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.

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 Solution structure of macromolecules using small angle neutron scattering and molecular simulations

2020 ◽  
Vol 236 ◽  
pp. 03003
Author(s):  
Jayesh S. Bhatt
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Solution Structure ◽  
Molecular Simulations ◽  
Liquid Solution ◽  
Scattering Data ◽  
Monte Carlo Techniques

An introductory account of using molecular simulations to deduce solution structure of macromolecules using small angle neutron scattering data is presented for biologists. The presence of a liquid solution provides mobility to the molecules, making it difficult to pin down their structure. Here a simple introduction to molecular dynamics and Monte Carlo techniques is followed by a recipe to use the output of the simulations along with the scattering data in order to infer the structure of macromolecules when they are placed in a liquid solution. Some practical issues to be watched for are also highlighted.

Solution structure of phosphorylase kinase studied using small-angle x-ray and neutron scattering

Biochemistry ◽  
1992 ◽  
Vol 31 (2) ◽  
pp. 437-442 ◽  
Author(s):  
S. J. Henderson ◽  
P. Newsholme ◽  
D. B. Heidorn ◽  
R. Mitchell ◽  
P. A. Seeger ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Solution Structure ◽  
Phosphorylase Kinase ◽  
X Ray

Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis

2011 ◽  
Vol 173 (3) ◽  
pp. 451-460 ◽  
Author(s):  
Osamu Miyashita ◽  
Christian Gorba ◽  
Florence Tama
Keyword(s):  
Normal Mode ◽  
Small Angle ◽  
Normal Mode Analysis ◽  
Scattering Data ◽  
Mode Analysis ◽  
Structure Modeling ◽  
Elastic Network ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

2019 ◽  
Vol 75 (6) ◽  
pp. 439-449 ◽  
Author(s):  
Thushara Welwelwela Hewage ◽  
Sofia Caria ◽  
Mihwa Lee
Keyword(s):  
Crystal Structure ◽  
Small Angle ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Protein ◽  
Coiled Coil ◽  
Scattering Data ◽  
Nucleic Acid Binding ◽  
Dimerization Domain ◽  
Orthorhombic Space Group

Splicing factor proline/glutamine-rich (SFPQ) is an essential RNA-binding protein that is implicated in many aspects of nuclear function. The structures of SFPQ and two paralogs, non-POU domain-containing octamer-binding protein and paraspeckle component 1, from theDrosophilabehavior human splicing protein family have previously been characterized. The unusual arrangement of the four domains, two RNA-recognition motifs (RRMs), a conserved region termed the NonA/paraspeckle (NOPS) domain and a C-terminal coiled coil, in the intertwined dimer provides a potentially unique RNA-binding surface. However, the molecular details of how the four RRMs in the dimeric SFPQ interact with RNA remain to be characterized. Here, a new crystal structure of the dimerization domain of human SFPQ in theC-centered orthorhombic space groupC2221with one monomer in the asymmetric unit is presented. Comparison of the new crystal structure with the previously reported structure of SFPQ and analysis of the solution small-angle X-scattering data revealed subtle domain movements in the dimerization domain of SFPQ, supporting the concept of multiple conformations of SFPQ in equilibrium in solution. The domain movement of RRM1, in particular, may reflect the complexity of the RNA substrates of SFPQ. Taken together, the crystal and solution structure analyses provide a molecular basis for further investigation into the plasticity of nucleic acid binding by SFPQ in the absence of the structure in complex with its cognate RNA-binding partners.

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.

scholarly journals Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis

2016 ◽  
Vol 18 (8) ◽  
pp. 5707-5719 ◽  
Author(s):  
Alejandro Panjkovich ◽  
Dmitri I. Svergun
Keyword(s):  
Normal Mode ◽  
Small Angle ◽  
Normal Mode Analysis ◽  
Conformational Transitions ◽  
Scattering Data ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Scattering ◽  
Insight Into

SREFLEX employs normal mode analysis for the flexible refinement of atomic models of biological macromolecules against solution scattering data, providing insight into conformational transitions.

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.

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