scholarly journals Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yunbeom Lee ◽  
Jong Goo Kim ◽  
Sang Jin Lee ◽  
Srinivasan Muniyappan ◽  
Tae Wu Kim ◽  
...  
Keyword(s):  
Structural Changes ◽  
Structure Refinement ◽  
Hydration Shell ◽  
Coherent Motion ◽  
Oligomeric State ◽  
Time Resolved ◽  
X Ray ◽  
Dependent Change ◽  
Refinement Method ◽  
Key Factor

AbstractUltrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

scholarly journals First steps towards time-resolved 'in-house' X-ray diffraction experiments

2014 ◽  
Vol 70 (a1) ◽  
pp. C775-C775 ◽  
Author(s):  
Radoslaw Kaminski ◽  
Jason Benedict ◽  
Elzbieta Trzop ◽  
Katarzyna Jarzembska ◽  
Bertrand Fournier ◽  
...  
Keyword(s):  
Excited State ◽  
Time Resolution ◽  
Structural Changes ◽  
Laser Pulses ◽  
High Repetition Rate ◽  
X Ray Diffraction ◽  
Laboratory Equipment ◽  
Time Resolved ◽  
X Ray ◽  
Ligand Charge Transfer

High-intensity X-ray sources, such as synchrotrons or X-ray free electron lasers, providing up to 100 ps time-resolution allow for studying very short-lived excited electronic states in molecular crystals. Some recent examples constitute investigations of Rh...Rh bond shortening,[1] or metal-to-ligand charge transfer processes in CuI complexes.[2] Nevertheless, in cases in which the lifetime of excited state species exceeds 10 μs it is now possible, due to the dramatic increase in the brightness of X-ray sources and the sensitivity of detectors, to use laboratory equipment to explore structural changes upon excitation. Consequently, in this contribution we present detailed technical description of the 'in-house' X-ray diffraction setup allowing for the laser-pump X-ray-probe experiments within the time-resolution at the order of 10 μs or larger. The experimental setup consists of a modified Bruker Mo-rotating-anode diffractometer, coupled with the high-frequency Nd:YAG laser (λ = 355 nm). The required synchronization of the laser pulses and the X-ray beam is realized via the optical chopper mounted across the beam-path. Chopper and laser capabilities enable high-repetition-rate experiments reaching up to 100 kHz. In addition, the laser shutter is being directly controlled though the original diffractometer software, allowing for collection of the data in a similar manner as done at the synchrotron (alternating light-ON & light-OFF frames). The laser beam itself is split into two allowing for improved uniform light delivery onto the crystal specimen. The designed setup was tested on the chosen set of crystals exhibiting rather long-lived excited state, such as, the Cu2Br2L2 (L = C5H4N-NMe2) complex, for which the determined lifetime is about 100 μs at 90 K. The results shall be presented. Research is funded by the National Science Foundation (CHE1213223). KNJ is supported by the Polish Ministry of Science and Higher Education through the "Mobility Plus" program.

scholarly journals Pressing the Limits of Rietveld Refinement

1988 ◽  
Vol 41 (2) ◽  
pp. 297 ◽  
Author(s):  
RA Young
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Site Occupancy ◽  
The Other ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Neutron Powder Diffraction Data ◽  
Refinement Method

Two examples are given, one with X-ray data and one with netltron data, of the determination of structural detail which appear to be at the edge of current possibility for the Rietveld structure-refinement method. In the first example, 2�2 wt% Sb substituted in CalO(P04)6F2 was located. X-ray powder diffraction data collected with special attention to intensity precision and scale constancy were used. The problem was solved through comparison of intra-sample site-occupancy ratios between Sb-doped and undoped samples. In the second example, high quality, high resolution neutron powder diffraction data were required. The problem was to distinguish between two subtly different models of kaolinite for which the R-weighted-pattern values differed only by 2 or 3 units in the third digit and, particularly, to understand the basis for the consistent programmatic choice of one of the models (PI) over the other. The answer was found in the calculated and 'observed' intensities for (h+ k)-odd reflections; although they were very small, less than 1% of the intensities of the main reflections, many of them were distinctly nonzero. Even though these reflections were not separately observable, because of overlap and small size, they nonetheless correlated with one model sufficiently better than the other to produce the consistent choice.

scholarly journals Time-resolved X-ray diffraction study of structural changes associated with the photocycle of bacteriorhodopsin.

1991 ◽  
Vol 10 (3) ◽  
pp. 521-526 ◽  
Author(s):  
M. H. Koch ◽  
N. A. Dencher ◽  
D. Oesterhelt ◽  
H. J. Plöhn ◽  
G. Rapp ◽  
...  
Keyword(s):  
Diffraction Study ◽  
Structural Changes ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray

scholarly journals A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

2012 ◽  
Vol 20 (1) ◽  
pp. 80-88 ◽  
Author(s):  
Tadashi Matsushita ◽  
Etsuo Arakawa ◽  
Wolfgang Voegeli ◽  
Yohko F. Yano
Keyword(s):  
Structural Changes ◽  
Vertical Direction ◽  
Sample Surface ◽  
Array Detector ◽  
Single Crystal Substrate ◽  
Time Resolved ◽  
Reflectivity Curve ◽  
X Ray ◽  
Monochromator Crystal ◽  
Crystal Substrate

An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energyE(wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed.

