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O Byron

Publications and source records attributed to O Byron.

27 records · Page 2Linked to original sources
PubMed1997

DT diaphorase exists as a dimer-tetramer equilibrium in solution.

The quaternary behaviour of DT diaphorase in solution has been investigated by hydrodynamics under a range of conditions. At neutral pH DT diaphorase is shown to exist as a tightly-associated homodimer in a dimer-tetramer equilibrium. Concentrations of the chaotropic agent potassium thiocyanate (KSCN) of greater than 200 mM result in irreversible loss of the FAD cofactor and denaturation of the homodimer though this agent appears to be ineffective in disrupting intermolecular association. These data conform to a model in which under extreme dissociation conditions, the folded dimer is in equilibrium with the unfolded monomer and are consistent with evidence from the X-ray structure and proposed catalytic mechanism where both monomers are catalytically interdependent.

Animals↗
PubMed1997

Characterisation of the low affinity interaction between rat cell adhesion molecules CD2 and CD48 by analytical ultracentrifugation.

CD2 is a cell adhesion molecule found on the plasma membrane of T-lymphocytes. Its counter-receptor in rat is the structurally related CD48. This interaction is believed to contribute to the adhesion of T-cells to other cells such as cytotoxic targets and antigen presenting cells. Cell-cell adhesion involves the formation of multiple cell adhesion molecule complexes at the cell surface and if cell-cell de-adhesion is to occur, these complexes need to be disrupted. The affinities of cell adhesion molecule interactions are suggested to be relatively weak to allow this de-adhesion of cell-cell interactions. The CD2/CD48 interaction has been studied using recombinant extracellular proteins and the affinity of the interaction of soluble recombinant rat CD2-CD48 has been determined (at 37 degrees C) using surface plasmon resonance (and shown to be weak), with the dissociation constant Kd = 60-90 microM. The values determined by surface plasmon resonance results could be affected by the immobilisation of the ligand on the chip and any self-association on the chip. We used three different analytical ultracentrifuge procedures which each allowed the interaction to be studied in free solution without the need for an immobilisation medium. Both sedimentation equilibrium (using direct analysis of the concentration distribution and also modelling of molecular weight versus concentration data) and sedimentation velocity at 5 degrees C yielded dissociation constants in the range of 20-110 microM, supporting the surface plasmon resonance findings showing that binding between these cell adhesion molecules is relatively weak. These studies also ruled out the presence of any significant self-association of the reactants which could lead to systematic error in the surface plasmon resonance results.

Animals↗
PubMed1997

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.

Algorithms↗
PubMed1997

Physical characterization and ATPase activity of 14S dynein fractions from Tetrahymena thermophila.

Using anion-exchange fast protein liquid chromatography, 14S dynein was separated into four fractions (designated 1-4). These fractions were distinguished with respect to polypeptide composition, and at least four unique heavy chains were identified. Each fraction was shown to exhibit ATPase activity. Fraction 2 has a specific activity 2-3 times greater than that of fractions 1, 3, and 4; the fractions showed a consistent trend of decreasing activity in the order 2 > 3 > 1 > 4. In all cases, the specific ATPase activity was reduced by high ionic strength, in contrast to 22S dynein, which was previously shown to exhibit increased activity under identical conditions. Electron microscopy analysis revealed that the four fractions of 14S dynein were structurally distinct. Fraction 1 comprises two globular head domains interconnected via two stems; fraction 2 consists of at least two clearly different globular structures; fraction 3 is a single globular head; and fraction 4 comprises three globular head domains interconnected by three stems to a basal structure. Further structural characterization using hydrodynamic techniques enabled a determination of mass and sedimentation coefficient for each fraction. Fraction 1 had a mass of 654 kDa and a sedimentation coefficient of 20.1 S. Fraction 2 had a variable mass due to association (616-966 kDa), and a sedimentation coefficient of 16.6 S, whereas fractions 3 and 4 had variable sedimentation coefficients but were of mass 701 kDa and 527 kDa respectively. Where possible, hydrodynamic parameters were utilized, in conjunction with electron microscopy data, to construct low-resolution hydrodynamic bead models to represent the fractions. Optimal models, which were consistent with all the available data, were produced for fractions 1 and 4. Bead modelling was also carried out for 22S dynein, using previously published data, to validate the 14S dynein modelling.

