Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bringing diffuse X-ray scattering into focus.

ABSTRACT: X-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.

SUBMITTER: Wall ME

PROVIDER: S-EPMC6078797 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Bringing diffuse X-ray scattering into focus.

Wall Michael E ME Wolff Alexander M AM Fraser James S JS

Current opinion in structural biology 20180216

X-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 c ...[more]

PMID: 29455056

Similar Datasets

Measuring and modeling diffuse scattering in protein X-ray crystallography.

Project description: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.

| S-EPMC4839442 | biostudies-literature

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Project description: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.diffuse is 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_xyz 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, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

| S-EPMC4528799 | biostudies-literature

Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease.

Project description:We have developed methods for obtaining and characterizing three-dimensional maps of the reciprocal-space distribution of diffuse x-ray scattering from protein crystals, and have used the methods to study the nature of disorder in crystals of Staphylococcal nuclease. Experimentally obtained maps are 99.5% complete in the reciprocal-space resolution range of 10 A-2.5 A, show symmetry consistent with the P41 space group of the unit cell, and are highly reproducible. Quantitative comparisons of the data with three-dimensional simulations imply liquid-like motions of the protein [Caspar, D. L. D., Clarage, J., Salunke, D. M. & Clarage, M. (1988) Nature (London) 332, 659-662], with a correlation length of 10 A and a root-mean-square displacement of 0.36 A.

| S-EPMC21023 | biostudies-literature

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

Project description:Protein 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 finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the 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.

| S-EPMC7062842 | biostudies-literature

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

Project description: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.

| S-EPMC5947722 | biostudies-literature

Topology and temperature dependence of the diffuse X-ray scattering in Na0.5Bi0.5TiO3 ferroelectric single crystals.

Project description:The results of high-resolution measurements of the diffuse X-ray scattering produced by a perovskite-based Na0.5Bi0.5TiO3 ferroelectric single crystal between 40 and 620?K are reported. The study was designed as an attempt to resolve numerous controversies regarding the average structure of Na0.5Bi0.5TiO3, such as the mechanism of the phase transitions between the tetragonal, P4bm, and rhombohedral | monoclinic, R3c?|?Cc, space groups and the correlation between structural changes and macroscopic physical properties. The starting point was to search for any transformations of structural disorder in the temperature range of thermal depoling (420-480?K), where the average structure is known to remain unchanged. The intensity distribution around the {032} pseudocubic reflection was collected using a PILATUS 100K detector at the I16 beamline of the Diamond Light Source (UK). The data revealed previously unknown features of the diffuse scattering, including a system of dual asymmetric L-shaped diffuse scattering streaks. The topology, temperature dependence, and relationship between Bragg and diffuse intensities suggest the presence of complex microstructure in the low-temperature R3c?|?Cc phase. This microstructure may be formed by the persistence of the higher-temperature P4bm phase, built into a lower-temperature R3c?|?Cc matrix, accompanied by the related long-range strain fields. Finally, it is shown that a correlation between the temperature dependence of the X-ray scattering features and the temperature regime of thermal depoling is present.

| S-EPMC4747085 | biostudies-other

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

Project description:X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-?s MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

| S-EPMC4273327 | biostudies-literature

Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.

Project description:In this study, the variance-covariance matrix of protein motions is used to compare several elastic network models within the theoretical framework of x-ray scattering from crystals. A set of 33 ultra-high resolution structures is used to characterize the average scaling behavior of the vibrational density of states and make comparisons between experimental and theoretical temperature factors. Detailed investigations of the vibrational density of states, correlations, and predicted diffuse x-ray scatter are carried out for crystalline Staphylococcal nuclease; correlations and diffuse x-ray scatter are also compared to predictions from the translation, libration, screw model and a liquid-like dynamics model. We show that elastic network models developed to best predict temperature factors without regard for the crystal environment have relatively strong long-range interactions that yield very short-ranged atom-atom correlations. Further, we find that the low-frequency modes dominate the variance-covariance matrix only for those models with a physically reasonable vibrational density of states, and the fraction of modes required to converge the correlations is higher than that typically used for elastic network model studies. The practical implications are explored using computed diffuse x-ray scatter, which can be measured experimentally.

| S-EPMC2955396 | biostudies-literature

Estimands: bringing clarity and focus to research questions in clinical trials.

Project description:Precise specification of the research question and associated treatment effect of interest is essential in clinical research, yet recent work shows that they are often incompletely specified. The ICH E9 (R1) Addendum on Estimands and Sensitivity Analysis in Clinical Trials introduces a framework that supports researchers in precisely and transparently specifying the treatment effect they aim to estimate in their clinical trial. In this paper, we present practical examples to demonstrate to all researchers involved in clinical trials how estimands can help them to specify the research question, lead to a better understanding of the treatment effect to be estimated and hence increase the probability of success of the trial.

| S-EPMC8724703 | biostudies-literature

Suboptimal Coding Metasurfaces for Terahertz Diffuse Scattering.

Project description:Coding metasurfaces, composed of only two types of elements arranged according to a binary code, are attracting a steadily increasing interest in many application scenarios. In this study, we apply this concept to attain diffuse scattering at THz frequencies. Building up on previously derived theoretical results, we carry out a suboptimal metasurface design based on a simple, deterministic and computationally inexpensive algorithm that can be applied to arbitrarily large structures. For experimental validation, we fabricate and characterize three prototypes working at 1?THz, which, in accordance with numerical predictions, exhibit significant reductions of the radar cross-section, with reasonably good frequency and angular stability. Besides the radar-signature control, our results may also find potentially interesting applications to diffusive imaging, computational imaging, and (scaled to optical wavelengths) photovoltaics.

| S-EPMC6085296 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data