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Biomedical subjects

D Chamberlain

Publications and source records attributed to D Chamberlain.

At least 37 records · Page 2Linked to original sources
PubMed1998

A synthetic holliday junction is sandwiched between two tetrameric Mycobacterium leprae RuvA structures in solution: new insights from neutron scattering contrast variation and modelling.

The interaction between homologous DNA molecules in recombination and DNA repair leads to the formation of crossover intermediates known as Holliday junctions. Their enzymatic processing by the RuvABC system in bacteria involves the formation of a complex between RuvA and the Holliday junction. To study the solution structure of this complex, contrast variation by neutron scattering was applied to Mycobacterium leprae RuvA (MleRuvA), a synthetic analogue of a Holliday junction with 16 base-pairs in each arm, and their stable complex. Unbound MleRuvA was octameric in solution, and formed an octameric complex with the DNA junction. The radii of gyration at infinite contrast were determined to be 3.65 nm, 2.74 nm and 4.15 nm for MleRuvA, DNA junction and their complex, respectively, showing that the complex was structurally more extended than MleRuvA. No difference was observed in the presence or absence of Mg2+. The large difference in RG values for the free and complexed protein in 65% 2H2O, where the DNA component is "invisible", showed that a substantial structural change had occurred in complexed MleRuvA. The slopes of the Stuhrmann plots for MleRuvA and the complex were 19 and 15 or less (x10(-5)), respectively, indicating that DNA passed through the centre of the complex. Automated constrained molecular modelling based on the Escherichia coli RuvA crystal structure demonstrated that the scattering curve of octameric MleRuvA in 65% and 100% 2H2O is explained by a face-to-face association of two MleRuvA tetramers stabilised by salt-bridges. The corresponding modelling of the complex in 65% 2H2O showed that the two tetramers are separated by a void space of about 1-2 nm, which can accommodate the width of B-form DNA. Minor conformational changes between unbound and complexed MleRuvA may occur. These observations show that RuvA plays a more complex role in homologous recombination than previously thought.

Amino Acid Sequence↗
PubMed1998

Possible arrangement of the five domains in human complement factor I as determined by a combination of X-ray and neutron scattering and homology modeling.

Human factor I is a multidomain plasma serine protease with one factor I-membrane attack complex (FIMAC) domain, one CD5 domain, two low-density lipoprotein receptor (LDLr) domains, and one serine protease (SP) domain and is essential for the regulation of complement. The domain arrangement in factor I was determined by X-ray and neutron scattering on serum-derived human factor I (sFI) and recombinant insect cell factor I (rFI). While the radii of gyration of both were the same at 4.05 nm and both had overall lengths of 14 nm, the cross-sectional radii of gyration were different at 1.70 nm for sFI and 1.57 nm for rFI. This difference was attributed to their different means of glycosylation which is complex-type for sFI and high-mannose-type for rFI. Homology models were constructed for the FIMAC, LDLr, and SP domains of factor I using related crystal structures, and CD5 was represented as a globular protein by referencing its electron microscopy dimensions. In these models, 38 of the 40 Cys residues in factor I were predicted to form internal disulfide bridges. The two remaining Cys residues at the N terminus of the FIMAC domain and at the center of the first LDLr domain were potentially not bridged. It was postulated that, if these two Cys residues were bridged to each other, the FIMAC, CD5, and LDLr-1 domains would form a compact triangular arrangement. This hypothesis was tested by automated scattering curve fit searches based on 9600 bilobal models, setting the FIMAC, CD5, and LDLr-1 domains as one lobe and the large SP domain as the other lobe. The searches gave a single small family of similar structures with a separation of 5.9 nm between the centers of the lobes which gave similar good X-ray and neutron fits for both sFI and rFI, despite the different glycosylations of sFI and rFI. These best-fit structures for factor I showed that this domain model is plausible, and suggested that the SP and the CD5 and LDLr-1 domains may present exposed surfaces in factor I whose roles are to interact separately with its substrates C3b and C4b and with cofactor proteins.

Amino Acid Sequence↗
PubMed1998

Adenovirus-mediated interleukin-10 gene transfer inhibits post-transplant fibrous airway obliteration in an animal model of bronchiolitis obliterans.

Bronchiolitis obliterans, a form of chronic allograft rejection characterized by progressive fibrous obliteration of the airways, is the major obstacle limiting prolonged survival of lung transplant recipients. To date, no effective therapy against this fatal complication exists. Interleukin-10 (IL-10), an anti-inflammatory and immunosuppressive cytokine, inhibits various T cell and antigen-presenting cell functions. We examined the effect of IL-10 in an animal model for bronchiolitis obliterans. A heterotopic tracheal transplant model was used. IL-10 was administered to the recipient either in its recombinant form by osmotic minipump or by adenoviral-mediated IL-10 gene transfer (Ad5E1mIL-10). Successful gene transfection and expression was confirmed by measuring circulating IL-10 protein. Tracheal allografts were assessed histologically based on a scoring system. IL-10 administration (in recombinant form or by gene transfer) inhibited the development of fibrous airway obliteration 3 weeks after transplantation in comparison to untreated controls (p < 0.05). This was demonstrated only if the delivery was initiated 5 days after transplantation and not if it was started at the time of transplantation. A single administration of the gene construct was sufficient to achieve the desired effect. We have shown that IL-10 can prevent the development of airway fibro-obliteration in this model. Gene transfection at a site distant from a graft can be used to produce a desired effect on the graft. IL-10 may be of major importance in the control of post-transplant bronchiolitis obliterans. The timing of its administration is critical and further studies are required to determine the mechanisms underlying the observed effects of IL-10.

