scholarly journals Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion

2004 ◽  
Vol 32 (5) ◽  
pp. 1638-1646 ◽  
Author(s):  
N. Carrasco
2008 ◽  
Vol 105 (46) ◽  
pp. 17682-17687 ◽  
Author(s):  
Jessica Bockhorn ◽  
Bharvi Balar ◽  
Dongming He ◽  
Eden Seitomer ◽  
Paul R. Copeland ◽  
...  

Selenomethionine (SeMet) is a potentially toxic amino acid, and yet it is a valuable tool in the preparation of labeled proteins for multiwavelength anomalous dispersion or single-wavelength anomalous dispersion phasing in X-ray crystallography. The mechanism by which high levels of SeMet exhibits its toxic effects in eukaryotic cells is not fully understood. Attempts to use Saccharomyces cerevisiae for the preparation of fully substituted SeMet proteins for X-ray crystallography have been limited. A screen of the viable S. cerevisiae haploid null allele strain collection for resistance to SeMet was performed. Deletion of the CYS3 gene encoding cystathionine gamma-lyase resulted in the highest resistance to SeMet. In addition, deletion of SSN2 resulted in both increased resistance to SeMet as well as reduced levels of Cys3p. A methionine auxotrophic strain lacking CYS3 was able to grow in media with SeMet as the only source of Met, achieving essentially 100% occupancy in total proteins. The CYS3 deletion strain provides advantages for an easy and cost-effective method to prepare SeMet-substituted protein in yeast and perhaps other eukaryotic systems.


1989 ◽  
Vol 111 (13) ◽  
pp. 4985-4986 ◽  
Author(s):  
Miguel Garcia-Garibay ◽  
John R. Scheffer ◽  
James Trotter ◽  
Fred Wireko

Author(s):  
Sosale Chandrasekhar

The origins of the molecular-chiral homogeneity that is the very basis of life remain a tantalizing mystery. Molecular chirality itself is manifest in its interaction with radiation, particularly as optical activity, although an intriguing alternative technique based in X-ray crystallography is being increasingly employed. Thus, X-ray diffraction with anomalous dispersion is currently believed to lead to the absolute configuration of a stereogenic center, the ultimate goal of structural chemistry. However, despite its apparently unerring consistency, the fundamental basis of the anomalous dispersion technique is itself enigmatic. This is because it is unclear how the technique not only distinguishes two enantiomeric lattices but also assigns the absolute configuration: all, apparently, in the absence of an external chiral influence! Indeed, as argued previously, it is highly likely that the technique succeeds because the X-rays employed are circularly polarized, itself a possible consequence of parity violation. All the same, the question of how the absolute configuration is assigned remains, as the chiral sense of the putative circular polarization of the X-rays is unknown. It is argued herein that the anomalous dispersion method is essentially based in the chirality of X-rays that must have entered–although unbeknownst as such–into the calculations leading to the absolute configuration. In fact, the enigma surrounding the anomalous dispersion method derives from uncertainties concerning the theory of X-ray diffraction itself, thus leading to the apparently inescapable conclusion that both methods are essentially empirical — but without detracting from the brilliance of the scientific achievements that led to these methods.          


Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.


Author(s):  
S. Cusack ◽  
J.-C. Jésior

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).


Author(s):  
Robert A. Grant ◽  
Laura L. Degn ◽  
Wah Chiu ◽  
John Robinson

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.


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