Protein crystal dynamics studied by time-resolved analysis of X-ray diffuse scattering

Nature ◽  
1989 ◽  
Vol 338 (6217) ◽  
pp. 665-666 ◽  
Author(s):  
G. U. Nienhaus ◽  
J. Heinzl ◽  
E. Huenges ◽  
F. Parak
2009 ◽  
Vol 42 (3) ◽  
pp. 392-400 ◽  
Author(s):  
I. B. Ramsteiner ◽  
A. Schöps ◽  
H. Reichert ◽  
H. Dosch ◽  
V. Honkimäki ◽  
...  

Diffuse X-ray scattering has been an important tool for understanding the atomic structure of binary systems for more than 50 years. The majority of studies have used laboratory-based sources providing 8 keV photons or synchrotron radiation with similar energies. Diffuse scattering is weak, with the scattering volume determined by the X-ray absorption length. In the case of 8 keV photons, this is not significantly different from the typical extinction length for Bragg scattering. If, however, one goes to energies of the order of 100 keV the scattering volume for the diffuse scattering increases up to three orders of magnitude while the extinction length increases by only one order of magnitude. This leads to a gain of two orders of magnitude in the relative intensity of the diffuse scattering compared with the Bragg peaks. This gain, combined with the possibility of recording the intensity from an entire plane in reciprocal space using a two-dimensional X-ray detector, permits time-resolved diffuse scattering studies in many systems. On the other hand, diffraction features that are usually neglected, such as multiple scattering, come into play. Four types of multiple scattering phenomena are discussed, and the manner in which they appear in high-energy diffraction experiments is considered.


2020 ◽  
Vol 118 (3) ◽  
pp. 487a
Author(s):  
Yuji C. Sasaki ◽  
Masahiro Kuramochi ◽  
Kazuhiro Mio ◽  
Hiroshi Sekiguchi ◽  
Ayana Sato-Tomita ◽  
...  
Keyword(s):  

1990 ◽  
Vol 23 (6) ◽  
pp. 509-514 ◽  
Author(s):  
H. Iwasaki ◽  
Y. Matsuo ◽  
K. Ohshima ◽  
S. Hashimoto

Through the high sensitivity of an area-detector Imaging Plate and the high brilliance of synchrotron radiation, changes in two-dimensional intensity distribution of X-ray diffuse scattering from an AgZn single-crystal having the B2-type structure were observed successively during the structural transition from the β′ phase to the ζ phase. It has been shown in a series of patterns taken at a time interval of 600 s that a diffuse intensity sheet extending parallel to the (111) relplane gradually loses its intensity without a precursive modulation while weak diffraction spots from the nuclei of the ζ phase appear superimposed on the sheet with a definite positional relation to the diffraction spots from the β′ phase. Promising aspects as well as the limits of the method applied to time-resolved measurements of structural changes are discussed.


2021 ◽  
Vol 77 (3) ◽  
pp. 173-185
Author(s):  
John R. Helliwell

The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure–function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.


2014 ◽  
Vol 70 (a1) ◽  
pp. C1748-C1748
Author(s):  
Marc Messerschmidt ◽  
Leonard Chavas ◽  
Sunil Ananthaneni ◽  
Hamidreza Dadgostar ◽  
Heinz Graafsma ◽  
...  

The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges


2020 ◽  
Vol 118 (3) ◽  
pp. 137a
Author(s):  
Yige Dong ◽  
Masahiro Kuramochi ◽  
Chiaki Takanashi ◽  
Kazuhiro Mio ◽  
Motomichi Doi ◽  
...  

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 172-181 ◽  
Author(s):  
Michael E. Wall

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.


2015 ◽  
Vol 177 ◽  
pp. 429-441 ◽  
Author(s):  
John R. Helliwell ◽  
Alice Brink ◽  
Surasak Kaenket ◽  
Victoria Laurina Starkey ◽  
Simon W. M. Tanley

Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a ‘crystal lattice free’ single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both ‘fresh’ and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as ‘NMR crystallography’ conclude the article.


Synchrotron X-radiation (SR) is intense, polychromatic and collimated. It is widely exploited, in macromolecular crystallography, particularly using a monochromatized short wavelength beam. The spectral curve of SR, however, ideally lends itself to use of Laue geometry, i. e. the original diffraction experimental arrangement based on a stationary crystal and a polychromatic X-ray beam. Rapid exposure times and time-resolved crystallography studies, e. g. of enzymes, are now possible. Historical objections to the use of Laue diffraction data, particularly the multiplicity distribution, have been found not to be as limiting as once thought. The credentials of the Laue method have been established through a variety of Laue crystal structure analyses, involving photographic film as detector. Recently a three-dimensional arrangement of films, known as a toast-rack, has been used to alleviate problems with spatially overlapping spots. This paper provides a review of these results and then reports several developments. In particular, one of the first Laue analyses using an image plate as detector, namely of a cobalt substituted concanavalin A crystal, is discussed. Recent experimental developments, also at the Daresbury synchrotron, are then described. First, a large toast-rack has been used to record Laue data from a protein crystal. Secondly, a transmission X-ray mirror has been constructed from thin mylar (1.5 μm) and used to provide a λ max filter instead of using aluminium foils. Thirdly, since the Laue method suffers from poor sampling of the low resolution data, a new method (known as LOT) has been introduced.


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