Interpretation of small-angle x-ray and neutron scattering data for perfluorosulfonated ionomer membranes

AbstractAn overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In the present study, the solution structure of the OLDN was investigated through integration of small-angle X-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis, and searched for the conformations that well reproduced the SAXS and SANS scattering curves. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.Statement of SignificanceOverlapping dinucleosomes (OLDNs) are intermediate structures formed through nucleosome collision promoted by nucleosome remodeling factor(s). To study the solution structure of OLDNs, a structural library containing a wide variety of conformations was prepared though simulations, and the structures that well reproduced the small angle X-ray and neutron scattering data were selected from the library. Simultaneous evaluation of the conformational variation in the global OLDN structures and in the histone tails is difficult using conventional MD simulations. We overcame this problem by combining multiple simulation techniques, and showed the importance of the histone tails for stabilizing the structures of OLDNs in solution.

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DENFERT version 2: extension of ab initio structural modelling of hydrated biomolecules to the case of small-angle neutron scattering data

Journal of Applied Crystallography ◽

10.1107/s1600576716003393 ◽

2016 ◽

Vol 49 (2) ◽

pp. 690-695 ◽

Cited By ~ 4

Author(s):

Alexandros Koutsioubas ◽

Sebastian Jaksch ◽

Javier Pérez

Keyword(s):

Neutron Scattering ◽

Ab Initio ◽

Small Angle ◽

Biological Molecules ◽

Scattering Data ◽

Data Sets ◽

X Ray ◽

User Input ◽

X Ray Scattering ◽

Objective Shape

Following the introduction of the program DENFERT [Koutsioubas & Pérez (2013). J. Appl. Cryst. 46, 1884–1888], which takes into account the hydration layer around solvated biological molecules during ab initio restorations of low-resolution molecular envelopes from small-angle X-ray scattering data, the present work introduces the second version of the program, which provides the ability to treat neutron scattering data sets. By considering a fully interconnected and hydrated model during the entire minimization process, it has been possible to simplify the user input and reach more objective shape reconstructions. Additionally, a new method is implemented for the subtraction of the contribution of internal inhomogeneities of biomolecules to the measured scattering. Validation of the overall approach is performed by successfully recovering the shape of various protein molecules from experimental neutron and X-ray solution scattering data.

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Structure and Property Characterization of Porous Low-k Dielectric Constant Thin Films using X-ray Reflectivity and Small Angle Neutron Scattering

MRS Proceedings ◽

10.1557/proc-612-d4.1.1 ◽

2000 ◽

Vol 612 ◽

Cited By ~ 3

Author(s):

Eric K. Lin ◽

Wen-li Wu ◽

Changming Jin ◽

Jeffrey T. Wetzel

Keyword(s):

Thin Films ◽

Neutron Scattering ◽

Small Angle ◽

Small Angle Neutron Scattering ◽

Coefficient Of Thermal Expansion ◽

Scattering Data ◽

Connectivity Matrix ◽

X Ray ◽

Porous Thin Films ◽

Low K

AbstractHigh-resolution X-ray reflectivity and small angle neutron scattering measurements are used as complementary techniques to characterize the structure and properties of porous thin films for use as low-k interlevel dielectric (ILD) materials. With the addition of elemental composition information, the average pore size, porosity, pore connectivity, matrix density, average film density, film thickness, coefficient of thermal expansion, and moisture uptake of porous thin films are determined. Examples from different classes of materials and two analysis methods for small angle neutron scattering data are presented and discussed.

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Quantification of the information in small-angle scattering data

Journal of Applied Crystallography ◽

10.1107/s1600576714024017 ◽

2014 ◽

Vol 47 (6) ◽

pp. 2000-2010 ◽

Cited By ~ 14

Author(s):

Martin Cramer Pedersen ◽

Steen Laugesen Hansen ◽

Bo Markussen ◽

Lise Arleth ◽

Kell Mortensen

Keyword(s):

Data Analysis ◽

Neutron Scattering ◽

Ray Tracing ◽

Information Content ◽

Small Angle ◽

Small Angle Scattering ◽

Scattering Data ◽

X Ray ◽

Angle Scattering ◽

Wide Range

Small-angle X-ray and neutron scattering have become increasingly popular owing to improvements in instrumentation and developments in data analysis, sample handling and sample preparation. For some time, it has been suggested that a more systematic approach to the quantification of the information content in small-angle scattering data would allow for a more optimal experiment planning and a more reliable data analysis. In the present article, it is shown how ray-tracing techniques in combination with a statistically rigorous data analysis provide an appropriate platform for such a systematic quantification of the information content in scattering data. As examples of applications, it is shown how the exposure time at different instrumental settings or contrast situations can be optimally prioritized in an experiment. Also, the gain in information by combining small-angle X-ray and neutron scattering is assessed. While solution small-angle scattering data of proteins and protein–lipid complexes are used as examples in the present case study, the approach is generalizable to a wide range of other samples and experimental techniques. The source code for the algorithms and ray-tracing components developed for this study has been made available on-line.

