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At least 1,261 records · Page 70Linked to original sources
PubMed1986

Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution.

The three-dimensional structure analysis of crystalline fungal catalase from Penicillium vitale has been extended to 2.0 A resolution. The crystals belong to space group P3(1)21, with the unit cell parameters of a = b = 144.4 A and c = 133.8 A. The asymmetric unit contains half a tetrameric molecule of 222 symmetry. Each subunit is a single polypeptide chain of approximately 670 amino acid residues and binds one heme group. The amino acid sequence has been tentatively determined by computer graphics model building (using the FRODO system) and comparison with the known sequence of beef liver catalase. The atomic model has been refined by the Hendrickson & Konnert (1981) restrained least-squares program against 68,000 reflections between 5 A and 2 A resolution. The final R-factor is 0.31 after 24 refinement cycles. The secondary and tertiary structure of the catalase has been analyzed.

Amino Acid Sequence↗
PubMed1987

Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles.

The calculation of induced dipole moments and of their contribution to electrostatic effects in proteins is implemented following the approach of Warshel. Isotropic polarizabilities are assigned to individual atoms, and the resulting deviation from pairwise interactions is treated by a self-consistent iterative procedure. We give a detailed description of how the formalism is implemented in molecular mechanics and molecular dynamics simulation procedures, and report results based on calculations performed on crystal structures of crambin, liver alcohol dehydrogenase and ribonuclease T1. We focus our analysis on evaluating the contribution of polarizability of the protein matrix to electrostatic energies, local fields, to dipole moments of peptide groups and of secondary structure elements in the polypeptide chain. Our calculations confirm that induced dipole moments in proteins provide important stabilizing contributions to electrostatic energies, and that these contributions cannot be mimicked by the usual approximations where either a continuum dielectric constant, or a distance-dependent dielectric function is used. We find that induced protein dipoles appreciably affect the magnitude and direction of local electrostatic fields in a manner that is strongly influenced by the microscopic environment in the protein. Most strongly affected are fields in charged groups that are involved in close interactions with other charged groups, while the influence on local fields of aliphatic groups is marginal. We find, moreover, that induction effects from surrounding protein atoms tend on average to increase peptide dipoles and helix macro-dipoles by about 16%, again reflecting electrostatic stabilization by the protein matrix, and show that (at least in the alpha/beta domain of alcohol dehydrogenase) the contribution of side-chains to this stabilization is significant.

Alcohol Dehydrogenase↗
PubMed1988

Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions.

The bacteriophage T3 connector, which consists of 12 copies of protein gp8, has been studied by image processing of electron micrographs from negatively stained ordered aggregates. A three-dimensional reconstruction of T3 connectors was obtained by collection of tilted views and using the direct Fourier method, up to 2.3 nm resolution. The reconstructed unit cell contains two connectors whose main structural features are essentially identical, but facing in opposite directions. The T3 connector has a height of about 10.9 nm, with two clearly defined domains: a wider one 14.4 nm in diameter, with 12 morphological units in the periphery, and a narrower one, 9.7 nm in diameter. There is a channel clearly defined in the narrower domain that almost closes along the wider domain. Comparison of the three-dimensional structure obtained for the connector of phages T3 and phi 29, and that of the neck extracted from phage phi 29 particles, reveals striking similarities and significant differences. A model for a general connector to account for the common functions carried out by these viral assemblies is discussed together with the possible role of the channel for DNA translocation.

Computer Graphics↗
PubMed1989

Three-dimensional structure of complexes of single-stranded DNA-binding proteins with DNA. IKe and fd gene 5 proteins form left-handed helices with single-stranded DNA.

Specimen-tilting in an electron microscope was used to determine the three-dimensional architecture of the helical complexes formed with DNA by the closely related single-stranded DNA binding proteins of fd and IKe filamentous viruses. The fd gene 5 protein is the only member of the DNA-helix-destabilizing class of proteins whose structure has been determined crystallographically, and yet a parameter essential to molecular modeling of the co-operative interaction of this protein with DNA, the helix handedness, has not been available prior to this work. We find that complexes formed by titrating fd viral DNA with either the fd or IKe gene 5 protein have a left-handed helical sense. Complexes isolated from Escherichia coli infected by fd virus are also found to be left-handed helical; hence, the left-handed fd helices are not an artefact of reconstitution in vitro. Because the proteins and nucleic acid of the complexes are composed of asymmetric units which cannot be fitted equivalently to right-handed and left-handed helices, these results rule out a previous computer graphics atomic model for the helical fd complexes: a right-handed helix had been assumed for the model. Our work provides a defined three-dimensional structural framework within which to model the protein-DNA and protein-protein interactions of two structurally related proteins that bind contiguously and co-operatively on single-stranded DNAs.

DNA, Bacterial↗
PubMed1989

Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2.

