Multi-speckle X-ray photon correlation spectroscopy in the ultra-small-angle X-ray scattering range

Möller, Johannes; Chushkin, Yuriy; Prévost, Sylvain; Narayanan, Theyencheri

doi:10.1107/s1600577516008092

Cited by 27 publications

(22 citation statements)

References 29 publications

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“…Using depolarized DLS, also rotational self-diffusion has been accessed (Dubin et al, 1971;Berne and Pecora, 2000). XPCS is a synchrotron-based technique, accessing length scales from the atomic scale up to a few micrometers (Grübel et al, 2008;Leheny, 2012;Möller et al, 2016). So far, it has only been used tentatively for protein dynamics because of the prevailing challenge of radiation damage (Vodnala et al, 2018), although XPCS could provide a unique time and length scale window for collective dynamics, and there may be ways to circumvent the problems (Verwohlt et al, 2018).…”

Section: Scattering Techniquesmentioning

confidence: 99%

Dynamics of proteins in solution

Grimaldo

Roosen-Runge

Zhang

et al. 2019

Quart. Rev. Biophys.

104

175

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The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

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Section: Scattering Techniquesmentioning

confidence: 99%

Dynamics of proteins in solution

Grimaldo

Roosen-Runge

Zhang

et al. 2019

Quart. Rev. Biophys.

104

175

View full text Add to dashboard Cite

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“…Geometrical models may fit low-angle X-ray scattering data (corresponding to relatively low-resolution information in real-space). High-quality solution X-ray scattering data at ultra-low to wide angles (Möller et al, 2016), however, can be obtained using modern synchrotron facilities, high solute concentrations, proper background measurement protocols in flow-cell setups , and online size exclusion chromatography (Graewert et al, 2015;Pérez & Koutsioubas, 2015).…”

Section: Introductionmentioning

confidence: 99%

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

Ginsburg¹,

Ben-Nun²,

Asor³

et al. 2018

Preprint

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<div>In this paper, we present our new computer program, D+, which uses the reciprocal-grid (RG) algorithm to efficiently compute X-ray scattering curves from solutions of complex structures at high-resolution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and by repeating this process for all the leaves and nodes of the tree. For very large structures, a Hybrid method can be used to avoid numerical artifacts. In the Hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. We present how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a protein data bank (PDB) file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. In addition, a python wrapper is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, we present a large number of tests and compare the results of D+ with other programs when possible and demonstrate the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number. D+ and its source code are freely available (https://scholars.huji.ac.il/uriraviv/software/d-software) for academic users and developers. </div>

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“…The USAXS and XPCS experiments were conducted at beamline ID02 (ESRF, Grenoble, France) in the pinhole scattering geometry. Details of the instrument can be found elsewhere (Mö ller et al, 2016). The sample-to-detector distance was set to 31 m, which corresponds to a scattering vector range of about 2 Â 10 À3 -10 À1 nm À1 at of 0.995 Å .…”

Section: Methodsmentioning

confidence: 99%

Multiple-scattering effects in SAXS and XPCS measurements in the ultra-small-angle region

2018

Self Cite

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An experimental study of the influence of multiple‐scattering events on data acquired by small‐angle X‐ray scattering (SAXS) and X‐ray photon correlation spectroscopy (XPCS) techniques in the ultra‐small‐angle range is presented. Both techniques rely on the single‐scattering assumption and any deviation may lead to erroneous interpretation of structural and dynamical results. Typical effects of multiple scattering on measured static and dynamic scattering from model colloidal suspensions are presented, and it is demonstrated that the same information content as in a single‐scattering experiment can be extracted after applying appropriate corrections. The perturbations induced by multiple scattering on resolution, photon statistics and speckle visibility are evaluated and the required optimal experimental conditions are discussed. In many cases, multiple scattering might be tolerable to a certain extent, especially if any shortcomings are outweighed by beneficial effects from counting statistics, acquisition time and signal‐to‐background ratio. The presented study may help to optimize future experiments and serve as a guide for data evaluation for this type of system.

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Multi-speckle X-ray photon correlation spectroscopy in the ultra-small-angle X-ray scattering range

Cited by 27 publications

References 29 publications

Dynamics of proteins in solution

Dynamics of proteins in solution

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

Multiple-scattering effects in SAXS and XPCS measurements in the ultra-small-angle region

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