Structural information on proteins obtainable from small-angle X-ray scattering with heavy-atom labeling. Application to solubilized bacteriorhodopsin

1988 ◽  
Vol 21 (4) ◽  
pp. 355-362 ◽  
Author(s):  
M. Kataoka ◽  
M. Nakasako ◽  
F. Tokunaga
2008 ◽  
Vol 81 (4) ◽  
pp. 541-551 ◽  
Author(s):  
Hiroyuki Kishimoto ◽  
Yuya Shinohara ◽  
Yoshiyuki Amemiya ◽  
Katsuaki Inoue ◽  
Yoshio Suzuki ◽  
...  

Abstract We investigated the hierarchical structure of silica, especially agglomerate structure, in stretched rubber by time-resolved two-dimensional ultra-small-angle X-ray scattering (2D-USAXS). Time-resolved 2D-USAXS measurements give us the in-situ structural information up to 5 μm during sample deformation. The results are summarized as follows: at first, the agglomerate is turned so that the long axis of the agglomerate is parallel to the stretching direction, and the “weakly-bonded agglomerates” weakly bonding between agglomerates is broken down. Second, the distance between agglomerates increases with the small deformation of agglomerate. Finally, the “tightly-bonded agglomerates” strongly bonding between agglomerates start to deform. Existence of silane-coupling agents causes the differences in the manner of agglomerate deformation. These kinds of structural information will be a key to understanding the origin of rubber reinforcement by filler such as carbon black and silica.


2007 ◽  
Vol 994 ◽  
Author(s):  
Myriam Dunmont ◽  
Vanessa Coulet ◽  
Gabrielle Regula ◽  
Françoise Bley

AbstractThe techniques of small angle X-ray scattering and transmission electron microscopy are applied to characterize the size distribution of nanocavities in a (111) Si wafer multi-implanted with He+ in the Mev range energy. The comparison between both methods shows that they all give access to the same structural information but small angle X-ray scattering additionally offers the possibility to monitor the cavity size distribution during a thermal treatment. Moreover, providing that the collected data are of good quality, the former method also allows the knowledge of the porosity of the implanted Si wafer.


2014 ◽  
Vol 47 (2) ◽  
pp. 788-798 ◽  
Author(s):  
Ying Su ◽  
Christian Burger ◽  
Benjamin S. Hsiao ◽  
Benjamin Chu

Cellulose nanofibers, extracted from wood pulps using the (2,2,6,6-tetramethylpiperidine-1-yl)oxyl (TEMPO)-mediated oxidation method, are low-cost, sustainable and high-performance materials with potential usage in many applications. The structural information of these cellulose nanofibers in aqueous suspension was characterized by synchrotron small-angle X-ray scattering (SAXS). A simplified ribbon model having a near rectangular cross section was found to give the best fit to the SAXS results. The analytical expression of the ribbon model also led to a higher calculation efficiency compared with the more conventional parallelepiped model. The extracted structural information included the cross-section size and size distribution of the cellulose nanofibers. For example, for nanofibers prepared from the dried pulp of the maritime pine, the size-weighted averages of thickness and width were 3.2 and 12.7 nm, respectively, and the corresponding standard deviations were 2.2 and 5.5 nm, respectively. The scattering results of the size-weighted average of the nanofiber width are also consistent with those determined directly from transmission electron microscopy.


2018 ◽  
Vol 51 (6) ◽  
pp. 1633-1640 ◽  
Author(s):  
Guangfeng Liu ◽  
Yiwen Li ◽  
Hongjin Wu ◽  
Xibo Wu ◽  
Xianhui Xu ◽  
...  

The biological small-angle X-ray scattering (BioSAXS) beamline (BL19U2) at the Shanghai Synchrotron Radiation Facility, China, is dedicated exclusively to small-angle scattering experiments for biological macromolecules in solution. With recent advances in data-analysis algorithms and X-ray detectors, SAXS becomes an ideal complementary technique to other structural and biophysical methods, but it can also be applied alone to obtain important structural information. Owing to the increasing interest in solution scattering studies from the biological community, the workload on BL19U2 has steadily risen. A major upgrade of BL19U2 was performed to improve the beamline data quality, to enrich the possible sample environments and to provide a user-friendly interface. These upgrades involved the major components of BL19U2, including the optical system (slits, beamstop), the electronics, the control and acquisition software, and the sample environments, which resulted in improvements to the collected angular range in BL19U2. These upgrades have significantly broadened the scope of macromolecule size (from kilodaltons to gigadaltons) analysed at the beamline. The dedicated BL19U2 BioSAXS beamline now offers fully automated data-collection and remote-control possibilities. These developments have paved the way for high-throughput studies that generate significant quantities of structure information over a short period of time.


2018 ◽  
Vol 25 (5) ◽  
pp. 1379-1388 ◽  
Author(s):  
Mao Oide ◽  
Yuki Sekiguchi ◽  
Asahi Fukuda ◽  
Koji Okajima ◽  
Tomotaka Oroguchi ◽  
...  

In structure analyses of proteins in solution by using small-angle X-ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X-ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper-dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper-dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.


FEBS Letters ◽  
1980 ◽  
Vol 116 (1) ◽  
pp. 107-110 ◽  
Author(s):  
B.K. Vainshtein ◽  
L.A. Feigin ◽  
Yu.M. Lvov ◽  
R.I. Gvozdev ◽  
S.A. Marakushev ◽  
...  

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