Oriented Crystallization of Amides on Collagen with Modification of the Collagen Lattice

1963 ◽  
Vol 7 ◽  
pp. 252-255 ◽  
Author(s):  
E. H. Shaw
Keyword(s):  
Carbonyl Group ◽  
Collagen Fiber ◽  
Saturated Solution ◽  
Fiber Axis ◽  
Layer Line ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Collagen Layer ◽  
Rat Tail

AbstractRat tail tendons were fixed in 4% formaldehyde at 250 g tension, soaked in nearly saturated solution of the amides involved, and dried while still under tension. X-ray diffraction patterns, taken with rotation around the collagen fiber axis, showed well-defined layer lines of the amide and usually substantial expansion of the collagen equatorial spacing.The layer lines on collagen, in two cases on abnormal or polymorphic axes, are clustered around the number 4.86 ± 0.33 Å, or a figure twice this, implying the presence of a repeating hydro gen-bond accepting group such as the carbonyl group at this interval. The prominent collagen layer line at 9.4 Å is approximately double this interval.

Cross Linking of Collagen by Hydrophobe Bonds

1971 ◽  
Vol 15 ◽  
pp. 527-533
Author(s):  
Edwin H. Shaw
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Collagen Fiber ◽  
Fiber Axis ◽  
Cross Linking ◽  
Methyl Groups ◽  
X Ray Diffraction ◽  
X Ray ◽  
Collagen Lattice ◽  
Rat Tail

Previous work on modification of the collagen lattice, presented at these meetings, has served to confirm the Ramachandran proposal for the structure of this important protein, together with information on the lengths and tensile strengths of these bonds, including hydrogen bonds, hydrophobe bonds, and Vander Waals attractions. Rat tail tendons were suspended in 2 M aqueous solutions of dimethylsulfoxide, acetone, trimethylamineoxide and 1,4-cyclohexanedione, all of which showed evidence of ligation by expansion of the collagen lattice and refinement of the 100 spot in the x-ray diffraction pattern run by rotation on the collagen fiber axis. In the case of trimethylamineoxide and cyclohexanedione, oriented crystallization also occurred, with the long direction of the molecule in the plane perpendicular to the fiber axis of collagen. With the monofunctional ligands, the -C=0 group forms a hydrogen bond to the N-H group in the Ramachandran standard revised model, leaving the methyl groups to form the hydrophobe bond.

Binding of Aliphatic Dihydroxy Compounds to Collagen with X-ray Diffraction Evidence for the Vander Waals Bond

1970 ◽  
Vol 14 ◽  
pp. 268-274
Author(s):  
E. H. Shaw
Keyword(s):  
Collagen Fiber ◽  
Fiber Axis ◽  
X Ray Diffraction ◽  
Extended Form ◽  
Core Diameter ◽  
X Ray ◽  
The Core ◽  
Collagen Lattice ◽  
Tail Tendon ◽  
Rat Tail

AbstractPrevious work presented by the author at these conferences has been summarized by G.N. Ramachandran in “Treatise on Collagen I , 177-8”. Epitactic crystallization of amides and diols in the collagen lattice of formalinized rat tail tendon, with equatorial expansion of the collagen lattice, was used to visualize the core diameter of each coil in the triple spiral at 7A and the vertical repeat of the hydrogen-bonding unit at 5.2A. Expansion of the non - formalinized collagen lattice has been observed as high as 20.1A when 1, 4-trans-(bisamino-methyl) - cyclo-hexane was inserted between the hexagonal array of protein spirals in the collagen lattice, the length of the inserted molecule being 13A. With dimensions based on Fisher - Hirschfelder - Taylor atomic models, with maximum extension of the dihydroxy compounds, the a. parameter of the expanded collagen would be expected to increase from 16.5A in the case of glycol to 20.6A in the case of 1, 5 - pentanediol, but actually the parameter decreases from 18.3A in the case of glycol to 16.2A in the case of 1, 5 - pentanediol. The larger figure in the case of glycol is explained by its hydrogen bonded dimerization. 1,3 propanediol fits in to the collagen lattice as its extended form. In the case of the other compounds, the chains are folded and fit together with Vander Waals bonding, and produce progressively smaller parameters for the a axis in collagen. In this nonaqueous equilibrium the non - formalinized collagen core diameter averages 7.7A ±0.2 and the spacing of hydrogen bond contacts along the collagen fiber axis is 4.8 ±0.2A.

