scholarly journals Increasing complexity in small-angle X-ray and neutron scattering experiments: from biological membrane mimics to live cells

Soft Matter ◽  
2021 ◽  
Author(s):  
Enrico F. Semeraro ◽  
Lisa Marx ◽  
Moritz P. K. Frewein ◽  
Georg Pabst
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Biological Membrane ◽  
Scattering Data ◽  
Live Cells ◽  
X Ray ◽  
Membrane Mimics ◽  
Complex Membrane

We review compositional models for analyzing small-angle X-ray and neutron scattering data of complex membrane mimics and live cells.

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

2020 ◽  
Vol 16 (4) ◽  
pp. e1007870 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Yong Wang ◽  
Sandro Bottaro ◽  
Sergei Grudinin ◽  
Lise Arleth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Scattering Data ◽  
X Ray ◽  
Dynamics Simulations

scholarly journals Structural Studies of Overlapping Dinucleosomes in Solution

2019 ◽  
Author(s):  
A. Matsumoto ◽  
M. Sugiyama ◽  
Z. Li ◽  
A. Martel ◽  
L. Porcar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Neutron Scattering ◽  
Small Angle ◽  
Solution Structure ◽  
Scattering Data ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Histone Tails ◽  
Nucleosome Remodeling ◽  
X Ray

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.

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

2016 ◽  
Vol 49 (2) ◽  
pp. 690-695 ◽  
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.

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

2000 ◽  
Vol 612 ◽  
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.

Quantification of the information in small-angle scattering data

2014 ◽  
Vol 47 (6) ◽  
pp. 2000-2010 ◽  
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.

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

2010 ◽  
Vol 44 (1) ◽  
pp. 221-224 ◽  
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.

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

1988 ◽  
Vol 21 (6) ◽  
pp. 629-638 ◽  
Author(s):  
T. P. Russell ◽  
J. S. Lin ◽  
S. Spooner ◽  
G. D. Wignall
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Scattering Data ◽  
X Ray

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

2019 ◽  
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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