A novel method for analysing molecular dynamics trajectories has been developed, which filters out high frequencies using digital signal processing techniques and facilitates focusing on the low-frequency collective motions of proteins. These motions involve low energy slow motions, which lead to important biological phenomena such as domain closure and allosteric effects in enzymes. The filtering method treats each of the atomic trajectories obtained from the molecular dynamics simulation as a "signal". The trajectories of each of the atoms in the system (or any subset of interest) are Fourier transformed to the frequency domain, a filtering function is applied and then an inverse transformation back to the time domain yields the filtered trajectory. The filtering method has been used to study the dynamics of the enzyme phospholipase A2. In the filtered trajectory, all the high frequency bond and valence angle vibrations were eliminated, leaving only low-frequency motion, mainly fluctuations in torsions and conformational transitions. Analysis of this trajectory revealed interesting motions of the protein, including concerted movements of helices, and changes in shape of the active site cavity. Unlike normal mode analysis, which has been used to study the motion of proteins, this method does not require converged minimizations or diagonalization of a matrix of second derivatives. In addition, anharmonicity, multiple minima and conformational transitions are treated explicitly. Thus, the filtering method avoids most of the approximations implicit in other investigations of the dynamic behaviour of large systems.

Binding Sites↗
PubMed1989

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Animals↗
PubMed1989

Enhancer binding protein (EBP1) makes base and backbone contacts over one complete turn of the DNA double helix.

The simian virus 40 (SV40) enhancer consists of multiple DNA sequence motifs that represent the binding sites for a large number of trans-acting factors. We have purified one such factor, EBP1, which binds to a region encompassing the "core" of the SV40 enhancer, and appears to be involved in transcriptional activation. The interaction of EBP1 with its recognition site has been analysed by nuclease protection and by a variety of chemical probes. Enhancer sequences protected from cleavage with DNase I in the presence of EBP1 extend from position 232 to 250 on one strand and from 233 to 251 on the other strand. Methylation protection and alkylation interference studies have identified purine bases and backbone phosphate groups that participate in the formation of a specific EBP1-DNA complex. Within a ten base-pair region, every purine base interferes with binding when methylated and six phosphate groups on each strand interfere with binding when the attached oxygen groups are ethylated. "Footprinting" with hydroxyl radicals, generated by the 1,10-orthophenanthroline-copper ion, revealed sugar residues in the binding site that were protected from cleavage in the presence of EBP1. Computer graphics analyses of the contact point data indicate that EBP1 makes base and backbone contacts with the DNA over one complete turn of the DNA double helix, and suggest a model in which EBP1 makes sequence-specific contacts in the major groove, although binding may be influenced by interactions in the minor groove. Comparison of the EBP1 contact points with that of other known DNA-binding proteins indicates that EBP1 employs a unique mechanism to recognize a specific DNA sequence.

Base Sequence↗
PubMed1990

Three-dimensional reconstruction of native Androctonus australis hemocyanin.

A sample of native 4 x 6-meric hemocyanin of Androctonus australis was negatively stained with the double-layer technique, and was observed by transmission electron microscopy under low-dose conditions with a 50 degree and 0 degree tilt. The three-dimensional reconstruction method from "Single-exposure, random conical tilt series" was then applied. Independent three-dimensional reconstructions were obtained from the top, side and 45 degree views. Despite a pronounced flattening effect, presumably due to the specimen preparation technique, the positions of the 24 subunits composing the oligomer were unequivocally determined. This experiment definitely solves the problem of the architectural organization of the subunits in the cheliceratan 4 x 6-meric hemocyanins. Moreover, distinction between the flip and flop faces and an attenuated rocking effect were observed.

Animals↗
PubMed1991

Human rhinovirus 14 complexed with antiviral compound R 61837.

The binding of the antirhinoviral agent R 61837 to human rhinovirus 14 has been examined by X-ray crystallographic methods. The compound R 61837 binds in the same pocket (underneath the canyon floor) as the "WIN" antirhinoviral agents. It does not penetrate as far into the pocket but causes similar conformational changes in the virus capsid. The movement of residues 1217 to 1221 of viral protein 1 (in the "FMDV loop") is more pronounced for R 61837 than for WIN compounds. Although both R 61837 and WIN antiviral agents partially fill the same hydrophobic pocket, atomic binding interactions differ, showing that considerable diversity in the nature of antiviral agents is possible.

Antiviral Agents↗
PubMed1992

Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies.

Computer-aided model building techniques have been used to construct three-dimensional model structures for hamster beta 2 adrenergic receptor. Experimental data were used as constraints to guide the model building procedure, and a number of rather strict criteria were applied to assess the physical plausibility of model structures. We present details of our best model structure to date, which is consistent with a large body of experimental data. We also discuss in detail our model building procedures and evaluation criteria, which we believe may be of general utility in modeling projects.

