%0 Journal Article %~ Pubmed %A Lee, Kristie %A Tan, Jacqueline %A Morris, Michael B %A Rizzoti, Karine %A Hughes, James %A Cheah, Pike See %A Felquer, Fernando %A Liu, Xuan %A Piltz, Sandra %A Lovell-Badge, Robin %A Thomas, Paul Q %T Congenital hydrocephalus and abnormal subcommissural organ development in sox3 transgenic mice. %B %D 2012 %V 7 %N 1 %P e29041 %@ 1932-6203 %X Congenital hydrocephalus (CH) is a life-threatening medical condition in which excessive accumulation of CSF leads to ventricular expansion and increased intracranial pressure. Stenosis (blockage) of the Sylvian aqueduct (Aq; the narrow passageway that connects the third and fourth ventricles) is a common form of CH in humans, although the genetic basis of this condition is unknown. Mouse models of CH indicate that Aq stenosis is associated with abnormal development of the subcommmissural organ (SCO) a small secretory organ located at the dorsal midline of the caudal diencephalon. Glycoproteins secreted by the SCO generate Reissner's fibre (RF), a thread-like structure that descends into the Aq and is thought to maintain its patency. However, despite the importance of SCO function in CSF homeostasis, the genetic program that controls SCO development is poorly understood. Here, we show that the X-linked transcription factor SOX3 is expressed in the murine SCO throughout its development and in the mature organ. Importantly, overexpression of Sox3 in the dorsal diencephalic midline of transgenic mice induces CH via a dose-dependent mechanism. Histological, gene expression and cellular proliferation studies indicate that Sox3 overexpression disrupts the development of the SCO primordium through inhibition of diencephalic roof plate identity without inducing programmed cell death. This study provides further evidence that SCO function is essential for the prevention of hydrocephalus and indicates that overexpression of Sox3 in the dorsal midline alters progenitor cell differentiation in a dose-dependent manner. %Z FOR Codes: 110903 60103 111603 %0 Journal Article %~ Pubmed %A Werner, Tim %A Morris, Michael B %A Dastmalchi, Siavoush %A Church, W Bret %T Structural modelling and dynamics of proteins for insights into drug interactions. %B Advanced drug delivery reviews %D 2012 %V %N %P %@ 1872-8294 %X Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets. %Z FOR Codes: 111602 30402 100499 %0 Journal Article %~ Pubmed %A Washington, Jennifer M %A Rathjen, Joy %A Felquer, Fernando %A Lonic, Ana %A Bettess, Michael D %A Hamra, Nancy %A Semendric, Ljiljana %A Tan, Boon Siang Nicholas %A Lake, Julie-Anne %A Keough, Rebecca A %A Morris, Michael B %A Rathjen, Peter D %T L-Proline induces differentiation of ES cells: a novel role for an amino acid in the regulation of pluripotent cells in culture. %B American journal of physiology. Cell physiology %D 2010 %V 298 %N 5 %P C982-92 %@ 1522-1563 %X The development of cell therapeutics from embryonic stem (ES) cells will require technologies that direct cell differentiation to specific somatic cell lineages in response to defined factors. The initial step in formation of the somatic lineages from ES cells, differentiation to an intermediate, pluripotent primitive ectoderm-like cell, can be achieved in vitro by formation of early primitive ectoderm-like (EPL) cells in response to a biological activity contained within the conditioned medium MEDII. Fractionation of MEDII has identified two activities required for EPL cell formation, an activity with a molecular mass of <3 kDa and a second, much larger species. Here, we have identified the low-molecular-weight activity as l-proline. An inhibitor of l-proline uptake, glycine, prevented the differentiation of ES cells in response to MEDII. Supplementation of the culture medium of ES cells with >100 M l-proline and some l-proline-containing peptides resulted in changes in colony morphology, cell proliferation, gene expression, and differentiation kinetics consistent with differentiation toward a primitive ectoderm-like cell. This activity appeared to be associated with l-proline since other amino acids and analogs of proline did not exhibit an equivalent activity. Activation of the mammalian target of rapamycin (mTOR) signaling pathway was found to be necessary but not sufficient for l-proline activity; addition of other activators of the mTOR