Manchester Interdisciplinary Biocentre

Manchester, United Kingdom

Manchester Interdisciplinary Biocentre

Manchester, United Kingdom
SEARCH FILTERS
Time filter
Source Type

Sattelle B.M.,Manchester Interdisciplinary Biocentre | Shakeri J.,Manchester Interdisciplinary Biocentre | Roberts I.S.,Oxford Road | Almond A.,Manchester Interdisciplinary Biocentre
Carbohydrate Research | Year: 2010

The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-strucutre at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without 15N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the β(1→3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the β(1→3) ψ dihedral (as previously predicted by simulation), while the β(1→4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties. © 2009 Elsevier Ltd. All rights reserved.


Courtot M.,Terry Fox Laboratory | Juty N.,European Bioinformatics Institute | Knupfer C.,Friedrich - Schiller University of Jena | Waltemath D.,University of Rostock | And 27 more authors.
Molecular Systems Biology | Year: 2011

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments. © 2011 EMBO and Macmillan Publishers Limited.


Dunstan M.S.,Manchester Interdisciplinary Biocentre | Barkauskaite E.,Paterson Institute for Cancer Research | Lafite P.,French National Center for Scientific Research | Knezevic C.E.,University of Illinois at Urbana - Champaign | And 5 more authors.
Nature Communications | Year: 2012

Poly(ADP-ribosyl)ation is a reversible post-translational protein modification involved in the regulation of a number of cellular processes including DNA repair, chromatin structure, mitosis, transcription, checkpoint activation, apoptosis and asexual development. The reversion of poly(ADP-ribosyl)ation is catalysed by poly(ADP-ribose) (PAR) glycohydrolase (PARG), which specifically targets the unique PAR (1ĝ€2ĝ€ 2-2ĝ€2) riboseĝ€"ribose bonds. Here we report the structure and mechanism of the first canonical PARG from the protozoan Tetrahymena thermophila. In addition, we reveal the structure of T. thermophila PARG in a complex with a novel rhodanine-containing mammalian PARG inhibitor RBPI-3. Our data demonstrate that the protozoan PARG represents a good model for human PARG and is therefore likely to prove useful in guiding structure-based discovery of new classes of PARG inhibitors. © 2012 Macmillan Publishers Limited. All rights reserved.


Mariani M.M.,Leibniz Institute for Analytical Sciences | Day P.J.R.,Manchester Interdisciplinary Biocentre | Deckert V.,Leibniz Institute for Analytical Sciences | Deckert V.,Institute of Photonic Technology
Integrative Biology | Year: 2010

Raman spectroscopy assesses the chemical composition of a sample by exploiting the inherent and unique vibrational chacteristics of chemical bonds. Initial applications of Raman were identified in the industrial and chemical sectors, providing a rapid non-invasive method to identify sample components or perform quality control assessments. Applications have since increased and sample sizes decreased, leading to the onset of micro-Raman spectroscopy. Coupling with microscopy enabled label-free sample analysis and the unveiling of total chemical composition. Latter adaptations of Raman have advanced into biomedical diagnostics and research. Alongside technical developments in filter systems and detectors, spectral peak intensities and improved signal-to-noise ratios have facilitated target molecule measurement within a variety of samples. Quantitative sample analysis applications of Raman have contributed to its increasing popularity. Through these exceptional capabilites, potential Raman spectroscopy utility in biomedical research applications has expanded, exemplifying why there is continued interest in this highly sensitive and often under-used technique. © The Royal Society of Chemistry.


Avis J.M.,Manchester Interdisciplinary Biocentre | Conn G.L.,Emory University | Walker S.C.,University of Michigan
Methods in Molecular Biology | Year: 2012

The use of in vitro transcribed RNA is often limited by sequence constraints at the 5′-end and the problem of transcript heterogeneity which can occur at both the 5′- and 3′-ends. This chapter describes the use of cis-acting ribozymes, 5′-end hammerhead (HH) and 3′-end hepatitis delta virus (HDV), for direct transcriptional processing to yield target RNAs with precisely defined ends. The method is focused on the use of the pRZ and p2RZ plasmids that are designed to simplify the production of such dual ribozyme templates. These plasmids each bear a 3′-HDV modified with a unique restriction site that allows the ribozyme to remain on the plasmid and, therefore, be omitted from the cloning procedure. The additional steps required to design a unique hammerhead ribozyme tailored to the 5′-end of each target RNA are detailed. In most cases, a transcriptional template bearing a 5′-HH ribozyme and a 3′-HDV ribozyme can be achieved by cloning a single PCR product into either the pRZ or p2RZ vector. Protocols for optimization of transcription yields from these templates and the isolation of the homogeneous target RNA are also described. © 2012 Springer Science+Business Media, LLC.


