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Register a new userGlobal Small-Angle Scattering Data Analysis of Inverted Hexagonal Phases
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We have developed a global analysis model for randomly oriented, fully hydrated inverted hexagonal (H$_text{II}$) phases formed by many amphiphiles in aqueous solution, including membrane lipids. The model is based on a structure factor for hexagonally packed rods and a compositional model for the scattering length density (SLD) enabling also the analysis of positionally weakly correlated H$_text{II}$ phases. For optimization of the adjustable parameters we used Bayesian probability theory, which allows to retrieve parameter correlations in much more detail than standard analysis techniques, and thereby enables a realistic error analysis. The model was applied to different phosphatidylethanolamines including previously not reported H$_text{II}$ data for diC14:0 and diC16:1 phosphatidylethanolamine. The extracted structural features include intrinsic lipid curvature, hydrocarbon chain length and area per lipid at the position of the neutral plane.
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Physically, disordered ensembles of non-homopolymeric polypeptides are expected to be heterogeneous; i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average values of end-to-end distance $R_{rm EE}$ and radius of gyration $R_{rm g}$. It was posited recently, however, that small-angle X-ray scattering (SAXS) data on conformational dimensions of disordered proteins can be rationalized almost exclusively by homopolymer ensembles. Assessing this perspective, chain-model simulations are used to evaluate the discriminatory power of SAXS-determined molecular form factors (MFFs) with regard to homogeneous versus heterogeneous ensembles. The general approach adopted here is not bound by any assumption about ensemble encodability, in that the postulated heterogeneous ensembles we evaluated are not restricted to those entailed by simple interaction schemes. Our analysis of MFFs for certain heterogeneous ensembles with more narrowly distributed $R_{rm EE}$ and $R_{rm g}$ indicates that while they deviates from MFFs of homogeneous ensembles, the differences can be rather small. Remarkably, some heterogeneous ensembles with asphericity and $R_{rm EE}$ drastically different from those of homogeneous ensembles can nonetheless exhibit practically identical MFFs, demonstrating that SAXS MFFs do not afford unique characterizations of basic properties of conformational ensembles in general. In other words, the ensemble to MFF mapping is practically many-to-one and likely non-smooth. Heteropolymeric variations of the $R_{rm EE}$--$R_{rm g}$ relationship were further showcased using an analytical perturbation theory developed here for flexible heteropolymers. Ramifications of our findings for interpretation of experimental data are discussed.
Exploiting small angle X-ray and neutron scattering (SAXS/SANS) on the same sample volume at the same time provides complementary nanoscale structural information at two different contrast situations. Compared with an independent experimental approach, the truly combined SAXS/SANS experimental approach ensures the exactness of the probed samples particularly for in-situ studies. Here, we introduce an advanced portable SAXS system that is dimensionally suitable for installation at D22 zone of ILL. The SAXS apparatus is based on a RIGAKU copper/molybdenum switchable microfocus rotating anode X-ray generator and a DECTRIS detector with a changeable sample-to-detector distance of up to 1.6 m in a vacuum chamber. A science case has been presented to demonstrate the uniqueness of the newly established method at ILL. Temporal structural rearrangements of both, organic stabilizing agents and organically capped gold colloidal particles during gold nanoparticle growth are simultaneously probed, enabling immediate correlated structural information. The newly established nano-analytical method at ILL will open the way for real time investigations of a wide range of innovative nanomaterials and will enable comprehensive in-situ studies on biological systems. A potential development of a fully-automated SAXS/SANS system with a common control environment and additional sample environments, permitting a continual and efficient operation of the system at the hands of ILL users, has also been introduced.
Small-angle neutron scattering (SANS) from cationic globular micellar solutions composed of sodium dodecyl sulfate (SDS) and in water was studied with contrast variation approach. Extensive computational studies have demonstrated that the distribution of invasive water is clearly an important feature for understanding the self-organization of SDS molecules and the stability of assemblies. However, in existing scattering studies the degree of hydration level was not examined explicitly. Here using the scheme of contrast variation, we establish a methodology of SANS to determine the intra-micellar radial dis-tributions of invasive water and SDS molecules from the evolving spectral lineshapes caused by the varying isotopic ratio of water. A detailed description hydration of SDS micelles is provided, which in an excellent agreement with known results of many existing simulations studies. Extension of our method can be used to provide an in-depth insight into the micellization phenomenon which is commonly found in many soft matter systems.
We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and artificial origin. Our analysis is based on a recently introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433 (2006)] which takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a collapse of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained before for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin, rather than being a problem with the proposed model.
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.
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