Upgrade of the CATS sample changer on FIP-BM30A at the ESRF: towards a commercialized standard

An upgraded version of the sample changer ;CATS' (Cryogenic Automated Transfer System) that was developed on the FIP-BM30A beamline at the ESRF is presented. At present, CATS is installed at SLS (three systems), BESSY (one system), DLS (two systems) and APS (four systems for the LSCAT beamline). It consists mainly of an automated Dewar with an assortment of specific grippers designed to obtain a fast and reliable mounting/dismounting rate without jeopardizing the flexibility of the system. The upgraded system has the ability to manage any sample standard stored in any kind of puck.

Bleaching of soda pulp of fibres of Musa textilis nee (abaca) with peracetic acid

In this work, we studied the influence of operational variables in the bleaching of soda pulp of Musa textilis nee (abaca) [viz. temperature (55-85 degrees C), bleaching time (30-150 min) and peracetic acid concentration oven dry pulp (0.5-4.5%)] on the kappa number and viscosity of the bleached pulp, as well as on the breaking length, burst index and brightness of paper sheets made from it. For this purpose, we used a central composite factorial design in order to identify the optimum operating conditions. In this way equations relating the dependent variables to the operational variables of the bleaching process were derived. These equations reproduce the dependent variables with errors less than 12% for all, except the viscosity which was predicted with errors less than 18%. Obtaining bleached pulp with the highest possible viscosity (1519 ml/g), and paper sheets with the maximum possible breaking length (6547 m) and burst index (5.00 kN/g), entails using a temperature of 55 degrees C, a peracetic acid concentration of 4.5% and a bleaching time of 150 min. This provides a brightness of 79.90%, which is only 6.53% lower than the maximum possible value (85.48%).

Optimization of pulping conditions of abaca. An alternative raw material for producing cellulose pulp

The influence of temperature (150-170 degrees C), pulping time (15-45 min) and soda concentration (5-10%) in the pulping of abaca on the yield, kappa, viscosity, breaking length, stretch and tear index of pulp and paper sheets, was studied. Using a factorial design to identify the optimum operating conditions, equations relating the dependent variables to the operational variables of the pulping process were derived that reproduced the former with errors lower than 25%. Using a high temperature, and a medium time and soda concentration, led to pulp that was difficult to bleach (kappa 28.34) but provided acceptable strength-related properties (breaking length 4728 m; stretch 4.76%; tear index 18.25 mN m2/g), with good yield (77.33%) and potential savings on capital equipment costs. Obtaining pulp amenable to bleaching would entail using more drastic conditions than those employed in this work.

X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing

Multi-wavelength anomalous dispersion (MAD) using brominated derivatives is considered a common and convenient technique for solving chemically synthesized nucleic acid structures. Here, it is shown that a relatively moderate X-ray dose (of the order of 5 x 10(15) photons mm(-2)) can induce sufficient debromination to prevent structure determination. The decrease in bromine occupancy with radiation dose can be accounted for by a simple exponential, with an estimated rate constant at the absorption-peak wavelength, 7.4 (0.8) MGy, that is not significantly different from its value at the absorption-edge wavelength, 9.2 (2.6) MGy (the given e.s.d.s assess the relative closeness of the two values, not their absolute accuracy, which is probably worse). Chemically, these results (and others) are consistent with bromine cleavage resulting from direct photodissociation and/or from the action of free electrons, rather than from the action of hydroxyl radicals originating from water dissociation. The free bromine species (Br(-)) diffuse too quickly, even in amorphous ice around 100 K, to allow the determination of a diffusion coefficient. From a practical point of view, it is suggested that a single data collection with a crystal consisting of iodinated instead of brominated derivatives could provide both anomalous scattering and SIR phase information by the progressive cleavage of iodine.

FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments

FIP is a French Collaborating Research Group (CRG) beamline at the European Synchrotron Radiation Facility (ESRF) dedicated exclusively to crystallography of biological macromolecules, with a special emphasis on multiwavelength anomalous diffraction data collection in the 0.7-1.81 A wavelength range. The optics, consisting of long cylindrical grazing-angle mirrors associated with a cryocooled double-crystal monochromator, delivers an optimal beam in the corresponding energy range. The high level of automation, which includes automated crystal centring, automated data-collection management and data processing, makes the use of this beamline very easy. This is illustrated by the large number of challenging structures that have been solved since 1999.

Structure and mechanism of chalcone synthase-like polyketide synthases

Polyketide synthases (PKS) produce an array of natural products with different biological activities and pharmacological properties by varying the starter and extender molecules that form the final polyketide. Recent studies of the simplest PKS, the chalcone synthase (CHS)-like enzymes involved in the biosynthesis of flavonoids, anthocyanin pigments, and antimicrobial phytoalexins, have yielded insight on the molecular basis of this biosynthetic versatility. Understanding the structure-function relationship in these PKS provides a foundation for manipulating polyketide formation and suggests strategies for further increasing the scope of polyketide biosynthetic diversity.

Automated data processing on beamline FIP (BM30A) at ESRF

Automation of protein crystallography synchrotron beamlines is becoming necessary to face challenging structural genomics projects. In this context, a program has been developed that processes diffraction frames using popular software but analyzes statistics and makes choices the way crystallographers usually do. This program includes the classical peak search, indexing, integration, scaling and anomalous signal analysis. The result, comparable with that obtained by standard users, is rapidly available, providing the required information for a more efficient use of the beam time.

Influence of the operating conditions in the acetone pulping of wheat straw on the properties of the resulting paper sheets

A central composite factor design was used to examine the influence of independent variables in the acetone pulping of wheat straw (processing temperature, time, and acetone concentration) on the yield of the resulting pulp, and on various physical properties of paper sheets (breaking length, stretch, burst index, tear index and brightness) obtained from it. Equations that related each dependent variable to the different independent variables were obtained, and these reproduced the experimental results for the yield, breaking, stretch, burst index and brightness obtained at temperatures, times, and acetone concentratons over the ranges 140-180 degrees C, 60-120 min and 40-80%, respectively, with errors less than 20%. Obtaining the optimum breakinig length, stretch, burst index and tear index for the paper sheets (3,456 m, 1.42%, 1.36 kN/g and 3.86 mNm2/g, respectively) entails using a high temperature; the processing time and acetone concentration only influence stretch, optimization of which requires using a short time and a low concentration. The optimum brightness (30.44%) is achieved with a low temperature, a short time and a medium acetone concentration. In order to minimize losses of solvent during its recovery and recycling while ensuring acceptable levels of the properties of the paper sheets, a high temperature, a low acetone concentration and a short time can be used; the brightness level thus obtained is only 10% lower than the optimum value.

Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module

Escherichia coli NADPH-sulfite reductase (SiR) is a 780 kDa multimeric hemoflavoprotein composed of eight alpha-subunits (SiR-FP) and four beta-subunits (SiR-HP) that catalyses the six electron reduction of sulfite to sulfide. Each beta-subunit contains a Fe4S4 cluster and a siroheme, and each alpha-subunit binds one FAD and one FMN as prosthetic groups. The FAD gets electrons from NADPH, and the FMN transfers the electrons to the metal centers of the beta-subunit for sulfite reduction. We report here the 1.94 A X-ray structure of SiR-FP60, a recombinant monomeric fragment of SiR-FP that binds both FAD and FMN and retains the catalytic properties of the native protein. The structure can be divided into three domains. The carboxy-terminal part of the enzyme is composed of an antiparallel beta-barrel which binds the FAD, and a variant of the classical pyridine dinucleotide binding fold which binds NADPH. These two domains form the canonic FNR-like module, typical of the ferredoxin NADP+ reductase family. By analogy with the structure of the cytochrome P450 reductase, the third domain, composed of seven alpha-helices, is supposed to connect the FNR-like module to the N-terminal flavodoxine-like module. In four different crystal forms, the FMN-binding module is absent from electron density maps, although mass spectroscopy, amino acid sequencing and activity experiments carried out on dissolved crystals indicate that a functional module is present in the protein. Our results clearly indicate that the interaction between the FNR-like and the FMN-like modules displays lower affinity than in the case of cytochrome P450 reductase. The flexibility of the FMN-binding domain may be related, as observed in the case of cytochrome bc1, to a domain reorganisation in the course of electron transfer. Thus, a movement of the FMN-binding domain relative to the rest of the enzyme may be a requirement for its optimal positioning relative to both the FNR-like module and the beta-subunit.

Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase

Chalcone synthase (CHS) catalyzes formation of the phenylpropanoid chalcone from one p-coumaroyl-CoA and three malonyl-coenzyme A (CoA) thioesters. The three-dimensional structure of CHS [Ferrer, J.-L., Jez, J. M., Bowman, M. E., Dixon, R. A., and Noel, J. P. (1999) Nat. Struct. Biol. 6, 775-784] suggests that four residues (Cys164, Phe215, His303, and Asn336) participate in the multiple decarboxylation and condensation reactions catalyzed by this enzyme. Here, we functionally characterize 16 point mutants of these residues for chalcone production, malonyl-CoA decarboxylation, and the ability to bind CoA and acetyl-CoA. Our results confirm Cys164's role as the active-site nucleophile in polyketide formation and elucidate the importance of His303 and Asn336 in the malonyl-CoA decarboxylation reaction. We suggest that Phe215 may help orient substrates at the active site during elongation of the polyketide intermediate. To better understand the structure-function relationships in some of these mutants, we also determined the crystal structures of the CHS C164A, H303Q, and N336A mutants refined to 1.69, 2.0, and 2.15 A resolution, respectively. The structure of the C164A mutant reveals that the proposed oxyanion hole formed by His303 and Asn336 remains undisturbed, allowing this mutant to catalyze malonyl-CoA decarboxylation without chalcone formation. The structures of the H303Q and N336A mutants support the importance of His303 and Asn336 in polarizing the thioester carbonyl of malonyl-CoA during the decarboxylation reaction. In addition, both of these residues may also participate in stabilizing the tetrahedral transition state during polyketide elongation. Conservation of the catalytic functions of the active-site residues may occur across a wide variety of condensing enzymes, including other polyketide and fatty acid synthases.

Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis

Chalcone synthase (CHS) is pivotal for the biosynthesis of flavonoid antimicrobial phytoalexins and anthocyanin pigments in plants. It produces chalcone by condensing one p-coumaroyl- and three malonyl-coenzyme A thioesters into a polyketide reaction intermediate that cyclizes. The crystal structures of CHS alone and complexed with substrate and product analogs reveal the active site architecture that defines the sequence and chemistry of multiple decarboxylation and condensation reactions and provides a molecular understanding of the cyclization reaction leading to chalcone synthesis. The structure of CHS complexed with resveratrol also suggests how stilbene synthase, a related enzyme, uses the same substrates and an alternate cyclization pathway to form resveratrol. By using the three-dimensional structure and the large database of CHS-like sequences, we can identify proteins likely to possess novel substrate and product specificity. The structure elucidates the chemical basis of plant polyketide biosynthesis and provides a framework for engineering CHS-like enzymes to produce new products.