Avis J.M.,Manchester Interdisciplinary Biocentre
Methods in molecular biology (Clifton, N.J.) | Year: 2012

The use of in vitro transcribed RNA is often limited by sequence constraints at the 5'-end and the problem of transcript heterogeneity which can occur at both the 5'- and 3'-ends. This chapter describes the use of cis-acting ribozymes, 5'-end hammerhead (HH) and 3'-end hepatitis delta virus (HDV), for direct transcriptional processing to yield target RNAs with precisely defined ends. The method is focused on the use of the pRZ and p2RZ plasmids that are designed to simplify the production of such dual ribozyme templates. These plasmids each bear a 3'-HDV modified with a unique restriction site that allows the ribozyme to remain on the plasmid and, therefore, be omitted from the cloning procedure. The additional steps required to design a unique hammerhead ribozyme tailored to the 5'-end of each target RNA are detailed. In most cases, a transcriptional template bearing a 5'-HH ribozyme and a 3'-HDV ribozyme can be achieved by cloning a single PCR product into either the pRZ or p2RZ vector. Protocols for optimization of transcription yields from these templates and the isolation of the homogeneous target RNA are also described.


Haward S.J.,University of Bristol | Odell J.A.,University of Bristol | Li Z.,Manchester Interdisciplinary Biocentre | Yuan X.-F.,Manchester Interdisciplinary Biocentre
Rheologica Acta | Year: 2010

Birefringent strands are key to understanding polymeric non-Newtonian flows, especially in extension. Utilising microfluidic extensional flow oscillatory rheometry coupled with microvelocimetry (μ-PIV), we report experiments on the genesis, steady state and decay of such strands, together with rheological consequences. For closely monodisperse atactic polystyrene, we report massive effects of the polymer on flow even at low concentrations. The often observed startup "overshoot" in stress and birefringence is observed at unprecedented dilution and discussed in terms of the local strain rate. Strand decay shows pronounced hysteresis. These factors are most important in modelling real flows such as cyclic and capillary entrance flows. Even with the closely monodisperse and well-characterised samples used, residual polydispersity plays a vital role in flow behaviour. © 2009 Springer-Verlag.


Haward S.J.,University of Bristol | Odell J.A.,University of Bristol | Li Z.,Manchester Interdisciplinary Biocentre | Yuan X.-F.,Manchester Interdisciplinary Biocentre
Rheologica Acta | Year: 2010

We apply micro-oscillatory cross-slot extensional flow to a semi-dilute poly(ethylene oxide) solution. Micro-particle image velocimetry (μPIV) is used to probe the real local flow field. Extreme flow perturbation is observed, where birefringent strands of extended polymer originate from the stagnation point. This coincides with a large increase in the extensional viscosity. The combination of stagnation point flow and μPIV enables us to investigate directly the stress and strain rates in the strand and so determine the true extensional viscosity of the localised strand alone. The Trouton ratio in the strand is found to be ~4000, amongst the highest values of Trouton ratio ever reported. Consideration of the flow in the exit channels surrounding the highly elastic strand suggests a maximum limit for the pressure drop across the device and the apparent extensional viscosity. This has implications for the understanding of high Deborah number extensional thinning reported in other stagnation point flow situations. © 2010 Springer-Verlag.


Haward S.J.,University of Bristol | Li Z.,Manchester Interdisciplinary Biocentre | Lighter D.,University of Bristol | Thomas B.,University of Bristol | And 2 more authors.
Journal of Non-Newtonian Fluid Mechanics | Year: 2010

We have studied the flow of thermodynamically ideal solutions of a high molecular weight (Mw=6.9MDa) atactic polystyrene in the θ solvent dioctyl phthalate (aPS in DOP) through a micro-fabricated 8:1 planar abrupt contraction geometry. The channel is much deeper than most micro-scale geometries, providing an aspect ratio of 16:1 and a good approximation to 2D flow in the narrow channel. The solutions span a range of concentration 0.03wt.%


Sattelle B.M.,Manchester Interdisciplinary Biocentre | Almond A.,Manchester Interdisciplinary Biocentre
Glycobiology | Year: 2011

Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid 4C 1 chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 μs to reach a conformational equilibrium, which comprised a metastable 4C 1 chair that underwent 4C 1 ↔ 1C 4 transitions at a predicted forward rate of 0.8 s -1 with an average 1C 4-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid 4C 1 chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 s -1) and a more stable 4C 1 conformer (0.2 kcal mol -1), suggesting that pivotal 3D intermediates (particularly 2SO, 1S5 and B2,5) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration. © 2011 The Author.

Loading Manchester Interdisciplinary Biocentre collaborators
Loading Manchester Interdisciplinary Biocentre collaborators