scholarly journals The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease

2015 ◽  
Vol 471 (2) ◽  
pp. 167-185 ◽  
Author(s):  
Gar Kay Hui ◽  
David W. Wright ◽  
Owen L. Vennard ◽  
Lucy E. Rayner ◽  
Melisa Pang ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Receptor Binding ◽  
Analytical Ultracentrifugation ◽  
Scattering Data ◽  
X Ray ◽  
Solution Structures ◽  
Binding Function ◽  
Atomistic Modelling ◽  
Modelling Approach

Detailed analytical ultracentrifugation and X-ray/neutron scattering data and a new atomistic modelling approach revealed asymmetric extended solution structures for human IgA1 that account for its receptor-binding function. IgA1 with different hinge O-galactosylation patterns showed similar structures.

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

X-ray diffraction, neutron scattering and EXAFS spectroscopy of monoclinic zirconia: analysis by Rietveld refinement and reverse Monte Carlo simulations

2002 ◽  
Vol 35 (4) ◽  
pp. 434-442 ◽  
Author(s):  
Markus Winterer ◽  
Robert Delaplane ◽  
Robert McGreevy
Keyword(s):  
Monte Carlo ◽  
Neutron Scattering ◽  
Rietveld Refinement ◽  
Local Structure ◽  
Exafs Spectroscopy ◽  
Scattering Data ◽  
Accurate Information ◽  
Reverse Monte Carlo ◽  
Monoclinic Zirconia ◽  
X Ray

Extended X-ray absorption fine structure (EXAFS) and neutron scattering data from monoclinic zirconia are analysed independently and simultaneously by reverse Monte Carlo (RMC) modelling. X-ray and neutron powder diffraction data are analysed by Rietveld refinement. The results are compared with respect to the local structure around the zirconium cations. Monoclinic zirconia was chosen as a model system for the comparison of structural information obtained by EXAFS spectroscopy and scattering methods because it is crystalline but also has some local disorder. In the case of zirconia, analysis of EXAFS spectra by RMC modelling results in reliable and accurate information on the local structure, consistent with neutron scattering and diffraction experiments.

The structure of monoclinic NaNiO2 as determined by powder X-ray and neutron scattering

1997 ◽  
Vol 12 (4) ◽  
pp. 239-241 ◽  
Author(s):  
Stefan Dick ◽  
Michaela Müller ◽  
Franziska Preissinger ◽  
Thomas Zeiske
Keyword(s):  
Neutron Scattering ◽  
Room Temperature ◽  
Scattering Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Distorted Octahedral Coordination ◽  
Distorted Octahedral ◽  
Jahn Teller ◽  
Na Ions ◽  
Starting Model

The crystal structure of low temperature NaNiO2 has been refined by Rietveld methods using powder X-ray diffraction and neutron scattering data. The starting model was based on parameters that had been obtained earlier by X-ray film methods. At room temperature NaNiO2 is monoclinic, C2/m, a=0.53192(2), b=0.28451(1), c=0.55826(4) nm, β=110.449(2)°. NaNiO2 has a layered structure. The Ni–O layer is formed by edge sharing of Jahn–Teller elonganted NiO6 octahedra with Ni–O distances of 0.1911(2) nm and 0.2144(4) nm. The Na ions between these layers also exhibit a distorted octahedral coordination with Na–O distances of 0.2328(2) nm and 0.2369(4) nm. The final R values were Rwp=0.069, RI=0.059, Rexp=0.059 for the neutron and Rwp=0.032, RI=0.034, Rexp=0.017 for the X-ray data.

scholarly journals Non-linearity of the collagen triple helix in solution and implications for collagen function

2017 ◽  
Vol 474 (13) ◽  
pp. 2203-2217 ◽  
Author(s):  
Kenneth T. Walker ◽  
Ruodan Nan ◽  
David W. Wright ◽  
Jayesh Gor ◽  
Anthony C. Bishop ◽  
...  
Keyword(s):  
Analytical Ultracentrifugation ◽  
Linear Structure ◽  
Small Degree ◽  
Scattering Data ◽  
Helical Conformation ◽  
End Effects ◽  
Helical Peptides ◽  
Atomistic Modelling ◽  
Triple Helices ◽  
Dynamics Simulations

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG)10unblocked, was compared with the blocked (POG)10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4–17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease.

Solution structures of complement components by X-ray and neutron scattering and analytical ultracentrifugation

2002 ◽  
Vol 30 (6) ◽  
pp. 996-1001 ◽  
Author(s):  
S. J. Perkins ◽  
H. E. Gilbert ◽  
M. Aslam ◽  
J. Hannan ◽  
V. M. Holers ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Complement System ◽  
Analytical Ultracentrifugation ◽  
Factor H ◽  
Protein Domain ◽  
Complement Receptor ◽  
Complement Components ◽  
X Ray ◽  
Solution Studies ◽  
The Complement System

The short consensus/complement repeat (SCR) domain (also known as the complement control protein domain) is the most abundant domain type in the complement system. Crystal and NMR structures for proteins that contain single and multiple SCR domains have now been published. These contain inter-SCR linkers of between three and eight residues, and the structures show much variability in inter-SCR orientations. X-ray and neutron scattering, combined with analytical ultracentrifugation and constrained modelling based on known subunit structures will yield a medium-resolution structure for the protein of interest. The fewer parameters that are associated with the structure of interest, the more defined the structure of interest becomes. These solution studies have been applied to several SCR-containing proteins in the complement system, most notably Factor H with 20 SCR domains, a complement receptor type 2 fragment with two SCR domains, and rat complement receptor-related protein (Crry) which contains five SCR domains. The results show great conformational variability in the inter-SCR orientation, and these will be reviewed. Even though the rotational orientation cannot be modelled, it is nonetheless possible to measure the degree of extension of the multi-SCR proteins and, from this, to obtain functionally useful results.

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.

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