A complete dielectric response model for liquid water: a solution of the Bethe ridge problem

We present a complete yet computationally simple model for the dielectric response function of liquid water over the energy-momentum plane, which, in contrast to earlier models, is consistent with the recent inelastic X-ray scattering spectroscopy data at both zero and finite momentum transfer values. The model follows Ritchie's extended-Drude algorithm and is particularly effective at the region of the Bethe ridge, substantially improving previous models. The present development allows for a more accurate simulation of the inelastic scattering and energy deposition process of low-energy electrons in liquid water and other biomaterials. As an example, we calculate the stopping power of liquid water for electrons over the 0.1-10 keV range where direct experimental measurements are still impractical and the Bethe stopping formula is inaccurate. The new stopping power values are up to 30-40% lower than previous calculations. Within the range of validity of the first Born approximation, the new values are accurate to within the experimental uncertainties (a few percent). At the low end, the introduction of Born corrections raises the uncertainty to perhaps approximately 10%. Thus the present model helps extend the ICRU electron stopping power database for liquid water down to about two orders of magnitude with a comparable level of uncertainty.     

Accurate electron inelastic cross sections and stopping powers for liquid water over the 0.1-10 keV range based on an improved dielectric description of the Bethe surface

Electron inelastic cross sections and stopping powers for liquid water over the 0.1-10 keV range are presented based on a recently developed dielectric response model for liquid water (D. Emfietzoglou, F. Cucinotta and H. Nikjoo, Radiat. Res. 164, 202-211, 2005) that is consistent with the experimental data over the whole energy-momentum plane. Both exchange and second-order Born corrections are included in a material-specific way using the dielectric functions of liquid water. The numerical results are fitted by simple analytic functions to facilitate their further use. Compared to previous studies, differential cross sections are shifted toward smaller energy losses resulting in smaller inelastic and stopping cross sections with differences reaching, on average, the approximately 20% and approximately 50% level, respectively. Contrary to higher energies, it is shown that the dispersion model for the momentum dependence of the dielectric functions (Bethe ridge) is as important as the optical model used. Within the accuracy of the experimental data (a few percent) upon which our dielectric model is based, the calculations are "exact" to first order, while the uncertainty of the results beyond first order is estimated at the 5-10% level. The present work overcomes the limitations of Bethe's theory at low energies by a self-consistent account of inner-shell effects and may serve to extend the ICRU electron stopping power database for liquid water down to 100 eV with a level of uncertainty similar to that for the higher-energy values.     

Small-angle X-ray scattering and differential scanning calorimetry studies on reversibly modified human-serum low density lipoproteins.

Small-angle x-ray scattering diagrams of human serum low density lipoprotein (LDL) were recorded at several temperatures in solutions of different freezing points. It was found that modifications of the x-ray patterns observed on cooling the lipoprotein samples below 0 degrees C are due to reversible alterations of the LDL surface structure induced by the freezing process (independent of temperature). With both intact and partially dehydrated LDL, differential scanning calorimetry (DSC) carried out in the body temperature range revealed a heat absorption characteristic of the transition from a liquid crystal to an isotropic liquid phase of cholesteryl esters within the lipoproteins (Deckelbaum, R. J., Shipley, R. J., Small, P. M., Lees, R. S., & George, P. K. (1975) Science 190, 392). However, small-angle x-ray scattering diagrams recorded with the same LDL sample before and after the partial removal of water were found to be very different: the scattering curve for intact LDL showed a strong band centered at (36 A)-1 which disappeared upon drying and reappeared upon restoring the water. Our results suggest that the presence of this signal strongly depends on the molecular structure of the lipoprotein surface.     

Differences in hydration structure near hydrophobic and hydrophilic amino acids.

