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  • Journal article
    van Thor JJ, Madsen A, 2015,

    A split-beam probe-pump-probe scheme for femtosecond time resolved protein X-ray crystallography

    , Structural Dynamics, Vol: 2, ISSN: 2329-7778

    In order to exploit the femtosecond pulse duration of X-ray Free-Electron Lasers (XFEL) operating in the hard X-ray regime for ultrafast time-resolved protein crystallography experiments, critical parameters that determine the crystallographic signal-to-noise (I/σI) must be addressed. For single-crystal studies under low absorbed dose conditions, it has been shown that the intrinsic pulse intensity stability as well as mode structure and jitter of this structure, significantly affect the crystallographic signal-to-noise. Here, geometrical parameters are theoretically explored for a three-beam scheme: X-ray probe, optical pump, X-ray probe (or “probe-pump-probe”) which will allow experimental determination of the photo-induced structure factor amplitude differences, ΔF, in a ratiometric manner, thereby internally referencing the intensity noise of the XFEL source. In addition to a non-collinear split-beam geometry which separates un-pumped and pumped diffraction patterns on an area detector, applying an additional convergence angle to both beams by focusing leads to integration over mosaic blocks in the case of well-ordered stationary protein crystals. Ray-tracing X-ray diffraction simulations are performed for an example using photoactive yellow protein crystals in order to explore the geometrical design parameters which would be needed. The specifications for an X-ray split and delay instrument that implements both an offset angle and focused beams are discussed, for implementation of a probe-pump-probe scheme at the European XFEL. We discuss possible extension of single crystal studies to serial femtosecond crystallography, particularly in view of the expected X-ray damage and ablation due to the first probe pulse.

  • Journal article
    Gu R-X, Corradi V, Singh G, Beis K, Tieleman Pet al., 2015,

    Conformational Changes of the ABC Transporter McjD Revealed by Molecular Dynamics Simulations

    , BIOPHYSICAL JOURNAL, Vol: 108, Pages: 89A-89A, ISSN: 0006-3495
  • Journal article
    Schreiber F, Kay S, Frankel G, Clare S, Goulding D, van de Vosse E, van Dissel JT, Strugnell R, Thwaites G, Kingsley RA, Dougan G, Baker Set al., 2015,

    The H<i>d</i>, H<i>j</i>, and H<i>z66</i> flagella variants of <i>Salmonella enterica</i> serovar Typhi modify host responses and cellular interactions

    , SCIENTIFIC REPORTS, Vol: 5, ISSN: 2045-2322
  • Journal article
    Huynh M-H, Liu B, Henry M, Liew L, Matthews SJ, Carruthers VBet al., 2015,

    Structural Basis of <i>Toxoplasma gondii</i> MIC2-associated Protein Interaction with MIC2

    , JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 290, Pages: 1432-1441
  • Journal article
    McEwan DG, Richter B, Claudi B, Wigge C, Wild P, Farhan H, McGourty K, Coxon FP, Franz-Wachtel M, Perdu B, Akutsu M, Habermann A, Kirchof A, Helfrich MH, Odgren PR, Van Hul W, Frangakis AS, Rajalingam K, Macek B, Holden DW, Bumann D, Dikic Iet al., 2015,

    PLEKHM1 Regulates <i>Salmonella</i>-Containing Vacuole Biogenesis and Infection

    , CELL HOST & MICROBE, Vol: 17, Pages: 58-71, ISSN: 1931-3128
  • Journal article
    De Simone A, Aprile FA, Dhulesia A, Dobson CM, Vendruscolo Met al., 2015,

    Structure of a low-population intermediate state in the release of an enzyme product.

