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At least 235 records · Page 13Linked to original sources
PubMed1994

Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.

The structure of the bacteriophage phi X174 was examined in a 2.7 A resolution map and refined, using 6.0 A to 3.0 A resolution data with F > or = 5 sigma (F). The final R-factor was 20.9% and the root-mean-square deviation from idealized bond lengths was 0.021 A. The Hendrickson-Konnert refinement was restrained by the phases derived from the molecular replacement icosahedral averaging procedure. The mature phage capsid consists of 60 copies of the F protein with 426 amino acids, the G protein with 175 amino acids and the J protein with 37 amino acids, as well as 12 copies of the H protein with 328 amino acids. The entire polypeptide chain of the F and G protein, all but the first N-terminal residue of the J protein, and 178 solvent molecules were included in the refinement calculations. The secondary structural features of the F, G and J proteins and their interactions with each other are described. The majority of the protein-protein interactions are between the icosahedral 5-fold related interfaces of the F and of the G proteins. These pentameric units of the F and G proteins form the 9S and 6S assembly intermediates, respectively. The J protein lacks any secondary structure and acts as a linking arm between the icosahedral 5-fold related F proteins. Water molecules were introduced only after phase extension to 2.7 A resolution had been completed. The F protein is associated with lower "thermal" parameters and exhibits greater water order in its environment than the G and J proteins. The largest thermal parameters occur in residues on the viral surface. The solvent contributes to the interactions between the proteins. There is an interface of solvent molecules between the F and the G pentamers which stabilizes the pentameric G protein spikes in a crater centered at each of the icosahedral 5-fold vertices of the F protein capsid. Sequence alignments of the F, G and J amino acid sequences for the homologous bacteriophages G4, alpha 3, phi K and phi X174 with respect to the phi X174 structure demonstrated the conservation of functionally important residues on the viral surface.

Amino Acid Sequence↗
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↗
PubMed2004

On the potential of normal-mode analysis for solving difficult molecular-replacement problems.

Molecular replacement (MR) is the method of choice for X-ray crystallographic data phasing when structural data of suitable homologues are available. However, MR may fail even in cases of high sequence homology when conformational changes arising for example from ligand binding or different crystallogenic conditions come into play. In this work, the potential of normal-mode analysis as an extension to MR to allow recovery from such drawbacks is demonstrated. Three examples are presented in which screening for MR solutions with templates perturbed in the direction of one or two normal modes allows a valid MR solution to be found where MR using the original template failed to yield a model that could ultimately be refined. It has been shown recently that half of the known protein movements can be modelled by displacing the studied structure using at most two low-frequency normal modes. This suggests that normal-mode analysis has the potential to break tough MR problems in up to 50% of cases. Moreover, even in cases where an MR solution is available, this method can be used to further improve the starting model prior to refinement, eventually reducing the time spent on manual model construction (in particular for low-resolution data sets).

Carrier Proteins↗
PubMed2006

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules.

The energetics and hydrogen bonding pattern of water molecules bound to proteins were mapped by analyzing structural data (resolution better than 2.3A) for sets of uncomplexed and ligand-complexed proteins. Water-protein and water-ligand interactions were evaluated using hydropatic interactions (HINT), a non-Newtonian forcefield based on experimentally determined logP(octanol/water) values. Potential water hydrogen bonding ability was assessed by a new Rank algorithm. The HINT-derived binding energies and Ranks for second shell water molecules were -0.04 kcal mol(-1) and 0.0, respectively, for first shell water molecules -0.38 kcal mol(-1) and 1.6, for active site water molecules -0.45 kcal mol(-1) and 2.3, for cavity water molecules -0.55 kcal mol(-1) and 3.3, and for buried water molecules -0.56 kcal mol(-1) and 4.4. For the last four classes, similar energies indicate that internal and external water molecules interact with protein almost equally, despite different degrees of hydrogen bonding. The binding energies and Ranks for water molecules bridging ligand-protein were -1.13 kcal mol(-1) and 4.5, respectively. This energetic contribution is shared equally between protein and ligand, whereas Rank favors the protein. Lastly, by comparing the uncomplexed and complexed forms of proteins, guidelines were developed for prediction of the roles played by active site water molecules in ligand binding. A water molecule with high Rank and HINT score is unlikely to make further interactions with the ligand and is largely irrelevant to the binding process, while a water molecule with moderate Rank and high HINT score is available for ligand interaction. Water molecule displaced for steric reasons were characterized by lower Rank and HINT score. These guidelines, tested by calculating HINT score and Rank for 50 water molecules bound in the active site of four uncomplexed proteins (for which the structures of the liganded forms were also available), correctly predicted the ultimate roles (in the complex) for 76% of water molecules. Some failures were likely due to ambiguities in the structural data.

Binding Sites↗
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↗
PubMed2001

Effect of windowing and zero-filled reconstruction of MRI data on spatial resolution and acquisition strategy.

