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PubMed2005

Protein-water displacement distributions.

The statistical properties of fast protein-water motions are analyzed by dynamic neutron scattering experiments. Using isotopic exchange, one probes either protein or water hydrogen displacements. A moment analysis of the scattering function in the time domain yields model-independent information such as time-resolved mean square displacements and the Gauss-deviation. From the moments, one can reconstruct the displacement distribution. Hydration water displays two dynamical components, related to librational motions and anomalous diffusion along the protein surface. Rotational transitions of side chains, in particular of methyl groups, persist in the dehydrated and in the solvent-vitrified protein structure. The interaction with water induces further continuous protein motions on a small scale. Water acts as a plasticizer of displacements, which couple to functional processes such as open-closed transitions and ligand exchange.

Biophysical Phenomena↗
PubMed2005

beta-lactoglobulin under high pressure studied by small-angle neutron scattering.

We used small-angle neutron scattering to study the effects of the high hydrostatic pressure on the structure of beta-lactoglobulin. Experiments were carried out at pH 7 on the dimeric form of the protein in a pressure range going from 50 MPa to 300 MPa. These measurements allow the protein size and the interactions between macromolecules to be studied during the application of pressure. Increasing pressure up to 150 MPa leads to a swollen state of the protein that gives rise to an increase of the radius of gyration by about 7%. Within this pressure range, we also show that the interaction between macromolecules weakens although it remains repulsive. The measurements show an aggregation process occurring above 150 MPa. From the spectra analysis, it appears that the aggregation occurs mainly by association of the dimeric units.

Animals↗
PubMed2005

Characterization of multimetric variants of ubiquitin carboxyl-terminal hydrolase L1 in water by small-angle neutron scattering.

Here, we illustrated that the morphological structures of ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) variants and Parkinson's disease (PD) exhibit good pathological correlation by a small-angle neutron scattering (SANS). UCH-L1 is a neuro-specific multiple functional enzyme, deubiquitinating, ubiquityl ligase, and also involved in stabilization of mono-ubiquitin. To examine the relationship between multiple functions of UCH-L1 and the configuration of its variants [wild-type, I93M (linked to familial Parkinson's disease), and S18Y (linked to reduced risk of Parkinson's disease)], in this report, we proposed that these were all self-assembled dimers by an application of a rotating ellipsoidal model; the configurations of these dimers were quite different. The wild-type was a rotating ellipsoidal. The globular form of the monomeric component deformed by the I93M mutation. Conversely, the S18Y polymorphism promoted the globularity. Thus, the multiple functional balance is closely linked to the intermolecular interactions between the UCH-L1 monomer and the final dimeric configuration.

Circular Dichroism↗
PubMed2005

Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics.

In this work we investigate the dynamic properties of hemoglobin in glycerolD(8)/D(2)O solution using incoherent elastic (ENS) and quasi-elastic (QENS) neutron scattering. Taking advantage of complementary energy resolutions of backscattering spectrometers at ILL (Grenoble), we explore motions in a large space-time window, up to 1 ns and 14 A; moreover, in order to cover the harmonic and anharmonic protein dynamics regimes, the elastic experiments have been performed over the wide temperature interval of 20-300 K. To study the dependence of the measured dynamics upon the protein quaternary structure, both deoxyhemoglobin (in T quaternary conformation) and carbonmonoxyhemoglobin (in R quaternary conformation) have been investigated. From the ENS data the mean square displacements of the non-exchangeable hydrogen atoms of the protein and their temperature dependence are obtained. In agreement with previous results on hydrated powders, a dynamical transition at about 220 K is detected. The results show interesting differences between the two hemoglobin quaternary conformations, the T-state protein appearing more rigid and performing faster motions than the R-state one; however, these differences involve motions occurring in the nanosecond time scale and are not detected when only faster atomic motions in the time scale up to 100 ps are investigated. The QENS results put in evidence a relevant Lorentzian quasi-elastic contribution. Analysis of the dependence of the Elastic Incoherent Structure Factor (EISF) and of the Lorentzian halfwidth upon the momentum transfer suggests that the above quasi-elastic contribution arises from the diffusion inside a confined space, values of confinement radius and local diffusion coefficient being compatible with motions of hydrogen atoms of the amino acid side chains. When averaged over the whole range of momentum transfer the QENS data put in evidence differences between deoxy and carbonmonoxy hemoglobin and confirm the quaternary structure dependence of the protein dynamics in the nanosecond time scale.

