scholarly journals Predicting data quality in biological X-ray solution scattering

2018 ◽  
Vol 74 (8) ◽  
pp. 727-738
Author(s):  
Chenzheng Wang ◽  
Yuexia Lin ◽  
Devin Bougie ◽  
Richard E. Gillilan
Keyword(s):  
Conformational Changes ◽  
Sample Path ◽  
Flow Time ◽  
Photon Flux ◽  
Detector Efficiency ◽  
Time Resolved ◽  
Short Sample ◽  
X Ray ◽  
Path Lengths ◽  
Flux Energy

Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.

The kinetics of conformational changes of α2 -macroglobulin determined by time resolved X-ray solution scattering

FEBS Letters ◽  
1994 ◽  
Vol 337 (2) ◽  
pp. 171-174 ◽  
Author(s):  
Hideo Arakawa ◽  
Takuji Urisaka ◽  
Hirotsugu Tsuruta ◽  
Yoshiyuki Amemiya ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Time Resolved ◽  
X Ray ◽  
Α2 Macroglobulin ◽  
Kinetics Of

The materials science X-ray beamline BL8 at the DELTA storage ring

2009 ◽  
Vol 16 (2) ◽  
pp. 264-272 ◽  
Author(s):  
Dirk Lützenkirchen-Hecht ◽  
Ralph Wagner ◽  
Ulrich Haake ◽  
Anke Watenphul ◽  
Ronald Frahm
Keyword(s):  
Materials Science ◽  
Photon Flux ◽  
Acquisition Time ◽  
Optical Components ◽  
Time Resolved ◽  
X Ray ◽  
Heavy Loads ◽  
Vacuum Systems ◽  
X Ray Absorption

The hard X-ray beamline BL8 at the superconducting asymmetric wiggler at the 1.5 GeV Dortmund Electron Accelerator DELTA is described. This beamline is dedicated to X-ray studies in the spectral range from ∼1 keV to ∼25 keV photon energy. The monochromator as well as the other optical components of the beamline are optimized accordingly. The endstation comprises a six-axis diffractometer that is capable of carrying heavy loads related to non-ambient sample environments such as, for example, ultrahigh-vacuum systems, high-pressure cells or liquid-helium cryostats. X-ray absorption spectra from several reference compounds illustrate the performance. Besides transmission measurements, fluorescence detection for dilute sample systems as well as surface-sensitive reflection-mode experiments have been performed. The results show that high-quality EXAFS data can be obtained in the quick-scanning EXAFS mode within a few seconds of acquisition time, enabling time-resolved in situ experiments using standard beamline equipment that is permanently available. The performance of the new beamline, especially in terms of the photon flux and energy resolution, is competitive with other insertion-device beamlines worldwide, and several sophisticated experiments including surface-sensitive EXAFS experiments are feasible.

scholarly journals Experimental and numerical study of ultra-short laser-produced collimated Cu Kα X-ray source

2017 ◽  
Vol 35 (3) ◽  
pp. 442-449 ◽  
Author(s):  
R. Rathore ◽  
V. Arora ◽  
H. Singhal ◽  
T. Mandal ◽  
J.A. Chakera ◽  
...  
Keyword(s):  
Laser Intensity ◽  
Numerical Study ◽  
Low Cost ◽  
Laser Pulses ◽  
Photon Flux ◽  
X Rays ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Short Laser Pulses

AbstractKα X-ray sources generated from the interaction of ultra-short laser pulses with solids are compact and low-cost source of ultra-short quasi-monochromatic X-rays compared with synchrotron radiation source. Development of collimated ultra-short Kα X-ray source by the interaction of 45 fs Ti:sapphire laser pulse with Cu wire target is presented in this paper. A study of the Kα source with laser parameters such as energy and pulse duration was carried out. The observed Kα X-ray photon flux was ~2.7 × 108 photons/shot at the laser intensity of ~2.8 × 1017 W cm−2. A model was developed to analyze the observed results. The Kα radiation was coupled to a polycapillary collimator to generate a collimated low divergence (0.8 mrad) X-ray beam. Such sources are useful for time-resolved X-ray diffraction and imaging studies.

Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects

2010 ◽  
Vol 66 (2) ◽  
pp. 270-280 ◽  
Author(s):  
Jeongho Kim ◽  
Kyung Hwan Kim ◽  
Jae Hyuk Lee ◽  
Hyotcherl Ihee
Keyword(s):  
Single Molecule ◽  
Reaction Dynamics ◽  
Liquid Solution ◽  
Substantial Improvement ◽  
Photon Flux ◽  
Solvation Dynamics ◽  
Structural Transitions ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray

In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100 ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of the X-ray free-electron laser (XFEL) will bring a substantial improvement in pulse duration, photon flux and coherence of X-ray pulses, making time-resolved X-ray diffraction even more powerful. This technical breakthrough is envisioned to revolutionize the field of reaction dynamics associated with time-resolved diffraction methods. Examples of candidates for the first femtosecond X-ray diffraction experiments using highly coherent sub-100 fs pulses generated from XFELs are presented in this paper. They include the chemical reactions of small molecules in the gas and solution phases, solvation dynamics and protein structural transitions. In these potential experiments, ultrafast reaction dynamics and motions of coherent rovibrational wave packets will be monitored in real time. In addition, high photon flux and coherence of XFEL-generated X-ray pulses give the prospect of single-molecule diffraction experiments.

scholarly journals Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

2018 ◽  
Author(s):  
Michael C. Thompson ◽  
Benjamin A. Barad ◽  
Alexander M. Wolff ◽  
Hyun Sun Cho ◽  
Friedrich Schotte ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Conformational Changes ◽  
Thermal Excitation ◽  
Relaxation Processes ◽  
Spectroscopic Techniques ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Solvent Molecules ◽  
Ray Scattering

AbstractCorrelated motions of proteins and their bound solvent molecules are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved methods hold promise for addressing this challenge but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature-jumps (T-jumps), through thermal excitation of the solvent, have been implemented to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform T-jump small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on a dynamic enzyme, cyclophilin A (CypA), demonstrating that these experiments are able to capture functional intramolecular protein dynamics. We show that CypA displays rich dynamics following a T-jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes in the enzyme. Two relaxation processes are resolved, which can be characterized by Arrhenius behavior. We also used mutations that have distinct functional effects to disentangle the relationship of the observed relaxation processes. A fast process is related to surface loop motions important for substrate specificity, whereas a slower process is related to motions in the core of the protein that are critical for catalytic turnover. These results demonstrate the power of time-resolved X-ray scattering experiments for characterizing protein and solvent dynamics on the μs-ms timescale. We expect the T-jump methodology presented here will be useful for understanding kinetic correlations between local conformational changes of proteins and their bound solvent molecules, which are poorly explained by the results of traditional, static measurements of molecular structure.

Continuous flow time-resolved small-angle x-ray scattering and X-ray absorption spectroscopy

2016 ◽  
Vol 44 (5) ◽  
pp. 537-546
Author(s):  
Guang Mo ◽  
Zhonghua Wu ◽  
Quan Cai ◽  
Zhihong Li ◽  
Xueqing Xing ◽  
...  
Keyword(s):  
Absorption Spectroscopy ◽  
Small Angle ◽  
Continuous Flow ◽  
Flow Time ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
X Ray Absorption ◽  
Ray Scattering

scholarly journals Structural Kinetics of MsbA Investigated by Stopped-Flow Time-Resolved Small-Angle X-Ray Scattering

Structure ◽  
2020 ◽  
Vol 28 (3) ◽  
pp. 348-354.e3 ◽  
Author(s):  
Inokentijs Josts ◽  
Yunyun Gao ◽  
Diana C.F. Monteiro ◽  
Stephan Niebling ◽  
Julius Nitsche ◽  
...  
Keyword(s):  
Small Angle ◽  
Flow Time ◽  
Stopped Flow ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

scholarly journals A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 585 ◽  
Author(s):  
Carl Caleman ◽  
Francisco Jares Junior ◽  
Oscar Grånäs ◽  
Andrew V. Martin
Keyword(s):  
Radiation Damage ◽  
Protein Dynamics ◽  
Conformational Changes ◽  
Bond Breaking ◽  
Time Resolved ◽  
Metal Centers ◽  
Disulfide Bonding ◽  
X Ray ◽  
Sample Structure ◽  
Effects Of Radiation

X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.

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