    , eLife, Vol: 4, ISSN: 2050-084X

    Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

  • Journal article
    Bubeck D, 2015,

    Unraveling Structural Polymorphism of Amyloid Fibers

    , Structure, Vol: 23, Pages: 10-11, ISSN: 0969-2126
  • Journal article
    Holden DW, 2015,

    Persisters unmasked

    , SCIENCE, Vol: 347, Pages: 30-32, ISSN: 0036-8075
  • Journal article
    Shah UV, Olusanmi D, Narang AS, Hussain MA, Tobyn MJ, Hinder SJ, Heng JYYet al., 2015,

    Decoupling the Contribution of Surface Energy and Surface Area on the Cohesion of Pharmaceutical Powders

    , Pharmaceutical Research, Vol: 32, Pages: 248-259, ISSN: 1573-904X

    PurposeSurface area and surface energy of pharmaceutical powders are affected by milling and may influence formulation, performance and handling. This study aims to decouple the contribution of surface area and surface energy, and to quantify each of these factors, on cohesion.MethodsMefenamic acid was processed by cryogenic milling. Surface energy heterogeneity was determined using a Surface Energy Analyser (SEA) and cohesion measured using a uniaxial compression test. To decouple the surface area and surface energy contributions, milled mefenamic acid was “normalised” by silanisation with methyl groups, confirmed using X-ray Photoelectron Spectroscopy.ResultsBoth dispersive and acid–base surface energies were found to increase with increasing milling time. Cohesion was also found to increase with increasing milling time. Silanised mefenamic acid possessed a homogenous surface with a surface energy of 33.1 ± 1.4 mJ/m2 , for all milled samples. The cohesion for silanised mefenamic acid was greatly reduced, and the difference in the cohesion can be attributed solely to the increase in surface area. For mefenamic acid, the contribution from surface energy and surface area on cohesion was quantified to be 57% and 43%, respectively.ConclusionsHere, we report an approach for decoupling and quantifying the contribution from surface area and surface energy on powder cohesion.

  • Journal article
    Guenther C, Kind B, Reijns MAM, Berndt N, Martinez-Bueno M, Wolf C, Tuengler V, Chara O, Lee YA, Huebner N, Bicknell L, Blum S, Krug C, Schmidt F, Kretschmer S, Koss S, Astell KR, Ramantani G, Bauerfeind A, Morris DL, Graham DSC, Bubeck D, Leitch A, Ralston SH, Blackburn EA, Gahr M, Witte T, Vyse TJ, Melchers I, Mangold E, Noethen MM, Aringer M, Kuhn A, Luethke K, Unger L, Bley A, Lorenzi A, Isaacs JD, Alexopoulou D, Conrad K, Dahl A, Roers A, Alarcon-Riquelme ME, Jackson AP, Lee-Kirsch MAet al., 2015,

    Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

    , JOURNAL OF CLINICAL INVESTIGATION, Vol: 125, Pages: 413-424, ISSN: 0021-9738
  • Journal article
    Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang Xet al., 2015,

    The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR

    , MOLECULAR MICROBIOLOGY, Vol: 95, Pages: 17-30, ISSN: 0950-382X
  • Journal article
    Douse CH, Vrielink N, Zhang W, Cota E, Tate EWet al., 2015,

    Targeting a Dynamic Protein-Protein Interaction: Fragment Screening against the Malaria Myosin A Motor Complex

    , CHEMMEDCHEM, Vol: 10, Pages: 134-143, ISSN: 1860-7179
  • Journal article
    Filloux A, 2015,


    , FEMS MICROBIOLOGY REVIEWS, Vol: 39, Pages: 1-1, ISSN: 0168-6445
  • Journal article
    Cho KH, Husri M, Amin A, Gotfryd K, Lee HJ, Go J, Kim JW, Loland CJ, Guan L, Byrne B, Chae PSet al., 2015,

    Maltose neopentyl glycol-3 (MNG-3) analogues for membrane protein study

    , ANALYST, Vol: 140, Pages: 3157-3163, ISSN: 0003-2654
  • Journal article
    Sadaf A, Cho KH, Byrne B, Chae PSet al., 2015,

