PubMed Health⌕ Search

Biomedical subjects

W Shepard

Publications and source records attributed to W Shepard.

18 recordsLinked to original sources

High-throughput sample handling and data collection at synchrotrons: embedding the ESRF into the high-throughput gene-to-structure pipeline.

An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.

Data Collection↗

The care and nurture of undulator data sets.

Undulator radiation is the X-ray source of choice for modern macromolecular crystallography beamlines. Here, the basic properties of undulator sources are described and it is indicated why they make such good X-ray sources for macromolecular crystallography. Collection of excellent data from these beamlines is not always straightforward; therefore, a number of rules are postulated for undulator data collection and guidelines are offered which will help to ensure a satisfactory experiment.

Crystallization↗

Crystallization of a recombinant form of the complete sequence of human gamma-interferon: characterization by small-angle X-ray scattering, mass spectrometry and preliminary X-ray diffraction studies.

The crystallization conditions of a recombinant form of the complete sequence of human gamma-interferon, designated r-hu IFN-gamma (RU 42369), have been determined after studying the behaviour of this protein in solution by small-angle X-ray scattering (SAXS) as a function of pH and salt type. IFN-gamma is difficult to crystallize without truncating at least the last five amino acids of the C-terminus; the SAXS results suggest viable crystallization conditions that led to crystals of r-hu IFN-gamma suitable for X-ray diffraction analysis. The crystals were grown in the presence of ammonium sulfate using vapour-diffusion techniques. The crystals, which diffract to 5 A resolution at best, belong to the primitive tetragonal space group P42(1)2 and have unit-cell parameters a = b = 123.4, c = 93.4 A. The protein contained in these crystals was analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), which verified the presence of the complete amino-acid sequence of r-hu IFN-gamma.

Crystallization↗

Structure of cytochrome c7 from Desulfuromonas acetoxidans at 1.9 A resolution.

Multihaem cytochromes play a key role in electron-transport reactions in the periplasm of sulfate- and sulfur-reducing bacteria. The redox proteins grouped in the c3 superfamily also display metal-reducing activities, which make them interesting biotechnological tools. The crystal structure of the fully oxidized cytochrome c7 from Desulfuromonas acetoxidans has been solved by combined molecular-replacement and MAD methods. The structure has been refined at 1.9 A resolution to an R value of 19.1% (R(free) = 24.3%) and includes three haems and 116 water molecules. The protein displays the cytochrome c3 fold in a highly minimized form, while haem 2 and the surrounding protein environment are missing. The geometry of haem packing and of the haem axial ligands and propionates are described and compared with that of c3 cytochromes. The crystal structure is compared with the solution structure recently obtained by NMR methods and with its homologue cytochromes of the c3 superfamily. Comparison of the high number of available structures makes it possible to analyze the structural role of the few highly conserved residues, in addition to the cysteines and histidines that link the porphyrin rings and the Fe atoms to the protein chain.

Amino Acid Sequence↗

Crystal structure of the S15-rRNA complex.

In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 ¿ resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.

Amino Acid Sequence↗

Low-resolution phase information in multiple-wavelength anomalous solvent contrast variation experiments.

The basic theory and principles of the multiple-wavelength anomalous solvent-contrast (MASC) method are introduced as a contrast-variation technique for generating low-resolution crystallographic phase information on the envelope of a macromolecule. Experimental techniques and practical considerations concerning the choice of anomalous scatterer, sample preparation and data acquisition are discussed. Test cases of crystals of three proteins of differing molecular weights from 14 kDa through to 173 kDa are illustrated. Methods for extracting the moduli of the anomalous structure factors from the MASC data are briefly discussed and the experimental results are compared with the known macromolecular envelopes. In all cases, the lowest resolution shells exhibit very large anomalous signals which diminish at higher resolution, as expected by theory. However, in each case the anomalous signal persists at high resolution, which is strong evidence for ordered sites of the anomalous scatterers. For the smaller two of these proteins the heavy-atom parameters could be refined for some of these sites. Finally, a novel method for phasing the envelope structure-factor moduli is presented. This method takes into account the relatively low number of observations at low resolution and describes the macromolecular envelope with a small number of parameters by presuming that the envelope is a compact domain of known volume. The parameterized envelope is expressed as a linear combination of independent functions such as spherical harmonics. Phasing starts from solutions of a sphere in the unit cell after positional refinement from random trials and the parameters describing the envelope are then refined against the data of structure-factor moduli. The preliminary results using simulated data show that the method can be used to reconstruct the correct macromolecular envelope and is able to discriminate against some false solutions.