Amino Acid Sequence↗
PubMed1990

A computergraphic investigation into the pharmacological role of the THC-cannabinoid phenolic moiety.

There has been much debate as to the nature of the cannabinoid-receptor interaction, whether by traditional interpretation or by means of membrane perturbation. Whichever hypothesis is correct, the structural requirements for pharmacological action need determination. Here, we report a computergraphic investigation into the role of the phenolic hydroxyl moiety in such a receptor interaction. It has been determined by molecular mechanics energy calculations and volume map determinations that the proton of the hydroxyl group may be involved in hydrogen bonding at the putative receptor site.

Computer Graphics↗
PubMed1990

The rational design and synthesis of haptens having specific activity as full agonists or full antagonists at the benzodiazepine receptor.

The use of computer graphics hardware, in conjunction with molecular modeling software, has allowed for a structural analysis of compounds that bind to the benzodiazepine receptor (BZR) in the nM range. The definition of additional binding requirements together with steric and/or hydrophobic limitations has been directly correlated with profiles of in vivo activity, both for full agonists and full antagonists. This information has been used for the rational design of haptens that contain the antigenic determinants necessary for the production of antibodies specific for either full agonists or for full antagonists at the BZR. The synthesis of these novel compounds has been completed.

Animals↗
PubMed1991

Corpus callosum: multiple parameter measurements in rodents and humans.

A magnified drawing of a human or a rodent corpus callosum is traced on a digitizing tablet. From this tracing the computer calculates callosal area, perimeter, length, and 99 widths, one for each percentile location along the longitudinal axis of the callosum. In addition, the human program encloses the callosum within a rectangle to obtain several other measures. The use of percentile widths allows one to generate a callosum profile to compare different clinical groups or different species. The human callosum program is compared to one recently reported by another research group.

Algorithms↗
PubMed1991

Chemosensory responses to mixtures: a model based on composition of receptor cell types.

Previous mixture models have assumed that members of a population of chemoreceptor cells are homogeneous in type, i.e., with either single shared or multiple independent receptor sites. In reality, many chemosensory systems actually consist of a heterogeneous population of receptor cells, consisting of both highly specific cells as well as more broadly and variably tuned cells. A mixed receptor composition model for binary mixtures is described which can be applied to chemosensory systems with heterogeneous receptor cell compositions. The model incorporates information on a) the number of receptor sites/transduction processes per cell, b) the specificity of receptor cells, and c) the contribution of the magnitude of response of each receptor cell to the overall response magnitude of the population of all receptor cells. The predictions of this model can be compared to behavioral responses of animals towards binary mixtures, or at any level of sensory processing which involves the input of the receptor cell population, in order to detect possible mixture interactions.

Animals↗
PubMed1996

A demonstration of virtual reality in free-flying honeybees: Apis mellifera.

Two experiments are reported on virtual reality illusion in free-flying honeybees. In the first experiment, subjects are trained on a simultaneous discrimination between two colored targets, one of which contains a sucrose reward. The ability to be influenced by a virtual reality illusion was assessed during an extinction test in which the training stimuli were a mirage of those used during acquisition. The results indicate that the bees consistently attempt to land on the previously rewarded color despite the fact that it is not there. In a second experiment, bees were unable to discriminate between two simultaneously presented, identically colored targets--one of which was real, the other a mirage.

Animals↗
PubMed1985

A high-speed point plotter for vision research.

An electronic interface is described that allows high speed plotting of points on an oscilloscope under the control of a computer. The storage and fast data manipulation done by the interface permit inexpensive computers of modest performance to produce complex displays which could otherwise be produced only by costly high speed computer graphics systems.

Data Display↗
PubMed1985

Intrinsic connectivity and receptive field properties in visual cortex.

In order to obtain insights into the mechanisms by which the cells in primary visual cortex generate their receptive field properties, we have investigated the intrinsic cortical circuitry by intracellular recording and dye injection. The dye injection technique in combination with 3-dimensional computer graphic reconstructions from serial sections allows us to visualize the full dendritic and axonal arbors of cells. We have also studied cells that are postsynaptic to the injected cells by serial EM reconstruction of the postsynaptic dendrites. Taken together, this methodology has extended our knowledge of interlaminar and horizontal cortical connections, and we present hypotheses on the relationship between these connections and specific receptive field features.

Animals↗
PubMed1987

A versatile programmable pattern generator.

A versatile visual pattern generator is described that can be programmed by a microcomputer and is developed as a part of a portable visual evoked potential analysis system. The hardware is contained on one printed circuit board (3" X 10", 7.5 X 25.5 cm) residing in an interface connector of a microcomputer (Apple II). The generator produces signals for commercial 50 Hz video monitors; a calibration procedure based on a photocell measurement corrects for the non-linear voltage intensity characteristic of the phosphor of the video monitor.

Computer Graphics↗