Rapid small-angle X-ray diffraction of a tonically contracting molluscan smooth muscle recorded with imaging plates

1989 ◽  
Vol 22 (1) ◽  
pp. 72-74 ◽  
Author(s):  
Y. Tajima ◽  
K. Okada ◽  
O. Yoshida ◽  
T. Seto ◽  
Y. Amemiya
Keyword(s):  
Small Angle ◽  
Structural Changes ◽  
High Sensitivity ◽  
Imaging Plate ◽  
Layer Line ◽  
X Ray Diffraction ◽  
Thin Filaments ◽  
X Ray ◽  
Area Detector ◽  
Diffraction Patterns

Small-angle X-ray diffraction patterns from the anterior byssus retractor muscles of Mytilus edulis contracting tonically in response to stimulation with acetylcholine were recorded in a 30 s exposure with synchrotron radiation and a high-sensitivity X-ray area detector called an imaging plate. The 190 Å layer line from the thin filaments increased in intensity with increase in tonic tension up to 6 x 104 kg m−2. Above this value, the layer-line intensity remained almost constant and comparable to that for a contracting skeletal muscle, indicating that the same structural changes of the thin filaments occur in both muscles.

scholarly journals X-ray diffraction patterns from chondroitin 4-sulphate, dermatan sulphate and heparan sulphate (Short Communication)

1973 ◽  
Vol 133 (3) ◽  
pp. 605-606.1 ◽  
Author(s):  
E. D. T. Atkins ◽  
T. C. Laurent
Keyword(s):  
Short Communication ◽  
Heparan Sulphate ◽  
Layer Line ◽  
X Ray Diffraction ◽  
Dermatan Sulphate ◽  
Acid Moiety ◽  
Sodium Salts ◽  
X Ray ◽  
Line Spacing ◽  
Diffraction Patterns

Ordered conformations from the sodium salts of chondroitin 4-sulphate, dermatan sulphate and heparan sulphate were observed by X-ray diffraction. Chondroitin 4-sulphate shows similar threefold helical character to that previously reported for chondroitin 6-sulphate and hyaluronates. Dermatan sulphate forms an eightfold helix with an axial rise per disaccharide of 0.93nm, which favours the l-iduronic acid moiety in the normal C1 chair form. The layer-line spacing and axial projection in heparan sulphate of 1.86nm favours a tetrasaccharide repeat with glycosidic linkages alternating β-d-(1→4) and α-d-(1→4).

scholarly journals Frog skeletal muscle thick filaments are three-stranded.

1983 ◽  
Vol 96 (6) ◽  
pp. 1797-1802 ◽  
Author(s):  
R W Kensler ◽  
M Stewart
Keyword(s):  
Skeletal Muscle ◽  
Optical Diffraction ◽  
Layer Line ◽  
X Ray Diffraction ◽  
Computer Image Analysis ◽  
X Ray ◽  
Thick Filaments ◽  
Diffraction Patterns ◽  
Meridional Reflection ◽  
Vertebrate Skeletal Muscle

A procedure has been developed for isolating and negatively staining vertebrate skeletal muscle thick filaments that preserves the arrangement of the myosin crossbridges. Electron micrographs of these filaments showed a clear periodicity associated with crossbridges with an axial repeat of 42.9 nm. Optical diffraction patterns of these images showed clear layer lines and were qualitatively similar to published x-ray diffraction patterns, except that the 1/14.3-nm meridional reflection was somewhat weaker. Computer image analysis of negatively stained images of these filaments has enabled the number of strands to be established unequivocally. Both reconstructed images from layer line data and analysis of the phases of the inner maxima of the first layer line are consistent only with a three-stranded structure and cannot be reconciled with either two- or four-stranded models.

Evaluation of Freezing Methods by Low Temperature X-Ray Diffraction

1977 ◽  
Vol 35 ◽  
pp. 330-333
Author(s):  
T. Gulik-Krzywicki ◽  
M.J. Costello
Keyword(s):  
Biological Materials ◽  
Molecular Organization ◽  
X Ray Diffraction ◽  
Glass Capillary ◽  
X Ray ◽  
Rate Dependent ◽  
Before And After ◽  
Freeze Etching ◽  
Diffraction Patterns ◽  
Set Up

Freeze-etching electron microscopy is currently one of the best methods for studying molecular organization of biological materials. Its application, however, is still limited by our imprecise knowledge about the perturbations of the original organization which may occur during quenching and fracturing of the samples and during the replication of fractured surfaces. Although it is well known that the preservation of the molecular organization of biological materials is critically dependent on the rate of freezing of the samples, little information is presently available concerning the nature and the extent of freezing-rate dependent perturbations of the original organizations. In order to obtain this information, we have developed a method based on the comparison of x-ray diffraction patterns of samples before and after freezing, prior to fracturing and replication.Our experimental set-up is shown in Fig. 1. The sample to be quenched is placed on its holder which is then mounted on a small metal holder (O) fixed on a glass capillary (p), whose position is controlled by a micromanipulator.