Aldose-Ketose Isomerases↗

MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association.

The monohemic cytochrome c552from Pseudomonas nautica (c552-Pn) is thought to be the electron donor to cytochrome cd1, the so-called nitrite reductase (NiR). It shows as high levels of activity and affinity for the P. nautica NiR (NiR-Pn), as the Pseudomonas aeruginosa enzyme (NiR-Pa). Since cytochrome c552is by far the most abundant electron carrier in the periplasm, it is probably involved in numerous other reactions. Its sequence is related to that of the c type cytochromes, but resembles that of the dihemic c4cytochromes even more closely. The three-dimensional structure of P. nautica cytochrome c552has been solved to 2.2 A resolution using the multiple wavelength anomalous dispersion (MAD) technique, taking advantage of the presence of the eight Fe heme ions in the asymmetric unit. Density modification procedures involving 4-fold non-crystallographic averaging yielded a model with an R -factor value of 17.8 % (Rfree=20.8 %). Cytochrome c552forms a tight dimer in the crystal, and the dimer interface area amounts to 19% of the total cytochrome surface area. Four tighly packed dimers form the eight molecules of the asymmetric unit. The c552dimer is superimposable on each domain of the monomeric cytochrome c4from Pseudomomas stutzeri (c4-Ps), a dihemic cytochrome, and on the dihemic c domain of flavocytochrome c of Chromatium vinosum (Fcd-Cv). The interacting residues which form the dimer are both similar in character and position, which is also true for the propionates. The dimer observed in the crystal also exists in solution. It has been hypothesised that the dihemic c4-Ps may have evolved via monohemic cytochrome c gene duplication followed by evolutionary divergence and the adjunction of a connecting linker. In this process, our dimeric c552structure might be said to constitute a "living fossile" occurring in the course of evolution between the formation of the dimer and the gene duplication and fusion. The availability of the structure of the cytochrome c552-Pn and that of NiR from P. aeruginosa made it possible to identify putative surface patches at which the docking of c552to NiR-Pn may occur.

Amino Acid Sequence↗

Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.

cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.

Base Pairing↗

The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins.

BACKGROUND: Leucocidins and gamma-hemolysins are bi-component toxins secreted by Staphylococcus aureus. These toxins activate responses of specific cells and form lethal transmembrane pores. Their leucotoxic and hemolytic activities involve the sequential binding and the synergistic association of a class S and a class F component, which form hetero-oligomeric complexes. The components of each protein class are produced as non-associated, water-soluble proteins that undergo conformational changes and oligomerization after recognition of their cell targets. RESULTS: The crystal structure of the monomeric water-soluble form of the F component of Panton-Valentine leucocidin (LukF-PV) has been solved by the multiwavelength anomalous dispersion (MAD) method and refined at 2.0 A resolution. The core of this three-domain protein is similar to that of alpha-hemolysin, but significant differences occur in regions that may be involved in the mechanism of pore formation. The glycine-rich stem, which undergoes a major rearrangement in this process, forms an additional domain in LukF-PV. The fold of this domain is similar to that of the neurotoxins and cardiotoxins from snake venom. CONCLUSIONS: The structure analysis and a multiple sequence alignment of all toxic components, suggest that LukF-PV represents the fold of any water-soluble secreted protein in this family of transmembrane pore-forming toxins. The comparison of the structures of LukF-PV and alpha-hemolysin provides some insights into the mechanism of transmembrane pore formation for the bi-component toxins, which may diverge from that of the alpha-hemolysin heptamer.

Amino Acid Sequence↗

Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.

A previous article [Fourme et al. (1995). J. Synchrotron Rad. 2, 36-48] presented the theoretical foundations of MASC, a new contrast-variation method using multiwavelength anomalous scattering, and reported the first experimental results. New experiments have been conducted both at the ESRF (Grenoble, France) and at LURE-DCI (Orsay, France), using cryocooled crystals of three proteins of known structures and very different molecular weights. Amplitudes of {GammaT(h)}, the 'normal' structure factors of the anomalously scattering part of the crystal including the solvent zone and the ordered anomalous scattering sites (if any), have been extracted from multiwavelength data. In the very low resolution range (d >/= 20 A), the agreement between experimental {GammaT(h)} and model values calculated from the bulk solvent is all the more satisfactory since the molecular weight of the protein is high. For spacings between 10 and 20 A, the agreement between experimental {GammaT(h)} and model values is also satisfactory if one takes into account ordered anomalous scatterer sites. Such sites have been found in the three cases.

