complex formation. These results are discussed.     

Methods of tissue characterization with ultrasonic spectroscopy, analysis of the results obtained, prospects for clinical application in a short time]

So far, to account for ultrasonic attenuation in soft tissues molecular scale relaxation theory is retained. In addition to these mechanisms, the authors have obtained experimental evidence proving the role also plaid by cellular scale resonance mechanisms. Moreover, in addition to incoherent diffusion, it has been found that some tissues exhibit some coherent diffusion. All these experimental findings allows us to establish the feasability of non invasive ultrasonic biopsies.     

Relaxation dynamics of the gel to liquid-crystalline transition of phosphatidylcholine bilayers. Effects of chainlength and vesicle size.

The relaxation kinetics of the gel to liquid-crystalline transition of five phosphatidylcholine (DC14PC to DC18PC) bilayer dispersions have been investigated using volume perturbation calorimetry, a steady-state technique which subjects a sample to sinusoidal changes in volume. Temperature and pressure responses to the volume perturbation are measured to monitor the relaxation to a new equilibrium position. The amplitude demodulation and phase shift of these observables are analyzed with respect to the perturbation frequency to yield relaxation times and amplitudes. In the limit of low perturbation frequency, the temperature and pressure responses are proportional to the equilibrium excess heat capacity and bulk modulus, respectively. At all temperatures, the thermal response data are consistent with a single primary relaxation process of the lipid. The less accurate bulk modulus data exhibit two relaxation times, but it is not clear whether they reflect lipid processes or are characteristic of the instrument. The observed thermal relaxation behavior of all multilamellar vesicles are quantitatively similar. The relaxation times vary from approximately 50 ms to 4 s, with a pronounced maximum at a temperature just greater than Tm, the temperature of the excess heat capacity maximum. Large unilamellar vesicles also exhibit a single relaxation process, but without a pronounced maximum in the relaxation time. Their relaxation time is approximately 80 ms over most of the transition range.     

Interaction between hydroxystilbamidine and DNA. II. Temperature jump relaxation study. Dynamics of nucleic acids and polynucleotides.

A temperature-jump relaxation study of the interaction of hydroxystilbamidine with DNA and synthetic polynucleotides has been performed. Two concentration dependent relaxation times tau1 and tau2 have been observed in the submillisecond range when detecting relaxation effects by means of light absorption. The longer of these two times (tau1) is also observed when using "blue" or "red" fluorescence detection. In the longer time scale the "red" fluorescence shows no other relaxation but the blue fluorescence shows two additional relaxation processes (tau3 and tau4) which correspond to an increase of fluorescence with temperature and which are independent of concentration. The experimental results clearly indicate that tau1 and tau2 are associated with the binding of the dye to strong and weak binding sites, respectively. A kinetic model is given to explain the results. It allows the determination of the four rate constants for the two binding reactions and yields equilibrium association constants in good agreement with those obtained from stoichiometric studies. The study of the effect of temperature, nature of the polymer, ionic strength and fraction of bound dye on tau3 and tau4 indicates that the dye acts only as a "blue" fluorescence probe of some processes involving the DNA or polynucleotide alone. These processes appear to be related with the dynamic structure of the polymers.     

Absolute measurement of enhanced fluctuations in assemblies of biomolecules by ultrasonic techniques.

By expressing the fluctuation-dissipation theorem explicitly, equations are obtained for the ultrasonic relaxation amplitudes that contain one single molecular parameter, i.e., the fluctuation, or the sum of fluctuations. The absolute measurement of this parameter is therefore possible. The equations apply to a two-state system, to a multistate system and to a linear Ising chain as well. In an aqueous medium, where molar volume changes are important, the ultrasonic relaxation amplitudes are proportional to the volume fluctuations. For assemblies of biomolecules that exhibit enhanced ultrasonic absorption on assembly it is possible to measure the increase on assembly of the sum of fluctuations. In view of application to tobacco mosaic virus protein aggregates, examples are given in which the fluctuations associated with two normal modes of relaxation are equally enhanced when the difference of conformational stability of the states is reduced. The corresponding observable changes of the ultrasonic spectra are described.     

Ultrasonic absorption studies of poly-benzyl-L-aspartate in mixed solvents, in relation to the helix-cell transition

Ultrasonic absorption measurements were carried out on solutions of polybenzyl-L -aspartate (PBLA) in chloroform–dichloroacetic acid (DCA) and in 1,2-dichloroethane (DCE)–DCA, in the range 3.9–155 MHZ . The helix–coil transition of PBLA produces an increase of absorption which is larger in CHCl₃–DCA than in DCE–DCA solutions. The influence of the solvent on the excess ultrasonic absorption suggests that solvation processes may be involved in these changes of absorption. The plots of the absorption vs. the volume fraction of DCA do not show any absorption maximum. This indicates that the ultrasonic absorption is not sensitive to the helix–coil equilibrium of PBLA in the frequency range investigated. A maximum value of 10⁹ S ^?1 has been obtained for the rate constant of growth of a helix region.     

