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J Raftery

Publications and source records attributed to J Raftery.

At least 19 recordsLinked to original sources
PubMed2001

The combination of molecular dynamics with crystallography for elucidating protein-ligand interactions: a case study involving peanut lectin complexes with T-antigen and lactose.

Peanut lectin binds T-antigen [Galbeta(1-3)GalNAc] with an order of magnitude higher affinity than it binds the disaccharide lactose. The crystal structures of the two complexes indicate that the higher affinity for T-antigen is generated by two water bridges involving the acetamido group. Fresh calorimetric measurements on the two complexes have been carried out in the temperature range 280-313 K. Four sets of nanosecond molecular-dynamics (MD) simulations, two at 293 K and the other two at 313 K, were performed on each of the two complexes. At each temperature, two somewhat different protocols were used to hydrate the complex in the two runs. Two MD runs under slightly different conditions for each complex served to assess the reliability of the approach for exploring protein-ligand interactions. Enthalpies based on static calculations and on MD simulations favour complexation involving T-antigen. The simulations also brought to light ensembles of direct and water-mediated protein-sugar interactions in both the cases. These ensembles provide a qualitative explanation for the temperature dependence of the thermodynamic parameters of peanut lectin-T-antigen interaction and for the results of one of the two mutational studies on the lectin. They also support the earlier conclusion that the increased affinity of peanut lectin for T-antigen compared with that for lactose is primarily caused by additional water bridges involving the acetamido group. The calculations provide a rationale for the observed sugar-binding affinity of one of the two available mutants. Detailed examination of the calculations point to the need for exercising caution in interpreting results of MD simulations: while long simulations are not possible owing to computational reasons, it is desirable to carry out several short simulations with somewhat different initial conditions.

Anti-Bacterial Agents↗
PubMed2001

Structure of lobster apocrustacyanin A1 using softer X-rays.

The molecular basis of the camouflage colouration of marine crustacea is often provided by carotenoproteins. The blue colour of the lobster carapace, for example, is intricately associated with a multimacromolecular 16-mer complex of protein subunits each with a bound astaxanthin molecule. The protein subunits of crustacyanin fall into two distinct subfamilies, CRTC and CRTA. Here, the crystal structure solution of the A(1) protein of the CRTC subfamily is reported. The problematic nature of the structure solution of the CRTC proteins (both C(1) and A(1)) warranted consideration and the development of new approaches. Three putative disulfides per protein subunit were likely to exist based on molecular-homology modelling against known lipocalin protein structures. With two such subunits per crystallographic asymmetric unit, this direct approach was still difficult as it involved detecting a weak signal from these sulfurs and suggested the use of softer X-rays, combined with high data multiplicity, as reported previously [Chayen et al. (2000), Acta Cryst. D56, 1064-1066]. This paper now describes the structure solution of CRTC in the form of the A(1) dimer based on use of softer X-rays (2 A wavelength). The structure solution involved a xenon derivative with an optimized xenon L(I) edge f" signal and a native data set. The hand of the xenon SIROAS phases was determined by using the sulfur anomalous signal from a high-multiplicity native data set also recorded at 2 A wavelength. For refinement, a high-resolution data set was measured at short wavelength. All four data sets were collected at 100 K. The refined structure to 1.4 A resolution based on 60 276 reflections has an R factor of 17.7% and an R(free) of 22.9% (3137 reflections). The structure is that of a typical lipocalin, being closely related to insecticyanin, to bilin-binding protein and to retinol-binding protein. This A(1) monomer or dimer can now be used as a search motif in the structural studies of the oligomeric forms alpha- and beta-crustacyanins, which contain bound astaxanthin molecules.

Amino Acid Sequence↗
PubMed2001

The 1.2 A resolution structure of the Con A-dimannose complex.

The complex between concanavalin A (Con A) and alpha1-2 mannobiose (mannose alpha1-2 mannose) has been refined to 1.2 A resolution. This is the highest resolution structure reported for any sugar-lectin complex. As the native structure of Con A to 0.94 A resolution is already in the database, this gives us a unique opportunity to examine sugar-protein binding at high resolution. These data have allowed us to model a number of hydrogen atoms involved in the binding of the sugar to Con A, using the difference density map to place the hydrogen atoms. This map reveals the presence of the protonated form of Asp208 involved in binding. Asp208 is not protonated in the 0.94 A native structure. Our results clearly show that this residue is protonated and hydrogen bonds to the sugar. The structure accounts for the higher affinity of the alpha1-2 linked sugar when compared to other disaccharides. This structure identifies different interactions to those predicted by previous modelling studies. We believe that the additional data presented here will enable significant improvements to be made to the sugar-protein modelling algorithms.

