scholarly journals Bringing Diffuse X-ray Scattering Into Focus

2017 ◽  
Author(s):  
Michael E. Wall ◽  
Alexander M. Wolff ◽  
James S. Fraser
Keyword(s):  
Diffuse Scattering ◽  
Conformational Ensemble ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Model Protein ◽  
Mean Structure ◽  
The Mean

AbstractX-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

scholarly journals Disorder in pentachloronitrobenzene, C6Cl5NO2: a diffuse scattering study

2007 ◽  
Vol 63 (4) ◽  
pp. 663-673 ◽  
Author(s):  
Lynne H. Thomas ◽  
T. Richard Welberry ◽  
Darren J. Goossens ◽  
Aidan P. Heerdegen ◽  
Matthias J. Gutmann ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Short Range ◽  
Scattering Data ◽  
X Ray ◽  
Monte Carlo Computer Simulation ◽  
X Ray Scattering ◽  
Scattering Study ◽  
The Mean ◽  
Diffraction Patterns ◽  
Local Relaxation

Monte Carlo computer simulation has been used to interpret and model observed single-crystal diffuse X-ray scattering data for pentachloronitrobenzene, C6Cl5NO2. Each site in the crystal contains a molecule in one of six different basic orientations with equal probability. However, no short-range order amongst these different orientations has been detected. The strong, detailed and very distinctive diffraction patterns can be accounted for almost entirely on the assumption of random occupancy of each molecular site, but with very large local relaxation displacements that tend to increase the neighbouring distances for contacts involving NO2...NO2 and NO2...Cl with a corresponding reduction for those involving Cl...Cl. The results show that the mean NO2...NO2 distance is increased by ∼ 0.6 Å, compared with that given by the average structure determination.

scholarly journals Diffuse X-Ray Scattering to Model Protein Motions

Structure ◽  
2014 ◽  
Vol 22 (2) ◽  
pp. 182-184 ◽  
Author(s):  
Michael E. Wall ◽  
Paul D. Adams ◽  
James S. Fraser ◽  
Nicholas K. Sauter
Keyword(s):  
X Ray ◽  
Protein Motions ◽  
X Ray Scattering ◽  
Model Protein ◽  
Ray Scattering

scholarly journals Measuring and modeling diffuse scattering in protein X-ray crystallography

2016 ◽  
Vol 113 (15) ◽  
pp. 4069-4074 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Lin Liu ◽  
Ana Gonzalez ◽  
Aaron S. Brewster ◽  
Nicholas K. Sauter ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Structure Refinement ◽  
Normal Modes ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
Diffuse Intensity ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Crystallography ◽  
Standard Data

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

scholarly journals Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 172-181 ◽  
Author(s):  
Michael E. Wall
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Diffuse Scattering ◽  
Md Simulations ◽  
Unit Cell ◽  
Protein Crystal ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Scattering ◽  
Ray Scattering

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

scholarly journals Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

2019 ◽  
Author(s):  
Steve P. Meisburger ◽  
David A. Case ◽  
Nozomi Ando
Keyword(s):  
Diffuse Scattering ◽  
Structural Information ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Dynamic Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Correlated Motions ◽  
Hinge Bending

AbstractProtein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a detailed diffuse scattering map from triclinic lysozyme that resolves both inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.

A Small-Angle X-Ray Scattering Study on Pre-Irradiated Malate Synthase. The Influence of Formate, Superoxide Dismutase, and Catalase on the X-Ray Induced Aggregation of the Enzyme

1985 ◽  
Vol 40 (5-6) ◽  
pp. 364-372 ◽  
Author(s):  
P. Zipper ◽  
R. Wilfing ◽  
M. Kriechbaum ◽  
H. Durchschlag
Keyword(s):  
Aqueous Solution ◽  
Superoxide Dismutase ◽  
Small Angle ◽  
Malate Synthase ◽  
X Ray ◽  
X Ray Scattering ◽  
X Irradiation ◽  
The Mean ◽  
Induced Aggregation ◽  
Ray Scattering

