Solution structure refinements

Xia B, Tsui V, Case DA, Dyson J, Wright PE (2002) Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water, J Biomol NMR, 22 317-331... 

The MM-EPR approach has been used successfully in a number of recent studies [205,206 328 329]. The most novel is that of the solution structure refinement of a dicopper(II) compound of a cyclic octapeptide[205] which is only the second structure of a dicopper(II) compound of this type of biologically important ligand and the first of a metal compound of an artificial cyclic octapeptide. An important development in this area is a new method for the simulation of EPR spectra (SOPHE)[325,326], which allows the simulation of coupled EPR spectra of polynuclear species with more than two metal centers with any electron spin 0, based on sets of parameters similar to those discussed above. 

Importing through to structure solution, structure refinement, and visualization. No Fourier contour map generation... 

The pioneering applications of molecular mechanics to coordination compounds were isomeric and conformational analyses [1,2]. Applications involving the computation of conformer equilibria discussed in this chapter are studies of solution structure refinements [217,255, 256], racemate separations [293-295], and the evaluation of conformer interconversion pathways [237, 238, 296]. The importance of conformer equilibria in the areas of electron-transfer rates and redox potentials is discussed in Chapter 11, and many examples discussed in the other chapters of Part II indicate how important the prediction of conformational equilibria is in various fields of coordination chemistry. 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

Recent developments and prospects of these methods have been discussed in a chapter by Schneider et al. (2001). It was underlined that these methods are widely applied for the characterization of crystalline materials (phase identification, quantitative analysis, determination of structure imperfections, crystal structure determination and analysis of 3D microstructural properties). Phase identification was traditionally based on a comparison of observed data with interplanar spacings and relative intensities (d and T) listed for crystalline materials. More recent search-match procedures, based on digitized patterns, and Powder Diffraction File (International Centre for Diffraction Data, USA.) containing powder data for hundreds of thousands substances may result in a fast efficient qualitative analysis. The determination of the amounts of different phases present in a multi-component sample (quantitative analysis) is based on the so-called Rietveld method. Procedures for pattern indexing, structure solution and refinement of structure model are based on the same method. 

EDXRD is a very powerful technique, although limitations include the requirement for synchrotron radiation. This Hmits the number of experiments that can be performed, due to the high cost and low availabihty of synchrotron beam time. Because of the large voliune of the reaction vessel and the geometry of the instrument, the peak resolution of the energy dispersive data is also rather poor (AE/E). This means that although it is possible to accurately monitor the course of a reaction, using the data for ab initio structure solution or structure refinement is precluded. 

An advantage of this approach is that diffraction patterns, which are not suitable for kinematical procedures, can be used now. The disadvantage is that this approach needs a model and is therefore only suitable for structure refinement but not for structure solution. 

An absorption correction was applied which resulted in transmission factors ranging from 0.891 to 0.991. Reflections with 20 < 50 were used for structure solution and refinement. 

For minerals and inorganic samples, low temperature is almost useless to improve structure solution and only marginally relevant to improve the refinement, unless dealing with host-guest materials like zeolites. In facts, for harder materials ambient temperature is already quite comparable and sometimes lower than the Debye temperature. Therefore, resolution is seldom a limitation for structure refinement of minerals at ambient temperature. On the contrary, for macromolecules and especially for proteins, the low temperature significantly increases the number of... 

The procedure of crystallography is concerned with the determination of the overall shape of the molecule by a low resolution study. Then the structure is refined to produce a high resolution structure. How far this refinement procedure can proceed is not certain. It is important to discover to what extent the solution structure resembles the X-ray structure. This comparison can be done at two levels, that of the overall fold and that of the high resolution structure. At the highest resolution it is... 

Solution and Refinement of the Structure. Scattering factors for the hydrogen (14) and nonhydrogen (15) atoms are those used previously. Anomalous dispersion terms (16) were included in Fc for rhodium and phosphorus atoms. For the processing of the data and solution and refinement of the structure procedures and computer programs standard in this laboratory were used. (See, e.g., Ref. 17).) Trial absorption corrections calculated for a random selection of reflections gave transmission factors in the range 0.71 to 0.73 therefore a full absorption correction was considered to be unnecessary. 

---