Standard, MR spin-warp sampling strategies acquire data on a rectangular k-space grid. That method samples data from the "corners" of k-space, i.e., data that lie in a region of k-space outside of an ellipse just inscribed in the rectangular boundary. Illustrative calculations demonstrate that the data in the corners of k-space contribute to the useful resolution only if an interpolation method such as a zero-filled reconstruction is used. The consequences of this finding on data acquisition and data windowing strategies are discussed. A further implication of this result is that the spatial resolution of images reconstructed with zero-filling (but without radial windowing) is expected to display angular dependence, even when the phase- and frequency-encoded resolutions are identical. This hypothesis is experimentally verified with a slit geometry phantom. It is also observed that images reconstructed without zero-filling do not display the angular dependence of spatial resolution predicted solely by the maximal k-space extent of the raw data. The implications of these results for 3D contrast-enhanced angiographic acquisitions with elliptical centric view ordering are explored with simulations.

Filtration↗
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↗
PubMed2006

Postconflict behavior in captive western lowland gorillas (Gorilla gorilla gorilla).

Postconflict (PC) behaviors, including reconciliation and consolation, have been observed in many primate and several nonprimate species. Using the PC-matched control (MC) method, PC behavior was examined in two groups (n=13) of captive western lowland gorillas, a species for which no conflict resolution data have been published. Analyses of 223 conflicts showed significantly more affiliation between former opponents after a conflict when compared to control periods, indicating reconciliation. Results also showed significantly more affiliation between the victim and a third-party after a conflict, indicating consolation. Both solicited and unsolicited consolation were observed. The majority of the affiliative interactions observed for both reconciliation and consolation were social proximity, which suggests that unlike most nonhuman primates, proximity, rather than physical contact, may be the main mechanism for resolving conflicts in western lowland gorillas. PC behavior was not uniform throughout the groups, but rather varied according to dyad type.

Animals↗
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↗
PubMed2004

From cells to tissues: fluorescence confocal microscopy in the study of histological samples.

Our knowledge of the genetic mechanisms controlling cell proliferation and differentiation usually originates from in vitro cultured cell line models. However, the definition of the molecular switches involved in control of homeostasis and the understanding of the changes occurring in neoplastic transformation require looking at single cells as the components of a complex tissue network. Histological examination of tissue samples can gain a substantial amount of information from high-resolution fluorescence analysis. In particular, confocal microscopy can help in the definition of functional pathways using multiparameter analysis. In this report, we present acquisition and analysis procedures to obtain high-resolution data from tissue sections. Confocal microscopy coupled to computational restoration, statistical evaluation of spatial correlations, and morphological analysis over large tissue areas were applied to colorectal samples providing a molecular fingerprint of the biological differences inferred from classical histological examination.

Animals↗
PubMed2006

Quantitative microscopy reveals 3D organization and kinetics of endocytosis in rat hepatocytes.

In order to demonstrate the power of quantitative microscopy, the endocytic apparatus of rat hepatocytes was reexamined using in situ liver and short term cultured hepatocyte couplets that were allowed to internalize endocytic markers for various time intervals. Correlative confocal light and electron microscopy demonstrate a tubulovesicular reticulum representing the endocytic apparatus. Volume and membrane area account for 2% of cell volume and 30% plasma membrane surface. Colocalization analysis demonstrated that pathway-specific ligands and fluid-phase markers enter EEA1-positive vesicles, the early endosomal compartment, immediately after internalization. These vesicles are translocated rapidly from basolateral to perinuclear and apical locations. Ligands are sorted within 5 min to their respective pathways. Sequential colocalization of an asialoglycoprotein-pulse with rab7 and lamp3 demonstrates that early endosomes change into or fuse with late endosomes and lysosomes. Alternatively, markers are sequestered into the common endosome consisting of rab11-positive, long tubules that originate from early endosomes and show an affinity for the transcytotic marker pIgA and its receptor. This compartment mediates transcytosis by delivering the receptor-ligand complex to the subapical compartment, a set of apical, rab11-positive vesicles, which are connected to the tubular reticulum. We conclude that vesicular traffic between preexisting compartments, maturation or fusion of endocytic organelles, and transport in tubules act in concert and together mediate transport between compartments of a tubulovesicular endocytic apparatus. In addition, we show that quantitative microscopy using high resolution data sets can detect and characterize kinetics of various parameters thus adding a dynamic component to 3D information.

Animals↗
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↗
PubMed2004

Electron ionization mass spectrometry as a tool for the investigation of the ortho effect in fragmentation of some Schiff bases derived from amphetamine analogs.

The electron ionization-induced fragmentation patterns of three forensically relevant Schiff bases, originating from the condensation between 2-, 3- and 4-methoxyamphetamine and the corresponding ketones, were studied. The proposed fragmentation routes and ion structures are supported by high-resolution data and B/E linked-scan and mass-analyzed ion kinetic energy spectra. The rationalization of the ortho effect, which is responsible for the formation of the [M-OCH3] fragment in the case of the imine bearing ortho-substituted methoxy group, is given.

Amphetamines↗