scholarly journals Merging in-solution X-ray and neutron scattering data allows fine structural analysis of membrane-protein detergent complexes

2018 ◽  
Author(s):  
Gaetan Dias-Mirandela ◽  
Giulia Tamburrino ◽  
Miloš T Ivanović ◽  
Felix M Strnad ◽  
Olwyn Byron ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Membrane Protein ◽  
Neutron Scattering ◽  
Structural Information ◽  
Scattering Data ◽  
Membrane Protein Complex ◽  
X Ray ◽  
Ab Initio Approach ◽  
Atomic Analysis ◽  
Sans Data

In-solution small angle X-ray and neutron scattering (SAXS/SANS) have become popular methods to characterize the structure of membrane proteins, solubilized by either detergents or nanodiscs. SANS studies of protein-detergent complexes usually require deuterium-labelled proteins or detergents, which in turn often lead to problems in their expression or purification. Here, we report an approach whose novelty is the combined analysis of SAXS and SANS data from an unlabeled membrane protein complex in solution in two complementary ways. Firstly, an explicit atomic analysis, including both protein and detergent molecules, using the program WAXSiS which has been adapted to predict SANS data. Secondly, the use of MONSA which allows to discriminate between detergent head- and tail-groups in an ab initio approach. Our approach is readily applicable to any detergent-solubilized protein and provides more detailed structural information on protein-detergent complexes from unlabeled samples than SAXS or SANS alone.

scholarly journals Merging In-Solution X-ray and Neutron Scattering Data Allows Fine Structural Analysis of Membrane–Protein Detergent Complexes

2018 ◽  
Vol 9 (14) ◽  
pp. 3910-3914 ◽  
Author(s):  
Gaëtan Dias Mirandela ◽  
Giulia Tamburrino ◽  
Miloš T. Ivanović ◽  
Felix M. Strnad ◽  
Olwyn Byron ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Membrane Protein ◽  
Neutron Scattering ◽  
Scattering Data ◽  
X Ray

scholarly journals Simultaneous SAXS/SANS Method at D22 of ILL: Instrument Upgrade

2021 ◽  
Vol 11 (13) ◽  
pp. 5925
Author(s):  
Ezzeldin Metwalli ◽  
Klaus Götz ◽  
Tobias Zech ◽  
Christian Bär ◽  
Isabel Schuldes ◽  
...  
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
High Energy ◽  
Scattering Data ◽  
Background Suppression ◽  
Experimental Conditions ◽  
Radiation Background ◽  
Saxs Data ◽  
X Ray ◽  
Sans Data

A customized portable SAXS instrument has recently been constructed, installed, and tested at the D22 SANS instrument at ILL. Technical characteristics of this newly established plug-and-play SAXS system have recently been reported (J. Appl. Cryst. 2020, 53, 722). An optimized lead shielding arrangement on the SAXS system and a double energy threshold X-ray detector have been further implemented to substantially suppress the unavoidable high-energy gamma radiation background on the X-ray detector. The performance of the upgraded SAXS instrument has been examined systematically by determining background suppression factors (SFs) at various experimental conditions, including different neutron beam collimation lengths and X-ray sample-to-detector distances (SDDX-ray). Improved signal-to-noise ratio SAXS data enables combined SAXS and SANS measurements for all possible experimental conditions at the D22 instrument. Both SAXS and SANS data from the same sample volume can be fitted simultaneously using a common structural model, allowing unambiguous interpretation of the scattering data. Importantly, advanced in situ/real time investigations are possible, where both the SAXS and the SANS data can reveal time-resolved complementary nanoscale structural information.

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 Understanding the properties of energy materials from their local structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C860-C860
Author(s):  
Hyunjeong Kim
Keyword(s):  
Structural Information ◽  
Lithium Ion ◽  
Structural Features ◽  
Scattering Data ◽  
Energy Materials ◽  
X Ray ◽  
Atomic Pair Distribution Function ◽  
Structure Probing ◽  
Atomic Pair ◽  
Pdf Analysis

Numerous energy materials with improved properties often show nano- or heavily disordered structural features which are hardly characterized by the conventional crystallographic technique alone. By using the atomic pair distribution function (PDF) analysis [1]on X-ray and neutron total scattering data, we have investigated various energy materials to elucidate structural features closely linked to their properties. Some of the examples are heavily disordered V1-xTixH2 for hydrogen storage [2] and layered Li1.2Mn0.567Ni0.166Co0.067O2 cathode material for lithium ion batteries. These materials possess an intricate structure and could easily lead to misleading results if one relies on only one structure probing technique. In this talk, I will show how their structural information was extracted from the x-ray and neutron PDFs obtained at BL22XU at SPring-8 and NOVA at J-PARC, respectively and how it was used with information available from other techniques to understand the properties of these energy materials.

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.

A Study of Tio2 Aerogels Pore and Ramified Structure by Small-Angle Neutron Scattering

1994 ◽  
Vol 376 ◽  
Author(s):  
Zhu Zhu ◽  
Min Lin ◽  
Geula Dagan ◽  
Micha Tomkiewicz
Keyword(s):  
Titanium Dioxide ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Gas Adsorption ◽  
Scattering Data ◽  
Morphological Parameters ◽  
Nitrogen Gas ◽  
Light Density ◽  
Sans Data

ABSTRACTThe microstructral characteristics of titanium dioxide aerogels were studied by Small Angle Neutron Scattering (SANS). A variety of models were used to extract the morphological parameters from the SANS data. The evaluation of scattering data was found to be consistent with nitrogen gas adsorption and TEM measurements of a model of aerogel consisting of a light density matrix in which meso- and macro-pores are embedded.

Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment

2014 ◽  
Vol 70 (2) ◽  
pp. 371-383 ◽  
Author(s):  
Søren A. R. Kynde ◽  
Nicholas Skar-Gislinge ◽  
Martin Cramer Pedersen ◽  
Søren Roi Midtgaard ◽  
Jens Baek Simonsen ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Small Angle ◽  
Structural Information ◽  
Protein Localization ◽  
Hybrid Approach ◽  
Small Angle Scattering ◽  
Phospholipid Bilayer ◽  
Scattering Data ◽  
Angle Scattering ◽  
Lipid Environment

Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein–lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.

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.

Sign in / Sign up

Export Citation Format

Share Document