scholarly journals Experimental phasing of MicroED data using radiation damage

2019 ◽  
Author(s):  
Michael W. Martynowycz ◽  
Johan Hattne ◽  
Tamir Gonen
Keyword(s):  
Radiation Damage ◽  
Structural Changes ◽  
Low Dose ◽  
Heavy Atom ◽  
Reciprocal Space ◽  
Difference Map ◽  
Continuous Rotation ◽  
Experimental Phasing ◽  
First Pass

AbstractWe present an example of an experimentally phased structure using only MicroED. The structure of a seven-residue peptide is determined starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a “low-dose dataset”. The data from the second pass were similarly merged to form a “damaged dataset.” Differences between these two datasets were used to calculate a Patterson difference map and to identify a single heavy atom site, from which initial phases were generated. The structure was then completed by iterative cycles of modeling and refinement.

Low-dose X-ray radiation induces structural alterations in proteins

2014 ◽  
Vol 70 (10) ◽  
pp. 2675-2685 ◽  
Author(s):  
Valentin Borshchevskiy ◽  
Ekaterina Round ◽  
Ivan Erofeev ◽  
Martin Weik ◽  
Andrii Ishchenko ◽  
...  
Keyword(s):  
Radiation Damage ◽  
Active Site ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Low Dose ◽  
Protein Structures ◽  
Data Set ◽  
Severe Problem ◽  
Structural Alterations ◽  
X Ray

X-ray-radiation-induced alterations to protein structures are still a severe problem in macromolecular crystallography. One way to avoid the influence of radiation damage is to reduce the X-ray dose absorbed by the crystal during data collection. However, here it is demonstrated using the example of the membrane protein bacteriorhodopsin (bR) that even a low dose of less than 0.06 MGy may induce structural alterations in proteins. This dose is about 500 times smaller than the experimental dose limit which should ideally not be exceeded per data set (i.e.30 MGy) and 20 times smaller than previously detected specific radiation damage at the bR active site. To date, it is the lowest dose at which radiation modification of a protein structure has been described. Complementary use was made of high-resolution X-ray crystallography and online microspectrophotometry to quantitatively study low-dose X-ray-induced changes. It is shown that structural changes of the protein correlate with the spectroscopically observed formation of the so-called bR orange species. Evidence is provided for structural modifications taking place at the protein active site that should be taken into account in crystallographic studies which aim to elucidate the molecular mechanisms of bR function.

Embedding Procedure for Water Swollen Samples

1970 ◽  
Vol 28 ◽  
pp. 504-505
Author(s):  
Ann M. Thomas ◽  
Virginia Shemeley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Ion Exchange ◽  
Structural Changes ◽  
Cross Linking ◽  
Ion Exchange Resins ◽  
Transmission Electron ◽  
First Pass ◽  
Exchange Resins

Those samples which swell rapidly when exposed to water are, at best, difficult to section for transmission electron microscopy. Some materials literally burst out of the embedding block with the first pass by the knife, and even the most rapid cutting cycle produces sections of limited value. Many ion exchange resins swell in water; some undergo irreversible structural changes when dried. We developed our embedding procedure to handle this type of sample, but it should be applicable to many materials that present similar sectioning difficulties.The purpose of our embedding procedure is to build up a cross-linking network throughout the sample, while it is in a water swollen state. Our procedure was suggested to us by the work of Rosenberg, where he mentioned the formation of a tridimensional structure by the polymerization of the GMA biproduct, triglycol dimethacrylate.

Anisotropic radiation damage of potassium tetracyano platinate (KCP)

1978 ◽  
Vol 36 (1) ◽  
pp. 392-393
Author(s):  
N. Uyeda ◽  
E. J. Kirkland ◽  
B. M. Siegel
Keyword(s):  
Electron Diffraction ◽  
Radiation Damage ◽  
Structural Changes ◽  
High Resolution Electron Microscopy ◽  
Radiation Sensitivity ◽  
Resolution Electron ◽  
Damage Process ◽  
Diffraction Patterns ◽  
Fading Rate

The direct observation of structural change by high resolution electron microscopy will be essential for the better understanding of the damage process and its mechanism. However, this approach still involves some difficulty in quantitative interpretation mostly being due to the quality of obtained images. Electron diffraction, using crystalline specimens, has been the method most frequently applied to obtain a comparison of radiation sensitivity of various materials on the quantitative base. If a series of single crystal patterns are obtained the fading rate of reflections during the damage process give good comparative measures. The electron diffraction patterns also render useful information concerning the structural changes in the crystal. In the present work, the radiation damage of potassium tetracyano-platinate was dealt with on the basis two dimensional observation of fading rates of diffraction spots. KCP is known as an ionic crystal which possesses “one dimensional” electronic properties and it would be of great interest to know if radiation damage proceeds in a strongly asymmetric manner.

Factors in Photographic Emulsions for Low Dose Electron Crystallography

1980 ◽  
Vol 38 ◽  
pp. 230-231
Author(s):  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
Radiation Damage ◽  
Low Dose ◽  
Damage Effect ◽  
Photographic Emulsion ◽  
Electron Crystallography ◽  
Electron Microscopic ◽  
X Ray ◽  
Signal Contrast ◽  
Diffraction Patterns ◽  
Photographic Emulsions

With the advances in preparing biological materials in a thin and highly ordered form, and in maintaining them hydrated under vacuum, electron crystallography has become an important tool for biological structure investigation at high resolution (1,2). However, the electron radiation damage would limit the capability of recording reflections with low intensities in an electron diffraction pattern. It has been demonstrated that the use of a low temperature stage can reduce the radiation damage effect and that one can expose the specimen with a higher dose in order to increase the signal contrast (3). A further improvement can be made by selecting a proper photographic emulsion. The primary factors in evaluating the suitability of photographic emulsion for recording low dose diffraction patterns are speed, fog level, electron response at low electron exposure, linearity, and usable range of exposure. We have compared these factors with three photographic emulsions including Kodak electron microscopic plate (EMP), Industrex AA x-ray film (AA x-ray) and Kodak nuclear track film (NTB3).

