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PubMed1999

The geometry of metal-ligand interactions relevant to proteins.

Geometrical data which could be of relevance in the structure determination, structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD contains crystallographic data from 'small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor </= 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal-donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using approximately 4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal-donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.

Carboxylic Acids↗
PubMed1999

The beamlines of ELETTRA and their application to structural biology.

Protein crystallographers are nowadays regular users of synchrotron radiation (SR) facilities for several applications. The goal of majority of users is simply to extract more accurate, higher resolution data from existing crystals; they use monochromatic radiation and the rotation method, in order to get a complete survey of the reciprocal space in a short time. In fact the brilliance of SR is essential, due to the weak scattering power of the samples, and because of their sensibility to radiation damage. Over the last few years, however, a general increase of interest for measurements at multiple wavelengths, which exploit the anomalous dispersion for the phase problem (multiwavelength anomalous diffraction--MAD), has generated the need of intense tuneable sources. For these applications, the emphasis is on accurate measurements of the small differences between the intensities of Bragg reflections at various energies across the absorption edge of an element present in the sample. The macromolecular diffraction beamline at ELETTRA, which is now running routinely since spring 1995, has been designed to provide a high flux--highly collimated tuneable X-rays source in the spectral range between 4 and 25 keV. The radiation source is the 57-pole wiggler, which delivers a very intense radiation up to 25 keV, and is shared and used simultaneously with the small angle X-ray scattering (SAXS) beamline. The front-end filter system has a cut-off energy at about 4 keV. The beamline optics consists of a pseudo-channel-cut double-crystal monochromator followed by a double focusing toroidal mirror. The tunability and the stability of the monochromator allows the user to perform MAD experiments, and for this purpose, a fluorescence probe for the exact calibration of the absorption edge is available on-line. The experimental station is based on an imaging plate area detector from MarResearch, with a sensible area of 345 mm in diameter. A cooled N2-stream is available to cool the sample crystal in order to reduce the radiation damage. SAXS is an experimental technique used to derive structural information about supra-molecular assemblies, amorphous materials and partly ordered systems (e.g. size and shape of large molecules). The high-flux SAXS beamline at ELETTRA is mainly intended for time-resolved studies on fast structural transitions in the sub-millisecond time region in solutions and in partly ordered systems, triggered by external or process parameters, with a SAXS resolution between 10 and 1400 A in real space. The source is the already mentioned 57-pole and the SAXS beamline accepts three discrete energies of its spectrum, namely 5.4, 8 and 16 keV. The beamline optics consists of a flat double-crystal monochromator and a double focusing toroidal mirror. A multi-purpose sample stage, movable along an optical table in order to optimise the sample to detect distance, allows to perform fast time-resolved relaxation studies based on temperature- or pressure-jumps as well as stopped flow experiments. Moreover, the users have option to install their own specialised sample surrounding equipment. The optimisation of the beamline with respect to high-flux and consequently high-flux density, allows to perform the following experiments: low contrast solution scattering, grazing incidence surface diffraction, micro-spot scanning, X-ray fluorescence analysis, time-resolved studies > or = 11 microseconds, simultaneous small- and wide-angle measurements on gels, liquid crystals, biopolymers, amorphous materials, muscles.

Crystallography, X-Ray↗
PubMed1990

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗
PubMed1999

Direct and indirect integration of event-related potentials, functional magnetic resonance images, and single-unit recordings.

Cognitive neuroimaging techniques vary along three primary dimensions: invasiveness, temporal resolution, and spatial resolution. Several of the major techniques excel on two of these three dimensions, but none of them excels on all three. In principle, multiple techniques with different strengths and weaknesses could be combined to obtain high temporal and spatial resolution data about human neural activity, and this article compares two approaches to combining microelectrode, hemodynamic, and electromagnetic measures of neural activity. The first approach involves using structural magnetic resonance images to provide a common reference frame for the mathematical estimation of neural activity, and the second approach involves parallel experimental manipulations and converging evidence. At present, neither approach is entirely satisfactory, and the integration of different measures of neural activity, therefore, requires a combination of direct and indirect approaches.

Action Potentials↗
PubMed2000

Mass spectrometric study of tricarbonyl (eta(6)-phenyl methanols) of chromium(0).

