The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA

We are developing a computational pipeline to use surveys of Affymetrix GeneChips as a discovery tool for unravelling some of the biology associated with post-transcriptional processing of RNA. This work involves the integration of a number of bioinformatics resources, from comparing annotations to processing images to determining the structure of transcripts. The rapidly growing datasets of GeneChips available to the community puts us in a strong position to discover novel biology about post-transcriptional processing, and should enable us to determine the mechanisms by which some groups of genes make co-ordinated changes in their production of isoforms.</jats:p

G-protein-coupled receptor dynamics: dimerization and activation models compared with experiment

Our previously derived models of the active state of the β2-adrenergic receptor are compared with recently published X-ray crystallographic structures of activated GPCRs (G-protein-coupled receptors). These molecular dynamics-based models using experimental data derived from biophysical experiments on activation were used to restrain the receptor to an active state that gave high enrichment for agonists in virtual screening. The β2-adrenergic receptor active model and X-ray structures are in good agreement over both the transmembrane region and the orthosteric binding site, although in some regions the active model is more similar to the active rhodopsin X-ray structures. The general features of the microswitches were well reproduced, but with minor differences, partly because of the unexpected X-ray results for the rotamer toggle switch. In addition, most of the interacting residues between the receptor and the G-protein were identified. This analysis of the modelling has also given important additional insight into GPCR dimerization: re-analysis of results on photoaffinity analogues of rhodopsin provided additional evidence that TM4 (transmembrane helix 4) resides at the dimer interface and that ligands such as bivalent ligands may pass between the mobile helices. A comparison, and discussion, is also carried out between the use of implicit and explicit solvent for active-state modelling.</jats:p