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SAXSMorph: a program for generating representative morphologies for two-phase materials from small-angle X-ray and neutron scattering data

Journal of Applied Crystallography ◽

10.1107/s0021889810048557 ◽

2010 ◽

Vol 44 (1) ◽

pp. 221-224 ◽

Cited By ~ 5

Author(s):

Bridget Ingham ◽

Haiyong Li ◽

Emily L. Allen ◽

Michael F. Toney

Keyword(s):

Neutron Scattering ◽

Small Angle ◽

Three Dimensional ◽

Scattering Data ◽

Visualization Tool ◽

Analysis Program ◽

Two Phase ◽

X Ray ◽

Phase Systems ◽

User Friendly

SAXSMorphis a free computer analysis program that generates three-dimensional representative morphologies of two-phase systems using small-angle X-ray or neutron scattering data. The morphologies thus generated have the correct length scales and degree of connectivity with respect to the sample and are a useful visualization tool. The program also offers statistical analysis of the generated morphology.SAXSMorphis written in Java and is user friendly and platform independent.

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Intercalibration of small-angle X-ray and neutron scattering data

Journal of Applied Crystallography ◽

10.1107/s0021889888004820 ◽

1988 ◽

Vol 21 (6) ◽

pp. 629-638 ◽

Cited By ~ 115

Author(s):

T. P. Russell ◽

J. S. Lin ◽

S. Spooner ◽

G. D. Wignall

Keyword(s):

Neutron Scattering ◽

Small Angle ◽

Scattering Data ◽

X Ray

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Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

10.1101/2019.12.26.888834 ◽

2019 ◽

Cited By ~ 2

Author(s):

Andreas Haahr Larsen ◽

Yong Wang ◽

Sandro Bottaro ◽

Sergei Grudinin ◽

Lise Arleth ◽

...

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

Small Angle ◽

Coarse Grained ◽

Scattering Data ◽

General Strategy ◽

X Ray ◽

Coarse Grained Simulations ◽

Dynamics Simulations

AbstractMany proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domain protein TIA-1 as an example, we here combine coarse-grained molecular dynamics simulations with previously measured small-angle scattering data to study the conformation of TIA-1 in solution. We show that while the coarse-grained potential (Martini) in itself leads to too compact conformations, increasing the strength of protein-water interactions results in ensembles that are in very good agreement with experiments. We show how these ensembles can be refined further using a Bayesian/Maximum Entropy approach, and examine the robustness to errors in the energy function. In particular we find that as long as the initial simulation is relatively good, reweighting against experiments is very robust. We also study the relative information in X-ray and neutron scattering experiments and find that refining against the SAXS experiments leads to improvement in the SANS data. Our results suggest a general strategy for studying the conformation of multi-domain proteins in solution that combines coarse-grained simulations with small-angle X-ray scattering data that are generally most easy to obtain. These results may in turn be used to design further small-angle neutron scattering experiments that exploit contrast variation through 1H/2H isotope substitutions.

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GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macromolecules in solution

Journal of Applied Crystallography ◽

10.1107/s1600576714005147 ◽

2014 ◽

Vol 47 (3) ◽

pp. 1132-1139 ◽

Cited By ~ 50

Author(s):

Francesco Spinozzi ◽

Claudio Ferrero ◽

Maria Grazia Ortore ◽

Alejandro De Maria Antolinos ◽

Paolo Mariani

Keyword(s):

Neutron Scattering ◽

Small Angle ◽

Heterogeneous Systems ◽

Software Tool ◽

Scattering Data ◽

Model Parameters ◽

X Ray ◽

High Data ◽

Link Functions ◽

Angle Scattering

Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here isGENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parametersviaphysical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.

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Size and Distribution: A Comparison of XRD, SAXS and SANS Study of II–VI Semiconductor Nanocrystals

Journal of Nanoscience and Nanotechnology ◽

10.1166/jnn.2008.370 ◽

2008 ◽

Vol 8 (3) ◽

pp. 1221-1227 ◽

Cited By ~ 18

Author(s):

Ashish K. Keshari ◽

Avinash C. Pandey

Keyword(s):

Neutron Scattering ◽

Small Angle ◽

Small Angle Neutron Scattering ◽

Quantum Confinement Effect ◽

Semiconductor Nanocrystals ◽

Spherical Particles ◽

Scattering Data ◽

Particle Sizes ◽

Saxs Data ◽

X Ray

The uniqueness of size dependent functional properties of II–VI semiconductor nanocrystals have led to the development of various techniques for determination of shape, size and distributions, although the accurate measurements of the particle sizes has always been a fundamental task in nanoscience and even become more crucial with the discovery of quantum confinement effect. Acomparison of the well established techniques X-ray diffraction (XRD), small angle X-ray scattering (SAXS) and small angle neutron scattering (SANS) with an emphasis on size and distribution of the prepared samples are reported in order to elaborate more precise techniques for the analysis of particles sizes. Modified Scherrer formula for spherical particles has been used to calculate the particle sizes from XRD spectra. Analysis of SAXS data has been reported using Guinier model. Small angle neutron scattering measurements has been performed for ZnO nanocrystals and the scattering data obtained is simulated for polydisperse sphere. The bare ZnO, ZnS and CdS and doped with Mn2+ systems are taken within the framework of our discussion. These materials were synthesized by chemical precipitation route and found to have size distribution from 2 to 6 nm for spherical particles. Sizes determined from various techniques are in good agreement with each other however small angle scattering technique is more reliable than XRD to determine the sizes of the nanoparticles.

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