Elasticity↗
PubMed2005

Influence of N-dodecyl-N,N-dimethylamine N-oxide on the activity of sarcoplasmic reticulum Ca(2+)-transporting ATPase reconstituted into diacylphosphatidylcholine vesicles: efects of bilayer physical parameters.

Sarcoplasmic reticulum Ca-transporting ATPase (EC 3.6.1.38) was isolated from rabbit white muscle, purified and reconstituted into vesicles of synthetic diacylphosphatidylcholines with monounsaturated acyl chains using the cholate dilution method. In fluid bilayers at 37 degrees C, the specific activity of ATPase displays a maximum (31.5+/-0.8 IU/mg) for dioleoylphosphatidylcholine (diC18:1PC) and decreases progressively for both shorter and longer acyl chain lengths. Besides the hydrophobic mismatch between protein and lipid bilayer, changes in the bilayer hydration and lateral interactions detected by small angle neutron scattering (SANS) can contribute to this acyl chain length dependence. When reconstituted into dierucoylphosphatidylcholine (diC22:1PC), the zwitterionic surfactant N-dodecyl-N,N-dimethylamine N-oxide (C12NO) stimulates the ATPase activity from 14.2+/-0.6 to 32.5+/-0.8 IU/mg in the range of molar ratios C12NO:diC22:1PC=0/1.2. In dilauroylphosphatidylcholines (diC12:0PC) and diC18:1PC, the effect of C12NO is twofold-the ATPase activity is stimulated at low and inhibited at high C12NO concentrations. In diC18:1PC, it is observed an increase of activity induced by C12NO in the range of molar ratios C12NO:diC18:1PC< or =1.3 in bilayers, where the bilayer thickness estimated by SANS decreases by 0.4+/-0.1 nm. In this range, the 31P-NMR chemical shift anisotropy increases indicating an effect of C12NO on the orientation of the phosphatidylcholine dipole N(+)-P- accompanied by a variation of the local membrane dipole potential. A decrease of the ATPase activity is observed in the range of molar ratios C12NO:diC18:1PC=1.3/2.5, where mixed tubular micelles are detected by SANS in C12NO+diC18:1PC mixtures. It is concluded that besides hydrophobic thickness changes, the changes in dipole potential and curvature frustration of the bilayer could contribute as well to C12NO effects on Ca(2+)-ATPase activity.

Animals↗
PubMed2006

Changes in vibrational modes of water and bioprotectants in solution.

Inelastic neutron scattering (INS) measurements have been performed on trehalose and sucrose/H(2)O mixtures at very low temperature as a function of concentration by using the TOSCA spectrometer at the ISIS Facility (DRAL, UK). The aim of this work is to investigate by INS the vibrational behaviour of water in presence of trehalose and sucrose in order to characterize the changes induced by these disaccharides on the H(2)O hydrogen-bonded network. In particular, we obtained information about the effects of the two disaccharides in the translational, librational and bending spectral regions of ice. The disaccharide bioprotective effectiveness can be linked by the high destructuring effect emphasised by the analysis of the librational modes region. On the other hand, the analysis of the vibrational region corresponding to the ice bending modes show a high "crystallinity" degree which can justify the cryptobiotic action of disaccharides.

Cryoprotective Agents↗
PubMed2005

The effect of electrolyte on the morphology of vesicles composed of the dialkyl polyoxyethylene ether surfactant 2C18E12.

Small-angle neutron-scattering (SANS) studies were performed on vesicles composed of 1,2-di-O-octadecyl-rac-glyceryl-3-(omega-methoxydodecaethylene glycol), in deuterium oxide (D2O) solutions with various ionic strengths of LiCl, NaCl and NaI. Gross vesicle morphologies, examined using freeze-fracture electron microscopy, showed that NaCl promoted the formation of multilamellar vesicles. Model fitting of the SANS data showed changes in bilayer parameters such as thickness and repeat spacings, in response to the presence of ions in the bulk solution. 2C18E12 vesicles in D2O are shown to exist as predominantly unilamellar structures with a bilayer thickness of approximately 51 A. Vesicles in increasing concentrations of LiCl and NaCl exhibit decreased layer thickness and increased lamelarity. Little change was observed for vesicles formed in NaI solutions. We suggest that these changes result from intrusion of E12 headgroups into the alkyl chain region of the vesicle bilayers, in response to the increase in concentration of ions present and their charge density.