A mass spectrometric study of several tricarbonyl (eta(6)-phenyl methanols) of chromium(0) was performed. Electron ionization (EI), chemical ionization (CI) and fast atom bombardment (FAB) mass spectra were acquired for each molecule, and compared in order to establish a general fragmentation pattern. The suggested pathways were investigated and confirmed by means of constant b/e linked scans and high resolution data. In addition a Hammett-McLafferty correlation for some peaks derived from the molecular ions was accomplished.

Chromium↗
PubMed2000

Probing acrylamide alkylation sites in cysteine-free proteins by matrix-assisted laser desorption/ionisation time-of-flight.

It is recognised that gel-separated proteins can experience a frequent modification provoked by the interaction of unpolymerized acrylamide monomers with the thiol group of cysteine to form a beta-cysteinyl-S-propionamide adduct. Other groups which have been implicated in this reaction include the hydroxyl group of tyrosine, the straightepsilon-amino group of lysine, and the free N-terminus. In a series of recent publications it has been demonstrated that at pH approximately 9.5 and in the presence of cysteine, none of these groups experienced measurable interaction with acrylamide monomers. To emphasise this conclusion we have used matrix-assisted laser desorption/ionisation with a reflectron time-of-flight mass spectrometer to examine a number of cysteine-free proteins incubated for various intervals with 30 mM acrylamide monomers at pH 9.5. These high resolution data suggest that, for short incubation times (>/=1 hour) and in the absence of cysteine, the straightepsilon-NH(2) group of lysine is the likely adduction site of acrylamide. Longer incubation times (>/=24 hours) with acrylamide monomers rendered the role of Cys as the favourite alkylation site less evident.

Acrylamide↗
PubMed2000

Electron impact fragmentation mechanisms of some cyclic esters with helical structures

The electron impact mass spectra of several cyclic esters with helical structures have been studied. Their fragmentation pathways were proposed and confirmed by mass-analyzed ion kinetic energy (MIKE) and high-resolution data. In general, the dominant fragmentation pathways in the spectra of these compounds originate from a alpha-cleavage with loss of a hydrogen or methyl group. The difference between hydrogen and methyl group loss greatly affects the subsequent fragmentations. Although, due to their helicity, these cyclic esters are optically active no stereo-related fragmentation pathway was observed. Copyright 2000 John Wiley & Sons, Ltd.

Journal Article↗
PubMed1988

A mass spectral study of cyclophosphamide concerning a thermally induced rearrangement reaction.

The electron impact mass spectra of cyclophosphamide (1) are very sensitive towards experimental conditions in view of the kind of sample handling, the type of mass spectrometer used and the temperature of evaporation. The reason for this phenomenon is the elimination of HCl from the molecular ion by a specific 1,5-hydrogen transfer yielding an ion at m/z 224 which is structurally related to the bicyclic compound 4 with its typical fragment ions at m/z 175 and 147. Thermal excitation of the sample increases the intensity of this fragmentation pathway. The fragmentation pattern of 1 and the thermally induced rearrangement reaction has been elucidated by means of isotopic labelling, high-resolution data, metastable ion analysis and some tandem mass spectrometric experiments. Various samples of 1 monohydrate and its commercially available preparations, which are triturates with sodium chloride, differing in the crystal size distribution, showed nearly identical mass spectra on two different magnetic mass spectrometers, provided that the materials were introduced as solids under careful control of the evaporation temperature. The fragmentation via m/z 224 prevails in case of non-crystalline, pre-dissolved samples on one of the instruments used which might be explained by a differing construction of the ion source and the sample cup holder. The conclusions of Mruzek et al. concerning different proportions of stereoisomers in pharmaceutical preparations of 1 lack any analytical evidence.

Chemical Phenomena↗
PubMedDate not supplied

An automated measurement system for characterization of RF and gradient coil parameters.

A fully automated laboratory-based measurement system for characterization of coil system parameters is presented. This method uses an inexpensive personal computer (PC)-controlled stepper motor positioning system in conjunction with a network/spectrum analyzer and an analog-to-digital converter (A/D) board that allows high resolution data acquisition in an unattended manner. A graphical interface was created for complete control of stepper motor movement, measurement, and data acquisition. The system is capable of performing a wide range of measurements that can, either individually or combined, characterize radiofrequency (RF) and gradient coils used in MRI. Measurement methods, theory, and results for conductor and shield current distributions, mutual impedance, and magnetic fields are given. Comparisons with theoretical calculations are included to validate the accuracy and utility of the system.