We use molecular dynamics to simulate recent neutron scattering experiments on aqueous solutions of N-acetyl-leucine-amide and N-acetyl-glutamine-amide, and break down the total scattering function into contributions from solute-solute, solute-water, water-water, and intramolecular correlations. We show that the shift of the main diffraction peak to smaller angle that is observed for leucine, but not for glutamine, is attributable primarily to alterations in water-water correlations relative to bulk. The perturbation of the water hydrogen-bonded network extends roughly two solvation layers from the hydrophobic side chain surface, and is characterized by a distribution of hydrogen bonded ring sizes that are more planar and are dominated by pentagons in particular than those near the hydrophilic side chain. The different structural organization of water near the hydrophobic solute that gives rise to the inward shift in the main neutron diffraction peak under ambient conditions may also provide insight into the same directional shift for pure liquid water as it is cooled and supercooled.     

Conformational changes of the lecithin headgroup in monolayers at the air/water interface

The headgroup conformation of the phospholipid dipalmitoyl-glycero-phosphocholine (DPPC) in monolayers at the air/water interface has been studied by neutron reflection in the fluid like liquid-expanded (LE) and in the crystal like solid (S) phase. Information on the headgroup conformation in the two phases has been obtained by scattering contrast variation of the lipid monolayer using four differently deuterated species of DPPC: perdeuterated, chain perdeuterated, choline group perdeuterated and selectively headgroup deuterated. Since the measurements were done mainly on a subphase of null reflecting water (i.e. water scattering contrast matched to the air) there is no subphase contribution to reflectivity and the simplest one layer model can be employed for the data analysis, thus minimising the number of free parameters. A remarkable change of the headgroup orientation was observed between the LE and the S phase. We found that the phosphate-nitrogen dipole of the DPPC headgroup exhibits an in-plane orientation with respect to the monolayer in the LE phase but it assumes a more parallel orientation to the surface normal at lateral pressures above 30 mN/m (S phase). Moreover, this conformational change is accompanied by a significant alteration of the headgroup hydration.Abbreviations DPPC Dipalmitoyl-Phosphatidylcholine - DMPC Dimyristoyl-Phosphatidylcholine - DPPE Dipalmitoyl-Phosphatidylethanolamine - DMPE Dimyristoyl-Phosphatidylethanolamine - DMPA Dimyristoyl-Phosphatic Acid - DMPG Dimyristoyl-Phosphatidylglycerol Correspondence to: T M. Bayed     

C-phycocyanin hydration water dynamics in the presence of trehalose: an incoherent elastic neutron scattering study at different energy resolutions

We present a study of C-phycocyanin hydration water dynamics in the presence of trehalose by incoherent elastic neutron scattering. By combining data from two backscattering spectrometers with a 10-fold difference in energy resolution we extract a scattering law S(Q,omega) from the Q-dependence of the elastic intensities without sampling the quasielastic range. The hydration water is described by two dynamically different populations--one diffusing inside a sphere and the other diffusing quasifreely--with a population ratio that depends on temperature. The scattering law derived describes the experimental data from both instruments excellently over a large temperature range (235-320 K). The effective diffusion coefficient extracted is reduced by a factor of 10-15 with respect to bulk water at corresponding temperatures. Our approach demonstrates the benefits and the efficiency of using different energy resolutions in incoherent elastic neutron scattering over a large angular range for the study of biological macromolecules and hydration water.     

Water and hermal diffusivity in a lipid-water smectic phase.

We report the first application of light scattering to measurement of the hydrodynamic relaxation of inhomogeneities in water concentration within a multilamellar, or smectic A, phospholipid water system (dipalmitoyl) phosphatidyl choline). Although the relaxation process in the multilamellar phase is different from the diffusion process in liquid phases, the relaxation rate can be described in terms of a diffusion coefficient. For diffusion parallel to the lamellae, diffusion coefficients ranging from 8 x 10(-7) to 2 x 10(-5) cm2/s were measured over a range of temperature and water concentrations. We describe a model that expresses the diffusion coefficient in terms of the chemical potential for water inside the multilamellar phase and the effective thickness of a "free water zone." The deduced thickness of this free water zone is in good agreement with estimates from X-ray diffraction results. The activation energy for the diffusion process is also deduced from the data, and is found to decrease monotonically with increasing water concentration. We also found the thermal diffusivity to be about 10(-3) cm2/s with only a weak temperature and water concentration dependence. The experimental technique is a new version of forced Rayleigh scattering. The method uses the phase information of the scattered light to improve the ability to detect weak signals. Experimental details are reported.     