Deuterium Oxide↗
PubMed2004

Bilayer thickness in unilamellar extruded 1,2-dimyristoleoyl and 1,2-dierucoyl phosphatidylcholine vesicles: SANS contrast variation study of cholesterol effect.

Small-angle neutron scattering on extruded unilamellar vesicles in water was used to study bilayer thickness when cholesterol (CHOL) was added at 44.4 mol% to 1,2-dimyristoleoylphosphatidylcholine (diC14:1PC) and 1,2-dierucoylphosphatidylcholine (diC22:1PC) bilayers. Using the (1)H(2)O/(2)H(2)O contrast variation and the small-angle form of Kratky-Porod approximation, the bilayer gyration radii at infinite contrast R(g,infinity) and the bilayer thickness parameters d(g,infinity) = 12(0.5)R(g,infinity) were obtained at 30 degrees C. Addition of cholesterol to diC14:1PC increased the d(g,infinity) from 3.72 +/- 0.02 to 4.26 +/- 0.01 nm, while in the diC22:1PC bilayers the d(g,infinity) change observed was within the experimental error: +0.23 +/- 0.23 nm.

Cholesterol↗
PubMed2005

Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties.

Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.

Animals↗
PubMed2006

Characterising the size and shape of polyamidoamines in solution as a function of pH using neutron scattering and pulsed-gradient spin-echo NMR.

Bioresponsive polymers are being developed as synthetic viral mimetics to enhance the intracellular delivery of macromolecular therapeutic agents such as genes, proteins and peptides. In this context we have designed pH-responsive, amphoteric polyamidoamines (PAAs) which change conformation on passing from a neutral pH (extracellular) to an acidic pH (endosomal and lysosomal) environments. PAAs have already demonstrated cytosolic delivery of genes and non-permeant toxins (e.g. gelonin and ricin A chain). The aim of this study was to use small-angle neutron scattering (SANS) to investigate the most likely shape of the hydrochloride salt form of one particular PAA (ISA23) in solution, under pH conditions that mimic those the polymer would be expected to encounter during endocytic internalisation (pH 7.4-3). It was shown that models based on a Gaussian coil representation of the polymer conformation described the SANS data better over this pH range than models based on a rod-like conformation. The conformation of ISA23 at 37 degrees C was expanded (radius of gyration approximately 80A) at pH approximately 3 but collapsed with an increase in pH (radius of gyration approximately 20A at pH 7.4), a conclusion also reached in a model-free analysis of the neutron data. Outside this pH range - at the extremes of high and low pH - the polymer coil collapsed and interpretation of the scattering was slightly complicated by the presence of a very weak structure factor indicating that the polymer coils are highly charged. The PAA concentration did not significantly affect the polymer size over the concentration range 10-50mg/ml. Characterisation of the dynamics of these polymer solutions - diffusion coefficients and viscosity -ostensibly suggest a very different conclusion with the polymer expanding as the pH is increased, but this arises due to weak aggregation of the amphoteric polymer coils.

Hydrogen-Ion Concentration↗
PubMed2004

Synthesis, characterization, and SANS studies of novel alkanediyl-alpha,omega-bis(hydroxyethylmethylhexadecylammonium bromide) cationic gemini surfactants.

A series of novel gemini cationic surfactants alkanediyl-alpha,omega-bis (hydroxyethylmethylhexadecylammonium bromide) with polymethylene spacer chain length of 4, 6, 8, and 10 carbon atoms was synthesized and characterized. Critical micellar concentrations of the gemini surfactants in aqueous solutions as determined by the surface tension and conductance measurements were observed to be in the range 1.39-3.63 microM. The critical micellar concentration was observed to increase initially with spacer length up to 6 methylene groups and to decrease thereafter with the increase in spacer length. The micellar microstructure in aqueous solutions examined through small angle neutron scattering (SANS) revealed that the extent of aggregation growth and variation in shapes of micelles strongly depend on head group polarity, spacer chain length, and temperature. The propensity to micellar growth with spacer chain length 4 was found to be much higher than with the longer spacer lengths. The fractional charge on the micelle increases with increased spacer chain length and temperature.

Cations↗
PubMed2005

Comparative analysis of the structure of sterically stabilized ferrofluids on polar carriers by small-angle neutron scattering.