Animals↗
PubMed1996

Investigations into the molecular size and shape of tomato extensin.

The molecular characteristics of soluble extensin from tomato have been investigated. An apparent molecular mass greater than 240 kDa has been previously observed with the shape-dependent method of gel-filtration chromatography [Brownleader and Dey (1993) Planta (Berlin) 191, 457-469]. Tomato extensin is a heavily glycosylated protein that does not migrate into SDS/polyacrylamide gels. This shape-dependent behaviour raises doubts about agreement between the observed apparent mass and the absolute value. The molecular mass measured with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was 72.3 kDa, with no evidence of any other species except a doubly charged ion. The sample was therefore considered to be monodisperse under the conditions used. Electron microscopy of soluble extensin showed the presence of particles 40-50 nm in length and 2.0-2.5 nm in width. A minority of these particles showed a central 'kink'. A number of smaller and generally wider particles (20 nm x 2-4 nm) were considered to be folded monomers and larger particles were thought to be dimers. Sedimentation analysis showed that extensin exists in a rapid monomer-dimer equilibrium in the concentration range and buffer used. Sedimentation equilibrium data gave a Kd of 8.5 microM and sedimentation velocity data generated a Kd between 1 and 10 microM. The concentration dependence of the measured sedimentation coefficient was used, together with hydrodynamic bead modelling, to define plausible shapes for monomer and dimer. This suggests that monomeric extensin is an elongated rod of length 40 nm and width 2 nm, which forms staggered dimers of average length 50 nm and width 3 nm. Extensin is an integral component of the primary cell wall. The physical characteristics (size, shape and form) of the rod-like extensin have been evaluated in this paper so that the role that extensin plays in primary cell wall architecture and during plant disease resistance can be more fully understood.

Cells, Cultured↗
PubMed1996

Crystal structure of a PDZ domain.

PDZ domains (also known as DHR domains or GLGF repeats) are approximately 90-residue repeats found in a number of proteins implicated in ion-channel and receptor clustering, and the linking of receptors to effector enzymes. PDZ domains are protein-recognition modules; some recognize proteins containing the consensus carboxy-terminal tripeptide motif S/TXV with high specificity. Other PDZ domains form homotypic dimers: the PDZ domain of the neuronal enzyme nitric oxide synthase binds to the PDZ domain of PSD-95, an interaction that has been implicated in its synaptic association. Here we report the crystal structure of the third PDZ domain of the human homologue of the Drosophila discs-large tumour-suppressor gene product, DlgA. It consists of a five-stranded antiparallel beta-barrel flanked by three alpha-helices. A groove runs over the surface of the domain, ending in a conserved hydrophobic pocket and a buried arginine; we suggest that this is the binding site for the C-terminal peptide.

Adaptor Proteins, Signal Transducing↗
PubMed1994

Modeling the bacterial protein toxin, pneumolysin, in its monomeric and oligomeric form.

Pneumolysin is a member of the family of related bacterial thiol-activated toxins, which share structural similarities and a proposed common cytolytic mechanism. Currently the molecular mechanism of membrane damage caused by these toxins remains a matter of controversy. A prerequisite for defining this mechanism is a detailed knowledge of the monomeric and oligomeric pneumolysin structures. We present for the first time details of the monomeric structure of a thiol-activated toxin, pneumolysin. Electron microscope images of metal-shadowed pneumolysin monomers show an asymmetric molecule composed of four domains. We have studied the conformation of pneumolysin monomer by low resolution hydrodynamic bead modeling procedures. The bead model dimensions and shape are derived solely from the electron micrographs. The bead model has been evaluated in terms of the predicted solution properties, which in turn have been compared to the experimental values of the sedimentation coefficient, s(20,w)0, obtained by analytical ultracentrifugation and the intrinsic viscosity, [eta]. Pneumolysin oligomers, observed as ring- and arc-shaped structures, were also examined by electron microscopy. Metal shadowing and negative staining methods were used to establish the overall dimensions of the oligomer and were used to produce a morphological model for the oligomer, incorporating monomer subunits based on the hydrodynamic bead model.

Animals↗