    Amphipathic Agents for Membrane Protein Study

  • Journal article
    Bertheleme N, Singh S, Dowell S, Byrne Bet al., 2015,

    Heterologous Expression of G-Protein-Coupled Receptors in Yeast

  • Journal article
    Williams DR, 2015,

    Particle Engineering in Pharmaceutical Solids Processing: Surface Energy Considerations

    , CURRENT PHARMACEUTICAL DESIGN, Vol: 21, Pages: 2677-2694, ISSN: 1381-6128
  • Journal article
    Zelina P, Blockus H, Zagar Y, Peres A, Friocourt F, Wu Z, Rama N, Fouquet C, Hohenester E, Tessier-Lavigne M, Schweitzer J, Roest Crollius H, Chedotal Aet al., 2014,

    Signaling switch of the axon guidance receptor Robo3 during vertebrate evolution

    , Neuron, Vol: 84, Pages: 1258-1272, ISSN: 0896-6273

    Development of neuronal circuits is controlled by evolutionarily conserved axon guidance molecules, including Slits, the repulsive ligands for roundabout (Robo) receptors, and Netrin-1, which mediates attraction through the DCC receptor. We discovered that the Robo3 receptor fundamentally changed its mechanism of action during mammalian evolution. Unlike other Robo receptors, mammalian Robo3 is not a high-affinity receptor for Slits because of specific substitutions in the first immunoglobulin domain. Instead, Netrin-1 selectively triggers phosphorylation of mammalian Robo3 via Src kinases. Robo3 does not bind Netrin-1 directly but interacts with DCC. Netrin-1 fails to attract pontine neurons lacking Robo3, and attraction can be restored in Robo3−/− mice by expression of mammalian, but not nonmammalian, Robo3. We propose that Robo3 evolution was key to sculpting the mammalian brain by converting a receptor for Slit repulsion into one that both silences Slit repulsion and potentiates Netrin attraction.

  • Journal article
    Sanfelice D, De Simone A, Cavalli A, Faggiano S, Vendruscolo M, Pastore Aet al., 2014,

    Characterization of the Conformational Fluctuations in the Josephin Domain of Ataxin-3

    , BIOPHYSICAL JOURNAL, Vol: 107, Pages: 2923-2931, ISSN: 0006-3495
  • Journal article
    Tenboer J, Basu S, Zatsepin N, Pande K, Milathianaki D, Frank M, Hunter M, Boutet S, Williams GJ, Koglin JE, Oberthuer D, Heymann M, Kupitz C, Conrad C, Coe J, Roy-Chowdhury S, Weierstall U, James D, Wang D, Grant T, Barty A, Yefanov O, Scales J, Gati C, Seuring C, Srajer V, Henning R, Schwander P, Fromme R, Ourmazd A, Moffat K, Van Thor JJ, Spence JCH, Fromme P, Chapman HN, Schmidt Met al., 2014,

    Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

    , Science, Vol: 346, Pages: 1242-1246, ISSN: 1095-9203

    Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.

  • Journal article
    Luther PK, Squire JM, 2014,

    The intriguing dual lattices of the Myosin filaments in vertebrate striated muscles: evolution and advantage.

    , Biology (Basel), Vol: 3, Pages: 846-865, ISSN: 2079-7737

    Myosin filaments in vertebrate striated muscle have a long roughly cylindrical backbone with cross-bridge projections on the surfaces of both halves except for a short central bare zone. In the middle of this central region the filaments are cross-linked by the M-band which holds them in a well-defined hexagonal lattice in the muscle A-band. During muscular contraction the M-band-defined rotation of the myosin filaments around their long axes influences the interactions that the cross-bridges can make with the neighbouring actin filaments. We can visualise this filament rotation by electron microscopy of thin cross-sections in the bare-region immediately adjacent to the M-band where the filament profiles are distinctly triangular. In the muscles of teleost fishes, the thick filament triangular profiles have a single orientation giving what we call the simple lattice. In other vertebrates, for example all the tetrapods, the thick filaments have one of two orientations where the triangles point in opposite directions (they are rotated by 60° or 180°) according to set rules. Such a distribution cannot be developed in an ordered fashion across a large 2D lattice, but there are small domains of superlattice such that the next-nearest neighbouring thick filaments often have the same orientation. We believe that this difference in the lattice forms can lead to different contractile behaviours. Here we provide a historical review, and when appropriate cite recent work related to the emergence of the simple and superlattice forms by examining the muscles of several species ranging back to primitive vertebrates and we discuss the functional differences that the two lattice forms may have.

