Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 2174243

The locked rotation function.

L A Tong·M G Rossmann
View original source ↗Export metadata ↓

Abstract

It frequently occurs that a biological assembly in a crystallographic asymmetric unit has more than one noncrystallographic symmetry operator. For instance, a tetramer might have the point group 222 or a spherical virus will have the point group 532. A self-rotation function searches for the direction and angle of rotation of the individual noncrystallographic symmetry operations, while a cross-rotation function searches for the relationship of a structure in one unit cell with similar structures in another cell. The power of the rotation function can be greatly enhanced by searching for all noncrystallographic symmetry operators simultaneously. The procedure described previously [Rossmann, Ford, Watson & Banaszak (1972). J. Mol. Biol. 64, 237-249] has been generalized. The increased power of this 'locked' rotation function permits a good determination of the orientation of an icosahedral virus in the presence of less than 1% of the possible diffraction data to 7 A resolution. In addition, the peak-to-noise ratio is substantially improved.

Explore related subjects

Bacteriophage phi X 174Chemical PhenomenaChemistry, PhysicalCrystallizationMacromolecular SubstancesMengovirusParvoviridaePlant ProteinsSoftwareVirionVirusesX-Ray DiffractionJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

L A Tong, M G Rossmann. 1990-10-01. The locked rotation function.. https://doi.org/10.1107/s0108767390005530

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

KEEP EXPLORING

Related citations

PubMed1992

DNA cleavage photoinduced by new water-soluble zinc porphyrins linked to 9-methoxyellipticine.

Two hybrid molecules based on a water-soluble zinc porphyrin covalently linked to 9-methoxyellipticine, 1 and 2, were studied as photoactivable DNA cleavers. The behaviour and efficiency of these photosensitizers were compared with the constitutive units of the hybrid molecules: meso-tetrakis(4-N-methylpyridiniumyl)porphyrinato-zinc(II) tetraacetate (ZnTMPyP, 3) and 9-methoxy-N2methylellipticinium acetate (9-OMe-NME, 4). On irradiation at 436 nm, the efficiency of these hybrids is similar to that of ZnTMPyP and 50-fold greater than that of haematoporphyrin derivative (HPD). This photoinduced DNA cleavage is markedly reduced in the absence of oxygen and also depends on the DNA base pair to porphyrin ratio. It is inhibited by N-acetylhistidine and sodium azide, unaffected by mannitol and superoxide dismutase (SOD) and enhanced when changing H2O for D2O. The same scavenger effects are observed on irradiation at 514 nm. At 313 nm, the efficiency of hybrids 1 and 2 is intermediate between those of ZnTMPyP and 9-OMe-NME. In these conditions, a slight inhibitory effect of mannitol is observed, suggesting the participation of radicals probably derived from partial decomposition of the porphyrins. At these three wavelengths, singlet oxygen seems to be the main species responsible for DNA cleavage. In contrast with expectation, the great affinity of these molecules for DNA does not enhance their efficiency as DNA cleavers. This effect is discussed taking into account the long lifetime of singlet oxygen which may be generated far from the target. These molecules which are only photoactivable in the presence of DNA appear to be an efficient "molecular light switch".

Bacteriophage phi X 174↗
PubMed1992

Structure determination of the bacteriophage phiX174.

The structure of the single-stranded DNA phage phiX174 has been determined to 3.4 A resolution. The crystal space group was P2(1) with one icosahedral particle per asymmetric unit, giving 60-fold noncrystallographic redundancy. Oscillation diffraction photographs were collected using synchrotron radiation at various wavelengths. The particle orientations in the unit cell were determined with a rotation function. Because cowpea mosaic virus has a similar external envelope to phiX174, it was used as a search model to find the approximately positions of the phiX174 particles in the unit cell relative to the crystallographic symmetry axes. An initial phase set to 12 A resolution was then based on the cowpea mosaic virus atomic structure. These phases were improved by 20 cycles of real-space molecular replacement averaging. The phase information was gradually extended to 3.4 A resolution by molecular replacement electron density averaging. One reciprocal lattice point was used for each extension followed by four cycles of averaging. The unusual particle capsid, with its 12 pentameric spikes, required the careful determination of a precise molecular envelope. This was redetermined at regular intervals, as was the particle center. The resultant electron density map was readily interpreted in terms of the F, G and J polypeptides in the capsid. A difference electron density map between full and partially empty particles showed some ordered DNA structure.

Bacteriophage phi X 174↗
PubMed1992

Reactions of glutathione with the catechol, the ortho-quinone and the semi-quinone free radical of etoposide. Consequences for DNA inactivation.

Etoposide [4'-demethylepipodophyllotoxin-9-(4,6-O-ethylidene-beta- D-glucopyranoside)] can be metabolized to DNA-inactivating catechol, ortho-quinone and semi-quinone free radical derivatives which may contribute to its cytotoxicity. In this paper, we examined in vitro whether glutathione (GSH), which is known to react easily with quinoid compounds, could interact with the active etoposide intermediates and in this way influence the cytotoxicity of the parent compound. To this end, reactions of GSH with the etoposide intermediates were studied, using HPLC and ESR measurements, together with the effects of GSH on the biological inactivation of single-stranded (ss) and double-stranded (RF) phi X174 DNA by these compounds. From the results it could be determined that: (a) GSH does not react with the catechol and, as a consequence, has no effect on the reaction of this intermediate of etoposide with ss and RF phi X174 DNA; (b) GSH reacts with the ortho-quinone most likely by formation of a conjugate and by two-electron reduction to the catechol, resulting in a partial protection of ss and RF phi X174 DNA against inactivation by this species; and (c) GSH protects ss phi X174 DNA against inactivation by the semi-quinone free radical of etoposide probably by conjugation with this species.

Bacteriophage phi X 174↗