PubMed Health⌕ Search

Biomedical subjects

James Raftery

Publications and source records attributed to James Raftery.

29 records · Page 2Linked to original sources
PubMed2003

Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

Carrier Proteins↗
PubMed2003

S-SWAT (softer single-wavelength anomalous technique): potential in high-throughput protein crystallography.

The drive for yet higher output of protein crystal structures sustains an interest in streamlining data-collection protocols. Highly organized automated robotics attend to one aspect. The data-collection elapsed time also depends on the number of wavelengths used, the data redundancy and the desired diffraction resolution limit. Synchrotron-radiation beamlines offer a centralized data-collection approach with considerable flexibility of choice of wavelength(s) with high beam intensity and fine collimation. The arrival of automated IPs (imaging plates) and CCDs (charge-coupled devices) with sample freezing has widened the scope for ease of data collection and achieving a high redundancy, the latter at the cost of elapsed time per sample. This paper reports a single-wavelength approach where a large optimized f" signal involving the Xe L1-absorption edge is harnessed. Even with modest data redundancy (7), a high-quality electron-density map was obtained from that single data set when combined with phase improvement methods. Two phasing protocols are compared for the same data set. Resolution extension (to 1.4 A), in this test, was also done but via a second data set. In future, with a tilted detector geometry, full diffraction resolution will be collectable in one experiment on the one beamline. Moreover, careful minimization of beamline Be window thickness on the new Daresbury SRS Multipole Wiggler Beamline 10 will maximize the 2-3 A (softer) wavelength intensity performance specification. The work has application to the harnessing of iodine f" optimized signals and enhanced sulfur f", as well as xenon f", in protein crystallography. This approach, softer-SWAT, should 'swat' many protein structures when it comes online.

Crystallography, X-Ray↗
PubMed2003

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase.

The enzyme hydroxymethylbilane synthase (HMBS, EC 4.3.1.8), 313 amino acid residues and MW 34 kDa, also known as porphobilinogen deaminase (PBGD), catalyses the stepwise polymerization of four molecules of porphobilinogen (PBG) to the linear tetrapyrrole 1-hydroxymethylbilane. Several crystallographic structures of HMBS have been previously determined, most recently including by time-resolved Laue protein crystallography of the Lys59Gln mutant form with reaction initiation undertaken by use of a flow cell carrying the substrate PBG. In this paper we review these structures and add new molecular graphics representations and analyses. Moreover we present a new structure refined at 1.66 A resolution using diffraction data recorded at cryo-temperature (100 K) in an attempt at trapping the polypeptide loop (residues 47 to 58) in the vicinity of the enzyme active site, missing in all previous structure determinations. This loop still has not appeared in the electron density maps, in spite of the advantage of cryo-temperature, but nevertheless the 1.66 A cryo-structure extends the ensemble of known HMBS structures. The cryomodel of protein, cofactor and 320 bound water molecules has been refined to a final R-factor and R-free of 0.198 and 0.247 respectively; the PDB deposition codes, coordinates and structure factors are 1GTK and R1GTKSF respectively. Finally a protein comparison study is presented of the Mycobacterium tuberculosis (MTb) HMBS, with the E. coli HMBS. This has been done as preparation for future structural studies on the MTb HMBS from this important disease bearing organism. The overall amino acid sequence identity is 41%. Most interestingly there is a two-residue reduction in length of the loop referred to above (Asp 50 and Gly 58 being missing in the MTb form). This gives the hope that this loop will be less flexible and thus might become visible to crystallographic analysis.

Crystallography, X-Ray↗
PubMed2002

The molecular basis of the coloration mechanism in lobster shell: beta-crustacyanin at 3.2-A resolution.

The binding of the carotenoid astaxanthin (AXT) in the protein multimacromolecular complex crustacyanin (CR) is responsible for the blue coloration of lobster shell. The structural basis of the bathochromic shift mechanism has long been elusive. A change in color occurs from the orange red of the unbound dilute AXT (lambda(max) 472 nm in hexane), the well-known color of cooked lobster, to slate blue in the protein-bound live lobster state (lambda(max) 632 nm in CR). Intriguingly, extracted CR becomes red on dehydration and on rehydration goes back to blue. Recently, the innovative use of softer x-rays and xenon derivatization yielded the three-dimensional structure of the A(1) apoprotein subunit of CR, confirming it as a member of the lipocalin superfamily. That work provided the molecular replacement search model for a crystal form of the beta-CR holo complex, that is an A(1) with A(3) subunit assembly including two bound AXT molecules. We have thereby determined the structure of the A(3) molecule de novo. Lobster has clearly evolved an intricate structural mechanism for the coloration of its shell using AXT and a bathochromic shift. Blue/purple AXT proteins are ubiquitous among invertebrate marine animals, particularly the Crustacea. The three-dimensional structure of beta-CR has identified the protein contacts and structural alterations needed for the AXT color regulation mechanism.

Amino Acid Sequence↗
PubMed2002

NHS activity. Running out of juice.

Productivity, as traditionally measured in the NHS, may have levelled off. The Department of Health has acknowledged productivity problems. Current measurement indicators do not take account of quality, so improvement to services may show up as decreases in efficiency. Quality improvements should be included in productivity measurement.

Efficiency, Organizational↗
PubMed2002

A simulation to evaluate screening for Helicobacter pylori infection in the prevention of peptic ulcers and gastric cancers.

A discrete event simulation model has evaluated a screening programme for Helicobacter pylori infection (H. pylori) in which individuals under the age of 50 years would be screened once. Eradication of H. pylori would reduce the peptic ulcer risk immediately and the gastric cancer risk after a fixed delay. The data were derived from published databases and peer reviewed papers. The simulation model, using variance reduction techniques, predicted that a screening programme would reduce morbidity and deaths but could cost around 19 million pounds for England and Wales in the first year of screening. A factorial design analysis showed the sensitivity of key variables. An increase in the opportunistic testing was found significantly to reduce the impact of screening.

Adult↗
PubMed2002

The development of a simulation model of the treatment of coronary heart disease.

A discrete event simulation models the progress of patients who have had a coronary event, through their treatment pathways and subsequent coronary events. The main risk factors in the model are age, sex, history of previous events and the extent of the coronary vessel disease. The model parameters are based on data collected from epidemiological studies of incidence and prognosis, efficacy studies. national surveys and treatment audits. The simulation results were validated against different sources of data. The initial results show that increasing revascularisation has considerable implications for resource use but has little impact on patient mortality.

Aged↗
PubMedDate not supplied

Cost-effectiveness of pharmacological interventions for smoking cessation: a literature review and a decision analytic analysis.

To evaluate the relative cost-effectiveness of nicotine replacement therapy (NRT) and bupropion SR for smoking cessation, the authors reviewed published studies and developed a decision analytic model from the UK National Health Services perspective. Irrespective of the methods or assumptions involved, the results of published studies consistently indicated that NRT for smoking cessation is cost-effective. No published studies have evaluated the relative cost-effectiveness of bupropion SR for smoking cessation. The results of the decision analyses indicated that, as compared with advice or counseling alone, the incremental cost per life-years saved is about $1,441-$3,455 for NRT, $920-$2,150 for bupropion SR, and $1,282-$2,836 for NRT plus bupropion SR. The cost-effectiveness of adding NRT and bupropion SR to advice or counseling for smoking cessation is better than many other accepted health care interventions.

Bupropion↗