Results of experiments on small-angle neutron scattering from ferrofluids on polar carriers (pentanol, water, methyl-ethyl-ketone), with double-layer sterical stabilization of magnetic nanoparticles, are reported. Several types of spatial structural organization are observed. The structure of highly stable pentanol-based samples is similar to that of stable ferrofluids based on organic non-polar carriers (e.g., benzene) with mono-layer covered magnetic nanoparticles. At the same time, the effect of the interparticle interaction on the scattering is stronger in polar ferrofluids because of the structural difference in the surfactant shell. The structure of the studied methyl-ethyl-ketone- and water-based ferrofluids essentially different from the previous case. The formation of large (>100 nm in size) elongated or fractal aggregates, respectively, is detected even in the absence of external magnetic field, which corresponds to weaker stability of these types of ferrofluids. The structure of the fractal aggregates in water-based ferrofluids does not depend on the particle concentration, but it is sensitive to temperature. A temperature increase results in a decrease in their fractal dimension reflecting destruction of the aggregates. In addition, in water-based ferrofluids these aggregates consist of small (radius approximately 10 nm) and temperature-stable primary aggregates.

Colloids↗
PubMed2005

In situ neutron reflectometry investigation of gold-chemisorbed PEO layers of varying chain density: relationship of layer structure to protein resistance.

In work reported previously [L.D. Unsworth, H. Sheardown, J.L. Brash, Langmuir 21 (2005) 1036] we investigated protein interactions with polyethylene oxide (PEO) layers formed by chemisorption of thiol-PEO on gold. It was shown that, as a function of surface chain density, protein adsorption passed through a minimum. In follow-on work reported here, neutron reflectometry (NR) was used to investigate the formation and properties (volume fraction and chain density) of such PEO layers in situ, i.e., in contact with water. Chain density was varied by varying solubility conditions (far from and near the cloud point) and chemisorption time. Neutron experiments were carried out using neutrons of de Broglie wavelength 2.37 A. Contrast matching techniques were used to improve sensitivity. Layers formed under high solubility conditions were found to have PEO volume fraction, layer thickness and chain density of 0.33, 28 A, and 0.56 chains/nm2, respectively, after 0.5 h chemisorption; and 0.31, 28.5 A, and 0.59 chains/nm2, respectively, after 11 h, suggesting that the layer is fully formed within 0.5 h. Both chain density and PEO volume fraction in the chemisorbed layers were significantly greater when the layers were formed under low solubility conditions. The PEO layers shown in our previous work to have maximum protein resistance were found to have a PEO volume fraction of approximately 40%. Moreover the limiting volume fraction in the PEO films formed under low solubility conditions was approximately 57%, a value similar to the solubility limit of PEO in aqueous solution, suggesting that local regions in the layers may be phase separated under these conditions. This may result in increased hydrophobicity and may explain why protein adsorption was found to increase on the layers of higher chain density.

Adsorption↗
PubMed2006

Clouding phenomenon and SANS studies on tetra-n-butylammonium dodecylsulfate micellar solutions in the absence and presence of salts.

Clouding phenomenon in aqueous micellar solutions of an anionic surfactant tetra-n-butylammonium dodecylsulfate (TBADS) has been observed as a function of surfactant concentration. Small-angle neutron scattering (SANS) experiments in these systems show clustering of micelles as the temperature approaches the cloud point (CP). The individual micelles and the clusters of micelles coexist at CP. The clustering of micelles depends on the surfactant concentration and temperature. It is proposed that clustering is due to depletion of H-bonded water present around the butyl chains at the micellar surface. This is associated with entropy gain which is considered to be the major thermodynamic factor related to micellar aggregation. The structures (clusters) that emerge depend on the relative lengths of the alkyl chains of the counterion and can be tuned by the temperature.

Micelles↗
PubMed2006

Structural variations in a family of orthodialkoxyarenes organogelators.

A series of low mass organic gelators (LMOGS) 1 to 6 whose chemical structures have in common an orthodialkoxyarene feature was prepared in order to compare the shape of their fibrillar network as investigated by small-angle neutron scattering (SANS) experiments. All members of the family exhibit a pronounced tendency to bundle formation by merging isolated fibers in extended packets of average diameter >500 A. Variations of the 2D packing symmetry are observed from hexagonal to square orderings with close derivatives of the reference member 2,3-didecyloxyanthracene (DDOA). Networks in which the fraction of isolated fibers is significant enough to allow for their SANS identification are those for 6,7-dichloro-2,3-didecyloxyanthracene (Cl(2)DDOA) and 2,3-dodecyloxy-9,10-anthraquinone (5). For this latter, the monodispersity of the cross-sections (thickness=74 A) is remarkable and the rectangular shape (b/a approximately 0.12) accounts for a merging mechanism into anisotropic bundles (ribbons).