Following the structural changes during zinc-induced crystallization of charged membranes using time-resolved solution X-ray scattering

Soft Matter ◽  
2011 ◽  
Vol 7 (4) ◽  
pp. 1512-1523 ◽  
Author(s):  
Moshe Nadler ◽  
Ariel Steiner ◽  
Tom Dvir ◽  
Or Szekely ◽  
Pablo Szekely ◽  
...  
Keyword(s):  
Structural Changes ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Charged Membranes ◽  
Induced Crystallization ◽  
Ray Scattering

Dynamical Response of the Electric Double Layer Structure of the DEME-TFSI Ionic Liquid to Potential Changes Observed by Time-Resolved X-ray Reflectivity

2016 ◽  
Vol 230 (4) ◽  
Author(s):  
Wolfgang Voegeli ◽  
Etsuo Arakawa ◽  
Tadashi Matsushita ◽  
Osami Sakata ◽  
Yusuke Wakabayashi
Keyword(s):  
Ionic Liquid ◽  
Double Layer ◽  
Time Scale ◽  
Electric Double Layer ◽  
Structural Changes ◽  
Layer Structure ◽  
Dynamical Response ◽  
Relaxation Processes ◽  
Time Resolved ◽  
X Ray

AbstractThe interface between the N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide (DEME-TFSI) ionic liquid and a gold (111) surface was investigated with time-resolved X-ray reflectivity in order to clarify the dynamics of structural changes of the electric double layer after changing the electrode potential. In the experiment, the potential was switched repeatedly between +1.5 V and −1.5 V every 2 s or every 0.3 s, while measuring the specular X-ray reflectivity. When the potential was switched every 2 s, the time dependence of the reflectivity was different from that of the accumulated charge. This indicates structural relaxation processes that occur on a slower time scale than the acummulation of the charge at the electric double layer.When the potential was switched every 0.3 s, on the other hand, the reflectivity changes followed the evolution of the charge of the electric double layer within the experimental precision, indicating that slow relaxation processes without charge transfer do not contribute significantly to structural changes at this time scale.

scholarly journals Observation of Transient Structural Changes on Hydrogen Absorption Process of LaNi4.75Sn0.25 by Time Resolved X-Ray Diffraction

2015 ◽  
Vol 79 (3) ◽  
pp. 124-130 ◽  
Author(s):  
Akihiko Machida ◽  
Kensuke Higuchi ◽  
Yoshinori Katayama ◽  
Kouji Sakaki ◽  
Hyunjeong Kim ◽  
...  
Keyword(s):  
Hydrogen Absorption ◽  
Structural Changes ◽  
Absorption Process ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

2003 ◽  
Vol 36 (2) ◽  
pp. 147-227 ◽  
Author(s):  
Michel H. J. Koch ◽  
Patrice Vachette ◽  
Dmitri I. Svergun
Keyword(s):  
High Resolution ◽  
Neutron Scattering ◽  
Small Angle ◽  
Structure Factor ◽  
Structural Changes ◽  
Biological Macromolecules ◽  
Time Resolved ◽  
Scattering Intensity ◽  
X Ray ◽  
Angle Scattering

1. Introduction 1482. Basics of X-ray and neutron scattering 1492.1 Elastic scattering of electromagnetic radiation by a single electron 1492.2 Scattering by assemblies of electrons 1512.3 Anomalous scattering and long wavelengths 1532.4 Neutron scattering 1532.5 Transmission and attenuation 1553. Small-angle scattering from solutions 1563.1 Instrumentation 1563.2 The experimental scattering pattern 1573.3 Basic scattering functions 1593.4 Global structural parameters 1613.4.1 Monodisperse systems 1613.4.2 Polydisperse systems and mixtures 1633.5 Characteristic functions 1644. Modelling 1664.1 Spherical harmonics 1664.2 Shannon sampling 1694.3 Shape determination 1704.3.1 Modelling with few parameters: molecular envelopes 1714.3.2 Modelling with many parameters: bead models 1734.4 Modelling domain structure and missing parts of high-resolution models 1784.5 Computing scattering patterns from atomic models 1844.6 Rigid-body refinement 1875. Applications 1905.1 Contrast variation studies of ribosomes 1905.2 Structural changes and catalytic activity of the allosteric enzyme ATCase 1916. Interactions between molecules in solution 2036.1 Linearizing the problem for moderate interactions: the second virial coefficient 2046.2 Determination of the structure factor 2057. Time-resolved measurements 2118. Conclusions 2159. Acknowledgements 21610. References 216A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

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