<i>STRATEGY</i>: a program to optimize the starting spindle angle and scan range for X-ray data collection

Ravelli, Raimond B. G.; Sweet, Robert M.; Skinner, John M.; Duisenberg, A. J. M.; Kroon, J.

doi:10.1107/s0021889897003543

Cited by 67 publications

(52 citation statements)

References 4 publications

(4 reference statements)

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“…The conformational changes observed on complexation are likely not induced by the crystal packing because they are identical in the two different crystal forms. Furthermore, we have recorded 15 N heteronuclear sequential quantum correlation spectra of CSPMbraA6 alone or in complex with BrC12OH (13). The superimposition of the spectra of the apo and complexed protein spectra has revealed Ͼ50% changes in the peak displacements, indicating that the extensive conformational changes observed in the crystal also occur in solution (13).…”

Section: Discussionmentioning

confidence: 99%

“…A single wavelength anomalous diffraction dataset was collected on ID-29 at the European Synchrotron Radiation Facility (Grenoble) at the Br-K edge ( ϭ 0.91965 Å, maximum f Љ; Table 1). Data were collected from a single crystal in an arbitrary setting by using a ADSC (Poway, CA) Quantum 4 detector after optimizing the oscillation range by using STRATEGY (15). All data were processed and reduced by using DENZO (16) and the CCP4 program suite (17).…”

Section: Methodsmentioning

confidence: 99%

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Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding

Campanacci

Lartigue

Hållberg

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

144

152

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Chemosensory proteins (CSPs) have been proposed to transport hydrophobic chemicals from air to olfactory or taste receptors. They have been isolated from several sensory organs of a wide range of insect species. The x-ray structure of CSPMbraA6, a 112-aa antennal protein from the moth Mamestra brassicae (Mbra), was shown to exhibit a novel type of ␣-helical fold. We have performed a structural and binding study of CSPMbraA6 to get some insights into its possible molecular function. Tryptophan fluorescence quenching demonstrates the ability of CSPMbraA6 to bind several types of semio-chemicals or surrogate ligands with M Kd. Its crystal structure in complex with one of these compounds, 12-bromo-dodecanol, reveals extensive conformational changes on binding, resulting in the formation of a large cavity filled by three ligand molecules. Furthermore, binding cooperativity was demonstrated for some ligands, suggesting a stepwise binding. The peculiar rearrangement of CSPMbraA6 conformation and the cooperativity phenomenon might trigger the recognition of chemicals by receptors and induce subsequent signal transduction.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding

Campanacci

Lartigue

Hållberg

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

144

152

View full text Add to dashboard Cite

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“…There are no good excuses for collecting data that are incomplete. There exist many programs which, following autoindexing of the ®rst image, will predict the optimum 9 range to collect and the 9 value at which to start data collection so that the completeness is maximized using the minimum beamtime (Leslie, 1993;Kabsch, 1993;Noble, 1996;Otwinowski & Minor, 1997;Ravelli et al, 1997). Table 1 shows the contrast between the 9 ranges for optimized data collection (Dauter, 1999) and that required in the worst-case scenario (crystal aligned with the lowest symmetry axis parallel to the beam and starting the 9 rotation from the worst possible place).…”

Section: Poor Diffraction And/or Incomplete Anomalous Datamentioning

confidence: 99%

Heavy-atom derivatization

Garman

Murray

2003

Acta Crystallogr D Biol Cryst

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Most of the standard methods of solving macromolecular structures involve producing a protein crystal that is derivatized by an anomalous scatterer or heavy atom (MIR, SIRAS, MAD, SAD etc.). The theoretical methodology which underpins the extraction of phase information from such derivatives is widely available in the literature. In addition, there are comprehensive sources of information on the chemistry of heavy‐atom compounds and the ligands with which they are known to interact, as well as the Heavy Atom Databank accessible on the World Wide Web. This contribution therefore aims to provide some information on the less well documented practical problems of firstly deciding on an overall strategy for derivatization and secondly performing the physical manipulations involved in producing heavy‐atom derivatives from native protein crystals and then cryocooling them. Ways to optimize the chances of isomorphous unit cells are suggested. Methods of determining whether or not the heavy atom is bound are outlined, including the powerful technique of PIXE (particle‐induced X‐ray emission).

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“…Data were collected on ID14-EH2 ( ϭ 0.933 Å) using the STRATEGY program (17) to determine the angular range for collection. For the time course experiment, a series of data sets were measured over the same oscillation range.…”

Section: Cloning Expression and Purification Of Recombinant Tryparementioning

confidence: 99%

Tryparedoxins from Crithidia fasciculata and Trypanosoma brucei

Alphey¹,

Gabrielsen²,

Micossi

et al. 2003

Journal of Biological Chemistry

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Tryparedoxin (TryX) is a member of the thioredoxin (TrX) fold family involved in the regulation of oxidative stress in parasitic trypanosomatids. Like TrX, TryX carries a characteristic Trp-Cys-Xaa-Xaa-Cys motif, which positions a redox-active disulfide underneath a tryptophan lid. We report the structure of a Crithidia fasciculata tryparedoxin isoform (CfTryX2) in two crystal forms and compare them with structures determined previously. Efforts to chemically generate crystals of reduced TryX1 were unsuccessful, and we carried out a novel experiment to break the redox-active disulfide, formed between Cys-40 and Cys-43, utilizing the intense x-radiation from a third generation synchrotron undulator beamline. A time course study of the S-S bond cleavage is reported with the structure of a TryX1 C43A mutant as the control. When freed from the constraints of a disulfide link to Cys-43, Cys-40 pivots to become slightly more solventaccessible. In addition, we have determined the structure of Trypanosoma brucei TryX, which, influenced by the molecular packing in the crystal lattice, displays a significantly different orientation of the active site tryptophan lid. This structural change may be of functional significance when TryX interacts with tryparedoxin peroxidase, the final protein in the trypanothione-dependent peroxidase pathway. Comparisons with chloroplast TrX and its substrate fructose 1,6-bisphosphate phosphatase suggest that this movement may represent a general feature of redox regulation in the trypanothione and thioredoxin peroxidase pathways.

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STRATEGY: a program to optimize the starting spindle angle and scan range for X-ray data collection

Cited by 67 publications

References 4 publications

Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding

Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding

Heavy-atom derivatization

Tryparedoxins from Crithidia fasciculata and Trypanosoma brucei

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