scholarly journals History of protein crystallography in China

2007 ◽  
Vol 362 (1482) ◽  
pp. 1035-1042 ◽  
Author(s):  
Zihe Rao
Keyword(s):  
Protein Crystallography ◽  
Three Dimensional ◽  
Porcine Insulin ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Subsequent Determination ◽  
History Of

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

The biological crystallography without crystals

2017 ◽  
Vol 12 (1) ◽  
pp. 55-72 ◽  
Author(s):  
В.Ю. Лунин ◽  
V.Y. Lunin
Keyword(s):  
Three Dimensional ◽  
Scattering Data ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Biological Objects ◽  
Standard Problem ◽  
Problems And Solutions

The main obstacle to the determination of the atomic structure of a biological macromolecule by X-ray structural analysis is the need to obtain a crystal of the object under study. This need is due to the complexity of the experimental registration of scattering from a separate molecule. However, it is not always possible to get crystals of biological objects. The development of experimental techniques, in particular the emergence of the X-ray free-electron lasers, allows to approach the practical solution of the problem of registration of the scattering from an isolated particle and thereby to obtain information about the three-dimensional structure of non-crystalline biological objects by X-ray diffraction methods. Sampling of experimental scattering data makes the task of the structure determination of a single particle equivalent to the standard problem of biological crystallography, which allows to extend the biological crystallography techniques to the study of isolated biological particles (individual cells, organelles, molecular machines and, in the future, biological macromolecules). This article is devoted to the state of the art in this area, problems and solutions.

scholarly journals Determination of the Three-dimensional Structure of Dislocations by Synchrotron White X-ray Topography Combined with a Topo-tomographic Technique

Materia Japan ◽  
2007 ◽  
Vol 46 (12) ◽  
pp. 823-823
Author(s):  
Seiji Kawado ◽  
Toshinori Taishi ◽  
Satoshi Iida ◽  
Yoshifumi Suzuki ◽  
Yoshinori Chikaura ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Tomographic Technique

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

An X-ray Diffraction Method for the Determination of Temperatures in Coke Reactions

1984 ◽  
Vol 28 ◽  
pp. 383-388 ◽  
Author(s):  
Jack L. Johnson ◽  
Seymour Katz
Keyword(s):  
Diffraction Method ◽  
Temperature History ◽  
Maximum Temperature ◽  
Slag Formation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Potential Source ◽  
History Of ◽  
Extract Information

Information about the conditions and reactions in a foundry cupola is essential to understand the thermochemistry of a cupola and thus improve its efficiency. A potential source of such information is coke taken from inside an operating cupola. In the region of the cupola that extends from the melt zone to the taphole, coke is directly involved in important chemical processes such as combustion, gasification, slag formation, iron sulfurization, carbon pickup, and oxide reduction. Coke is also suspected of being involved in the transport of silicon to the liquid iron. Each of these processes produces characteristic physical and/or chemical changes in the coke, making it possible to extract information about the processes from an examination of coke pieces taken from within an operating cupola. A program to study such coke samples is in progress. To effectively interpret these data it is necessary to know the temperature history of the coke being examined, especially the maximum temperature attained by the coke piece in the cupola.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

Structure determination of a partially ordered layered silicate material with an NMR crystallography approach

2017 ◽  
Vol 73 (3) ◽  
pp. 184-190 ◽  
Author(s):  
Darren Henry Brouwer ◽  
Sylvian Cadars ◽  
Kathryn Hotke ◽  
Jared Van Huizen ◽  
Nicholas Van Huizen
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Three Dimensional ◽  
Layered Silicate ◽  
Silicate Layer ◽  
Silicate Material ◽  
X Ray Diffraction ◽  
X Ray ◽  
Nmr Crystallography

Structure determination of layered materials can present challenges for conventional diffraction methods due to the fact that such materials often lack full three-dimensional periodicity since adjacent layers may not stack in an orderly and regular fashion. In such cases, NMR crystallography strategies involving a combination of solid-state NMR spectroscopy, powder X-ray diffraction, and computational chemistry methods can often reveal structural details that cannot be acquired from diffraction alone. We present here the structure determination of a surfactant-templated layered silicate material that lacks full three-dimensional crystallinity using such an NMR crystallography approach. Through a combination of powder X-ray diffraction and advanced 29Si solid-state NMR spectroscopy, it is revealed that the structure of the silicate layer of this layered silicate material templated with cetyltrimethylammonium surfactant cations is isostructural with the silicate layer of a previously reported material referred to as ilerite, octosilicate, or RUB-18. High-field 1H NMR spectroscopy reveals differences between the materials in terms of the ordering of silanol groups on the surfaces of the layers, as well as the contents of the inter-layer space.

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