  • Journal article
    Young JC, Clements A, Lang AE, Garnett JA, Munera D, Arbeloa A, Pearson J, Hartland EL, Matthews SJ, Mousnier A, Barry DJ, Way M, Schlosser A, Aktories K, Frankel Get al., 2014,

    The Escherichia coli effector EspJ blocks Src kinase activity via amidation and ADP ribosylation

    , Nature Communications, Vol: 5, ISSN: 2041-1723

    The hallmark of enteropathogenic Escherichia coli (EPEC) infection is the formation of actin-rich pedestal-like structures, which are generated following phosphorylation of the bacterial effector Tir by cellular Src and Abl family tyrosine kinases. This leads to recruitment of the Nck–WIP–N-WASP complex that triggers Arp2/3-dependent actin polymerization in the host cell. The same phosphorylation-mediated signalling network is also assembled downstream of the Vaccinia virus protein A36 and the phagocytic Fc-gamma receptor FcγRIIa. Here we report that the EPEC type-III secretion system effector EspJ inhibits autophosphorylation of Src and phosphorylation of the Src substrates Tir and FcγRIIa. Consistent with this, EspJ inhibits actin polymerization downstream of EPEC, Vaccinia virus and opsonized red blood cells. We identify EspJ as a unique adenosine diphosphate (ADP) ribosyltransferase that directly inhibits Src kinase by simultaneous amidation and ADP ribosylation of the conserved kinase-domain residue, Src E310, resulting in glutamine-ADP ribose.

  • Journal article
    Hohenester E, 2014,

    Signalling complexes at the cell-matrix interface

    , CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 29, Pages: 10-16, ISSN: 0959-440X
  • Journal article
    Engelman A, Cherepanov P, 2014,

    Retroviral Integrase Structure and DNA Recombination Mechanism.

    , Microbiol Spectr, Vol: 2

    Due to the importance of human immunodeficiency virus type 1 (HIV-1) integrase as a drug target, the biochemistry and structural aspects of retroviral DNA integration have been the focus of intensive research during the past three decades. The retroviral integrase enzyme acts on the linear double-stranded viral DNA product of reverse transcription. Integrase cleaves specific phosphodiester bonds near the viral DNA ends during the 3' processing reaction. The enzyme then uses the resulting viral DNA 3'-OH groups during strand transfer to cut chromosomal target DNA, which simultaneously joins both viral DNA ends to target DNA 5'-phosphates. Both reactions proceed via direct transesterification of scissile phosphodiester bonds by attacking nucleophiles: a water molecule for 3' processing, and the viral DNA 3'-OH for strand transfer. X-ray crystal structures of prototype foamy virus integrase-DNA complexes revealed the architectures of the key nucleoprotein complexes that form sequentially during the integration process and explained the roles of active site metal ions in catalysis. X-ray crystallography furthermore elucidated the mechanism of action of HIV-1 integrase strand transfer inhibitors, which are currently used to treat AIDS patients, and provided valuable insights into the mechanisms of viral drug resistance.

  • Journal article
    Spathi C, Young N, Heng JYY, Vandeperre LJM, Cheeseman CRet al., 2014,

    A simple method for preparing super-hydrophobic powder from paper sludge ash

    , Materials Letters, Vol: 142, Pages: 80-83, ISSN: 1873-4979

    Paper sludge ash (PSA) is a readily available waste material generated by the paper recycling industry. This work reports on the production of hydrophobic powders by dry milling PSA in the presence of a fatty acid surface functionalising agent. Optimum laboratory processing involves dry milling for 8 h with a 4 wt.% addition of stearic acid and this produced a super-hydrophobic powder with a water contact angle of 153°. Different chain length fatty acids were investigated but stearic acid produced the highest hydrophobicity. The super-hydrophobicity of PSA results from the micro-particulate texture induced by dry milling with simultaneous formation of calcium stearate self-assembling surface monolayers chemically bonded to fracture surfaces.

