scholarly journals Direct Evidence of Conformational Changes Associated with Voltage-Gating in a Voltage Sensor Protein by Time-Resolved X-Ray/Neutron Interferometry

2014 ◽  
Vol 106 (2) ◽  
pp. 743a
Author(s):  
J.K. Blasie ◽  
A. Tronin ◽  
J.W. Strzalka ◽  
I. Kuzmenko ◽  
D. Worcester ◽  
...  
Langmuir ◽  
2014 ◽  
Vol 30 (16) ◽  
pp. 4784-4796 ◽  
Author(s):  
Andrey Y. Tronin ◽  
C. Erik Nordgren ◽  
Joseph W. Strzalka ◽  
Ivan Kuzmenko ◽  
David L. Worcester ◽  
...  

2008 ◽  
Vol 72 (1) ◽  
pp. 201-204 ◽  
Author(s):  
A. Sumoondur ◽  
S. Shaw ◽  
I. Ahmed ◽  
L. G. Benning

AbstractIn this study, direct evidence for the formation of magnetite via a green rust intermediate is reported. The Fe(II) induced transformation of ferrihydrite, was quantified in situ and under O2-free conditions using synchrotron-based time-resolved energy dispersive X-ray diffraction. At pH 9 and Fe(II)/Fe(III) ratios of 0.5 and 1, rapid growth (6 min) of sulphate green rust and its subsequent transformation to magnetite was observed. Electron microscopy confirmed these results, showing the initial rapid formation of hexagonal sulphate green rust particles, followed by the corrosion of the green rust as magnetite growth occurred, indicating that the reaction proceeds via a dissolution-reprecipitation mechanism. At pH 7 and Fe(II)/Fe(III) ratio of 0.5, sulphate green rust was the stable phase, with no transformation to magnetite.


FEBS Letters ◽  
1994 ◽  
Vol 337 (2) ◽  
pp. 171-174 ◽  
Author(s):  
Hideo Arakawa ◽  
Takuji Urisaka ◽  
Hirotsugu Tsuruta ◽  
Yoshiyuki Amemiya ◽  
Hiroshi Kihara ◽  
...  

2018 ◽  
Vol 74 (8) ◽  
pp. 727-738
Author(s):  
Chenzheng Wang ◽  
Yuexia Lin ◽  
Devin Bougie ◽  
Richard E. Gillilan

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.


1985 ◽  
Vol 51 ◽  
Author(s):  
Kouichi Murakami ◽  
Hans C. Gerritsen ◽  
Hedser Van Brug ◽  
Fred Bijkerk ◽  
Frans W. Saris ◽  
...  

ABSTRACTWe report time-resolved X-ray absorption and extended X-ray absorption fine structure (EXAFS) measurements on amorphous silicon under nanosecond pulsed-laser irradiation. Each measurement was performed with one laser shot in the X-ray energy range from 90 to 300 eV. An X-ray absorption spectrum for induced liquid Si (liq*Si) was first observed above an energy density of 0.17 J/cm2. It differs significantly from the spectrum for amorphous Si and characteristically shows the disappearance of the Si-L(II,III) edge structure at around 100 eV. This phenomenon is interpreted in terms of a significant reduction in the 3s-like character of the unfilled part of the conduction band of liq*Si compared to that of amorphous Si. This is the first direct evidence that liq*Si has a metallic-like electronic structure. Timeresolved EXAFS results are also discussed briefly.


2018 ◽  
Author(s):  
Michael C. Thompson ◽  
Benjamin A. Barad ◽  
Alexander M. Wolff ◽  
Hyun Sun Cho ◽  
Friedrich Schotte ◽  
...  

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.


Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 585 ◽  
Author(s):  
Carl Caleman ◽  
Francisco Jares Junior ◽  
Oscar Grånäs ◽  
Andrew V. Martin

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.


2017 ◽  
Vol 24 (5) ◽  
pp. 1086-1091 ◽  
Author(s):  
Minoru Kubo ◽  
Eriko Nango ◽  
Kensuke Tono ◽  
Tetsunari Kimura ◽  
Shigeki Owada ◽  
...  

X-ray free-electron lasers (XFELs) have opened new opportunities for time-resolved X-ray crystallography. Here a nanosecond optical-pump XFEL-probe device developed for time-resolved serial femtosecond crystallography (TR-SFX) studies of photo-induced reactions in proteins at the SPring-8 Angstrom Compact free-electron LAser (SACLA) is reported. The optical-fiber-based system is a good choice for a quick setup in a limited beam time and allows pump illumination from two directions to achieve high excitation efficiency of protein microcrystals. Two types of injectors are used: one for extruding highly viscous samples such as lipidic cubic phase (LCP) and the other for pulsed liquid droplets. Under standard sample flow conditions from the viscous-sample injector, delay times from nanoseconds to tens of milliseconds are accessible, typical time scales required to study large protein conformational changes. A first demonstration of a TR-SFX experiment on bacteriorhodopsin in bicelle using a setup with a droplet-type injector is also presented.


Author(s):  
Sebastian Westenhoff ◽  
Elena Nazarenko ◽  
Erik Malmerberg ◽  
Jan Davidsson ◽  
Gergely Katona ◽  
...  

Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.


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