Examination of Rabbit Fc Crystals

1968 ◽  
Vol 26 ◽  
pp. 140-141
Author(s):  
J. P. Robinson ◽  
P. G. Lenhert
Keyword(s):  
Molecular Weight ◽  
Flat Plate ◽  
Phosphate Buffer ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutral Ph ◽  
Small Crystals ◽  
Carbon Coated ◽  
Diffraction Patterns

Crystallographic studies of rabbit Fc using X-ray diffraction patterns were recently reported. The unit cell constants were reported to be a = 69. 2 A°, b = 73. 1 A°, c = 60. 6 A°, B = 104° 30', space group P21, monoclinic, volume of asymmetric unit V = 148, 000 A°3. The molecular weight of the fragment was determined to be 55, 000 ± 2000 which is in agreement with earlier determinations by other methods.Fc crystals were formed in water or dilute phosphate buffer at neutral pH. The resulting crystal was a flat plate as previously described. Preparations of small crystals were negatively stained by mixing the suspension with equal volumes of 2% silicotungstate at neutral pH. A drop of the mixture was placed on a carbon coated grid and allowed to stand for a few minutes. The excess liquid was removed and the grid was immediately put in the microscope.

Control of the phase composition of advanced calcium phosphates using an x-ray diffractometer with a curved position-sensitive detector

2020 ◽  
Vol 86 (6) ◽  
pp. 29-35
Author(s):  
V. P. Sirotinkin ◽  
O. V. Baranov ◽  
A. Yu. Fedotov ◽  
S. M. Barinov
Keyword(s):  
Phase Composition ◽  
Calcium Phosphates ◽  
Position Sensitive Detector ◽  
Sensitive Detector ◽  
X Ray Diffraction ◽  
X Ray ◽  
Impurity Phases ◽  
Position Sensitive ◽  
Diffraction Peaks ◽  
Diffraction Patterns

The results of studying the phase composition of advanced calcium phosphates Ca10(PO4)6(OH)2, β-Ca3(PO4)2, α-Ca3(PO4)2, CaHPO4 · 2H2O, Ca8(HPO4)2(PO4)4 · 5H2O using an x-ray diffractometer with a curved position-sensitive detector are presented. Optimal experimental conditions (angular positions of the x-ray tube and detector, size of the slits, exposure time) were determined with allowance for possible formation of the impurity phases during synthesis. The construction features of diffractometers with a position-sensitive detector affecting the profile characteristics of x-ray diffraction peaks are considered. The composition for calibration of the diffractometer (a mixture of sodium acetate and yttrium oxide) was determined. Theoretical x-ray diffraction patterns for corresponding calcium phosphates are constructed on the basis of the literature data. These x-ray diffraction patterns were used to determine the phase composition of the advanced calcium phosphates. The features of advanced calcium phosphates, which should be taken into account during the phase analysis, are indicated. The powder of high-temperature form of tricalcium phosphate strongly adsorbs water from the environment. A strong texture is observed on the x-ray diffraction spectra of dicalcium phosphate dihydrate. A rather specific x-ray diffraction pattern of octacalcium phosphate pentahydrate revealed the only one strong peak at small angles. In all cases, significant deviations are observed for the recorded angular positions and relative intensity of the diffraction peaks. The results of the study of experimentally obtained mixtures of calcium phosphate are presented. It is shown that the graphic comparison of experimental x-ray diffraction spectra and pre-recorded spectra of the reference calcium phosphates and possible impurity phases is the most effective method. In this case, there is no need for calibration. When using this method, the total time for analysis of one sample is no more than 10 min.

Infrared spectroscopic study of the YPO4-YCrO4 system

1985 ◽  
Vol 50 (10) ◽  
pp. 2139-2145
Author(s):  
Alexander Muck ◽  
Eva Šantavá ◽  
Bohumil Hájek
Keyword(s):  
Spectroscopic Study ◽  
Infrared Spectra ◽  
Point Of View ◽  
Mixed Crystals ◽  
Crystal Symmetry ◽  
Infrared Spectroscopic Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Infrared Spectroscopic ◽  
Diffraction Patterns

The infrared spectra and powder X-ray diffraction patterns of polycrystalline YPO4-YCrO4 samples are studied from the point of view of their crystal symmetry. Mixed crystals of the D4h19 symmetry are formed over the region of 0-30 mol.% YPO4 in YCrO4. The Td → D2d → D2 or C2v(GS eff) correlation is appropriate for both PO43- and CrO43- anions.

scholarly journals Deep learning for visualization and novelty detection in large X-ray diffraction datasets

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Lars Banko ◽  
Phillip M. Maffettone ◽  
Dennis Naujoks ◽  
Daniel Olds ◽  
Alfred Ludwig
Keyword(s):  
Thin Film ◽  
Crystal Structure ◽  
Artificial Intelligence ◽  
Deep Learning ◽  
Novelty Detection ◽  
Structural Similarity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Post Hoc

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.

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