A liquid diffraction analysis of sarcoplasmic reticulum. I. Compositional variation.

Intensities of x-ray scattering from a series of fragmented rabbit muscle sarcoplasmic reticulum (SR) samples have been measured over the range x = 0.05 to s = 0.25. By varying the relative concentrations of lipid and protein (chiefly the Mg++-dependent, Ca++- stimulated ATPase) in the membranes of this series, and by employing methods of analysis appropriate to the scattering from binary liquid mixtures, we have identified the separable contributions of protein and lipid, and the protein-lipid interaction contributions to the total scattering profiles. The shape of the protein term is consistent with scattering from a cylindrical ATPase particle 142 A in length and 35 A in diameter. These data imply that the dominant ATPase species is monomeric. The protein-lipid interaction term has been analyzed by a novel treatment based on a determination of the pair correlation function between the electrons of the protein molecule with the electrons of the lipid bilayer in terms of the asymmetry of the transbilayer disposition of the protein. Applied to our results, the analysis indicates a fully asymmetric disposition of ATPase, in which one end of the molecule is contiguous with either the lumenal or cytoplasmic surface of the bilayer.     

Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data

The implications of protein-water interactions are of importance for understanding the solution behavior of proteins and for analyzing the fine structure of proteins in aqueous solution. Starting from the atomic coordinates, by bead modeling the scattering and hydrodynamic properties of proteins can be predicted reliably (Debye modeling, program HYDRO). By advanced modeling techniques the hydration can be taken into account appropriately: by some kind of rescaling procedures, by modeling a water shell, by iterative comparisons to experimental scattering curves (ab initio modeling) or by special hydration algorithms. In the latter case, the surface topography of proteins is visualized in terms of dot surface points, and the normal vectors to these points are used to construct starting points for placing water molecules in definite positions on the protein envelope. Bead modeling may then be used for shaping the individual atomic or amino acid residues and also for individual water molecules. Among the tuning parameters, the choice of the scaling factor for amino acid hydration and of the molecular volume of bound water turned out to be crucial. The number and position of bound water molecules created by our hydration modeling program HYDCRYST were compared with those derived from X-ray crystallography, and the capability to predict hydration, structural and hydrodynamic parameters (hydrated volume, radius of gyration, translational diffusion and sedimentation coefficients) was compared with the findings generated by the water-shell approach CRYSOL. If the atomic coordinates are unknown, ab initio modeling approaches based on experimental scattering curves can provide model structures for hydrodynamic predictions.     

Supramolecular assembly using helical peptides

We investigated supramolecular assemblies of various hydrophobic helical peptides. The assemblies were formed at the air/water interface or in aqueous medium. The hexadecapeptide, Boc-(Ala-Aib)₈-OMe (BA16M), was reported to take α-helical structure by X-ray analysis. Several derivatives were prepared, which have the repeating sequence of Ala-Aib, Lys(Z)-Aib or Leu-Aib, or have the terminal chemically modified. CD spectra of the peptides indicated helical conformation in ethanol solution. The surface pressure-area isotherms of the peptide monolayers showed an inflection at the surface area corresponding to the cross section along the helix axis, and the monolayers were collapsed by further compression. All the helical peptides oriented their helix axis parallel to the air/water interface on the basis of the results of transmission IR spectra and RAS of the monolayers transferred onto substrates.A small mound was observed in the isotherm of BA16M and other derivatives, which was ascribed to the phase transition from the liquid state to the solid state. One mol% of FITC-labeled peptide was mixed into the monolayers to visualize the phase separation of the solid and liquid states at the surface pressure of the coexisting region. Various shapes of the dark domain were observed at the top of the mound in the isotherms by fluorescence microscopy. The helical peptides formed two-dimensional crystals at the air/water interface when they were compressed to the solid state.An amino-terminated helical peptide, HA16B, was suspended in an aqueous medium by a sonication method and transparent dispersion was obtained. The dynamic light scattering measurement of the dispersion revealed the particle size of 75 nm with a narrow size distribution. The molecular assembly of the helical peptide in water was called “Peptosome”, because it takes a vesicular structure.     