Ultrasonic absorption studies of protein-buffer interactions

The acoustic absorption of protein solutions in the presence of phosphate and other buffering ions has been studied in the physiological pH range. Buffers containing hydroxyl residues as titratable groups cause a pronounced increase of protein sound absorption, which is attributed to relaxation processes of proton transfer reactions between buffer ions and accessible imidazole and -amino groups of the protein surface. Amino group based buffers like Good's buffers do not induce additional sound absorption. Measurement of the ultrasonic absorption as a function of pH and of buffer concentration, and corresponding parameter fitting of the equation describing proton transfer relaxation processes has been used to evaluate equilibrium parameters. For the imidazole group of the amino acid histidine a pK value of 6.22 and for the imidazole group of the protein lysozyme a pK value of 5.71 have been determined. In hemoglobin the ligand-linked pK changes have been monitored by recording ultrasonic titration curves.     

Dynamics of human serum albumin studied by acoustic relaxation spectroscopy

Sonic absorption spectra of solutions of human serum albumin (SA) in water and in aqueous phosphate buffer systems have been measured between 0.2 and 2000 MHz at different temperatures (15-35 degrees C), pH values (1.8-12.3), and protein concentrations (1-40 g/L). Several spectra, indicating relaxation processes in the whole frequency range, have been found. The spectra at neutral pH could be fitted well with an analytical function consisting of the asymptotic high frequency absorption and two relaxation contributions, a Debye-type relaxation term with discrete relaxation time and a term with asymmetric continuous distribution of relaxation times. Both relaxation contributions were observed in water and in buffer solutions and increased with protein concentration. The contribution represented by a Debye-type term is practically independent of temperature and was attributed to cooperative conformational changes of the polypeptide chain featuring a relaxation time of about 400 ns. The distribution of the relaxation times corresponding to the second relaxation contribution was characterized by a short time cutoff, between about 0.02 and 0.4 ns depending on temperature, and a long time tail extending to microseconds. Such relaxation behavior was interpreted in terms of solute-solvent interactions reflecting various hydration layers of HSA molecules. At acid and alkaline pH, an additional Debye-type contribution with relaxation time in the range of 30-100 ns exists. It seems to be due to proton transfer reactions of protein side-chain groups. The kinetic and thermodynamic parameters of these processes have been estimated from these first measurements to indicate the potential of acoustic spectra for the investigation of the elementary kinetics of albumin processes.     

Plant responses to metal toxicity

Metal toxicity for living organisms involves oxidative and/or genotoxic mechanisms. Plant protection against metal toxicity occurs, at least in part, through control of root metal uptake and of long distance metal transport. Inside cells, proteins such as ferritins and metallothioneins, and glutathion-derived peptides named phytochelatins, participate in excess metal storage and detoxification. Low molecular weight organic molecules, mainly organic acids and amino acids and their derivatives, also play an important role in plant metal homeostasis. When these systems are overloaded, oxidative stress defense mechanisms are activated. Molecular and cellular knowledge of these processes will be necessary to improve plant metal resistance. Occurrence of naturally tolerant plants which hyperaccumulate metals provides helpful tools for this research.     

Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding

Two fundamentally different mechanisms of ligand binding are commonly encountered in biological kinetics. One mechanism is a sequential multistep reaction in which the bimolecular binding step is followed by first-order steps. The other mechanism includes the conformational transition of the macromolecule, before the ligand binding, followed by the ligand binding process to one of the conformational states. In stopped-flow kinetic studies, the reaction mechanism is established by examining the behavior of relaxation times and amplitudes as a function of the reactant concentrations. A major diagnostic tool for detecting the presence of a conformational equilibrium of the macromolecule, before the ligand binding, is the decreasing value of one of the reciprocal relaxation times with the increasing [ligand]. The sequential mechanism cannot generate this behavior for any of the relaxation times. Such dependence is intuitively understood on the basis of approximate expressions for the relaxation times that can be comprehensively derived, using the characteristic equation of the coefficient matrix and polynomial theory. Generally, however, the used approximations may not be fulfilled. On the other hand, the two kinetic mechanisms can always be distinguished, using the approach based on the combined application of pseudo-first-order conditions, with respect to the ligand and the macromolecule. The two experimental conditions differ profoundly in the extent of the effect of the ligand on the protein conformational equilibrium. In a large excess of the ligand, the conformational equilibrium of the macromolecule, before the ligand binding, is strongly affected by the binding process. However, in a large excess of the macromolecule, ligand binding does not perturb the internal equilibrium of the macromolecule. As a result, the normal mode, affected by the conformational transition, is absent in the observed relaxation process. In the case of a sequential mechanism, the number of relaxation times is not altered by different pseudo-first-order conditions. Thus, the approach provides a strong diagnostic criterion for detecting the presence of the conformational transition of the macromolecule and establishing the correct mechanism. Application of this approach is illustrated for the binding of 3'-O-(N-methylantraniloyl)-5'-diphosphate to the E. coli DnaC protein.     

Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model

Photosynthetic eukaryotes house two photosystems with distinct light absorption spectra. Natural fluctuations in light quality and quantity can lead to unbalanced or excess excitation, compromising photosynthetic efficiency and causing photodamage. Consequently, these organisms have acquired several distinct adaptive mechanisms, collectively referred to as non-photochemical quenching (NPQ) of chlorophyll fluorescence, which modulates the organization and function of the photosynthetic apparatus. The ability to monitor NPQ processes fluorometrically has led to substantial progress in elucidating the underlying molecular mechanisms. However, the relative contribution of distinct NPQ mechanisms to variable light conditions in different photosynthetic eukaryotes remains unclear. Here, we present a mathematical model of the dynamic regulation of eukaryotic photosynthesis using ordinary differential equations. We demonstrate that, for Chlamydomonas, our model recapitulates the basic fluorescence features of short-term light acclimation known as state transitions and discuss how the model can be iteratively refined by comparison with physiological experiments to further our understanding of light acclimation in different species.     

Relaxational contributions to protein compressibility from ultrasonic data

The ultrasonic absorption spectra of proteins in solution generally show relaxational behaviour. There will be a corresponding dispersion of sound velocities accompanying each relaxation. The compressibility of the protein as measured by sound velocity techniques will therefore include a relaxational contribution. We have evaluated this contribution for a number of proteins and found that in some cases the relaxational contribution is a significant fraction of the total compressibility. The relaxational contribution will be large only if the molecule has a large number of degrees of freedom with low force constants. However, such motions are likely to be those involved in the biological functioning of the molecule. Care is needed in interpreting the relaxation spectrum since proton transfer processes give large apparent relaxational compressibilities.     

Relaxation spectra of two-step mechanisms as measured by the NADH-binding to glutamate dehydrogenase

Temperature-jump relaxation experiments performed with glutamate dehydrogenase and the reduced coenzyme nicotinamide adenosine dinucleotide show two clearly separated relaxation times. Three of the simplest and most plausible mechanisms attributable to two relaxation times are treated here theoretically and the concentration dependence of the relaxation times is determined in each case with different experimental conditions. This makes it possible to distinguish between the mechanisms and also to determine the rate constants of the different reaction steps.     

Anomalies of nanosecond ultrasonic relaxation in the lipid bilayer transition

The frequency dependence of ultrasonic velocity as well as absorption in a suspension of sonicated dipalmitoylphosphatidylcholine vesicles was measured by a differential ultrasonic resonator. The frequency was scanned between 1.3 and 13 MHz and the temperature was varied from 25 to 47°C. A pronounced relaxation was observed in the time range of 10 ns. The data were analyzed assuming a single relaxation which appeared to be a good approximation. The relaxation time as well as relaxation strength increased anomalously in the vicinity of the gel-to-liquid crystal transition of 41.5°C. This result represents the first definite evidence of the critical slowing down in the lipid bilayer and is discussed in terms of the Landau theory of phase transition. The possible biological significance of the mechanical relaxation is also presented.     

Ultrasonic evidence for structural relaxation in large unilamellar liposomes

The ultrasonic absorption of large unilamellar vesicles (average diameter 0.2 micron) was determined in the frequency range 0.5-5 MHz. The liposomes were composed of a 4:1 mixture by weight of dipalmitoyl phosphatidylcholine and dipalmitoyl phosphatidylglycerol. They were studied with and without cholesterol or gramicidin incorporated into the bilayer. A large increase in absorption occurs at the solid to liquid-crystalline phase transition temperature (42 degrees C) of the pure lipid vesicles. This increase in absorption is interpreted as a structural relaxation of the 'melting' fatty acid chains occurring with an average relaxation time of 76 ns. The liposomes were also found to be extremely permeable near the transition temperature. Essentially complete release of cytosine arabinoside, a small water-soluble molecule, occurred at 42 degrees C. Addition of cholesterol or gramicidin to the bilayer of the liposomes broadened the ultrasonic absorption and reduced the efflux of cytosine arabinoside at the phase transition. No increase in absorption was observed at the transition temperature in the presence of 50 mol% of cholesterol. Gramicidin, in addition to broadening the transition, slows the isomerization of bonds in the hydrocarbon chains of the lipids. A concentration of 5 mol% gramicidin increased the average relaxation time to 211 ns.     