Calibration↗
PubMed1990

Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.

Structures have been determined of Bacillus stearothermophilus "apo" and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-bisphosphate. The "apo" lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 A to 3 A resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 A resolution data, in a restrained least-squares refinement in which the molecular symmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the "apo"-enzyme. Further refinement proceeded with the isomorphous holo-enzyme from Bacillus stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 A and 1.7 degrees r.m.s. deviation from idealized bond lengths and angles, respectively. Two sulfate ions per subunit were included in the final model of the "apo"-form--one at the substrate binding site and one close to the molecular P-axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the "apo" model. This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with nicotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose 1,6-bisphosphate were also analyzed.

Amino Acid Sequence↗
PubMed1990

Crystallographic refinement of human serum retinol binding protein at 2A resolution.

Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R-factor of 18.1% with 2A resolution data. The protein topology results in an anti-parallel beta-barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.

Amino Acid Sequence↗
PubMed1993

Growth and analysis of crystal forms of toxic shock syndrome toxin 1.

Native toxic shock syndrome toxin 1 (TSST-1) purified from Staphylococcus aureus has been crystallized in four different forms. The highest resolution data (2.05 A) was collected from orthorhombic crystals belonging to the space group C222(1). The unit cell dimensions are a = 108.7 A, b = 177.5 A, c = 97.6 A. Rotation function analysis of this form indicates that there is trimer of toxin molecules in the asymmetric unit with a local 3-fold axis parallel to the crystallographic c axis. Crystals of a double mutant of TSST-1 have been grown which has a single molecule in the asymmetric unit and diffract to 1.9 A. The space group is P2(1) with unit cell parameters of a = 44.4 A, b = 34.0 A, c = 55.2 A, beta = 93.0 degrees.

Bacterial Toxins↗
PubMed1993

Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism.

The crystal structure of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 has been refined at 1.9 A resolution at two different pH values, the pH of crystallization (pH 6.2) and the pH of optimal activity (pH 8.2), to final R-factors of 16.8% and 16.4%, respectively. Both models show good stereochemical quality. Two non-glycine residues have main-chain torsion angles that are located outside the "allowed" regions in a Ramachandran plot. One of them is the nucleophilic residue Asp124, which, together with the two other active site residues His289 and Asp260, is situated in an internal, predominantly hydrophobic cavity. The other residue, Asn148, helps stabilize the conformations of two of these active-site residues, Asp124 and Asp260. Comparison of the models at pH 6.2 and pH 8.2 revealed one major structural difference. At pH 6.2, a salt-bridge is present between the N epsilon 2 atom of His289 and the O delta 1 atom of Asp124, while at pH 8.2, this salt-bridge is absent, indicating that the N epsilon 2 atom of the histidine residue is mostly deprotonated at the pH of optimum activity. This is in agreement with the putative reaction mechanism in which the O delta 1 atom of Asp124 performs a nucleophilic attack on the substrate, resulting in an intermediate ester. This ester is subsequently cleaved by a hydrolytic water molecule. The high-resolution data sets clearly show the exact position of this water molecule. It is in an ideal position for donating a proton to the N epsilon 2 atom of His289 and subsequently cleaving the covalently bound intermediate ester, releasing the alcohol product. Detailed investigation of both refined models showed a number of unusual structural features. Four out of 11 helices contain an internal proline residue other than in the first turn. Two other alpha-helices have adopted in their central part a 3(10) conformation. A novel four-residue turn between a helix and a strand, the alpha beta 4 turn, is located at the site of the bend in the central eight-stranded beta-sheet of the dehalogenase structure.

Amino Acid Sequence↗
PubMed1995

Refined crystal structure of spinach ferredoxin reductase at 1.7 A resolution: oxidized, reduced and 2'-phospho-5'-AMP bound states.