Bilayer thickness and lipid interface area in unilamellar extruded 1,2-diacylphosphatidylcholine liposomes: a small-angle neutron scattering study

Small-angle neutron scattering (SANS) experiments have been performed on large unilamellar liposomes prepared from 1,2-dilauroylphosphatidylcholine (DLPC), 1,2-dimyristoyl-phosphatidylcholine (DMPC) and 1,2-distearoylphosphatidylcholine (DSPC) in heavy water by extrusion through polycarbonate filters with 500 A pores. The neutron scattering intensity I(Q) in the region of scattering vectors Q corresponding to 0.0015 A(-2) < or = Q(2) < or = 0.0115 A(-2) was fitted using a step function model of bilayer neutron scattering length density and supposing that the liposomes are spherical and have a Gaussian distribution of radii. Using the lipid volumetric data, and supposing that the thickness of bilayer polar region equals to d(H) = 9+/-1 A and the water molecular volume intercalated in the bilayer polar region is the same as in the aqueous bulk aqueous phase, the steric bilayer thickness d(L), the lipid surface area A(L) and the number of water molecules per lipid molecule N intercalated in the bilayer polar region were obtained: d(L) = 41.58+/-1.93 A, A(L) = 57.18+/-1.00 A(2) and N = 6.53+/-1.93 in DLPC at 20 degrees C, d(L) = 44.26+/-1.42 A, A(L) = 60.01+/-0.75 A(2) and N = 7.37+/-1.94 in DMPC at 36 degrees C, and d(L) = 49.77+/-1.52 A, A(L) = 64.78+/-0.46 A(2) and N = 8.67+/-1.97 in DSPC at 60 degrees C. After correcting for area thermal expansivity alpha approximately 0.00417 K(-1), the lipid surface area shows a decrease with the lipid acyl chain length at 60 degrees C: A(L) = 67.56+/-1.18 A(2) in DLPC, A(L) = 66.33+/-0.83 A(2) in DMPC and A(L) = 64.78+/-0.46 A(2) in DSPC. It is also shown that a joint evaluation of SANS and small-angle X-ray scattering on unilamellar liposomes can be used to obtain the value of d(H) and the distance of the lipid phosphate group from the bilayer hydrocarbon region d(H1).     

Phytantriol-Based In Situ Liquid Crystals with Long-Term Release for Intra-articular Administration

The purpose of this study was to develop an injectable in situ liquid crystal formulation for intra-articular (IA) administration, and in situ forming a viscous liquid crystalline gel with long-term release of sinomenine hydrochloride (SMH) upon water absorption. The pseudo-ternary phase diagram of phytantriol (PT)-ethanol (ET)-water was constructed, and isotropic solutions were chosen for further optimization. The physicochemical properties of isotropic solutions were evaluated, and the phase structures of liquid crystalline gels formed by isotropic solutions in excess water were confirmed by crossed polarized light microscopy (CPLM) and small-angle X-ray scattering (SAXS). In vitro drug release studies were conducted by using a dialysis membrane diffusion method. The optimal in situ cubic liquid crystal (ISV₂) (PT/ET/water, 64:16:20, w/w/w) loaded with 6 mg/g of SMH showed a suitable pH, showed to be injectable, and formed a cubic liquid crystalline gel in situ with minimum water absorption within the shortest time. The optimal ISV₂ was able to sustain the drug release for 6 days. An in situ hexagonal liquid crystal (ISH₂) system was prepared by addition of 5% vitamin E acetate (VitEA) into PT in the optimal ISV₂ system to improve the sustained release of SMH. This ISH₂ (PT/VitEA/ET/water, 60.8:3.2:16:20, w/w/w/w) was an injectable isotropic solution with a suitable pH range. The developed ISH₂ was found to be able to sustain the drug release for more than 10 days and was suitable for IA injection for the treatment of rheumatoid arthritis (RA).KEY WORDS: in situ cubic liquid crystal, in situ hexagonal liquid crystal, phytantriol, sinomenine hydrochloride, sustained drug release     

