FFT method to compute solution X-ray scattering curves.

F A Rey; C Dumas

doi:10.1016/0300-9084(84)90200-1

Home/Archive/PubMed

PubMed · 6733154

FFT method to compute solution X-ray scattering curves.

F A Rey·C Dumas

View original source ↗Export metadata ↓

Abstract

We present an efficient algorithm to compute X-ray intensities scattered by macromolecules in solution, from atomic positions found in crystal structures. The algorithm applies the Fast Fourier Transform to an electron density map created from the atomic coordinates and corrected for solvent density. We compute scattering curves for both allosteric forms of E. coli aspartate carbamoyltransferase. Calculated intensities are in agreement with the ones measured by Moody et al. which shows that the structures observed in solution in the presence or in the absence of a substrate analogue do correspond to those of two crystal forms analyzed by Lipscomb and collaborators .

Explore related subjects

Aspartate Carbamoyltransferase Fourier Analysis Mathematics Methods Protein Conformation Radiation, Ionizing Scattering, Radiation X-Rays Journal Article Research Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

F A Rey, C Dumas. 1984. FFT method to compute solution X-ray scattering curves.. https://doi.org/10.1016/0300-9084(84)90200-1

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed1995

Reactivation of the ATCase domain of the URA2 gene complex: a positive selection method for Ty insertions and chromosomal rearrangements in Saccharomyces cerevisiae.

Genetic rearrangements such as deletions or duplications of DNA sequences are rarely detected in the yeast Saccharomyces cerevisiae. We have developed a screening system using the URA2 gene coding for the bi-functional CPSase-ATCase (carbamyl phosphate synthetase - aspartate transcarbamylase) to select positively for these kinds of events. Nonsense mutations in the CPSase region cause a complete loss of the ATCase activity because of their strong polar effect. Thirty-seven ATCase+ revertants were isolated from a strain containing three nonsense mutations in the proximal CPSase region. Genetic and structural analysis of the URA2 locus in these strains allowed us to characterize two major classes of revertants. In the first, an entire copy of a Ty transposon was found to be inserted in the CPSase coding domain. This event, which represents a new form of Ty-mediated gene activation was further analysed by mapping the Ty integration site in 26 strains. In a second class of revertants, we observed chromosomal rearrangements and, in particular, duplication of the ATCase region and its integration in a new chromosomal environment in which this sequence becomes active.

Aspartate Carbamoyltransferase↗

PubMed1995

Evidence for substrate stabilization in regulation of the degradation of Bacillus subtilis aspartate transcarbamylase in vivo.

Aspartate transcarbamylase (ATCase) is rapidly degraded in Bacillus subtilis cells that are starved for a carbon or nitrogen source or a required amino acid. The hypothesis that ATCase degradation may be regulated in vivo by protection of the enzyme by substrate binding was tested by studies of a mutant ATCase (Arg99 to Ala, R99A), which binds substrate so poorly that it fails to support pyrimidine-independent growth in a pyrB strain, but still has 10% of normal activity when saturated with substrates. Unlike normal ATCase, R99A ATCase was degraded rapidly in exponentially growing cells. Degradation of the mutant enzyme was two-fold slower in a relA strain, as was degradation of the normal ATCase. The stability of purified R99A ATCase to denaturation by heat or guanidine hydrochloride was identical to that of wild-type ATCase, as was its circular dichroic spectrum. The wild-type and R99A ATCase were degraded identically in vitro by subtilisin, except that the mutant enzyme was much less effectively protected against cleavage by carbamyl phosphate, as expected. The carbamyl phosphate pool in glucose-limited B. subtilis cells was only one-third of the pool in exponentially growing cells. These results indicate that protection of ATCase by carbamyl phosphate binding could be one of the elements that regulate ATCase stability in vivo. However, carbamyl phosphate pools were the same in cells grown with ammonium ions and with a mixture of 20 common amino acids, conditions under which ATCase stability in vivo differs. Thus, other means of regulating ATCase degradation must also exist.

Aspartate Carbamoyltransferase↗

PubMed1995

Recovery of gene function by gene duplication in Saccharomyces cerevisiae.

A prototroph revertant (Rev9) selected from an ATCase- mutant of the URA2 gene containing three nonsense mutations was shown to contain two ATCase coding sequences. We cloned both ATCase coding areas to show that the duplicated locus (dl9) was the only functional one. Its size corresponded roughly to the second half of the URA2 wild-type gene. Sequence analysis of the 5' end of dl9 indicated that this duplicated sequence was inserted within the intergenic region close to the MRS3 gene and was transcribed from an unknown promoter divergently from the MRS3 gene. The event leading to the revertant strain Rev9 included a rearrangement that increased the size of chromosome X by about 60 kb. In agreement with such a rearrangement, recombination was undetectable in the vicinity of the locus dl9. Genetic mapping confirms that the MRS3 gene is 2 cM distal to the URA2 gene on the right arm of chromosome X.

Aspartate Carbamoyltransferase↗