The crystal structure of spinach ferredoxin-NADP(+)-oxidoreductase (FNR), determined by multiple isomorphous replacement at 2.6 A resolution, has been refined at 1.7 A resolution to an R-factor of 17.9%. The structure of FNR bound to the competitive inhibitor 2'-phospho-5'-AMP (P-AMP) has also been refined at 1.7 A to an R-factor of 17.4% and dithionite-reduced/P-AMP-bound FNR has been refined at 2.0 A to an R-factor of 14.9%. The P-AMP-bound structure was used to construct a model for the binding of NADP+. Over 200 solvation sites were included in each structure, and many of the best defined solvation sites stabilize buried turns. A bulk solvent correction obviated the need for a low-resolution data cutoff. An acidic side-chain likely to be responsible for the low pH requirement for crystallization has been identified. Three large networks of the hydrophobic side-chains help define the FNR structure. One of these contains a large cavity far from the active site, which coincides with the lone site of sequence heterogeneity in FNR, and may provide a site for membrane attachment. The reduced structure shows that Ser96 moves toward atom N-5 of FAD and a water molecule moves toward atom N-1 of FAD, while the flavin moiety remains planar. Possible sources of a proton that must be picked up upon reduction are discussed.

Binding Sites↗
PubMed1994

Crystallization and preliminary crystallographic analysis of NADPH:FMN oxidoreductase from Vibrio harveyi.

Crystals of NADPH:FMN oxidoreductase from Vibrio harveyi have been obtained and characterized by X-ray diffraction. This enzyme plays a role in the generation of light in luminescent bacteria by providing reduced FMN to luciferase. Large, high quality crystals were grown using polyethylene glycol 6000 at pH 7.0. They crystallize in the monoclinic space group P2(1) with cell dimensions a = 51.2 A, b = 85.9 A, c = 58.1 A, beta = 109.3 degrees, and diffract to 1.8 A. We expect two molecules per asymmetric unit. High resolution data sets have been recorded and a search is under way for heavy-atom derivatives.

Crystallization↗
PubMed1994

Towards atomic interpretation of F-actin filament three-dimensional reconstructions.

We have recorded dark field images of negatively stained F-actin filaments polymerized with 2 mM MgCl2 and 50 mM KCl with a scanning transmission electron microscope and computed 3-D reconstructions using a helical parameter search to optimize simultaneously the helical repeat length, the radial position of the filament axis, and the helical selection rule. The resulting optimized averaged filament 3-D reconstruction at 2.5 nm resolution is remarkably similar to an atomic model of the F-actin filament. By comparison, several structural features of the reconstruction can be interpreted at the level of distinct secondary structure elements, and predictions made by the atomic model could be verified: for instance, the density connecting the two long-pitch helical strands in our reconstruction co-localizes with an extended beta-hairpin, the "hydrophobic loop" (i.e. residues 262 to 274), which according to the atomic model establishes the major intersubunit contact between the two long-pitch helical strands. The most pronounced structural variations among individual filament 3-D reconstructions were observed in (1) the details of the intersubunit contact pattern between the two long-pitch helical strands, and (2) the exact size and shape of subdomain 2 of the F-actin molecule, which appears rather flexible and easily deformed. In addition, we found that all phenotypes of F-actin filament 3-D reconstructions that arise from small deviations from the optimal helical parameters or from lowering the nominal resolution exhibited stronger intersubunit contacts between than along the two long-pitch helical strands, a structural feature that has been emphasized for a number of F-actin filament 3-D reconstructions in the past. Since this is clearly at variance with the relative strength of the intersubunit contacts as predicted by the atomic model, it may represent an artifactual structural feature arising from low-resolution data or suboptimal helical data processing, and should therefore be interpreted with caution in terms of indicating chemical, mechanical or conformational states of the F-actin filament.

Actins↗
PubMed1995

Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution.

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution using MIR phases in combination with density modification (space group P6; a = 195.6 A, c = 97.6 A; dimer of 1460 amino acid residues/asymmetric unit; VM = 3.26 A3/Da). The refined crystallographic R-value was 0.219 (Rfree = 0.268) using 2-fold restraints with a 4 sigma cutoff and 8.0 to 3.0 A resolution data. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 10(6) Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the center of the dodecamer and contribute to dodecamer stabilization. The "linker" domain, residues 108 to 160, consists of short alpha-helices separated by a loop that fills in the PLP pocket. The third domain, residues 161 to 413, is an alpha/beta domain containing a seven stranded beta-sheet that resembles the PLP-binding domain of the aspartate aminotransferases. The fourth domain, residues 414 to 569, resembles the "small" domain of the aspartate aminotransferases, but is significantly larger due to insertions. The remaining carboxy-terminal domain, residues 570 to 730, is organized into multiple antiparallel loops and seven alpha-helices that help form a deep channel leading to the PLP-binding site.

Amino Acid Sequence↗