Effects of suspensoids (turbidity) on penetration of solar radiation in aquatic ecosystems

In mainland Australia and in southern Africa, the aridity of the climate and sparse vegetative cover increase the susceptibility of the soils to erosion, and as a consequence surface waters are usually turbid. The inanimate suspensoids in such waters, the tripton fraction of the limnologist, are responsible for virtually all the light scattering, and also, by virtue of the yellow-brown humic materials adsorbed on their surface, for a substantial part of the light absorption. Spectral absorption data for suspensoids in terms of theirin situ absorption coefficient values, and the contribution of suspensoids to absorption of photosynthetically available radiation (PAR) are given for certain Australian water bodies.To understand the effect of suspensoids on attenuation of the solar flux with depth, the scattering coefficient must also be known, and this can be determined from the nephelometric turbidity or from up- and down-welling irradiance measurements. The effect of particle size on scattering efficiency is discussed.An equation expressing the vertical attenuation coefficient for downward irradiance as a function of absorption coefficient, scattering coefficient and solar altitude is presented, and is used to explore the effects of absorption due to dissolved colour and suspensoids, and the effects of scattering by suspensoids, on the penetration of PAR.Suspensoids, by increasing the rate of attenuation of the solar flux with depth, can greatly diminish the euphotic depth of a water body, with a consequent decrease in the ratio of the euphotic to the mixed depth: thus turbidity can reduce productivity of a water body substantially below that which might be expected on the basis of nutrient availability. Shallow turbid waters of low intrinsic colour can, however, be highly productive. By diminishing the depth of the layer within which solar energy is dissipated as heat, suspensoids can greatly modify the hydrodynamic behaviour of water bodies, and this also has far-reaching ecological consequences.Suspensoids drastically impair the visual clarity of water, a fact of major significance for the aquatic fauna, as well of aesthetic significance for humanity. The reciprocal of the Secchi depth is more correctly thought of as a guide to the vertical contrast attenuation coefficient rather than to the vertical attenuation coefficient for irradiance. The reflectivity of a water body, being at any wavelength proportional to the backscattering coefficient divided by the absorption coefficient, is highly dependent on the concentration, and optical character, of the suspensoids present. This has implications not only for the appearance (colour, muddiness) of the water to an observer, but also for the remote sensing of water composition by air- or satellite-borne radiometric sensors.     

Solution structure of halophilic malate dehydrogenase from small-angle neutron and X-ray scattering and ultracentrifugation