Adenoviruses, Human↗
PubMed1998

Molecular structures from low angle X-ray and neutron scattering studies.

Molecular structures can be extracted from solution scattering analyses of multidomain or oligomeric proteins by a new method of constrained automated scattering curve fits. Scattering curves are calculated using a procedure tested by comparisons of crystal structures with experimental X-ray and neutron data. The domains or subunits in the protein of interest are all represented by atomic coordinates in order to provide initial constraints. From this starting model, hundreds or thousands of different possible structures are computed, from each of which a scattering curve is computed. Each model is assessed for steric overlap, radii of gyration and R-factors in order to leave a small family of good fit models that corresponds to the molecular structure of interest. This method avoids the tedium of curve fitting by hand and error limits on the ensuing models can be described. For single multidomain proteins, the key constraint is the correct stereochemical connections between the domains in all the models. Successful applications to determine structures are summarised for the Fab and Fc fragments in immunoglobulin G, the three domain pairs in the Fc subunit of immunoglobulin E and the seven, domains in carcinoembryonic antigen. For oligomeric proteins, the key constraint is provided by symmetry and successful analyses were performed for the association of the monomers of the bacterial amide sensor protein AmiC to form trimers and pentameric serum amyloid P component to form decameric structures. The successful analysis of the heterodimeric complex of tissue factor and factor VIIa required the use of constraints provided from biochemical data. The outcome of these analyses is critically appraised, in particular the biological significance of structures determined by these solution scattering curve fits.

Animals↗
PubMed1998

Human complement factor I: its expression by insect cells and its biochemical and structural characterisation.

Factor I is a five-domain plasma serine protease which is essential for the regulation of the complement system. In order to express this, the factor I coding sequence was cloned into a recombinant baculovirus system, which was used to infect Trichoplusia ni cells. Using the native factor I leader sequence, recombinant factor I (rFI) was secreted into the culture medium. Purified rFI was recognised by polyclonal antisera and by the factor I-specific monoclonal antibody MRC-OX21. SDS PAGE showed that rFI was processed into two chains with molecular weights of 48,000 and 36,000. Amino acid sequence analysis showed that the N-terminal sequences of the rFI chains were the same as those of serum-derived factor I (sFI), confirming that processing was correct. Since both molecular weights were less than those observed for sFI, this is attributed to the replacement of complex-type oligosaccharides by high mannose ones in rFI. C3(NH,) cleavage assays showed that rFI had 55% the activity of sFI. Circular dichroism and Fourier transform infrared spectroscopy showed that the protein folding of rFI and sFI were very similar. Both had a secondary structure low in alpha-helix and high in beta-sheet, as expected from crystal structure and multiple sequence alignment analyses. It is inferred that the reduced activity of rFI is attributable to its changed glycosylation. The availability of rFI and structures for the domains in factor I makes possible new approaches to determine the molecular basis of its interactions with factor H and C3b.

Animals↗
PubMed1998

A rationale for staged teaching of basic life support.

Basic life support is a crucial part of the Chain of Survival. Unfortunately, however the skill is complex and cannot readily be acquired--let alone retained--in the course of a single training session. Although the problem has long been recognised, no new strategies have been widely implemented to counter the problem. We believe that staged teaching of CPR might provide a solution, and we have devised a program to test this new method. It involves three stages of instruction that we have called bronze, silver, and gold standards. The bronze standard involves opening the airway and providing chest compression without active ventilation: this alone may widen the window of opportunity for successful defibrillation in adult victims in out-of-hospital cardiac arrest. Ventilation is introduced at silver stage using a ratio of 50:5, with emphasis on its value in the resuscitation of children being used as motivation to bring people back for a second period of instruction. The gold stage teaches conventional CPR. A pilot study has been encouraging and a randomized trial on skill acquisition and skill retention is planned.

Adult↗
PubMed1998

Utility of electron microscopy in the assessment of transthoracic needle lung biopsy specimens.

RATIONALE AND OBJECTIVES: The authors determine the usefulness of electron microscopy (EM) in the workup of patients with certain intrathoracic masses undergoing transthoracic needle biopsy (TNB). METHODS: Over a 4-year period, 1603 patients underwent TNB at our institution. Of these, 79 had EM examination of the aspirated material. The study is a retrospective review of this latter group. Previous use of EM for TNB had suggested that it may he helpful in those with pleural, chest wall, and mediastinal lesions. The 40 men and 39 women had pulmonary (n = 49), mediastinal (n = 17), pleural (n = 10), and chest wall (n = 3) lesions. RESULTS: The adequate specimen rate was 59% (47 of 79) for light microscopy (LM) and 37% (29 of 79) for EM. Of the 28 patients with satisfactory specimens for both LM and EM, the correct diagnosis was obtained by LM 79% (22 of 28) and EM 96% (27 of 28) of the time. Electron microscopy was most helpful in patients with mediastinal (6 of 6 correct versus 3 of 6 for LM) and pleural (3 of 3 versus 1 of 3) lesions. CONCLUSIONS: In specific circumstances, EM can be a very useful adjunct to LM in patients undergoing TNB. Problems with sample adequacy must be addressed.

