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.

scholarly journals Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

2015 ◽  
Vol 71 (8) ◽  
pp. 1657-1667 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Pavel V. Afonine ◽  
Thomas C. Terwilliger ◽  
Michael E. Wall ◽  
Colin J. Jackson ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Positional Distribution ◽  
Data Bank ◽  
Bragg Diffraction ◽  
Structural Refinement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Displacements ◽  
Technological Advances ◽  
Structural Ensembles

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool,phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case,phenix.diffuseis applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures,phenix.tls_as_xyzbuilds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

scholarly journals 20 YEARS OF LEPTIN: Insights into signaling assemblies of the leptin receptor

2014 ◽  
Vol 223 (1) ◽  
pp. T9-T23 ◽  
Author(s):  
Frank Peelman ◽  
Lennart Zabeau ◽  
Kedar Moharana ◽  
Savvas N Savvides ◽  
Jan Tavernier
Keyword(s):  
Electron Microscopy ◽  
Energy Homeostasis ◽  
Leptin Receptor ◽  
Structural Information ◽  
Cell Types ◽  
Activation Mechanism ◽  
Peripheral Cell ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering

Leptin plays a central role in the control of body weight and energy homeostasis, but is a pleiotropic cytokine with activities on many peripheral cell types. In this review, we discuss the interaction of leptin with its receptor, and focus on the structural and mechanistic aspects of the extracellular aspects of leptin receptor (LR) activation. We provide an extensive overview of all structural information that has been obtained for leptin and its receptor via X-ray crystallography, electron microscopy, small-angle X-ray scattering, homology modeling, and mutagenesis studies. The available knowledge is integrated into putative models toward a recapitulation of the LR activation mechanism.

scholarly journals Diffuse X-ray scattering from correlated motions in a protein crystal

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Steve P. Meisburger ◽  
David A. Case ◽  
Nozomi Ando
Keyword(s):  
Protein Crystal ◽  
X Ray ◽  
X Ray Scattering ◽  
Correlated Motions ◽  
Ray Scattering

scholarly journals Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

2015 ◽  
Author(s):  
Andrew Van Benschoten ◽  
Pavel Afonine ◽  
Thomas Terwilliger ◽  
Michael Wall ◽  
Colin Jackson ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Positional Distribution ◽  
Data Bank ◽  
Bragg Diffraction ◽  
Structural Refinement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Displacements ◽  
Technological Advances ◽  
Structural Ensembles

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. While Bragg diffraction describes the average positional distribution of crystalline atoms, many different models can fit this distribution equally well. Diffuse X-ray scattering can reduce this degeneracy by directly reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to Translation-Libration-Screw (TLS) refinement, which models rigid body displacement for segments of the macromolecule. To enable calculation of diffuse scattering from TLS refined structures, phenix.tls_models builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how X-ray diffuse scattering can extend macromolecular structural refinement, validation, and analysis.

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 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 Monitoring protein precipitates by in-house X-ray powder diffraction

2013 ◽  
Vol 28 (S2) ◽  
pp. S458-S469 ◽  
Author(s):  
Kenny Ståhl ◽  
Christian G. Frankær ◽  
Jakob Petersen ◽  
Pernille Harris
Keyword(s):  
Powder Diffraction ◽  
Protein Crystal ◽  
Data Sets ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Parameters ◽  
X Ray Scattering ◽  
Source Organism ◽  
Peak Asymmetry ◽  
Overlapping Peaks

Powder diffraction from protein powders using in-house diffractometers is an effective tool for identification and monitoring of protein crystal forms and artifacts. As an alternative to conventional powder diffractometers a single crystal diffractometer equipped with an X-ray micro-source can be used to collect powder patterns from 1 µl samples. Using a small-angle X-ray scattering (SAXS) camera it is possible to collect data within minutes. A streamlined program has been developed for the calculation of powder patterns from pdb-coordinates, and includes correction for bulk-solvent. A number of such calculated powder patterns from insulin and lysozyme have been included in the powder diffraction database and successfully used for search-match identification. However, the fit could be much improved if peak asymmetry and multiple bulk-solvent corrections were included. When including a large number of protein data sets in the database some problems can be foreseen due to the large number of overlapping peaks in the low-angle region, and small differences in unit cell parameters between pdb-data and powder data. It is suggested that protein entries are supplied with more searchable keywords as protein name, protein type, molecular weight, source organism etc. in order to limit possible hits.

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 A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter

2012 ◽  
Vol 46 (1) ◽  
pp. 234-241 ◽  
Author(s):  
Chae Un Kim ◽  
Jennifer L. Wierman ◽  
Richard Gillilan ◽  
Enju Lima ◽  
Sol M. Gruner
Keyword(s):  
High Pressure ◽  
Biological Samples ◽  
Protein Crystal ◽  
High Background ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
X Ray Scattering ◽  
Alternative Method ◽  
Helium Gas ◽  
Diffraction Imaging

High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydratedviavapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryocooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.

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