Data from small-angle X-ray and neutron scattering and ultracentrifugation experiments on solutions of malate dehydrogenase from Halobacterium maris mortui are analysed together to yield a model for the enzyme particle formed by the protein and its interactions with water and salt in the solvent. The halophilic enzyme is stable only in high concentrations of salt and the model has structural features that are absent from non-halophilic malate dehydrogenase. The complementarity of the information derived from the three experimental methods is discussed extensively and quantitatively. It derives from the fact that mass density (ultracentrifugation), electron density (X-rays) and neutron scattering density are independent of each other. Each method gives a different "view" of the same particle, and an analysis of the combined data provided thermodynamic and structural parameters with, apart from the chemical composition of the solutions, only one other assumption: a constant partial specific volume for water equal to 1.00 cm3 g-1. Both the insights gained by this novel approach and its limitations are carefully pointed out. In solvents between 1 M and 5 M-NaCl, the enzyme forms a particle of invariant volume, consisting of a protein dimer (87,000 g mol-1) with which are associated 0.87 g of water and 0.35 g of salt per gram of protein. The partial specific volume of the protein calculated from the combined experimental data is 0.753(+/- 0.030) cm3 g-1, in good agreement with the value calculated from the amino acid composition. The particle has a radius of gyration of 32 A and an equivalent Stokes radius of 43 A. By combining the data from the X-ray and neutron scattering studies, the radii of gyration of the protein moiety alone and of the associated water and salt distribution were calculated. They are 28 A and about 40 A, respectively. The large-angle scattering curves show that the shapes of the particle and of the protein moiety alone are similar. At very low resolution they can be approximated by an ellipsoid of axial ratio 1:1:0.6 (or 1:1:1.5). At higher resolution, it becomes apparent that the particle has a significantly larger interface with solvent than an homogeneous ellipsoid or globular protein. The model has a globular protein core similar to non-halophilic malate dehydrogenase, with about 20% of the protein extending loosely out of the core, forming the large interface with solvent. The main interactions with water and salt take place on this outer part.     

Floating lipid bilayers: models for physics and biology

Progress in the determination of structure and fluctuation spectrum of a floating bilayer system, as well as potential applications for biological studies, is reviewed. The system described here was first introduced by Charitat et al. (Eur Phys J B 8:583–593, 1999) and consists of a planar bilayer floating at 2–3?nm away from an adsorbed one on a solid surface in contact with bulk water. This model has been widely used for surface scattering studies using both neutrons and synchrotron radiation and its use in studies of relevance for physics and biology research areas will be described, together with the progress towards the production of complex biomimetic samples for use with scattering techniques.     

On the “swelling” of mitochondria under palmitic acid,calcium, and hypotension treatment

The high-amplitude swelling of mitochondria is critically considered. In contrast to numerous statements by some authors about a marked swelling of isolated liver mitochondria under the influence of palmitic acid, calcium ions, or hypotension, we have shown that mitochondria are generally not subject to highamplitude swelling. According to optical-microscopy data even during long-lasting incubation (in distilled water) where full hypotension takes place, the size of liver mitochondria (approximately 1 µm) can be enlarged by no more than by 40%. Under short-lasting hypotension or the addition of palmitic acid the mitochondrial diameter becomes greater by only 20% or remains virtually unchanged. The light scattering of the mitochondrial suspension measured using a photometer according to the decrease in optical density declines by 2.5 times. A decrease in the light scattering in hypotension or via the addition of palmitic acid or calcium (in an isotonic medium) occurs because of damage (even destruction) to the outer membrane, rather than due to the swelling of mitochondria, as was previously believed. The inner membrane is not significantly expanded. The destruction of the outer membrane reduces the probability of light scattering by each mitochondrion at the boundary layer of the water/membrane interface. Release of substances from the matrix resulting in a decrease of its refractive index may additionally contribute to the decrease in light scattering. Palmitic acid and calcium (at concentrations of 10 to 100 µM) cause permeabilization and disruption of the outer membrane gradually, over several minutes. Full hypotension activates this process very rapidly, viz., within a fraction of a second. Under low ionic-strength conditions, the addition of calcium leads to neutralization of negative charges on the membrane surface, which induces aggregation of mitochondria, thus enhancing light scattering and creating the illusion of mitochondrial swelling.     

Static and dynamic light scattering approach to the hydration of hemoglobin and its supertetramers in the presence of osmolites.