Anisotropy↗
PubMed2005

Solution structure of the chicken skeletal muscle troponin complex via small-angle neutron and X-ray scattering.

Troponin is a Ca2+-sensitive switch that regulates the contraction of vertebrate striated muscle by participating in a series of conformational events within the actin-based thin filament. Troponin is a heterotrimeric complex consisting of a Ca2+-binding subunit (TnC), an inhibitory subunit (TnI), and a tropomyosin-binding subunit (TnT). Ternary troponin complexes have been produced by assembling recombinant chicken skeletal muscle TnC, TnI and the C-terminal portion of TnT known as TnT2. A full set of small-angle neutron scattering data has been collected from TnC-TnI-TnT2 ternary complexes, in which all possible combinations of the subunits have been deuterated, in both the +Ca2+ and -Ca2+ states. Small-angle X-ray scattering data were also collected from the same troponin TnC-TnI-TnT2 complex. Guinier analysis shows that the complex is monomeric in solution and that there is a large change in the radius of gyration of TnI when it goes from the +Ca2+ to the -Ca2+ state. Starting with a model based on the human cardiac troponin crystal structure, a rigid-body Monte Carlo optimization procedure was used to yield models of chicken skeletal muscle troponin, in solution, in the presence and in the absence of regulatory calcium. The optimization was carried out simultaneously against all of the scattering data sets. The optimized models show significant differences when compared to the cardiac troponin crystal structure in the +Ca2+ state and provide a structural model for the switch between +Ca2+ and -Ca2+ states. A key feature is that TnC adopts a dumbbell conformation in both the +Ca2+ and -Ca2+ states. More importantly, the data for the -Ca2+ state suggest a long extension of the troponin IT arm, consisting mainly of TnI. Thus, the troponin complex undergoes a large structural change triggered by Ca2+ binding.

Animals↗
PubMed2006

Conformation of the HIV-1 Gag protein in solution.

A single multi-domain viral protein, termed Gag, is sufficient for assembly of retrovirus-like particles in mammalian cells. We have purified the human immunodeficiency virus type 1 (HIV-1) Gag protein (lacking myristate at its N terminus and the p6 domain at its C terminus) from bacteria. This protein is capable of assembly into virus-like particles in a defined in vitro system. We have reported that it is in monomer-dimer equilibrium in solution, and have described a mutant Gag protein that remains monomeric at high concentrations in solution. We report that the mutant protein retains several properties of wild-type Gag. This mutant enabled us to analyze solutions of monomeric protein. Hydrodynamic studies on the mutant protein showed that it is highly asymmetric, with a frictional ratio of 1.66. Small-angle neutron scattering (SANS) experiments confirmed its asymmetry and yielded an R(g) value of 34 A. Atomic-level structures of individual domains within Gag have previously been determined, but these domains are connected in Gag by flexible linkers. We constructed a series of models of the mutant Gag protein based on these domain structures, and tested each model computationally for its agreement with the experimental hydrodynamic and SANS data. The only models consistent with the data were those in which Gag was folded over, with its N-terminal matrix domain near its C-terminal nucleocapsid domain in three-dimensional space. Since Gag is a rod-shaped molecule in the assembled immature virion, these findings imply that Gag undergoes a major conformational change upon virus assembly.

Circular Dichroism↗
PubMed2003

Proteins in action: the physics of structural fluctuations and conformational changes.

Structural dynamics is essential for the biological function of proteins. Results from new experimental techniques should be compared with those from previous experiments in order to obtain a consistent picture of the physics of intramolecular fluctuations and conformational changes. The high intensity and time structure of synchrotron radiation have made possible time-resolved X-ray structure analysis and the determination of phonon density spectra through the Mössbauer effect. By combining results from Mössbauer absorption spectroscopy, incoherent neutron scattering, low-temperature crystallography and optical spectroscopy, a physical picture of protein dynamics emerges.

Absorptiometry, Photon↗