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• Conference paper
  Hedberg S, Quigley A, Heng JYY, Williams DR, Liddell Jet al., 2014,

  Self-interaction chromatography (SIC) of mabs: New methods for estimating the dead volume in SIC and using sic to predict mab stability

  , Pages: 897-907

  Protein-protein molecular interactions are known to be involved in protein solution aggregation behaviour; however the mechanisms leading to protein aggregation are still not fully understood. The osmotic second virial coefficient (B22) is a fundamental physiochemical property that describes proteinprotein interactions in solution, which can be a useful tool to predict aggregation propensity of proteins. This work includes two experimental SIC studies on both model proteins and therapeutic mAbs of different sizes. The first study is an evaluation of two different experimental techniques used to determine SIC dead volumes and the second study uses SIC results for mAb to predict stability. Accurate dead retention volumes are essential for the accurate determinations of B22. The traditional method of estimating dead volume for SIC includes the use of a dead column (without protein immobilised) where the retention volume for proteins can be established. For this technique the dead volume was established for the proteins over a wide range of solution conditions (pH and salt concentrations), and then compared with a new method, where a number of non-interacting dextrans of different molecular weights (MW) (including the MW's of the protein) were employed to find the dead retention volume. The results for the traditional technique with a dead column changed depending on the protein used; only certain model proteins kept a constant dead retention volume when the pH was changing under a constant high salt concentration to minimise protein-surface interactions. Several proteins, including the mAb, exhibited an increased dead retention volume especially when exposed to lower pH. From this it can be concluded that there is no absolute dead volume that can be determined by this technique which are independent of solution conditions. The new technique involving dextrans gives a better overall result for the dead volume for proteins such as mAbs. The second study shows that the SI

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• Journal article
  Hamilton ML, Franco E, Deák Z, Schlodder E, Vass I, Nixon PJet al., 2014,

  Investigating the photoprotective role of cytochrome b-559 in photosystem II in a mutant with altered ligation of the haem

  , Plant and Cell Physiology, Vol: 55, Pages: 1276-1285, ISSN: 0032-0781

  Despite many years of study, the physiological role of cytochrome b-559 (Cyt b-559) within the photosystem II (PSII) complex still remains unclear. Here we describe the analysis of a mutant of the green alga Chlamydomonas reinhardtii in which the His ligand to the haem, provided by the alpha subunit, has been replaced by a Cys residue. The mutant is unable to grow photoautotrophically but can assemble oxygen-evolving PSII supercomplexes to 15-20% of the levels found in the wild-type control. Haem is still detected in the isolated PSII supercomplexes but at sub-stoichiometric levels consistent with weaker binding to the mutated cytochrome. Analysis of PSII activity in cells indicates slowed electron transfer in the mutant between plastoquinones QA and QB. We show that PSII activity in the mutant is more sensitive to chronic photoinhibition than the WT control because of two effects: a faster rate of damage and an impaired PSII repair cycle at the level of synthesis and/or incorporation of D1 into PSII. We also demonstrate that Cyt b-559 plays a role during the critical stage of assembling the Mn 4CaO5 cluster. Overall we conclude that Cyt b-559 optimises electron transfer on the acceptor side of PSII and plays physiologically important roles in the assembly, repair and maintenance of the complex. © 2014 The Author 2014.

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  • Citations: 19
• Journal article
  Liu B, Shadrin A, Sheppard C, Mekler V, Xu Y, Severinov K, Matthews S, Wigneshweraraj Set al., 2014,

  The sabotage of the bacterial transcription machinery by a small bacteriophage protein.

  , Bacteriophage, Vol: 4, ISSN: 2159-7073

  Many bacteriophages produce small proteins that specifically interfere with the bacterial host transcription machinery and thus contribute to the acquisition of the bacterial cell by the bacteriophage. We recently described how a small protein, called P7, produced by the Xp10 bacteriophage inhibits bacterial transcription initiation by causing the dissociation of the promoter specificity sigma factor subunit from the host RNA polymerase holoenzyme. In this addendum to the original publication, we present the highlights of that research.

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• Journal article
  Sugiura M, Azami C, Koyama K, Rutherford AW, Rappaport F, Boussac Aet al., 2014,

  Modification of the pheophytin redox potential in <i>Therrnosynechococcus elongatus</i> Photosystem II with PsbA3 as D1

  , BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, Vol: 1837, Pages: 139-148, ISSN: 0005-2728
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  • Citations: 29
• Journal article
  van Thor JJ, Warren MM, Lincoln CN, Chollet M, Lemke HT, Fritz DM, Schmidt M, Tenboer J, Ren Z, Srajer V, Moffat K, Graber Tet al., 2014,

  Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein

  , FARADAY DISCUSSIONS, Vol: 171, Pages: 439-455, ISSN: 1359-6640
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  • Citations: 13
• Journal article
  Jones C, Filloux A, 2014,

  Gene Amplification and qRT-PCR

  , PSEUDOMONAS: METHODS AND PROTOCOLS, Vol: 1149, Pages: 457-468, ISSN: 1064-3745
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  • Citations: 1
• Journal article
  Mickleburgh I, Kafasla P, Cherny D, Llorian M, Curry S, Jackson RJ, Smith CWJet al., 2014,