Aldose-Ketose Isomerases↗

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.

BACKGROUND: The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood. RESULTS: The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the presence of cobalt hexammine. The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheared G.A mismatches, are intercalated and stacked on top of each other without any interstrand Watson-Crick base pairing. The cobalt hexammine cation appears to participate only in crystal cohesion. CONCLUSIONS: The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.

Crystallography, X-Ray↗

Protein Crystallography at Ultra-Short Wavelengths: Feasibility Study of Anomalous-Dispersion Experiments at the Xenon K-edge.

A protein crystallography experiment at the xenon K-edge (lambda = 0.358 A) has been successfully carried out at the materials science beamline (BL2/ID11) of the ESRF. The samples used in this methodological study were crystals of porcine pancreatic elastase, a 26 kDa protein of known structure. The diffraction data are of excellent quality. The combination of isomorphous replacement and anomalous dispersion of a single xenon heavy-atom derivative allowed accurate phase determination and the computation of a high-quality electron density map of the protein molecule. This is the first fully documented report on a complete protein crystallography experiment, from data collection up to phase determination and calculation of an electron density map, carried out with data obtained at ultra-short wavelengths. Experimental considerations as well as possible advantages and drawbacks of protein crystallography at very short and ultra-short wavelengths are discussed.

Journal Article↗

High-pressure krypton gas and statistical heavy-atom refinement: a successful combination of tools for macromolecular structure determination.

The noble gas krypton is shown to bind to crystallized proteins in a similar way to xenon [Schiltz, Prangé & Fourme (1994). J. Appl. Cryst. 27, 950-960]. Preliminary tests show that the major krypton binding sites are essentially identical to those of xenon. Noticeable substitution is achieved only at substantially higher pressures (above 50 x 10(5) Pa). As is the case for xenon, the protein complexes with krypton are highly isomorphous with the native structure so that these complexes can be used for phase determination in protein crystallography. Krypton is not as heavy as xenon, but its K-absorption edge is situated at a wavelength (0.86 A) that is readily accessible on synchrotron radiation sources. As a test case, X-ray diffraction data at the high-energy side of the K edge were collected on a crystal of porcine pancreatic elastase (molecular weight of 25.9 kDa) put under a krypton gas pressure of 56 x 10(5) Pa. The occupancy of the single Kr atom is approximately 0.5, giving isomorphous and anomalous scattering strengths of 15.2 and 1.9 e, respectively. This derivative could be used successfully for phase determination with the SIRAS method (single isomorphous replacement with anomalous scattering). After phase improvement by solvent flattening, the resulting electron-density map is of exceptionally high quality, and has a correlation coefficient of 0.85 with a map calculated from the refined native structure. Careful data collection and processing, as well as the correct statistical treatment of isomorphous and anomalous signals have proven to be crucial in the determination of this electron-density map. Heavy-atom refinement and phasing were carried out with the program SHARP, which is a fully fledged implementation of the maximum-likelihood theory for heavy-atom refinement [Bricogne (1991). Crystallographic Computing 5, edited by D. Moras, A. D. Podjarny & J. C. Thierry, pp. 257-297. Oxford: Clarendon Press]. It is concluded that the use of xenon and krypton derivatives, when they can be obtained, associated with statistical heavy-atom refinement will allow one to overcome the two major limitations of the isomorphous replacement method i.e. non-isomorphism and the problem of optimal estimation of heavy-atom parameters.

Journal Article↗

New insights on DNA recognition by ets proteins from the crystal structure of the PU.1 ETS domain-DNA complex.