Abstract The sulfhydryl enzyme malate synthase from baker’s yeast was X-irradiated with 6 kGy in air-saturated aqueous solution (enzyme concentration: ≃ 10 mg/ml; volume: 120 μl), in the absence or presence of the specific scavengers formate, superoxide dismutase, and catalase. After X-irradiation, a small aliquot of the irradiated solutions was tested for enzymic activity while the main portion was investigated by means of small-angle X-ray scattering. Additionally, an unir­radiated sample without additives was investigated as a reference. Experiments yielded the fol­lowing results: 1. X-irradiation in the absence of the mentioned scavengers caused considerable aggregation, fragmentation, and inactivation of the enzyme. The dose Dt37 for total (= repairable + non­-repayable) inactivation resulted as 4.4 kGy. The mean radius of gyration was found to be about 13 nm. The mean degree of aggregation was obtained as 5.7, without correction for fragmenta­tion. An estimation based on the thickness factor revealed that about 19% of material might be strongly fragmented. When this amount of fragments was accordingly taken into account, a value of 7.1 was obtained as an upper limit for the mean degree of aggregation. The observed retention of the thickness factor and the finding of two different cross-section factors are in full accord with the two-dimensional aggregation model established previously (Zipper and Durchschlag, Radiat. Environ. Biophys. 18, 99 - 121 (1980)). 2. The presence of catalytic amounts of superoxide dismutase and/or catalase, in the absence of formate, during X-irradiation reduced both aggregation and inactivation significantly. 3. The presence of formate (10 or 100 mᴍ) during X-irradiation led to a strong decrease of aggregation and inactivation. This effect was more pronounced with the higher formate concen­tration or when superoxide dismutase and/or catalase were simultaneously present during X-irradiation. The presence of formate also reduced the amount of fragments significantly. 4. The results clearly show that the aggregation and inactivation of malate synthase upon X-irradiation in aqueous solution are mainly caused by OH·; to a minor extent O·̄2 and H2O2 are additionally involved in the damaging processes.

Evolution of Interfacial Roughness Correlations of Fe Au Films Grown on Mgo(001) Substrates

1996 ◽  
Vol 440 ◽  
Author(s):  
P. C. Chow ◽  
R. Paniago ◽  
R. Forrest ◽  
S. C. Moss ◽  
S. S. P. Parkin ◽  
...  
Keyword(s):  
Thin Films ◽  
Diffuse Scattering ◽  
Perfect Match ◽  
Grazing Incidence ◽  
Interface Roughness ◽  
Metallic Structures ◽  
X Ray ◽  
Dimensional Image ◽  
X Ray Scattering ◽  
Image Plate Detector

AbstractThe growth by sputtering of a series of thin films of Fe/Au on MgO(001) substrates was analyzed using Bragg and diffuse X-ray scattering. The Fe (bcc) layer grows rotated by 45° with respect to the MgO – Au(fcc) (001) epitaxial orientation, resulting in an almost perfect match between the two metallic structures. By collecting the X-ray diffuse scattering under grazing incidence using a 2-dimensional image plate detector, we mapped the reciprocal space of these films. We characterized the correlated interface roughness starting with a buffer of Fe in which only three interfaces are present. The propagation of the roughness was subsequently characterized for Fe/Au multilayers with 40 and 100 bilayers. We observe an enlargement of the surface features as a function of time, evidenced by the longer lateral cutoff length measured for thicker films.

scholarly journals Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy

2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Lassa Virus ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Ray Scattering

Diffuse X-ray scattering from tiny sample volumes

2005 ◽  
Vol 220 (12) ◽  
Author(s):  
Gene E. Ice ◽  
Rozaliya I. Barabash ◽  
Wenjun Liu
Keyword(s):  
Local Structure ◽  
Diffuse Scattering ◽  
High Performance ◽  
Sensitive Area ◽  
X Ray ◽  
X Ray Scattering ◽  
Defect Content ◽  
Ray Scattering

AbstractThe emergence of intense synchrotron X-ray sources, efficient focusing optics and high-performance X-ray sensitive area detectors allows for measurements of diffuse scattering from cubic micron-scale sample vol umes. Here we present an experiment that illustrates methods for studying the local structure and defect content of tiny sample volumes. In the experiment, an X-ray microbeam illuminating about ∼5 μm

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