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  • Conference paper
    Yuan Q, Gould I, Kidley N, 2017,

    Density functional theory study on triplet intermolecular hydrogen transfer between cycloxydim and chlorothalonil

    , 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
  • Conference paper
    Khanna T, Barter L, Gould I, 2017,

    Development and application of the AMBER molecular mechanics force field to investigate herbicide interaction in plants

    , 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
  • Journal article
    Barlow NE, Smpokou E, Friddin MS, Macey R, Gould I, Turnbull C, Flemming AJ, Brooks NJ, Ces O, Barter LMCet al., 2017,

    Engineering plant membranes using droplet interface bilayers

    , Biomicrofluidics, Vol: 11, ISSN: 1932-1058

    Droplet interface bilayers (DIBs) have become widely recognised as a robust platform for constructing model membranes and are emerging as a key technology for the bottom-up assembly of synthetic cell-like and tissue-like structures. DIBs are formed when lipid-monolayer coated water droplets are brought together inside a well of oil, which is excluded from the interface as the DIB forms. The unique features of the system, compared to traditional approaches (e.g., supported lipid bilayers, black lipid membranes, and liposomes), is the ability to engineer multi-layered bilayer networks by connecting multiple droplets together in 3D, and the capability to impart bilayer asymmetry freely within these droplet architectures by supplying droplets with different lipids. Yet despite these achievements, one potential limitation of the technology is that DIBs formed from biologically relevant components have not been well studied. This could limit the reach of the platform to biological systems where bilayer composition and asymmetry are understood to play a key role. Herein, we address this issue by reporting the assembly of asymmetric DIBs designed to replicate the plasma membrane compositions of three different plant species; Arabidopsis thaliana, tobacco, and oats, by engineering vesicles with different amounts of plant phospholipids, sterols and cerebrosides for the first time. We show that vesicles made from our plant lipid formulations are stable and can be used to assemble asymmetric plant DIBs. We verify this using a bilayer permeation assay, from which we extract values for absolute effective bilayer permeation and bilayer stability. Our results confirm that stable DIBs can be assembled from our plant membrane mimics and could lead to new approaches for assembling model systems to study membrane translocation and to screen new agrochemicals in plants.

  • Journal article
    Frampton CS, Murray JI, Spivey AC, 2017,

    Crystal structure of 1-methylimidazole 3-oxide monohydrate.

    , Acta Crystallographica Section E: Crystallographic Communications, Vol: 73, Pages: 372-374, ISSN: 2056-9890

    1-Methylimidazole 3-N-oxide (NMI-O) crystallizes as a monohydrate, C4H6N2O·H2O, in the monoclinic space group P21 with Z' = 2 (mol-ecules A and B). The imidazole rings display a planar geometry (r.m.s. deviations = 0.0008 and 0.0002 Å) and are linked in the crystal structure into infinite zigzag strands of ⋯NMI-O(A)⋯OH2⋯NMI-O(B)⋯OH2⋯ units by O-H⋯O hydrogen bonds. These chains propagate along the b-axis direction of the unit cell.

  • Journal article
    French PMW, Görlitz F, Kelly D, Warren S, Alibhai D, West L, Kumar S, Alexandrov Y, Munro I, McGinty J, Talbot C, Serwa R, Thinon E, Da Paola V, Murray EJ, Stuhmeier F, Neil M, Tate E, Dunsby Cet al., 2017,

    Open source high content analysis utilizing automated fluorescence lifetime imaging microscopy

    , Jove-Journal of Visualized Experiments, Vol: 119, ISSN: 1940-087X

    We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe herethe functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in μ Manager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.

  • Journal article
    Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PM, Chin JW, Gervasio FL, Tate EW, Katan Met al., 2017,

    Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    , Scientific Reports, Vol: 7, ISSN: 2045-2322

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.

  • Conference paper
    Andrews N, Davis S, Hay C, Kumar S, Ramel M-C, Bugeon L, McGinty J, Dallman MJ, French PMWet al., 2017,

    Functional imaging of live Zebrafish using fluorescence lifetime optical projection tomography

    , Conference on Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XV, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
  • Journal article
    Barlow NE, Bolognesi G, Flemming AJ, Brooks N, Barter LMC, Ces Oet al., 2016,

    Multiplexed droplet Interface bilayer formation

    , Lab on a Chip, Vol: 16, Pages: 4653-4657, ISSN: 1473-0197

    We present a simple method for the multiplexed formation ofdroplet interface bilayers (DIBs) using a mechanically operatedlinear acrylic chamber array. To demonstrate the functionality ofthe chip design, a lipid membrane permeability assay is performed.We show that multiple, symmetric DIBs can be created andseparated using this robust low-cost approach.

  • Journal article
    Boyd C, Parsons ES, Smith RAG, Seddon JM, Ces O, Bubeck Det al., 2016,

    Disentangling the roles of cholesterol and CD59 in intermedilysin pore formation

    , Scientific Reports, Vol: 6, ISSN: 2045-2322

    The plasma membrane provides an essential barrier, shielding a cell from the pressures of its external environment. Pore-forming proteins, deployed by both hosts and pathogens alike, breach this barrier to lyse target cells. Intermedilysin is a cholesterol-dependent cytolysin that requires the human immune receptor CD59, in addition to cholesterol, to form giant β-barrel pores in host membranes. Here we integrate biochemical assays with electron microscopy and atomic force microscopy to distinguish the roles of these two receptors in mediating structural transitions of pore formation. CD59 is required for the specific coordination of intermedilysin (ILY) monomers and for triggering collapse of an oligomeric prepore. Movement of Domain 2 with respect to Domain 3 of ILY is essential for forming a late prepore intermediate that releases CD59, while the role of cholesterol may be limited to insertion of the transmembrane segments. Together these data define a structural timeline for ILY pore formation and suggest a mechanism that is relevant to understanding other pore-forming toxins that also require CD59.

  • Journal article
    Salzmann CG, Slater B, Radaelli PG, Finney JL, Shephard JJ, Rosillo-Lopez M, Hindley Jet al., 2016,

    Detailed crystallographic analysis of the ice VI to ice XV hydrogen ordering phase transition

    , JOURNAL OF CHEMICAL PHYSICS, Vol: 145, ISSN: 0021-9606

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