Biomedical subjects
Publications and source records attributed to Alexandre Urzhumtsev.
The connectivity-based phasing method has been applied independently to three neutron diffraction data sets obtained from the same crystal of tRNA(Asp)-aspartyl-tRNA synthetase complex but at different concentrations of D(2)O/H(2)O, thus masking different components of the crystal. The obtained low-resolution images correlate perfectly with the solvent level.
A simultaneous analysis of several rotation functions allows identification of the model orientation in situations when a single rotation function fails to find the answer. Multiple rotation functions can be obtained by the usual modification of the search model or by variation of the resolution at which the function is calculated. A specially suitable case is a search with several NMR models. When the orientation of the model becomes available, its position can be found much more easily; low-resolution data can help in such a search. Many difficult cases of molecular replacement can be solved by new tools discussed in the article.
A bulk-solvent correction is regularly used for macromolecular refinement. The flat model of the bulk solvent is considered to be the most reliable. It is shown that the standard procedure does not always result in the optimal values of the bulk-solvent correction parameters. A method to obtain the best values for parameters k(sol) and B(sol) of the flat-solvent model is discussed. The values of correctly determined parameters for crystallographic structures deposited in the Protein Data Bank are clustered around k(sol) = 0.35 e A(-3) and B(sol) = 46 A(2), which have a reasonable physical meaning. Such a distribution allows the use of these mean values of solvent parameters for many practical applications when refined parameters cannot be obtained, especially when an atomic model in the unit cell is not yet known.
In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.
Low-resolution reflections (approximately 15 A and lower) are very useful for the translation search in molecular replacement because they are less sensitive to model errors compared with the traditionally used reflections of resolution 4-10 A. At low resolution, however, the contribution from the bulk solvent is quite significant and corresponding structure factors calculated from a macromolecular model cannot be compared with experimental values if this contribution is neglected. The proposed method provides a way of fast translation searches where low-resolution reflections are taken into account. Test calculations using several experimental data sets show a dramatic improvement in the signal after the bulk-solvent correction and low-resolution reflections were included in the calculation; this improvement allowed unambiguous identification of the solution.