signaling pathway failed to alter the ES cell phenotype. This is the first report describing a role for amino acids in the regulation of pluripotency and cell differentiation and identifies a novel role for the imino acid l-proline. %Z FOR Codes: 60103 60601 %0 Journal Article %~ Pubmed %A Morris, Michael B %A Dastmalchi, Siavoush %A Church, W Bret %T Rhodopsin: structure, signal transduction and oligomerisation. %B The International Journal of Biochemistry & Cell Biology %D 2009 %V 41 %N 4 %P 721-4 %@ 1878-5875 %X Rhodopsin was the first G protein-coupled receptor (GPCR) for which a high-resolution crystal structure was obtained. Several crystal structures have now been solved representing different activation states of the receptor. These structures, together with those from lower resolution techniques (e.g. electron microscopy), shed light on the stepwise process by which energy from an extracellular photon is transduced across the membrane to the intracellular compartment thereby activating signalling mechanisms responsible for very low-level light detection. Controversy remains in several areas including: (i) transmembrane helix movements responsible for the transduction process, (ii) the stoichiometry of coupling to G proteins and their mode of activation, (iii) the role, if any, of receptor oligomerisation and (iv) the suitability of using structures of this GPCR as templates for modelling the structures of other GPCRs, and their mechanisms of activation. %Z FOR Codes: 1101 %0 Journal Article %~ Pubmed %A Dastmalchi, Siavoush %A Church, W Bret %A Morris, Michael B %T Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. %B BMC bioinformatics [electronic resource] %D 2008 %V 9 Suppl 1 %N %P S14 %@ 1471-2105 %X BACKGROUND: G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to approximately 60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the first GPCR for which high-resolution structures have been completed but significant variations in structure are likely to exist among the GPCRs. Because of this, considerable effort has been expended on developing in silico tools for refining structures of individual GPCRs. We have developed REPIMPS, a modification of the inverse-folding software Profiles-3D, to assess and predict the rotational orientation and vertical position of helices within the helix bundle of individual GPCRs. We highlight the value of the method by applying it to the Baldwin GPCR template but the method can, in principle, be applied to any low- or high-resolution membrane protein template or structure. RESULTS: 3D models were built for transmembrane helical segments of 493 GPCRs based on the Baldwin template, and the models were then scored using REPIMPS and Profiles-3D. The compatibility scores increased significantly using REPIMPS because it takes into account the physicochemical properties of the (lipid) environment surrounding the helix bundle. The arrangement of helices in the helix bundle of the 493 models was then altered systematically by rotating the individual helices. For most GPCRs in the set, changes in the rotational position of one or more helices resulted in significant improvement in the compatibility scores. In particular, for most GPCRs, a rotation of helix VII by 240-300 degrees resulted in improved scores. Bovine rhodopsin modelled using this method showed 3.31 A RMSD to its crystal structure for 198 Calpha atom pairs, suggesting the utility of the method even when starting with idealised structures such as the Baldwin template. CONCLUSION: We have developed an in silico tool which can be used to test the validity of, and refine, models of GPCRs with respect to helix rotation and vertical position based on the physicochemical properties of amino acids and the surrounding environment. The method can be applied to any multi-pass membrane protein and potentially can be used in combination with other high-throughput methodologies to generate and refine models of membrane proteins. %Z FOR Codes: 110106 %0 Book Section %A Morris, Michael %A Rathjen, Jennifer %A Keough, Rebecca A %A Rathjen, P.D %T Biology of Embryonic Stem Cells %B Human Embryonic Stem Cells %D 2005 %C United States %I Garland Science/BIOS Scientific Publishers %V %N %P 1-28 %@ 9781859962787 %E Odorico, Jon S. %E Zhang, Su-Chun %E Pedersen, Roger A. %X %Z FOR Codes: 100404 111401