Defects in Ultrasonic Vocalization of Cadherin-6 Knockout Mice

Background

Although some molecules have been identified as responsible for human language disorders, there is still little information about what molecular mechanisms establish the faculty of human language. Since mice, like songbirds, produce complex ultrasonic vocalizations for intraspecific communication in several social contexts, they can be good mammalian models for studying the molecular basis of human language. Having found that cadherins are involved in the vocal development of the Bengalese finch, a songbird, we expected cadherins to also be involved in mouse vocalizations.

Methodology/Principal Findings

To examine whether similar molecular mechanisms underlie the vocalizations of songbirds and mammals, we categorized behavioral deficits including vocalization in cadherin-6 knockout mice. Comparing the ultrasonic vocalizations of cadherin-6 knockout mice with those of wild-type controls, we found that the peak frequency and variations of syllables were differed between the mutant and wild–type mice in both pup-isolation and adult-courtship contexts. Vocalizations during male-male aggression behavior, in contrast, did not differ between mutant and wild–type mice. Open-field tests revealed differences in locomotors activity in both heterozygote and homozygote animals and no difference in anxiety behavior.

Conclusions/Significance

Our results suggest that cadherin-6 plays essential roles in locomotor activity and ultrasonic vocalization. These findings also support the idea that different species share some of the molecular mechanisms underlying vocal behavior.     

Solid state NMR investigation of the molecular dynamics of cocoon silks produced by different Bombyx mori (Lepidoptera) strains

Cocoons produced by different strains of Bombyx mori larvae were investigated by a combination of several high- and low-resolution 1H and 13C solid-state NMR techniques in order to characterize and compare their dynamic behavior at a molecular level. A detailed interpretation in terms of molecular motions in these very complex systems was possible thanks to the integrated analysis of different relaxation measurements and high-resolution selective experiments. Untreated cocoons of all strains were found to be mainly constituted by two different types of rigid domains and by a third one, more mobile, due to physisorbed water molecules. Dynamic processes in the MHz and kHz ranges were characterized by means of different 1H and 13C relaxation times. Cocoons arising from different strains exhibit a different content of physisorbed water and also slightly different dynamic behavior, especially in the MHz regime.     

Proteins involved in uptake, intracellular transport and basolateral secretion of fat-soluble vitamins and carotenoids by mammalian enterocytes

Our understanding of the molecular mechanisms responsible for fat-soluble vitamin uptake and transport at the intestinal level has advanced considerably over the past decade. On one hand, it has long been considered that vitamin D and E as well as β-carotene (the main provitamin A carotenoid in human diet) were absorbed by a passive diffusion process, although this could not explain the broad inter-individual variability in the absorption efficiency of these molecules. On the other hand, it was assumed that preformed vitamin A (retinol) and vitamin K1 (phylloquinone) absorption occurred via energy-dependent processes, but the transporters involved have not yet been identified. The recent discovery of intestinal proteins able to facilitate vitamin E and carotenoid uptake and secretion by the enterocyte has spurred renewed interest in studying the fundamental mechanisms involved in the absorption of these micronutrients. The proteins identified so far are cholesterol transporters such as SR-BI (scavenger receptor class B type I), CD36 (cluster determinant 36), NPC1L1 (Niemann–Pick C1-like 1) or ABCA1 (ATP-Binding Cassette A1) displaying a broad substrate specificity, but it is likely that other membrane proteins are also involved. After overviewing the metabolism of fat-soluble vitamins and carotenoids in the human upper gastrointestinal lumen, we will focus on the putative or identified proteins participating in the intestinal uptake, intracellular transport and basolateral secretion of these fat-soluble vitamins and carotenoids, and outline the uncertainties that need to be explored in the future. Identifying the proteins involved in intestinal uptake and transport of fat-soluble vitamins and carotenoids across the enterocyte is of great importance, especially as some of them are already targets for the development of drugs able to slow cholesterol absorption. Indeed, these drugs may also interfere with lipid vitamin uptake. A better understanding of the molecular mechanisms involved in fat-soluble vitamin and carotenoid absorption is a priority to better optimize their bioavailability.     

Application of pressure-modulated differential scanning calorimetry to the determination of relaxation kinetics of multilamellar lipid vesicles

We report an extension of the recently published PMDSC method that permitted synchronous determination of heat capacity and expansibility when using slow, defined pressure formats in a DSC scan. Here we applied continuously opposing pressure changes that are fast compared to the time constants of the DSC instrument to study relaxation kinetics of phospholipids. Investigations of multilamellar vesicles of DPPC or DSPC in water revealed for both lipids relaxation times of about 30 s at the maximum of the main transition peak and about 15 s at the maximum of the pretransition. The relaxation times in the transition range are proportional to heat capacity of main- and pretransition. The molecular origin of the relaxation processes appears to stem from pressure-induced water fluxes between the interbilayer region and the bulk water phase.