Biomedical subjects

Giovanni L Cascarano

Publications and source records attributed to Giovanni L Cascarano.

4 recordsLinked to original sources

PubMed2005

Phasing at resolution higher than the experimental resolution.

Limited experimental resolution is a unavoidable feature in macromolecular crystallography: it may hinder or make difficult the determination of the crystal structure. A novel procedure is presented which from an approximate electron-density map extrapolates the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit. Applications to a set of test structures show that the extrapolation can be successfully accomplished. As a consequence, the phase estimates of the observed reflections are subsequently improved and the interpretability of the corresponding electron-density map increases. The use of the extrapolated values for the non-measured reflections provides additional information for the map, which shows a resolution higher than the experimental resolution.

Algorithms↗

PubMed2003

Separated and aligned molecular fibres in solid state self-assemblies of cyclodextrin [2]rotaxanes.

The conformations of two [2]rotaxanes, each comprising alpha-cyclodextrin as the rotor, a stilbene as the axle and 2,4,6-trinitrophenyl substituents as the capping groups, have been examined in solution and in the solid state, using (1)H NMR spectroscopy and X-ray crystallography, respectively. In solution, introducing substituents onto the stilbene prevents the cyclodextrin from being localized over one end of the axle. Instead the cyclodextrin moves back and forth along the substituted stilbene. In the solid state, the axles of the rotaxanes form extended molecular fibres that are separated from each other and aligned along a single axis. The molecular fibres are strikingly similar to those formed by the axle component of one of the rotaxanes in the absence of the cyclodextrin, but in the latter case they are neither separated nor all aligned.

Crystallography, X-Ray↗

PubMed2003

Ab initio protein phasing at 1.4 A resolution: the new phasing approach of SIR2003-N.

New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.

Algorithms↗

PubMed2003

Ab initio protein phasing at 1.4 A resolution.

All the techniques today available for the ab initio crystal structure solution of proteins require that the atomicity condition is satisfied. Accordingly, diffraction data at resolution equal or better than 1.2 A are necessary. This condition reduces the role of the ab initio techniques in macromolecular crystallography. The computer program SIR2002 has been modified in such a way that it may succeed also with 1.4 A resolution diffraction data. The modifications concern all the modules of the program: the modified program also benefits by the efficiency of a figure of merit.

Collagen↗