D2AM, a beamline with a high-intensity point-focusing fixed-exit monochromator for multiwavelength anomalous diffraction experiments

D2AM is a french CRG beamline installed at the ESRF (European Synchrotron Radiation Facility) in Grenoble, with half of the time dedicated to biological macromolecule crystallography and half to materials science studies (diffraction, wide-angle and small-angle scattering). It is constructed at the front-end BM02 of the ESRF storage ring, using the X-ray beam from a 0.8 T bending magnet. D2AM entered into routine operation at the end of 1994, and is used either for single-wavelength or for multiwavelength anomalous diffraction studies. The beam is monochromated by an Si[111] two-crystal monochromator with a resolution of about 2 x 10(-4). The first crystal is water cooled. The X-ray photon energy covers the range between 6.5 keV (lambda approximately 1.9 A) and 17 keV (lambda approximately 0.7 A), a domain of energy with many K or L absorption edges of heavy atoms of interest for biological macromolecules studies and in materials science. The X-ray beam is focused in the vertical plane by two long curved mirrors and in the horizontal plane by the second crystal of the monochromator which is given an adjustable sagittal curvature. A spot size of 0.3 x 0.1 mm (FWHM) is measured at the sample position. Both mirrors are cut out of a 6"-diameter 1.1 m-long Si single crystal, polished and coated with a 400 A Pt thin film. The rugosity is better than 4 A r.m.s. and the longitudinal slope error is better than 5 x 10(-6) rad r.m.s. The first mirror is water cooled, the second is not. The beam intensity on the sample is about 10(11) photon s(-1) on a 0.3 x 0.3 mm focus area at 100 mA in the storage ring of the ESRF. The harmonic rejection ratio obtained with the two mirrors is better than 10(-5) for lambda/3. The combined optical system, mirror/monochromating-crystals/mirror, used on D2AM constitutes altogether a high-intensity point-focusing fixed-exit monochromator, which has the additional property that the energy resolution is not dependent on the beam divergence in use. Its stability and resolution are perfectly adapted to multiwavelength anomalous diffraction studies. The alignment of the mirrors and the monochromator is fully automated, taking 5 min, with the exception of the adjustment of the sagittal focusing. During multiwavelength diffraction experiments the wavelength is changed by a fast single monochromator rotation. Neither realignment of the mirrors nor readjustment of the beam focusing are necessary. The stability and reproducibility of the selected X-ray photon energy is better than 0.5 eV.

Data compression for diffraction patterns

Efficient coding (lossless) and compression (lossy) of diffraction patterns is important in protein crystallography experiments because of storage and transmission limitations. The goal is to reduce the bit-rate significantly while keeping diffraction peak intensity distortion at an acceptable level. This paper presents an overview of coding and compression techniques more or less adapted to such problems. A large part of this study is dedicated to time-frequency-transform based compression algorithms and some of their extensions. Wavelet based software has been developed and tested. Results are compared with the discrete cosine transform (DCT) and other classical algorithms. These tools seem attractive and very promising for analyzing and compressing signals with singularities and transient phenomena such as diffraction peaks. Tests were performed on a standard protein crystallography data set coming from the CCD detector of D2AM beamline at the European Synchrotron Radiation Facility at Grenoble. These were compressed with DCT and wavelet-based algorithms. It appears that alterations of the result of the processing of restored images remain very weak for compression rates up to 10. These preliminary results indicate that the proposed wavelet method is a good standard technique for efficient compression of diffraction patterns.

Observations of middle ear pressures. Commentary with movie

Previous direct measurements of middle ear pressure in ears with serous otitis resulted in the range of from 0 to -10 mm H2O pressure. To confirm these findings we attempted to quantify middle ear pressures by doing myringotomies in serous otitis patients through sterile saline solution. We compared the rate of aspiration of the saline in ears with serous otitis to the rate of aspiration of saline after an experimental myringotomy in an ear model in which known pressures were imposed. To record our findings we used motion picture photography. Layering a film of sterile oil suspension of oxytetracycline and hydrocortisone over dry tympanic membrane perforations resulted in the demonstration of a pulsatile positive pressure of about 6 mm water in many of the ears which we tested. The oil film often formed an external bubble which ruptured after several minutes. In some ears there was no change in pressure and in only a small percentage there was evidence of a decreased pressure by absorption of air in the middle ear during the period of observation. This positive pressure is unrelated to swallowing and suggests that the current theories of middle ear aeration via opening of the eustachian tube may not be valid. These findings were demonstrated with motion picture film.