We used static and dynamic light scattering for comparing the mass (MW) and hydrodynamic radius (R(h)) of several hemoglobin systems, namely human hemoglobin, bovine hemoglobin, human hemoglobin cross-linked with a sebacyl residue, and bovine hemoglobin cross-linked with an adipoyl residue. We measured the MW and R(h) of these systems in 0.1M phosphate buffer at pH 7.0 in the absence and in the presence of either betaine or glycerol up to 1.7 molal concentrations. The 90 degrees scattering was measured with a photon counting machine equipped with a diode laser at 783 nm. The Rayleigh ratio [R(theta)] of the instrument was estimated using R(theta) = 7.19E-6 cm(-1) for toluene at 783 nm. The refractive index increment of hemoglobin solutions was measured using a laser beam at 750 nm. We estimated a value dn/dc = 0.210 cm3/g in the absence and dn/dc = 0.170 in the presence of 1.7 molal osmolites. For all systems both in liganded and unliganded form, the static light scattering data showed a 16% mass increase with increasing concentration of osmolites. The hydrodynamic radii of all investigated systems in the presence and absence of osmolites were close to 3.17 nm. Assuming a partial specific volume nu = 0.739 for hemoglobin, and using spherical geometry, the estimated average hydration volume of hemoglobin was 32.6 L/mole in the absence of osmolites. It decreased to 23.5 L/mole in the presence of 1.7 molal osmolites. Assuming that the density of water in the hydration volume is D = 1.0 g/cm3, the hydration of Hb was 0.51 gH2O/gHb, with a surface density of 0.20 molH2O/A2. The hydration decreased to 0.33 gH2O/gHb and 0.14 molH2O/A2 in the presence of 1.7 molal osmolites. The decreased hydration was compensated by the increased mass (i.e., decreased surface area per unit volume) so that the thickness of the water shell around these proteins remained close to a single layer of water molecules. These findings indicate that the combination of static and dynamic light scattering offer unique means for investigating the relevance of water activity on the structure and function of biological macromolecules. In the case of hemoglobin, the data suggest that the decreased oxygen affinity in the presence of osmolites reported by Colombo et al. (M. F. Colombo, D. C. Rau, and V. A. Parsegian Science, 1992, Vol. 256, pp. 655-659), as due to ligand linked water binding on hemoglobin surface, is part of a complex phenomenon involving the hydration shell of hemoglobin and the formation of low affinity supertetrameric molecules.     

Internal dynamics and protein-matrix coupling in trehalose-coated proteins

We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q(B) containing or Q(B) deprived reaction centre from R. sphaeroides. Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein-matrix interactions observed in our samples may shed light on the protein-solvent coupling also in liquid aqueous solutions.     

Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements

Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To understand these biological processes, knowledge of solvent structure around the nucleic acids is critical. Yet, because they are often disordered, ions and water evade detection by x-ray crystallography and other high-resolution methods. Small-angle x-ray scattering (SAXS) is uniquely sensitive to the spatial correlations between solutes and the surrounding solvent. Thus, SAXS provides an experimental constraint to guide or test emerging solvation theories. However, the interpretation of SAXS profiles is nontrivial because of the difficulty in separating the scattering signals of each component: the macromolecule, ions, and hydration water. Here, we demonstrate methods for robustly deconvoluting these signals, facilitating a more straightforward comparison with theory. Using SAXS data collected on an absolute intensity scale for short DNA duplexes in solution with Na⁺, K⁺, Rb⁺, or Cs⁺ counterions, we mathematically decompose the scattering profiles into components (DNA, water, and ions) and validate the decomposition using anomalous scattering measurements. In addition, we generate a library of physically motivated ion atmosphere models and rank them by agreement with the scattering data. The best-fit models have relatively compact ion atmospheres when compared to predictions from the mean-field Poisson-Boltzmann theory of electrostatics. Thus, the x-ray scattering methods presented here provide a valuable measurement of the global structure of the ion atmosphere that can be used to test electrostatics theories that go beyond the mean-field approximation.