Transcription factors belonging to the ets family regulate gene expression and share a conserved ETS DNA-binding domain that binds to the core sequence 5'-(C/A)GGA(A/T)-3'. The domain is similar to alpha+beta ("winged") helix-turn-helix DNA-binding proteins. The crystal structure of the PU.1 ETS domain complexed to a 16-base pair oligonucleotide revealed a pattern for DNA recognition from a novel loop-helix-loop architecture (Kodandapani, R., Pio, F., Ni. C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R. A., and Ely, K. R. (1996) Nature 380, 456-460). Correlation of this model with mutational analyses and chemical shift data on other ets proteins confirms this complex as a paradigm for ets DNA recognition. The second helix in the helix-turn-helix motif lies deep in the major groove with specific contacts with bases in both strands in the core sequence made by conserved residues in alpha3. On either side of this helix, two loops contact the phosphate backbone. The DNA is bent (8 degrees) but uniformly curved without distinct kinks. ETS domains bind DNA as a monomer yet make extensive DNA contacts over 30 A. DNA bending likely results from phosphate neutralization of the phosphate backbone in the minor groove by both loops in the loop-helix-loop motif. Contacts from these loops stabilize DNA bending and may mediate specific base interactions by inducing a bend toward the protein.

Amino Acid Sequence↗

The Multiwavelength Anomalous Solvent Contrast (MASC) Method in Macromolecular Crystallography.

The wavelength dependence of anomalous scattering of X-rays, due to atoms randomly dispersed in the solvent phase of a macromolecular crystal, is a way of producing solvent-density contrast variation with perfect isomorphism. The largest contrast variations are obtained by tuning the X-ray wavelength near an absorption edge of the anomalous-scattering species. In this method, which we call MASC, the anomalous partial structure is an extended uniform electron density, in contrast to the few punctual ordered scatterers in the multiwavelength anomalous-dispersion (MAD) method. MASC is, in principle, applicable to the determination of the molecular envelope and of low-resolution structure-factor phases. Structure factors (lambda)F(+/-h) leads to a set of equations which can be solved to give |G(h)| and |(0)F(h)|, the modulus of the envelope and of the total ;normal' structure factors, respectively, and Deltavarphi = (varphi(0)(F)-varphi(G)). The moduli {|G|} behave like structure-factor amplitudes from small-molecule crystals, and the estimation of their phases can be carried out by statistical direct methods. Then, the phase of (0)F(h) and finally the conventional (e.g. in vacuum) protein structure factor F(p)(h) can be determined. As in the MAD method, the strength of MASC signals can be quantified by Bijvoet and dispensive ratios, for which practical expressions are derived in the case of zero contrast. The behaviour of these ratios at increasing resolution is discussed, using approximations for |G(h)| and |Delta(h)| , respectively, derived from Porod's law and assuming a random distribution of atoms in the solvent excluding volume. Expected values of anomalous ratios are calculated for a hypothetical MASC experiment based on the known three-dimensional structure of kallikrein A, using a solvent with 3.5 M ammonium selenate to ensure zero contrast, and wavelength tuning near the Se K-absorption edge. The main steps of a MASC experiment are discussed in the context of a MAD-like data collection optimized for accurate measurements of intensities of anomalous pairs at low resolution. Finally, the results of preliminary experiments on two protein crystals are reported. The first, a partial single-wavelength data collection, used anomalous scattering of selenium at the K edge and gave anomalous ratios with the expected behaviour. The second one, at three wavelengths, used anomalous scattering of ytterbium at the L(III) edge. In this case, effects from solvent as well as from ordered lanthanide ions were demonstrated.

Journal Article↗

Active site geometry in the high oxido-reduction potential rusticyanin from Thiobacillus ferrooxidans.

Rusticyanin is a blue copper protein involved in the oxidation of iron catalyzed by Thiobacillus ferrooxidans. This protein is characterized by a high oxido-reduction potential and a high stability at low pH. The three dimensional structure of this protein is still unknown and in order to investigate the geometric properties of the copper center which could be correlated to the high oxido-reduction potential, we have studied rusticyanin by UV-Visible, EPR and NMR spectroscopies, at different pH values. Our results suggest that rusticyanin is stable between pH 2 and pH 9 and that the copper center does not undergo significant geometric modifications in this pH range. Moreover, the copper atom could be buried more deeply in the protein than in other type I copper proteins and the atomic distance Cu-S(Met), one of the four bonds involved in copper coordination, is probably shorter in rusticyanin than in other cupredoxins. These two properties of the copper site are expected to be responsible, in part, for the high oxido-reduction potential observed in rusticyanin.

Azurin↗