Adult↗
PubMed1998

Analogy and solution scattering modelling: new structural strategies for the multidomain proteins of complement, cartilage and the immunoglobulin superfamily.

Many immunologically relevant proteins possess multidomain structures. Molecular structures both at the level of the individual domain and that of the intact protein are required for a full appreciation of function and control. Two recently developed structural approaches are reviewed here. Analogy modelling methods are based on the current understanding of many protein structures, and make possible the identification of folds for superfamilies of unknown structures. An integrated multidisciplinary predictive approach has been successfully applied to the von Willebrand factor type A, proteoglycan tandem repeat and factor I/membrane attack complex domains. The available experimental and predictive evidence is assembled in order to identify a known three-dimensional structure related to the unknown one of interest. Neutron and X-ray scattering curve modelling provides information on the full multidomain structure in solution. As scattering curves can be calculated from known atomic structures, the present availability of structures for many domains in conjunction with tight constraints based on these structures and the covalent connections between them results in a small family of allowed best-fit structures for a given scattering curve. The curve-fit procedure can be automated, and whole multidomain structures can be determined to a positional precision of the order of 0.2-1 nm. Such models are informative on the steric accessibility of each domain and their functional activity, and this is illustrated for antibody, cell-surface and complement proteins.

Animals↗
PubMed1997

Lymphocytic airway infiltration as a precursor to fibrous obliteration in a rat model of bronchiolitis obliterans.

BACKGROUND: Bronchiolitis obliterans is the most significant complication adversely affecting prolonged survival of lung allograft recipients. The evolution from the initial insult to the final pathologic entity is largely unknown. The aim of this study was to characterize the evolution of transplant-induced fibrous airway obliteration in a rat tracheal transplant model of bronchiolitis obliterans. METHODS: Tracheal segments were transplanted from Brown Norway rats to Brown Norway rats (isografts) or to Lewis rats (allografts). Grafts were implanted into a subcutaneous pouch and an abdominal omental wrap. They were harvested at 14 different time points (from 1 day to 1 year after transplantation) and assessed histologically. RESULTS: The fibrous airway obliteration developed only in allografts showing a triphasic time course: an initial ischemic phase (observed in both isografts and allografts) was followed by a marked lymphocytic infiltrative phase with complete epithelial loss (observed only in allografts, P<0.01), and finally by an obliterative phase with fibrous obliteration of the allograft airway lumen (P<0.01). CONCLUSIONS: This animal model shows a distinct and reproducible triphasic time course in the development of obliterative airway lesions in allografts. It confirms that the mechanism leading to airway obliteration is immune mediated as only allografts showed this lesion and that lymphocytic infiltration is a precursor of the lesion in this model. The insights into the different phases demonstrated may lead to novel approaches regarding the type and timing of therapeutic interventions.

Animals↗
PubMed1997

Oligomerization of the amide sensor protein AmiC by x-ray and neutron scattering and molecular modeling.

AmiC is the negative regulator of the amidase operon which is involved in amide metabolism in the cytosol of Pseudomonas aeruginosa. Crystal structures show that AmiC contains two large domains that are very similar to the periplasmic leucine-isoleucine-valine binding protein (LivJ) of Escherichia coli. Synchrotron X-ray and neutron (in 100% 2H2O buffer) scattering data were obtained for AmiC in the presence of its substrate acetamide and its anti-inducer butyramide which binds more weakly to AmiC than acetamide. Guinier analyses to obtain radius of gyration RG and molecular weight Mr values showed that AmiC formed trimers whose formation was favored in the presence of acetamide and which exhibited concentration-dependent properties at concentrations between 0.4 and 2 mg/mL. Above 2 mg/mL, where trimers predominated, the RG data were identical within 0.05 nm for AmiC-acetamide and AmiC-butyramide with mean X-ray and neutron RG values of 3.35 and 3. 28 nm, respectively. Scattering curve fits constrained by the crystal structure of AmiC-acetamide were evaluated in order to describe a model for trimeric AmiC. A translational search of parallel alignments of three monomers to form a symmetric AmiC homotrimer gave a good X-ray curve fit. Combinations of calculated curves for monomeric, dimeric, trimeric, and tetrameric AmiC as seen in the crystal structure of AmiC gave reasonable but weaker X-ray curve fits which did not favor the existence of tetrameric AmiC. It is concluded that AmiC exhibits novel ligand-dependent oligomerization properties in solution when these are compared to other members of the periplasmic binding protein superfamily, where AmiC exists in monomeric and trimeric forms, the proportions of which depend on the presence of acetamide or butyramide.

Bacterial Proteins↗