  • Journal article
    Kelwick R, MacDonald JT, Webb AJ, Freemont Pet al., 2014,

    Developments in the Tools and Methodologies of Synthetic Biology

    , Frontiers in Bioengineering and Biotechnology, Vol: 2
  • Journal article
    Foerster A, Planamente S, Manoli E, Lossi NS, Freemont PS, Filloux Aet al., 2014,

    Coevolution of the ATPase ClpV, the Sheath Proteins TssB and TssC, and the Accessory Protein TagJ/HsiE1 Distinguishes Type VI Secretion Classes

  • Journal article
    Satoh-Takayama N, Serafini N, Verrier T, Rekiki A, Renauld J-C, Frankel G, Di Santo JPet al., 2014,

    The Chemokine Receptor CXCR6 Controls the Functional Topography of Interleukin-22 Producing Intestinal Innate Lymphoid Cells

    , IMMUNITY, Vol: 41, Pages: 776-788, ISSN: 1074-7613
  • Journal article
    Shah UV, Olusanmi D, Narang AS, Hussain MA, Tobyn MJ, Heng JYYet al., 2014,

    Decoupling the contribution of dispersive and acid-base components of surface energy on the cohesion of pharmaceutical powders

    , International Journal of Pharmaceutics, Vol: 475, Pages: 592-596, ISSN: 1873-3476

    This study reports an experimental approach to determine the contribution from two different components of surface energy on cohesion. A method to tailor the surface chemistry of mefenamic acid via silanization is established and the role of surface energy on cohesion is investigated. Silanization was used as a method to functionalize mefenamic acid surfaces with four different functional end groups resulting in an ascending order of the dispersive component of surface energy. Furthermore, four haloalkane functional end groups were grafted on to the surface of mefenamic acid, resulting in varying levels of acid-base component of surface energy, while maintaining constant dispersive component of surface energy. A proportional increase in cohesion was observed with increases in both dispersive as well as acid-base components of surface energy. Contributions from dispersive and acid-base surface energy on cohesion were determined using an iterative approach. Due to the contribution from acid-base surface energy, cohesion was found to increase ∼11.7× compared to the contribution from dispersive surface energy. Here, we provide an approach to deconvolute the contribution from two different components of surface energy on cohesion, which has the potential of predicting powder flow behavior and ultimately controlling powder cohesion.

  • Journal article
    Hoyer LL, Oh S-H, Jones R, Cota Eet al., 2014,

    A proposed mechanism for the interaction between the Candida albicans Als3 adhesin and streptococcal cell wall proteins

    , Frontiers in Microbiology, Vol: 5, ISSN: 1664-302X

    C. albicans binds various bacteria, including the oral commensal Streptococcus gordonii. Published reports documented the role of C. albicans Als3 and S. gordonii SspB in this interaction, and the importance of the Als N-terminal domain (NT-Als) in C. albicans adhesion. Here, we demonstrate that Als1 also binds S. gordonii. We also describe use of the NT-Als crystal structure to design mutations that precisely disrupt peptide-binding cavity (PBC) or amyloid-forming region (AFR) function in Als3. C. albicans displaying Als3 PBC mutant proteins showed significantly reduced binding to S. gordonii; mutation of the AFR did not affect the interaction. These observations present an enigma: the Als PBC binds free C termini of ligands, but the SspB C terminus is covalently linked to peptidoglycan and thus unavailable as a ligand. These observations and the predicted SspB elongated structure suggest that partial proteolysis of streptococcal cell wall proteins is necessary for recognition by Als adhesins.

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