RESUMEN
Sequences of the ubiquitin-conjugating enzyme (UBC or E2) family were used as a test set to investigate issues associated with the high-throughput comparative modelling of protein structures. A semi-automatic method was initially developed with particular emphasis on producing models of a quality suitable for structural comparison. Structural and sequence features of the E2 family were used to improve the sequence alignment and the quality of the structural templates. Initially, failure to correct for subtle structural inconsistencies between templates lead to problems in the comparative analysis of the UBC electrostatic potentials. Modelling of known UBC structures using Modeller 4.0 showed that multiple templates produced, on average, no better models than the use of just one template, as judged by the root-mean-squared deviation between the comparative model and crystal structure backbones. Using four different quality-checking methods, for a given target sequence, it was not possible to distinguish the model most similar to the experimental structure. The UBC models were thus finally modelled using only the crystal structure template with the highest sequence identity to the target to be modelled, and producing only one model solution. Quality checking was used to reject models with obvious structural anomalies (e.g., bad side-chain packing). The resulting models have been used for a comparison of UBC structural features and of their electrostatic potentials. The work was extended through the development of a fully automated pipeline that identifies E2 sequences in the sequence databases, aligns and models them, and calculates the associated electrostatic potential.
Asunto(s)
Biología Computacional/métodos , Proteómica/métodos , Enzimas Ubiquitina-Conjugadoras/química , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Automatización , Cristalografía por Rayos X , Bases de Datos de Proteínas , Modelos Biológicos , Modelos Moleculares , Modelos Teóricos , Datos de Secuencia Molecular , Prolina/química , Conformación Proteica , Estructura Terciaria de Proteína , Control de Calidad , Análisis de Secuencia de Proteína , Programas Informáticos , Electricidad Estática , Homología Estructural de Proteína , TemperaturaRESUMEN
The Humber Estuary Shoreline Management Plan provides the framework for investment in defences to reduce the risk of flooding to people, property and the environment. A key issue is the rise in sea level, which is reducing the standard of protection provided and is increasing erosion. The plan is developed from detailed geomorphological and ecological studies, and extensive consultation with interested organisations and the community. It takes into account the urban and industrial development on the floodplain, high-grade agricultural land, the historic environment and the Humber's status as an outstanding site for wildlife, which is protected under the Habitats Directive. A key aim is wherever possible to work with natural processes. Another is to ensure that there is no net loss of protected inter-tidal habitat. The options investigated include changes to the existing alignment of the embankments. The overall strategy provides for a continuing line of defence around the estuary and tidal rivers but with the use of managed retreat in some places. The creation of new inter-tidal habitat by this means is to gain more stable and cost-effective defences, and to offset the loss of protected sites, including by coastal squeeze. Further studies are in progress to appraise potential managed retreat sites.
Asunto(s)
Conservación de los Recursos Naturales , Planificación en Desastres , Desastres , Ambiente , Animales , Animales Salvajes , Ecosistema , Contaminación Ambiental/prevención & control , Humanos , Suelo , Reino Unido , Abastecimiento de AguaRESUMEN
Self-organizing molecular field analysis (SOMFA) is a novel technique for three-dimensional quantitative structure-activity relations (3D-QSAR). It is simple and intuitive in concept and avoids the complex statistical tools and variable selection procedures favored by other methods. Our calculations show the method to be as predictive as the best 3D-QSAR methods available. Importantly, steric and electrostatic maps can be produced to aid the molecular design process by highlighting important molecular features. The simplicity of the technique leaves scope for further development, particularly with regard to handling molecular alignment and conformation selection. Here, the method has been used to predict the corticosteroid-binding globulin binding affinity of the "benchmark" steroids, expanded from the usual 31 compounds to 43 compounds. Test predictions have also been performed on a set of sulfonamide endothelin inhibitors.
Asunto(s)
Diseño de Fármacos , Modelos Moleculares , Endotelinas/antagonistas & inhibidores , Esteroides/química , Relación Estructura-Actividad , Sulfonamidas/química , Transcortina/químicaRESUMEN
A molecular dynamics-based approach to receptor mapping is proposed, based on the method of Rizzi (Rizzi, J. P.; et al. J. Med. Chem. 1990, 33, 2721). In Rizzi's method, the interaction energy between a series of drug molecules and probe atoms (which mimic functional groups on the receptor, such as hydrogen bond donors) was calculated. These interactions were calculated on a three-dimensional grid within a molecular mechanics parameters, were placed at these minima. The distances between the dummy atom sites were monitored during molecular dynamics simulations and plotted as distance distribution functions. Important distances within the receptor became apparent, as drugs with a common mode of binding share similar peaks in the distance distribution functions. In the case of specific 5HT3 ligands, the important donor--acceptor distance within the receptor has a range of ca. 7.9--8.9 A. In the case of specific beta 2-adrenergic ligands, the important donor--acceptor distances within the receptor lie between ca. 7--9 A and between 8 and 10 A. These distances distribution functions were used to assess three different models of the beta 2-adrenergic G-protein-coupled receptor. The comparison of the distance distribution functions for the simulation with the actual donor--acceptor distances in the receptor models suggested that two of the three receptor models were much more consistent with the receptor-mapping studies. These receptor-mapping studies gave support for the use of rhodopsin, rather than the bacteriorhodopsin template, for modeling G-protein-coupled receptors but also sounded a warning that agreement with binding data from site-directed mutagenesis experiments does not necessarily validate a receptor model.
Asunto(s)
Receptores Adrenérgicos beta 2/química , Receptores Histamínicos H3/química , Agonistas Adrenérgicos/química , Secuencia de Aminoácidos , Animales , Agonistas de los Receptores Histamínicos/química , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Ratas , Relación Estructura-ActividadRESUMEN
A method is described for the quantitation of total skeletal activity during bone scans. The method requires a single plasma sample only, taken at the time of imaging. The ratio of % injected dose of 51Cr EDTA to that of 99Tcm MDP is calculated from this sample following combined injection of the two radiopharmaceuticals. The 51Cr EDTA level corrects for the glomerular filtration of 99Tcm MDP. Using this method, which only requires a gamma counter, significant differences from normal controls have been shown in patients with osteomalacia, renal osteodystrophy, Paget's disease and hypercalcaemia. The method provides routine quantitative data to add to the imaging information in the bone scan.