  The organization of RNA contacts by PTB for regulation of <i>FAS</i> splicing

  , NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 8605-8620, ISSN: 0305-1048
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  • Citations: 11
• Journal article
  Darbari VC, Lawton E, Lu D, Burrows PC, Wiesler S, Joly N, Zhang N, Zhang X, Buck Met al., 2014,

  Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA plus activator

  , NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 9249-9261, ISSN: 0305-1048
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  • Citations: 1
• Journal article
  Barraud N, Moscoso JA, Ghigo J-M, Filloux Aet al., 2014,

  Methods for Studying Biofilm Dispersal in <i>Pseudomonas aeruginosa</i>

  , PSEUDOMONAS: METHODS AND PROTOCOLS, Vol: 1149, Pages: 643-651, ISSN: 1064-3745
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  • Citations: 26
• Journal article
  Muhl D, Filloux A, 2014,

  Site-Directed Mutagenesis and Gene Deletion Using Reverse Genetics

  , PSEUDOMONAS: METHODS AND PROTOCOLS, Vol: 1149, Pages: 521-539, ISSN: 1064-3745
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  • Citations: 13
• Journal article
  Wang H, Shun M-C, Li X, Di Nunzio F, Hare S, Cherepanov P, Engelman Aet al., 2014,

  Efficient transduction of LEDGF/p75 mutant cells by complementary gain-of-function HIV-1 integrase mutant viruses

  , MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT, Vol: 1
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  • Citations: 25
• Journal article
  Filloux A, Ramos J-L, 2014,

  Pseudomonas Methods and Protocols Preface

  , PSEUDOMONAS: METHODS AND PROTOCOLS, Vol: 1149, Pages: V-V, ISSN: 1064-3745
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  • Citations: 5
• Journal article
  Reeve B, Sanderson T, Ellis T, Freemont Pet al., 2014,

  How Synthetic Biology Will Reconsider Natural Bioluminescence and Its Applications

  , BIOLUMINESCENCE: FUNDAMENTALS AND APPLICATIONS IN BIOTECHNOLOGY, VOL 2, Vol: 145, Pages: 3-30, ISSN: 0724-6145
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  • Citations: 10
• Journal article
  Percy MG, Gruendling A, 2014,

  Lipoteichoic Acid Synthesis and Function in Gram-Positive Bacteria

  , ANNUAL REVIEW OF MICROBIOLOGY, VOL 68, Vol: 68, Pages: 81-100, ISSN: 0066-4227
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  • Citations: 253
• Journal article
  Filloux A, 2013,

  Fit and resistant is a worst case scenario with bacterial pathogens

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 20360-20361, ISSN: 0027-8424
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  • Citations: 1
• Journal article
  Ha K, Buchan JG, Alvarado DM, Mccall K, Vydyanath A, Luther PK, Goldsmith MI, Dobbs MB, Gurnett CAet al., 2013,

  MYBPC1 mutations impair skeletal muscle function in zebrafish models of arthrogryposis

  , HUMAN MOLECULAR GENETICS, Vol: 22, Pages: 4967-4977, ISSN: 0964-6906
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  • Citations: 41
• Journal article
  Jones C, Hachani A, Manoli E, Filloux Aet al., 2013,

  An rhs Gene Linked to the Second Type VI Secretion Cluster Is a Feature of the Pseudomonas aeruginosa Strain PA14

  , Journal of Bacteriology, Vol: 196, Pages: 800-810, ISSN: 1098-5530

  The type VI secretion system (T6SS) of Gram-negative bacteria has been involved in various processes, notably bacterial competition and eukaryotic cell subversion. Most Pseudomonas aeruginosa strains possess three T6SS gene clusters, but only the function of the first T6SS (H1-T6SS) has been clearly elucidated. It is involved in the secretion of three toxins (Tse1 to -3) that target bacterial competitors. In the case of the H2- and H3-T6SS, no clear function has been assigned, and only one effector has been associated with these systems. Yet the H2-T6SS was proposed to promote P. aeruginosa internalization in nonphagocytic epithelial cells. Although the H2-T6SS genetic organization is conserved across P. aeruginosa isolates, one feature is the presence of an additional transcriptional unit in the PA14 strain H2-T6SS cluster, which is divergent from the core H2-T6SS genes. A specific set of four genes encodes an Hcp protein (Hcp2), a VgrG protein (VgrG14), an Rhs element (PA14_43100 or RhsP2), and a protein with no homologies with previously characterized proteins (PA14_43090). In this study, we engineered a P. aeruginosa PA14 strain carrying an arabinose-inducible H2-T6SS on the chromosome. We showed that arabinose induction readily promotes assembly of the H2-T6SS, as seen by monitoring Hcp2 secretion. We further studied the secretion fate of VgrG14 and RhsP2, but these were not detectable in the extracellular medium. We finally investigated whether activation of the PA14 H2-T6SS gene cluster could influence phenotypic traits such as internalization in eukaryotic cells, and we reported noteworthy differences compared to strain PAO1, which may be accounted for by the described genetic differences.