Low-dose aspirin prevents age-related endothelial dysfunction in a mouse model of physiological aging

2008 ◽  
Vol 294 (4) ◽  
pp. H1562-H1570 ◽  
Author(s):  
Hélène Bulckaen ◽  
Gaétan Prévost ◽  
Eric Boulanger ◽  
Géraldine Robitaille ◽  
Valérie Roquet ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Endothelial Dysfunction ◽  
Protective Effect ◽  
Structural Changes ◽  
Low Dose ◽  
Age Groups ◽  
Dose Aspirin ◽  
Age Related ◽  
Low Dose Aspirin ◽  
Old Mice

The age-related impairment of endothelium-dependent vasodilatation contributes to increased cardiovascular risk in the elderly. For primary and secondary prevention, aspirin can reduce the incidence of cardiovascular events in this patient population. The present work evaluated the effect of low-dose aspirin on age-related endothelial dysfunction in C57B/J6 aging mice and investigated its protective antioxidative effect. Age-related endothelial dysfunction was assessed by the response to acetylcholine of phenylephrine-induced precontracted aortic segments isolated from 12-, 36-, 60-, and 84-wk-old mice. The effect of low-dose aspirin was examined in mice presenting a decrease in endothelial-dependent relaxation (EDR). The effects of age and aspirin treatment on structural changes were determined in mouse aortic sections. The effect of aspirin on the oxidative stress markers malondialdehyde and 8-hydroxy-2′-deoxyguanosine (8-OhdG) was also quantified. Compared with that of 12-wk-old mice, the EDR was significantly reduced in 60- and 84-wk-old mice ( P < 0.05); 68-wk-old mice treated with aspirin displayed a higher EDR compared with control mice of the same age (83.9 ± 4 vs. 66.3 ± 5%; P < 0.05). Aspirin treatment decreased 8-OHdG levels ( P < 0.05), but no significant effect on intima/media thickness ratio was observed. The protective effect of aspirin was not observed when treatment was initiated in older mice (96 wk of age). It was found that low-dose aspirin is able to prevent age-related endothelial dysfunction in aging mice. However, the absence of this effect in the older age groups demonstrates that treatment should be initiated early on. The underlying mechanism may involve the protective effect of aspirin against oxidative stress.

scholarly journals The magic triangle goes MAD: experimental phasing with a bromine derivative

2010 ◽  
Vol 66 (4) ◽  
pp. 374-380 ◽  
Author(s):  
Tobias Beck ◽  
Tim Gruene ◽  
George M. Sheldrick
Keyword(s):  
Functional Groups ◽  
Heavy Atom ◽  
Anomalous Dispersion ◽  
Proteinase K ◽  
Nonspecific Binding ◽  
Heavy Atoms ◽  
Carboxylate Groups ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Bromine Derivative

Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteinsviahydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br Kedge was successfully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.

Derelaxation of Amorphous Silicon by Ion Implantation: Optical Characterization

1991 ◽  
Vol 235 ◽  
Author(s):  
R. Reitano ◽  
M. G. Grimaldi ◽  
P. Baeri ◽  
E. Bellandi ◽  
A. Borghesi ◽  
...  
Keyword(s):  
Amorphous Silicon ◽  
Short Range ◽  
Short Range Order ◽  
Structural Changes ◽  
Low Dose ◽  
Near Infrared ◽  
Ion Irradiation ◽  
Infrared Region ◽  
Range Order ◽  
Density Of State

ABSTRACTThe transition between relaxed and unrelaxed amorphous silicon can be obtained by thermal treatment of the unrelaxed amorphous or by low dose ion irradiation of the relaxed material. In both cases a variation in the short range order has been invoked to explain the behavior of the structural changes probed by various techniques. In this work we study the influence of such changes on the optical properties of a-Si in the region of the transition between the relaxed and the unrelaxed states. We show that a progressive variation of the optical constant in the visible-near infrared region upon derelaxation occurs. Therefore, significant modifications of the electron density of state in the region above the optical gap are associated with the changes in the short range order probed by Raman spectroscopy.

scholarly journals Exploiting subtle structural differences in heavy-atom derivatives for experimental phasing

2014 ◽  
Vol 70 (7) ◽  
pp. 1873-1883 ◽  
Author(s):  
Jimin Wang ◽  
Yue Li ◽  
Yorgo Modis
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Data Sets ◽  
Diarrhea Virus ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Structural Differences ◽  
Structure Determinations ◽  
Weak Derivatives ◽  
Viral Diarrhea Virus

Structure determination using the single isomorphous replacement (SIR) or single-wavelength anomalous diffraction (SAD) methods with weak derivatives remains very challenging. In a recent structure determination of glycoprotein E2 from bovine viral diarrhea virus, three isomorphous uranium-derivative data sets were merged to obtain partially interpretable initial experimental maps. Small differences between them were then exploited by treating them as three independent SAD data sets plus three circular pairwise SIR data sets to improve the experimental maps. Here, how such subtle structural differences were exploited for experimental phasing is described in detail. The basis for why this approach works is also provided: the effective resolution of isomorphous signals between highly isomorphous derivatives is often much higher than the effective resolution of the anomalous signals of individual derivative data sets. Hence, the new phasing approaches outlined here will be generally applicable to structure determinations involving weak derivatives.

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