Concanavalin A↗
PubMed2001

Stroke rehabilitation after hospital discharge: a randomized trial comparing domiciliary and day-hospital care.

OBJECTIVES: To compare the effectiveness and costs of a new domiciliary rehabilitation service for elderly stroke patients with geriatric day-hospital care. DESIGN: Randomized controlled trial. PARTICIPANTS: Stroke patients aged 55+ who required further rehabilitation after hospital discharge or after referral to geriatricians from the community. SETTING: Poole area, East Dorset, a mixed urban/rural area on the south coast of England. MAIN OUTCOMES: Primary-changes between hospital discharge and 6-month follow-up in physical function as measured by Barthel index. Secondary-changes over this period in Rivermead Mobility Index and mental state (Philadelphia Geriatric Centre Morale Scale) and differences in social activity (Frenchay Activities Index) and generic health status (SF-36). Health service and social service cost per patient were compared for the two groups. RESULTS: 180 patients were eligible and 140 (78%) were randomized. The groups were well balanced for age, sex, social class and initial Barthel index. We achieved follow-up in 88% of subjects who were alive at 6 months. We detected no significant differences in patient outcomes, although there was a non-significant improvement in measures of physical function and social activity in the domiciliary group. Domiciliary patients had more physiotherapy time per session and more district nurse time, and made greater use of social service day centres and home helps. Total cost per patient did not differ significantly between the two groups, with reduced health service costs in the domiciliary arm offset by higher social service costs. CONCLUSION: No significant differences were detected in the effectiveness of the two services. Neither service influenced patients' mental state, and their social activity remained low. Total costs were similar. A mixed model of day-hospital and domiciliary care may be most cost-effective for community stroke rehabilitation, but this requires further evaluation.

Aged↗
PubMed2001

Hampshire depression project: changes in the process of care and cost consequences.

Records of patients included in a trial of educating practice teams about the management of depression were examined to determine changes in the process of care. There were no significant differences in the proportions recognised or treated for depression. Only 15% of those with possible, and 26% of those with probable, major depressive disorder were prescribed recommended doses and duration of antidepressants. The education apparently delayed a switch away from tricyclics while achieving a similar outcome. However health service costs were mainly non-psychiatric, and there were no significant savings as a result.

Antidepressive Agents↗
PubMed2000

Anticoagulation management in primary care: a trial-based economic evaluation.

The demand for anticoagulation management is increasing because of a widening of the indications of treatment. A primary care clinic using near-patient testing and computer decision support software is one model of care to meet this increased demand. The study aimed to determine the cost and cost-effectiveness of primary care-based anticoagulation management in comparison with 'traditional' hospital care-based provision by means of a cost-effectiveness analysis using data from a Birmingham-based multicentre randomized controlled trial. The costs per patient per year in primary care were pound170 [95% confidence interval (CI) pound149-190] vs. pound69 (95% CI pound57-81). Sensitivity analysis demonstrated that the cost in primary care could be reduced to under pound100 per patient per year under plausible changes in the variables. Primary care provides similar levels of control to secondary care for patients on anticoagulation therapy. There is an increased cost of managing patients in primary care and at no point did primary care become a lower cost option than secondary care. Local decision-makers need to assess the increased cost of primary care anticoagulation management in terms of the potential reductions in high-cost serious adverse events.

Aged↗
PubMed2000

Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography.

The correct positions of the deuterium (D) atoms of many of the bound waters in the protein concanavalin A are revealed by neutron Laue diffraction. The approach includes cases where these water D atoms show enough mobility to render them invisible even to ultra-high resolution synchrotron-radiation X-ray crystallography. The positions of the bound water H atoms calculated on the basis of chemical and energetic considerations are often incorrect. The D-atom positions for the water molecules in the Mn-, Ca- and sugar-binding sites of concanavalin A are described in detail.

Binding Sites↗
PubMed2000

Apocrustacyanin A1 from the lobster carotenoprotein alpha-crustacyanin: crystallization and initial X-ray analysis involving softer X-rays.

The A1 subunit of the carotenoprotein alpha-crustacyanin, isolated from lobster carapace, has been crystallized using the vapour-diffusion method. The crystals, grown in solutions of ammonium sulfate containing methylpentanediol (MPD), diffracted to 2. 0 A. The crystals are stable to radiation. The space group of the crystals is P2(1)2(1)2(1). The unit-cell parameters are a = 41.9, b = 80.7, c = 110.8 A. 'Standard structure determination' has been unsuccessful within this crustacyanin family. Instead, an approach based on the S atoms is being undertaken involving softer X-rays at the SRS, Daresbury.

Animals↗