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• Journal article
  Islam M, Gor J, Perkins SJ, Ishikawa Y, Baechinger HP, Hohenester Eet al., 2013,

  The Concave Face of Decorin Mediates Reversible Dimerization and Collagen Binding

  , JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 288, Pages: 35526-35533
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  • Citations: 27
• Journal article
  Gupta SS, Maetzig T, Maertens GN, Sharif A, Rothe M, Weidner-Glunde M, Galla M, Schambach A, Cherepanov P, Schulz TFet al., 2013,

  Bromo- and Extraterminal Domain Chromatin Regulators Serve as Cofactors for Murine Leukemia Virus Integration

  , JOURNAL OF VIROLOGY, Vol: 87, Pages: 12721-12736, ISSN: 0022-538X
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  • Citations: 107
• Journal article
  Corbalan N, Runti G, Adler C, Covaceuszach S, Ford RC, Lamba D, Beis K, Scocchi M, Vincent PAet al., 2013,

  Functional and Structural Study of the Dimeric Inner Membrane Protein SbmA

  , JOURNAL OF BACTERIOLOGY, Vol: 195, Pages: 5352-5361, ISSN: 0021-9193
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  • Citations: 29
• Journal article
  Runti G, Ruiz MDCL, Stoilova T, Hussain R, Jennions M, Choudhury HG, Benincasa M, Gennaro R, Beis K, Scocchi Met al., 2013,

  Functional Characterization of SbmA, a Bacterial Inner Membrane Transporter Required for Importing the Antimicrobial Peptide Bac7(1-35)

  , JOURNAL OF BACTERIOLOGY, Vol: 195, Pages: 5343-5351, ISSN: 0021-9193
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  • Citations: 74
• Journal article
  Devi S, Williams D, 2013,

  Morphological and Compressional Mechanical Properties of Freeze-Dried Mannitol, Sucrose, and Trehalose Cakes

  , JOURNAL OF PHARMACEUTICAL SCIENCES, Vol: 102, Pages: 4246-4255, ISSN: 0022-3549
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  • Citations: 20
• Conference paper
  Carlsson E, Zhang M, Ding JL, Byrne Bet al., 2013,

  Gly601 residue of human SARM is critical for interaction with other TLR adaptor proteins

  , Annual Congress of the British-Society-for-Immunology, Publisher: WILEY-BLACKWELL, Pages: 180-180, ISSN: 0019-2805
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• Journal article
  Glassford SE, Byrne B, Kazarian SG, 2013,

  Recent applications of ATR FTIR spectroscopy and imaging to proteins

  , BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, Vol: 1834, Pages: 2849-2858, ISSN: 1570-9639
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  • Citations: 186
• Journal article
  Muniz-Feliciano L, Van Grol J, Portillo J-AC, Liew L, Liu B, Carlin CR, Carruthers VB, Matthews S, Subauste CSet al., 2013,

  <i>Toxoplasma gondii</i>-Induced Activation of EGFR Prevents Autophagy Protein-Mediated Killing of the Parasite

  , PLOS PATHOGENS, Vol: 9, ISSN: 1553-7366
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  • Citations: 86
• Journal article
  Chae PS, Kruse AC, Gotfryd K, Rana RR, Cho KH, Rasmussen SGF, Bae HE, Chandra R, Gether U, Guan L, Kobilka BK, Loland CJ, Byrne B, Gellman SHet al., 2013,

  Novel Tripod Amphiphiles for Membrane Protein Analysis

  , CHEMISTRY-A EUROPEAN JOURNAL, Vol: 19, Pages: 15645-15651, ISSN: 0947-6539
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  • Citations: 42
• Journal article
  van Heel M, 2013,

  Finding trimeric HIV-1 envelope glycoproteins in random noise

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: E4175-E4177, ISSN: 0027-8424
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  • Citations: 48
• Journal article
  Lu Z, Bergeron JRC, Atkinson RA, Schaller T, Veselkov DA, Oregioni A, Yang Y, Matthews SJ, Malim MH, Sanderson MRet al., 2013,

  Insight into the HIV-1 Vif SOCS-box-ElonginBC interaction

  , Open Biology, Vol: 3, Pages: 1-11, ISSN: 2046-2441

  The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

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• Journal article
  Ali SSM, Heng JYY, Nikolaev AA, Waters KEet al., 2013,

  Introducing inverse gas chromatography as a method of determining the surface heterogeneity of minerals for flotation

  , POWDER TECHNOLOGY, Vol: 249, Pages: 373-377, ISSN: 0032-5910
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  • Citations: 38
• Journal article
  Zhou Z, Mogensen MM, Powell PP, Curry S, Wileman Tet al., 2013,

  Foot-and-Mouth Disease Virus 3C Protease Induces Fragmentation of the Golgi Compartment and Blocks Intra-Golgi Transport

  , JOURNAL OF VIROLOGY, Vol: 87, Pages: 11721-11729, ISSN: 0022-538X
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  • Citations: 31

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